Authorea's Blog

Blogging for the 21st Century

Host articles, preprints, files, data, code, more

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At Authorea, we made it possible to host data behind figures in your documents from the very beginning. Starting today, however, you can add arbitrary datasets and files to your Authorea document.

It's easy! Start a new document or open an existing one and in the toolbar select Insert 👉File, then select a file to host (Figure 1). The hosted file will look like this:

DOIs are now free! One-click publishing for preprints, articles, data and code

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As of today, you can assign DOIs to your content for free At Authorea, we have been offering publishing tools to authors for a long time. DOIs are the industry standard for registering content with the scholarly record by getting a persistent identifier. (What is a DOI?).As of today, we're making it possible for everyone to publish content in one click. Just sign up to Authorea with an account and follow the steps below:

Writing a response to reviewers

You recently submitted your first manuscript for publication, and you were pleased when the editor decided to send the manuscript out for peer review. Now you have gotten the reviews back, and the editor has asked you to revise your manuscript in light of the reviewers' comments. How should you tackle this task?
The comprehensive guide by \citet{Noble_2017} "Ten simple rules for writing a response to reviewers" gives you some concrete tips to organize and write a compelling letter for reviewers addressing their comments.
Rule 6 states:
Use typography to help the reviewer navigate your response:
Use changes of typeface, color, and indenting to discriminate between 3 different elements: the review itself, your responses to the review, and changes that you have made to the manuscript.
If you are writing your manuscript in Authorea, you can now very easily produce a changelog of your manuscript (the changes you have made to the manuscript) which you can export as PDF and include in your response to reviewers.

and 1 collaborator

Here's our product roadmap for the next 12 months, so that you know what is keeping us busy these days, and what to expect from Authorea.

Authorea is acquired by Atypon and joins the Wiley family

# We have some big news 🙊

What the future of research writing and publishing could look like

Research writing and publishing is broken. Hyperbole you say? Perhaps, but I am not sure how else to describe a system where I could have a child faster than I could formally publish a research paper \cite{Björk2013}. A system where I can no longer access some of my own work now that I have left academia or even worse a system where the public could never really access my work despite funding it through Federal grants \cite{Bj_rk_2017}. Sure, there are some cases where these statements are not true but for the most part they are and that is troubling. The list of problems goes on: papers have become harder to read over time and increasingly full of hype or spin \cite{Plav_n_Sigray_2017,Vinkers_2015}, the literature becomes more biased everyday--devoid of "negative results," and most work is largely irreproducible \cite{Collaboration2015,Begley2012} or at the very least never independently verified. So, yes, research publishing is broken and research is being hurt by how it is communicated.  How did it get this way and how can we improve it?
Historically, researchers primarily communicated amongst each other by giving talks, publishing books, and writing letters. In 1655 research publishing was formalized with the launch of the first journal, Philosophical Transactions \cite{Oldenburg_1665}. The process remained largely unchanged until the 1960's and 70's, when peer review was introduced (this was facilitated by new technologies like photocopying). And that's mostly it–nothing else has changed despite even the introduction of the industry-changing world wide web. Compare Einstein's 1916 publication \cite{1915SPAW.......844E} on the prediction of gravitational waves to the publication detecting gravitational waves \cite{Abbott_2016}–100 years difference, massive changes in research technologies, identical format and largely the same publication process.

Getting Started with Authorea🚶‍

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Up-Goer Five Challenge: Explain Your Research Using the Ten Hundred Most Common Words

“If you can't explain it to a six year old, you don't understand it yourself.”Writing is hard. Writing about complex concepts is even harder. Writing about complex concepts with little writing training, that's research communication. And while research writing is difficult and often under-taught, it is critical to the success of a researcher and research. Implicit in the dictum publish or perish, is that you must write. Researchers write papers, syllabi, grants, progress reports and a variety of different documents on a daily basis. Yet researchers don't typically write for the public...or for fun. Today, we'd like to change that, with the Up Goer Five Challenge! A contest that challenges researchers to use only the ten hundred most common words to explain their research. We're offering everyone that participates in the Upgoer five challenge a free premium membership on Authorea for a year! We think such a challenge is great for PIs, postdocs, students, and anyone doing research and it is great for the community and public. We also think it's quite fun!To enter, follow these steps:Signup at authorea.com/signup to create an account.Upon signup, select the group "Up-Goer Five" to join the challenge.Describe your research using the ten hundred most common words with the Up-Goer five text editor. Copy and paste your entry into a public Authorea document.Hit "Publish" on the toolbar to publish your document to the Up-Goer five group.Assign a digital object identifier (DOI) to make it citable.Share it socially and challenge your friends! (#upgoerfive)

The most powerful platform for scientific blogging 💪

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When you think of blogging you might think of a blog for cuddly cats, party parrots, the '90s, or celebrity gossip (we will not link to any of those, except cuddly cats). You probably do not think of ground breaking research, original ideas, and a powerful mechanism for research communication. And while you may be largely right, there is a world of blogging that is extremely important, a community that we wish to empower and serve with our latest feature release at Authorea, scientific blogging. In this post we wish to highlight how blogging can improve research, improve researchers career prospects, and why researchers should use a system designed for research blogging, like Authorea.Blogging as a place for correcting the scientific recordBlogging has proven to be integral towards maintaining and correcting the scientific literature. In fact, in many cases it is blogs and other forums where scientific fraud as well as common errors are first highlighted and ultimately corrected \cite{Yeo_2016}.  Blogging as a place for publishing "grey literature"Blogging allows researchers to post different types of content, ranging from journal clubs, peer reviews, single-figure observations, class essays, opinions, etc. There is a huge value to the research community to share "different" types of content, blogging allows researchers to easily do that. Blogging as a place of public outreachNearly all original peer-review publications are paywalled. Meaning it is difficult, if not impossible, for the majority of the world to legally access scientific research. Blogs, however, are nearly all completely open and accessible. More than that, they are also often times accessible in language. The discoveries and recommendations for which society invests substantial economic and human capital, should be directly disseminated by the people who really understand them, and not by the media and the political class, who often over-hype and in some case even distort the results. Blogging can be the long sought bridge between academia and the general public, something increasingly becoming required by grant agencies.Blogging as a way to advance your careerBlogs are by and large thought of as a distraction from communicating scientific ideas in a way that "counts." However, blogs can in many cases have a much larger impact on your career by providing you a forum to communicate with the world. Not all careers and hirers have such a limited way of thinking as tenure committees. Want to start blogging today? Create a group with us for free here. Want a custom design? Email us at hi@authorea.com

Q&A with protocols.io

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What is your mission?We founded Authorea with the mission of accelerating and opening up scientific discovery. We were frustrated that a writing tool didn't fully suit the needs of researchers -- especially researchers in a web-first, data-driven world.  Our mission is to reinvent how research documents are written and shared to capture the power of the web. In short, we allow researchers to create 21st century documents for 21st century research.What is the story behind Authorea?Authorea was started by two physicists, Alberto Pepe and Nathan Jenkins, who met while working at CERN in Geneva. CERN is the birthplace of the World Wide Web. The web was initially created to be a scientific information network that would allow researchers to share and disseminate scientific insights as fast as possible . The web today touches many facets of our lives: we produce massive volumes of content for the web, in HTML. Yet, scientific information is by and large still written, published and exchanged in formats which are not fully web compatible. PDFs and Microsoft Word documents, for example, are printer-centric rather than web-centric. Our plan with Authorea was to bring the writing process and its products (scientific manuscripts) to the web.We're a small group of former researchers from variety of different backgrounds, including life sciences, physics, math, computer science, and even the classics!

Authorea and the American Association for Cancer Research Partner to Streamline Research Editing & Publishing

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Authorea and BioRxiv partner to bring preprints into 21st century

and 4 collaborators

BROOKLYN, NY, July 18, 2017 -- Authorea, the collaborative document editor for researchers, today announced a partnership and direct submission agreement with bioRxiv, the leading preprint server for biological research. The agreement enables researchers writing documents on Authorea to submit preprints directly to bioRxiv with one-click.Josh Nicholson, Chief Research Officer at Authorea says: "bioRxiv is having a tremendous impact in the life sciences. We're excited to work with bioRxiv and their highly engaged community to offer more powerful preprinting capabilities for authors. Authorea's mission is to accelerate scientific discovery by making tools that help researchers write and disseminate their work. bioRxiv is an important partner in this pursuit. "bioRxiv, a non-profit service of Cold Spring Harbor Laboratory funded in part by the Chan Zuckerberg Initiative,  has emerged as the go-to place for life scientists to preprint scholarly research. Today, hundreds of preprints a month are posted, the rate of submission is rising rapidly, and the service now contains more than 11,000 preprints. As life-scientist support swells dramatically, bioRxiv will demonstrate that preprinting in the life sciences is critical to advance the body of research faster than could otherwise be done.Richard Sever, co-founder of bioRxiv, says: "bioRxiv's goal is to speed up research by allowing authors to share work as quickly and easily as possible. Authorea has created a great, next-generation authoring tool for scientists, and we're delighted to integrate with them to allow direct submission. Hopefully this is just the first step in a partnership that will make writing, sharing and discovering papers easier."You can learn more about directly submitting to bioRxiv here.

Turn-key research writing and publishing with Authorea for groups and teams

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Authorea aims to make research writing and dissemination more effective and modern for all of research. That means academic research as well as tech, biotech, pharma, real estate, and financial research, to mention a few. One question we receive almost across all groups when discussing how Authorea might be able to help researchers is: "Can we customize the appearance of articles and profile pages to use on our own site?" Our answer: "Yes, soon." Today, we're happy to introduce the ability for groups, labs, teams, private companies, and large organizations to customize the appearance of their organization page as well as their documents (see Fig \ref{303825}). This group-based feature is currently available only to licensed groups (see pricing page).

Authorea and SSRN Partner to Offer Authors a Better Way to Write and Edit Documents

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BROOKLYN, NY, September 12, 2017 -- Authorea, the online document editor for researchers, has partnered with the SSRN, one of the world's leading preprint repositories with recent expansion in the life and physical sciences. The partnership allows researchers to write and edit their documents on Authorea and directly publish their work at SSRN with a few simple clicks.Authorea, launched in 2014, has developed a new way for researchers to write, edit, and collaborate on research documents and today serves over 100,000 researchers from all disciplines.SSRN, launched in 1994, allows researchers to freely share working papers, conference papers, and preprints across 30 disciplines, including Economics, Law, Philosophy, Biology, Chemistry, and others. With over 700,000 research papers, it is the second largest preprint server in the world.Gregg Gordon, CEO of SSRN, says, "Authorea has developed a powerful editor for researchers that makes document editing and collaboration easy. We're excited to be working with Authorea to bring a new way of writing and submission to our community of researchers and are keen on advancing this partnership further over time. Authorea is a dynamic tool enabling scholars to easily write mathematical and scientific formulas all in one document without cumbersome formatting often associated with complicated computations."Josh Nicholson, Chief Research Officer at Authorea, says: “We're excited to partner with SSRN to offer a better way for researchers to write, edit, and publish their documents. Authorea was founded to bring document editing into the 21st century and we're happy to partner with SSRN towards this goal."Step-by-step instructions: How to submit to SSRNSSRN Template: https://www.authorea.com/templates/ssrnPress ContactAdyam Ghebre,Outreach, Authorea+1 (646) 598-9285About AuthoreaAuthorea is an online document editor for research and the place where scientific collaboration happens. Authorea is trusted worldwide by leading researchers writing and publishing content in every discipline, from astrophysics to zoology. The online document editor supports a wide range of markup languages and scientific integrations, including the most popular citation management, graphing, and visualization plugins. Authorea is on a mission to accelerate science through a superior web-based research-writing platform that delivers powerful tools and capabilities to researchers.

The arXiv of the future will not look like the arXiv

and 2 collaborators

The arXiv is the most popular preprint repository in the world. Since its inception in 1991, the arXiv has allowed researchers to freely share publication-ready articles prior to formal peer review. The growth and the popularity of the arXiv emerged as a result of new technologies that made document creation and dissemination easy, and cultural practices that incentivized collaboration and data sharing. The arXiv represents a unique place in the history of research communication and the Web itself, however it has arguably changed very little since its creation.  Here we look at the strengths and weaknesses of arXiv in an effort to identify what possible improvements can be made based on new technologies not previously available. Based on this, we argue that a modern arXiv might in fact not look at all like the arXiv of today.

The American Astronomical Society & Authorea Partner for Enhanced Collaborative Document Editing and Direct Submission

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BROOKLYN, NY, July 29 2017 -- Authorea, the online document editor for researchers,  has partnered with the American Astronomical Society (AAS), the world's leading organization for astrophysicists and astronomers. With the partnership, researchers wishing to publish in AAS journals can now use Authorea to prepare their manuscripts and submit directly to any AAS journal for publication. The integration ensures documents automatically conform to AAS journal submission requirements, substantially reducing formatting time and effort.

From Collaborative Authoring to Collaborative Reviewing

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Publishing needs to keep up with research writingModern research is written collaboratively, online, and with more accompanying data and media than ever before. The number of collaborators is going up \cite{Adams_2012} and in many cases the time to publish is going up as well \cite{Powell_2016} -- it's truly a time of great change in the research world. At the same time, researchers have more publication options than ever before \cite{Larsen_2010}. The proliferation of publication options means that researchers have endless options for their work. How do researchers choose the best venue for their work? What happens when the first venue declines to publish a piece -- how do the authors find an alternative? How can publishers evolve to these changing demands? Most of the time submission is grueling for authorsAs most seasoned authors know, the submission process is neither easy nor enjoyable. Often there is a long road ahead of submit-reject-reformat-submit-revise-resubmit-proof. It's not fun. One of the most vexing issue for authors is the intense amount of formatting that goes into conforming to a particular journal style. Submission requirements are vastly different from publication to publication and the result is that authors must spend enormous amounts of time preparing manuscripts.Enter AuthoreaAuthorea is an online document editor that is collaborative and format-neutral. Authorea helps researchers write a manuscript in a vanilla style and then output to thousands of styles (see fig \ref{391184}). Authorea users, which number close to 100,000 and are growing daily, may also submit directly to hundreds of journals.

The Society for Neuroscience & Authorea Partner for One-Click Submissions

BROOKLYN, NY, May 22, 2017 -- Authorea, the online home for researchers to write and disseminate documents, has partnered with Society for Neuroscience (SfN), the world's leading neuroscience organization. With the partnership researchers interested in submitting to SfN may use Authorea to submit manuscripts directly to eNeuro and The Journal of Neuroscience with one click. The integration greatly reduces formatting and data entry overhead for Authorea users by ensuring documents conform to SfN submission requirements automatically.
With the recent launch of its flagship document editor, Authorea has become the go-to place for researchers to write scholarly articles. Researchers have the freedom to write in multiple markup languages, store data alongside in-progress documents, establish collaborative workflows, insert and format citations, and much more. Submitting directly to the world's leading publishers allows any researcher writing on Authorea to have many options for publication.
Josh Nicholson, Chief Research Officer at Authorea, says: “We're happy to be working with Society for Neuroscience to make collaboration and publication easier for neuroscientists. We're excited to work with such an important and engaged community.”
Society for Neuroscience is the world's largest and most prestigious neuroscience organization with over 40,000 international physicians and scientists. Founded in 1969 it publishes some of the world's leading research in the field of neuroscience.
Templates for submission to SfN can be found below
Press Contact
+1 (646) 598-9285
Authorea is an online document editor for research and the place where scientific collaboration happens. Authorea is trusted worldwide by leading researchers writing and publishing content in every discipline, from astrophysics to zoology. The online document editor supports a wide range of markup languages and scientific integrations, including the most popular citation management, graphing, and visualization plugins. Authorea is on a mission to accelerate science through a superior web-based research-writing platform that delivers powerful tools and capabilities to researchers.

The Preprint Citation Bump

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# Abstract

Preprints are widely acknowledged to be beneficial to the research community. However, the career implications of an author preprinting their work are unclear. Here we discuss the implications of researchers preprinting their work in terms of precedence, visibility and citation impact, and manuscript editing. In short, we show that researchers that preprint their work have a citation boost ranging from 83% to 269% and that preprints can in practice improve your manuscript and that can limit "scooping."

# What are preprints?

Preprints are publication-ready research articles that have yet to undergo peer review and be formally published. They are free, openly accessible, and widely reusable under permissive copyright licenses.  They accelerate research communication by putting dissemination under researcher control. While preprints are widely viewed as beneficial for research and are the norm in certain disciplines like physics, math, computer science, and statistics, preprinting is relatively new in other disciplines, like the life sciences, psychology, sociology and others.  In these fields - that are new to preprints - questions and confusion can arise around preprinting, potentially hampering their uptake and utility.

# The benefits of preprinting

Below we highlight the benefits of preprinting your work at the individual level in an effort to encourage researchers to take control of their research. This article aims to show that preprinting is not just good for the community, but also good for the individual scientist, as outlined in "The selfish scientist’s guide to preprint posting" \cite{Kriegeskorte}.

## Preprints allow researchers to claim precedence on a discovery

With funding rates at an all-time historic low (see figure \ref{849950}) researchers are hyper-competitive in many aspects of their careers. This competition, while good to an extent, can severely limit data sharing and open discussion, two practices necessary for the advancement of research.  One particular fear of researchers is that they might be "scooped," (ie their discovery is shared by someone else first).

Why the ArXiv of the future will look like Authorea

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What is the ArXiv?The arXiv, or actually, ar$$\chi$$iv (pronounced "archive", since $$\chi$$ = "chi" 🤓 ) is the most popular preprint repository in the world. (Read: What is a preprint?) It was started in 1991 by physicist Paul Ginsparg (hi Paul! 👋 ) to become a way to quickly and freely give the scientific community access to the submission-ready research papers, as e-prints. While the arXiv initially covered only the fields of physics and astronomy, it grew over time to encompass other fields, such as computer science, quantitative biology, statistics, and quantitative finance. The rise of arXiv has been mostly limited to fields that use LaTeX, a typesetting system for math-heavy documents. This is because:  (1) the most efficient way to submit papers to arXiv is by uploading a LaTeX file which gets compiled to PDF, and (2) pre-printing has historically been a practice popular in the hard sciences --- at CERN, it was performed via inter-library exchange of scanned papers before the web even existed \cite{pepe2005cern}. However, in recent years, pre-prints are catching on as a free (and legal!) mechanism to openly and quickly share research also in the life sciences (see ASAPbio, and BiorXiv, for example).How do ArXiv and Authorea compare?At first glance, ArXiv and Authorea may not seem related to one another. ArXiv is a content repository, while Authorea is a content creation system. However, Authorea - with the launch of a number of publishing features - is quickly becoming an open repository, as well. We think that the open research repository of the future will have a lot of the features and traits that Authorea is developing. Here's why:1. A scholarly repository is more than a PDF dumpThere is growing consensus in scholarly communication circles that academic publishing needs to move "beyond the PDF" (see the manifesto of Force 11). PDFs are a great portable format for printing, but they are not the best format to share, discuss, and read on the web. Every article on arXiv is a PDF (built from LaTeX). As such, it is static, 2-dimensional and non-actionable. It is not a stretch to say that a paper in PDF is merely a digital photograph of a piece of paper. We can, and are doing, better than that. Authorea's repository is a collection of Open Access and Open Science (i.e. data driven) web native papers.

Three Scientific Papers With Pets as Authors 🐾

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The majority of the world's population has not and will not ever publish a scientific paper. That fact is even more true for pets. Yes, dogs, cats, hamsters. Pets. Surprisingly, however, there are papers with pets as authors. Here's a selection of three articles coauthored by our furry friends.

# 1. Hamster: Tisha 🐹

Do you have a paper with a Nobel laureate? No? Well... Hamster Tisha does! The pet hamster of the physics Nobel laureate Andrew Geim was co author on the publication "Detection of earth rotation with a diamagnetically levitating gyroscope" \cite{Geim_2001}. Go Tisha!

Opening Citations to Open Research

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The importance of citations in scholarshipCitations are arguably one of the defining features of research communication. Linking the corpus of knowledge together, across time and space, they connect Einstein's work at the beginning of last century \cite{Einstein_1906} to researchers writing important physics research today \cite{Stanislavsky_2017}. This web of knowledge is immensely powerful for the analysis of ideas over time and for determining what might be important or not. If you imagine the scholarly corpus as a brain you can think of scholarly citations as its neural connections.

Authorea Researcher Spotlight - Dr. Joe Bathelt

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Dr. Joe Bathelt, a scientist at the MRC Cognition & Brain Sciences Unit at the University of Cambridge, researches brain mechanisms of typical and atypical cognitive development in children, with a particular focus on neural constraints. We interview Dr. Bathelt to find out more about his research and why he chose Authorea to write his recent paper, now published in Cerebral Cortex.

Rockefeller University Press & Authorea Make Collaboration and Submission Easier For Authors Through Partnership

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BROOKLYN, NY, March 20, 2017 – Authorea, the online collaborative document editor for researchers, has partnered with Rockefeller University Press (RUP), a leading publisher in the life sciences, to offer better collaboration and submission options for scientists. With this partnership, researchers writing on Authorea can submit directly to The Journal of Cell Biology, The Journal of Experimental Medicine, or The Journal of General Physiology with one-click submission.
Authorea has integrated with a growing list of journals in the past year as it pushes to become the one-stop shop for researchers to write collaborative work and disseminate it widely. Researchers writing on Authorea can write in multiple markup languages (including rich text, Markdown, and LaTeX), can easily search, insert, and format citations, as well as automatically format their manuscripts for submission to leading publishers like RUP.
The Rockefeller University Press provides scientists and the public with peer-reviewed results of groundbreaking research and vital news and information they can trust. With a strong commitment to quality and integrity, RUP strives to publish excellent science using the latest technologies. It carries out rigorous and fair peer-review, applying the highest standards of novelty, mechanistic insight, data integrity, and general interest. All three journals are led by active scientists in partnership with professional editors, ensuring that RUP represents the communities it serves.
Rob O’Donnell, Director of Publishing Technologies at RUP, says: “RUP journals have allowed format-neutral submission for years, making the process fast and efficient for authors. We are happy to integrate with Authorea, who take that efficiency one step further by allowing authors to submit to JCB, JEM, or JGP directly from the authoring tool.”
Josh Nicholson, Chief Research Officer at Authorea, says: “We want to make research more robust, open, and impactful. Rockefeller University Press publishes some of the most important journals and research in the world and we’re happy to partner with them to make the writing, submission, and ultimately publication process easier for researchers.”
The partnership makes formatting and submitting extremely simple for researchers so that they spend less time formatting and more time on their essential work. With this integration,
Press Contact
+1 (646) 598-9285
Authorea is the online document editor for research and the place where scientific collaboration happens. Authorea is trusted worldwide by leading researchers writing and publishing content in every discipline, from astrophysics to zoology. The online document editor supports a wide range of markup languages and scientific integrations, including the most popular citation management, graphing, and visualization plugins. Authorea is on a mission to accelerate science through a superior web-based research-writing platform that delivers powerful tools and capabilities to researchers.

American Geophysical Union and Authorea Partner to Offer One-Click Submission of Manuscripts

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BROOKLYN, NY, March 28, 2017 – Authorea, an online collaborative editor for research documents, has partnered with the American Geophysical Union (AGU) to offer one-click direct submission of articles written on Authorea to a collection of leading earth and space science journals published by AGU.
AGU, founded in 1919, is a not-for-profit professional organization representing 60,000 members in 137 countries. AGU publishes over 6,000 articles annually across its catalog of journals. Authorea has now integrated direct submission to the following AGU journals:
• Earth and Space Science
• Earth’s Future
• Geochemistry, Geophysics, Geosystems
• GeoHealth
• Geophysical Research Letters
• Global Biogeochemical Cycles
• Journal of Advances in Modeling Earth Systems
• Journal of Geophysical Research:
– Atmospheres
– Biogeosciences
– Earth Surface
– Oceans
– Planets
– Space Physics
– Solid Earth
• Paleoceanography
• Reviews of Geophysics
• Space Weather
• Tectonics
Authorea provides industry leading writing tools for researchers. Authors may write in multiple markup languages (including richtext, Markdown, and LaTeX), can search and insert citations from the web or from another reference manager, and can insert data sources and rich media into the document itself.
The partnership streamlines the formatting and submission process for authors. Whereas before authors could spend hours or days formatting documents to meet submission requirements, Authorea automatically formats, packages, and sends submissions to the journal, greatly reducing the time cost of submission for authors.
Josh Nicholson, Chief Research Officer at Authorea, says: “We’re excited to partner and work with AGU to make the editing and submission of research articles easier and more efficient for earth and space science researchers. AGU publishes some of the world’s most important research and we’re excited to integrate to make publishing more streamlined and effective.”
Brooks Hanson, Director of Publications at AGU, says: “As a leader in scientific collaboration and innovative publishing, we’re always looking for ways to improve our publications, scientific collaboration, and the experience for our authors. In partnering with Authorea, AGU provides our authors and researchers with another tool to simplify the submission process allowing them to spend more time focused on their research and less on formatting submissions.”
Press Contact
+1 (646) 598-9285
Authorea is the online document editor for research and the place where scientific collaboration happens. Authorea is trusted worldwide by leading researchers writing and publishing content in every discipline, from astrophysics to zoology. The online document editor supports a wide range of markup languages and scientific integrations, including the most popular citation management, graphing, and visualization plugins. Authorea is on a mission to accelerate science through a superior web-based research-writing platform that delivers powerful tools and capabilities to researchers.

Introducing the 21st-century preprint: HTML, versioned, citable, data-rich.

and 2 collaborators

Authorea was founded with the mission of improving how researchers write and publish their findings. We created a platform that allows researchers to write across formats, to automatically add and format citations from over 86,594,377 scholarly documents, to directly submit to a growing list of leading journals, and to collaborate easily across continents and disciplines with superior version control.  We built Authorea to be the most powerful editor for researchers because we believe that research is fundamentally important in all aspects of life.  Today, we're happy to announce our latest addition to the Authorea toolset: the ability for researchers assign a digital object identifier (DOI) to their Authorea documents.  With this release, you can now write, cite, host data, and preprint on Authorea.What is a preprint?Preprints are publication-ready research papers that are made public before peer review and formal publication. Preprints are designed to address the speed of scientific communication, the accessibility of knowledge and the existing tendency to report mostly positive results.  Preprints have a long history in research dissemination and are part of the story about how the web was created. They have long been used in physics and math with nearly 10,000 preprints posted per month at ar$$\chi$$iv and are starting to gain rapid adoption in other disciplines like the life sciences.  In fact, the growth of preprints in other disciplines was named one of Science's events that shaped 2016.

A New Version Control System for Research Writing

and 2 collaborators

Today, we're happy to announce the release of a new and improved version control for Authorea documents: History view. What is version control?A version control or revision control system automatically records changes to a piece of text over time. As a result, a document will contain underneath it the story of how it came together -- who made which contributions and when -- with the ability to track changes on a granular level over time. The Authorea system is based on Git, the most popular version control system in the world and one originally developed by the creator of the Linux operating system.

Without Data, Are We Just Telling Nice Stories?

At the foundation of research is data.  The papers we write and the figures we make revolve around it and it is what we spend countless hours collecting. And yet, most raw data remains absent from major studies \cite{Alsheikh_Ali_2011}.  This is a problem that has received much attention the past few weeks,  with preliminary findings being released from the Cancer Reproducibility Project, a large multi-year effort to see how robust top cancer studies are \cite{2017}.  Like previous studies in psychology \cite{2015} and cancer \cite{Begley_2012}, the findings from the reproducibility project, that a large percentage of findings are irreproducible or at least very difficult to reproduce raise serious questions and doubts about how we conduct and communicate our research.
Authorea was founded to reinvent the research article so that it is data-rich, interactive, transparent, and replicable.  Not only did we want to make Authorea a place where researchers could collaborate easier and communicate their results more quickly, we also wanted to make sure that the data behind the study could be easily shared.  This is why each article on Authorea is a repository in itself that allows you to host data directly within your article.  We enabled integrations with Jupyter notebooks and various data visualization tools not just to make the document more aesthetically pleasing, but to make it easier to analyze each other's work.  A quote in The Atlantic summarized one problem we're working to fix quite well:
"If people had deposited raw data and full protocols at the time of publication, we wouldn’t have to go back to the original authors," says Iorns. That would make it much easier for scientists to truly check each other’s work.- The Atlantic
We believe that static snapshots of research living in PDFs behind paywalls are inimical to the advancement of research and the findings from the various efforts looking at reproducibility in research support this.  Authorea is first and foremost a modern collaborative editor--we want to make it easy to write your work and utilize the power of the web-- but we're much more than this, with preprint capabilities (DOIs coming soon), direct submissions to journals, and data hosting, we are working to make research communication more robust on numerous levels. Why should the most important documents in the world be shared and disseminated so poorly? They don't have to be and in fact, we're seeing encouraging signs that the next generation of researchers will do it differently.
The following are just a few student papers all utilizing open data sets and analyses on Authorea.
We hope you'll join us and write your next paper with us.  How we make research more robust as a community starts with us as individuals.

The Fitbit of Research Writing

and 1 collaborator

At Authorea we're constantly thinking about how to make research writing easier, faster, and more robust from initial idea all the way through publication. Beyond stressing over making Authorea an impeccable experience and tool for researchers, we also like to think outside of the box for new innovative features that may not be on our immediate radar but are things we'd like to focus on at some point in the near future. Authorea X, if you like.
Today, we'd like to ask for your feedback on one of the new ideas we're working on. We actively sought your feedback when we redesigned our new editor and would like to continue to involve researchers in the development of Authorea as much as possible. After all, we're building a great experience for you!
In our latest brainstorming session, we discussed how we could help researchers improve their writing beyond what we're currently doing.  Specifically, how could we make the writing process one informed by data?  We identified a few key things we thought were important to the researcher based on requests as well as on our own observations and came up with what we're tentatively calling: "the Authorea Fitbit of research writing."

## The Authorea Fitbit of research

While there are numerous metrics aimed at measuring the output of a researcher and the impact of their work \cite{Abbott_2010}, there is no easy way to track how a researcher is writing.  Some researchers have started manually keeping track of their writing progress on Twitter like the online #acwrimo community or the "thesis-writing tracker" by Achintya Rao of CERN but this is somewhat laborious and really just added work.  We think we can do better than a daily tally.  We can automatically track your writing patterns and share with you in a useful dashboard your typical behavior as well as your progress over a certain period of time. With such a system we would hope to be able to provide answers to the following:
• What time do I write most frequently at?
• What are the most common words that I use?
• How frequently do I write?
• How many words am I writing per day, per week, and per year?
These are the things that we think researchers may like to know and thus we started quickly mocking up what this could look like on Authorea.  Our mocks are just initial sketches, heavily inspired by Github, and we hope, with your feedback, that they could become something very useful to researchers.  What would you track about your writing if you could? Tweet at us @authorea or leave a comment on Facebook or this article!

eLife and Authorea Partner to Simplify Submission For Authors

and 1 collaborator

Sample of Science and Authorea Partner for Better Writing Experience

and 1 collaborator

NEW YORK, NY, January 18, 2016 -- Sample of Science and the collaborative writing platform Authorea have partnered to empower researchers around the world to share materials samples more efficiently. Development of novel materials is a growing area of research and the Sample of Science and the Authorea partnership makes it easier for researchers to write brief descriptions of their materials and share the samples with other scientists.
"Sample of Science is solving an important problem in the field of chemistry and materials sciences. We are happy that Authorea can serve as the writing platform for submissions to Sample of Science. If samples from experiments are made more openly accessible, it can help make research more efficient -- something we value greatly” said Alberto Pepe, CEO of Authorea. “Authorea and Sample of Science share a passion for giving researchers great tools that help them do better work.”
Sharing samples of newly synthesized materials is an important step in the research cycle. For example, a carbon material developed in Berlin can subsequently be validated or utilized by research groups in Boston. Scientists who want to increase the visibility of their research and facilitate new experiments can write brief descriptions of their novel materials samples using the Authorea platform. All materials, together with brief descriptions, will be made available on the Sample of Science portal.
Felix Evert, managing director of Sample of Science, is certain that the partnership will improve the research process for scientists who synthesize novel materials. “Better science is all about enabling researchers to disseminate the right information more efficiently. Authorea is an excellent digital writing tool. The lean online template for submission of brief sample descriptions is ideal for chemists and materials scientists who want to communicate their findings quickly," Evert explains.

Sample of Science was founded in 2015 as a digital platform which connects researchers synthesizing novel materials with researchers who need them. The platform publishes open access description of novel materials and facilitates interdisciplinary collaborations based on materials from experiments. The company is located at the Freie Universität Berlin which is also one of the first cooperation partners of Sample of Science. www.sampleofscience.com
Felix Evert
Phone +49 162 276 2928
Authorea is the online document editor for researchers that is accelerating scientific discover. Authorea is trusted worldwide by leading researchers writing and publishing content in every discipline, from astrophysics to zoology. The online document editor supports a wide range of markup languages and scientific integrations, including the most popular citation management, graphing, and visualization plugins. www.authorea.com
Phone +1 646 598-9285

Introducing the Editor of the Future

and 3 collaborators

Authorea is on a mission to build the best research document editor and publishing platform ever made. We believe that the best way to accelerate scientific discovery is to give full control of document creation and distribution to the researcher, and that the best way to do that is to build a web-based editor that enables researchers to collaborate and disseminate their work seamlessly.
Authorea,  like many research projects, started with a question: Why is the research writing process so slow? We started with the rough notion that the internet age was failing to deliver optimal tools for things like collaborative writing and submitting works to publishers.  We refined this core idea and launched Authorea two years ago.
Since then, we've devoted tens of thousands of hours to understand how to build software that makes it easier for researchers to do groundbreaking work. At the beginning of this year, we started building our new editor -- Authorea Beta -- the editor that will bring Authorea to the mainstream to benefit researchers in every discipline.
Today, we're happy to share with you Authorea Beta. Writing research online has tremendous potential for collaboration, dissemination, and discovery. We're here to bring writing online to researchers and we'll be with you every step.

Authorea: accelerating discovery through online collaboration

# Authorea: our pitch.

It has been said that in order to cure cancer, we must first cure cancer research. At Authorea we're improving how researchers work and make breakthrough discoveries by tackling one of the most important parts of the research cycle, which is as important as research itself: scientific communication. Our mission is to reinvent the scientific article - the main vehicle of scientific dissemination - that hasn’t changed in format and scope since the birth of the scientific method. We're bringing the power of the modern web to a process that has not changed in 400 years in order to make research more open, collaborative, accessible, transparent and data-driven. In scientific terms, we're a paradigm shift. Join us as we write the future of research, literally.

Authorea Researcher Spotlight: Achintya Rao

Achintya Rao, a science communicator who works with the CMS Collaboration at CERN’s Large Hadron Collider in Geneva, Switzerland, is currently pursuing his PhD in Science Communication. We first met Achintya when chatting with him through our support chat and then later in person at OpenCon 2016, where he gave a talk on Open Data and Culture Change at CERN. We're pleased Achintya uses Authorea and we enjoyed following up with him here to learn more about his research and how he uses Authorea for it.

Introducing Our New Editor

and 1 collaborator

# A new era

Fall marks a new era for Authorea. Summer was already very eventful -- 8,200+ custom journal templates, increased rendering speed, dictionary support for new languages, improved article metadata, better import and export functionality, and many more improvements (see our product roadmap). Fall is going to be even more eventful! We are launching a modern design and an improved rich-text editor! Our editor "rewrite" marks the culmination of months of work and it is the biggest project we've undertaken since founding Authorea. We hope you'll like it.

We'll be rolling out the new Editor to all our users over the next few weeks after our private beta test. You'll get a message very soon with a link to opt-in.

There is a chance that the Beta Editor is already active for your account. Want to turn it on? Go to your User Settings, then click Editor Preferences and if available, select your Default Editor to be Beta. Every new article you will create from the top navbar (Create New) will be in Authorea Beta.

Here are some of the updates we think you’ll find exciting:

# A modern new look

It took a long time but we finally have a dashing new look: familiar and easy to use like most modern word processors, and at the same time perfectly tailored for the writing needs of researchers. And this is just the beginning. We will continue improving your reading and writing experience.

The death of the term paper, the rise of students as authors.

Scholarly publishing is hard, really hard.  Researchers submit their manuscripts to journal after journal after journal in hopes of publishing their work in the most prestigious outlet. Because of how long and strenuous the publishing process is it's been compared to birth, a battlefield, and a lottery.  Individual student publishing at the graduate or undergraduate level is nearly unheard of--we'd like to change that.

Authorea Acquires Scientific Publisher The Winnower

and 1 collaborator

BROOKLYN, NY, NOVEMBER 10, 2016 --

Authorea (http://www.authorea.com), the online collaborative platform for researchers, today announced it has acquired The Winnower (https://www.thewinnower.com), a pioneering research publisher that offers advanced publishing tools to individual authors.
With the acquisition, Authorea enhances the foremost online platform for researchers to write, cite, collaborate, host data, and publish all in one place. The acquisition follows a financing round led by Lux Capital and joined by Bloomberg Beta, the John S. and James L. Knight Foundation, TechHammer, ff Venture Capital, and New York Angels.

"We are building a powerful toolset for researchers to collaborate," said Authorea CEO Dr. Alberto Pepe. “We're supporting a research model that puts the author first, allowing him or her to write technical research documents online -- with a data layer underneath -- and to control fully the output and dissemination of that effort. We're pleased to welcome aboard the team at The Winnower, which will help provide additional publishing options to our researchers."

The Winnower, founded by Dr. Joshua Nicholson in 2014, is a leading publisher of preprints and grey literature -- outputs that are often overlooked by traditional publishers.

"The Winnower offers traditional research publishing tools, such as a digital object identifier and permanent archival, to non-traditional documents like Reddit r/science Ask-Me-Anything (AMA) transcripts, blog posts, preprints, grant applications, citizen science reports, and more," said Dr. Nicholson. "We're delighted to join the forward-thinking team at Authorea. We share the mission of accelerating scientific discovery through superior research communication tools, and a big part of that is providing authors the tools to control their research from initial spark to output."

##

What might peer review look like in 2030? Find out at SpotOn16.

SpotOn London is back for a one day conference on Saturday, November 5th at Wellcome Collection. The event is jointly held by BioMed Central, Digital Science and the Wellcome Trust. It is part of a series of community events aimed at researchers, science communicators, and anyone interested in science policy.

Creating a domino effect: what can we all do, however small, to make research more open and reproducible?

Issues related to research transparency and reproducibility are becoming increasingly recognized for their importance in communicating and conducting research. However, practices by most academics could be improved.

Open Sourcing Our Exporter

and 1 collaborator

A common workflow in submitting scientific work to a peer-reviewed venue, such as a journal or conference, is to adhere to specially provided submission guidelines. To many this story is painfully familiar: your document must satisfy a long enumeration of requirements, including an official citation style, font face, margin and font sizes, single- or multi-column, frontmatter arrangements, ... The list goes on.

The work on styling a finished document alone is known to take anywhere from a day to a week, irrespective of which tool you used - Word and LaTeX users alike had to sweat it out. What makes this situation a nightmare rather than an annoyance, however, is that more often than not a manuscript is rejected and needs to be resubmitted to a different venue, where this tedious procedure needs to be repeated from scratch. And that process can repeat for several iterations. As academics are urged to publish their work as quickly and often as possible, this type of friction accumulates.

Essay Contest: How has social media enhanced your research?

Social media is generally discouraged in science today. A recent article, "I'm a serious academic, not a professional Instagrammer" castigated scholars with active online social lives. Most advisors won't ask you to "tweet out our paper" or "write a blog post about our findings" and it's likely that you'd close Twitter or Reddit if your colleague or advisor walked by. Some conferences have taken it so far as to enforce a "no tweeting" policy. But social networking is here to stay and will likely become even more integrated into our lives and research.

The Value of Ignorance in Science

and 4 collaborators

Last Thursday, September 22nd, we held our 5th New York open science meetup (#opensciencenyc). Science journalists, Columbia faculty members, and enthusiasts from our open science meetup group came out to hear Dr. Stuart Firestein talk about ignorance in scientific research and why it is necessary and valuable (yes, you read that right).

Reinventing Peer Review

Peer review is arguably necessary for effective communication amongst researchers.  Authors, editors, and the public rely on peer review to ensure a first measure of trust in scientific communication.  While peer review is considered to be integral in scholarly communication by most, its shortcomings are becoming evident. Former editor of JAMA and NEJM Drummond Rennie once said, "if peer review was a drug it would never be allowed onto the market." Is this true? Does peer review, as it is done today, cause more harm than good?

Publish and Prosper: Reddit AMA with Authorea Co-Founder and CEO, Alberto Pepe

and 2 collaborators

Hello world! This Thursday, September 15th from 1:00 - 3:00 pm EST, Authorea Co-Founder and CEO, Alberto Pepe will be participating in Reddit's r/science Ask Me Anything (a.k.a. AMA) series. AMAs were created by the Reddit community as an opportunity for interesting individuals to field questions about anything – and everything! AMAs hosted on Reddit have become an exciting platform for people to have direct discussions and gain insight into the lives of unique individuals, like President Barack Obama, Sir David Attenborough, Bill Gates, Elon Musk and many others. Thursday's AMA discussion topic, "Publish and Prosper; How to Challenge Elsevier" will touch on:how to break the cycle of the individual in academia and squash the collective obsession with academic rankings; how open science and open scholarship will positively shape the future of academic publishing and increase the rate of scientific discovery;introduce the 'paper of the future'; whereby a static paper is no longer viewed as an acceptable form of submission, rather a digital-born format that allows the reader to access and interact with the most important elements of a researcher's work: the data and code.Join the discussion by posting your questions as early as 9:00 am EST! Alberto will be live starting at 1:00 pm EST.https://redd.it/52vtf7

Do the right thing: 11 Courageous Retractions

and 3 collaborators

Retraction Watch is a blog that tracks retractions in science -- and it's probably a site you never want your research to be on. To many, retracting your work means that you've committed fraud, and in most cases can be the end of a researcher's career. However, that's not always the case: in fact, retracting your work for the right reasons can even be good for your career and good for science (﻿Lu 2013). Retraction Watch highlights cases where scientists did not retract their work due to fraud, but rather because it was "the right thing."  Here we take the opportunity to further highlight these pieces and the courageous scientists that did the right thing despite an enormous stigma.

We believe the future of scholarly communication will be more dynamic than it is today. By definition, this will require more corrections and retractions.  Authorea was built to show the full history of a document, from creation to final publication. We allow annotations of the literature and believe that a more dynamic and robust form of communication is the future -- it's what we're building. Join us!

6 Publisher Policies Antithetical to Research

and 3 collaborators

How researchers communicate with one another and the world has changed very little over the last 350 years. Attempts to improve the process have been implemented throughout the years, not all of which have been to the benefit of research. Here we highlight some policies implemented by various publishers that we believe are antithetical to research communication and what we're doing to try to fix them.

65 out of the 100 most cited papers are paywalled.

and 1 collaborator

The web was built specifically to share research papers amongst scientists. Despite this being the first goal of the modern web, most research is still published behind a paywall. We have recently highlighted famous math papers that reside behind a paywall as well as ten papers that have achieved a near rockstar status in research and the public. Here we systematically look at the top one hundred cited papers of all time and find that 65% of these papers are not open. Stated another way, THE WORLD’S MOST IMPORTANT RESEARCH IS INACCESSIBLE FROM THE MAJORITY OF THE WORLD. A few facts about the top 100 cited papers: 1. The weighted average of all the paywalls is: $32.33, rounding to the nearest cent. 2. There are 1, 088, 779 citations of the Open Access articles, so, if they cost the same on average as the Paywalled articles and were paid for individually, they would cost a total of:$35, 199, 108.44–that’s 14 Bugatti Veyrons, or enough to buy everyone in New York City a Starbucks Tall coffee and chocolate chip cookie. In comparison, the total amount for the paywalled articles, assuming everyone bought the paywalled articles individually, is $54, 722, 252.80. 3. That’s 23 Bugatti Veyrons, or enough to buy everyone in New York City a footlong from Subway. 4. Although 65% of the most cited papers are paywalled, only 61% of those paper’s citations are from paywalled journals. Thus the open access articles in this list are, on average, cited more than the paywalled ones. Paywalling the laws of the universe. and 1 collaborator PYTHAGORAS’ THEOREM a² + b² = c² _Pythagoras, 530 BC_ -------------------------------- -------------------------------------------------------------------------------------------------------------------------------------------- ------------------------------ --------- LOGARITHMS logxy = logx + logy _John Napier, 1610_ CALCULUS$ f}{ t} = {h}$_Newton, 1668_ LAW OF GRAVITY$F = G {r^2}$_Newton, 1687_ THE SQUARE ROOT OF MINUS ONE i² = −1 _Euler, 1750_ EULER’S FORMULA FOR POLYHEDRA V − E + F = 2 _Euler, 1751_ NORMAL DISTRIBUTION$\psi(x) = {} e^{2~\rho^2}$_C. F. Gauss, 1810_ WAVE EQUATION${\partial t^2} = c^2 {\partial x^2}$_J. D‘Ambert, 1746_ FOURIER TRANSFORM f(ω)=∫−∞∞f(x)e−2 π i x ωdx _J. Fourier, 1822_ NAVIER-STOKES EQUATION$\rho \left ( }{\partial t} + \cdot \nabla \right ) = - \nabla p + \nabla \cdot T + f$_C. Navier, G. Stokes, 1845_ MAXWELL’S EQUATIONS ∇ ⋅ E = 0 _J. C. Maxwell, 1865_$\nabla \times E = - {e} {\partial t}$∇ ⋅ H = 0$\nabla \times H = {e} {\partial t}$SECOND LAW OF THERMODYNAMICS dS ≥ 0 _L. Boltzmann, 1874_ PAYWALL RELATIVITY E = mc² _Einstein, 1905_ PAYWALL SCHRÖDINGER’S EQUATION$ \hbar {\partial t} \psi = H \psi$_E. Schrödinger, 1927_ PAYWALL INFORMATION THEORY H = −∑p(x)logp(x) _C. Shannon, 1949_ PAYWALL CHAOS THEORY xt + 1 = k xt(1 − xt) _Robert May, 1975_ PAYWALL BLACK-SCHOLES EQUATION${2} \sigma^2 S^2 {\partial S^2} + r S {\partial S} + {\partial t} - r V = 0$_F. Black, M. Scholes, 1990_ PAYWALL EULER’S TRANSFORMATION$^\infty (-1)^n a_n = ^\infty (-1)^n {2^{n+1}}$_Euler, 1755_ PAYWALL RUSSELL’S PARADOX Let R = {x ∣ x ∉ x}, then R ∈ R ⇔ R ∉ R _Russell, 1902_ GÖDEL’S INCOMPLETENESS THEOREM G(x):=¬Prov(sub(x, x)) ⇒ PA ⊢ G(⌜G⌝) ↔ ¬Prov(⌜G(⌜G⌝)⌝) _Gödel, 1931_ Sweet, Sweet Irony: 7 Papers That Should be Open Access But Aren't and 2 collaborators What better way to argue for the benefits of open access than to publish a research paper with restricted access rights? While open access has been shown to be beneficial for researchers and the public by numerous studies (some of which are listed below), these same papers make it pretty self-evident that the move to full open access is going to take some time. It is true that more and more open access articles appear each year -- some predict that the volume of open access publications will overtake subscription publications by 2018 -- yet despite the increase in publishers and researchers adopting open access as a modus operandi, paywalls still remain on the vast majority of articles, including many which tout the benefits of open research. The following is a list of articles that while advocating for open research remain, ironically, behind paywalls: 10 Famous Articles Still Behind a Paywall and 2 collaborators Some research findings have permeated all parts of our culture -- so much so that we often take the actual ideas and access to them for granted. Would you believe that Einstein's "Does the Inertia of a Body Depend Upon Its Energy Content?" remains behind a paywall, despite being more than 100 years old? Here we show 10 famous papers that have achieved a similar "rockstar" status in the public imagination yet are still subject to paywalls. At Authorea, we believe that open communication is the key to advancing research. We're working every day to make it possible for researchers to have full control over their work and its dissemination. Interactive and discoverable preprints and 3 collaborators Scholarly communication is advancing culturally and technologically towards a better future. There are an increasing number of disciplines and people publishing their content under open-access licenses, publishing their work as preprints, and publishing different types of content from data to posters to single figures. We're happy to be part of this push towards a more dynamic and transparent system of communication. In fact, it's one of the reasons we exist--to improve how leading researchers and student's alike communicate their ideas amongst each other and to the world. These are the world's most important ideas, how we communicate them is important. 9th Annual Imagine Science Film Festival x Authorea and 2 collaborators Authorea is delighted to announce a landmark sponsorship with Imagine Science Film Festival, a not-for-profit organization that fosters collaboration between scientists and filmmakers. The sponsorship is part of Authorea's ongoing commitment to heighten the relevance of scientists' research as a benefit to society and to cultivate collaboration across disciplines and borders. We're excited for the opportunity to reach a broader audience with the Imagine Science Film Festival, as they inspire passion for science through film and art. "The Imagine Science Film Festival is a conversation between scientists, filmmakers, and artists to explore the latest scientific advances and theories in unique and thought-provoking ways." - Nate Dorr, Director of Programming Research Olympics and 2 collaborators The 2016 Olympics have captivated the world -- records are breaking, medal counts are climbing, and nationalism is roaring! It's all very exciting. It should get even more exciting in Tokyo in four years time at the 2020 games when several new sports are scheduled to be introduced, including surfing, skateboarding, and... research! Okay, research definitely won't be included, but what if it were? How would each country fare? Here we look at research output vs. Olympic prowess on a per-country basis. 8,249 more reasons to use Authorea Write, edit, submit, revise, resubmit, resubmit, resubmit, resubmit.... Okay, you get the point: we send our manuscripts to lots of journals. The time formatting and reformatting manuscripts is a pain and it is one we are working to ease. Your valuable time should be spent on your research, not tiresome formatting. Today, we've added 8,249 article templates to Authorea! With the addition of these templates we now make it easy for you to write your article for just about any journal out there. We hope you won't submit to all 8,000+ different journals but at least you now have the power to do so! We've also made it easy for users to create their own templates, so if you see a template missing, please feel free to create one.So...How does it work? It couldn't be any simpler. Just browse our template section for inspiration. Don't start from scratch. Our templates give you a mold that you can shape to your liking. Working feverishly on a research paper, grant proposal, university thesis or a class project? We do them all. Focus on your writing on the web, and enjoy Authorea's single streamlined web view of scholarly text. Once finished, you're truly finished - forget about formatting issues. With just a couple of clicks through our Export flow, you're ready to send in that submission! Authorea's journal templates follow correct citations guidelines outlined by the journals, at no extra effort for our authors.We're really just getting started. If you need to send a printout to a colleague in draft shape, line-numbered and double-spaced, it's a selection away. Different journal? Same breeze. Your text, data, visuals, and citations will be updated automatically behind the scenes. In the unlikely event you hit a hurdle, our 24/7 support team will be happy to quality control your article and quickly get it back on the fast track to getting published.This is the first step towards making the writing and publication process as seamless as possible but we've got lot's more coming. We hope you'll join us so that we can make scholarly writing and publishing more effective and more enjoyable. Happy writing! Open Science Meetup with Stuart Firestein and 1 collaborator Authorea is excited to announce our 5th NYC Open Science Meetup on Thursday, Sept 22nd, 2016! Academics Turned Founders: Andrew Preston, Publons and 1 collaborator Peer review is an important issue in scholarly communication. Arguably, it is the defining characteristic between a blog and a scholarly article. Authorea believes in exploring new models of peer review in ways that peer reviewers can be rewarded and recognized. Accordingly, we offer authors and the public at large the ability to annotate documents, to write post-publication peer reviews, and to post work immediately and openly. Publons, an innovative young company co-founded by Andrew Preston and Daniel Johnston, was started specifically to improve how peer review is coordinated, accomplished, and rewarded. We've known Andrew for a few years and are happy to have him as our first interviewee in a new series we're calling Academics Turned Founders. What's Open Access Good For? Absolutely everything! and 5 collaborators Research: the process by which we understand the world, ourselves, and other phenomena ranging from the alpha helix of a protein to the societal movements in politics is what life is. That may be a bit too grandiose, but research is an integral part of advancing humankind forward.Said differently, research is the engine by which progress occurs. Yet, performing successful research is something that is not easy. Unlocking the secrets of life is a laborious task and it requires cooperation amongst people in real time as well as those that came before us. Key to this progress is clarity, completeness, and access. One might guess that this is the what defines the research publishing community. One might be wrong.Scholarly research is for the most part locked behind expensive paywalls in forms that resemble more of something like a trophy than a document used for conveying important of pieces of research in the best manner possible. While there are lots of things occurring in scholarly research that don't make sense, one blatant one stands out. We charge researchers to access other researchers documents-- not in the name of sustainability, but in the name of profit. In fact, we had to invent a word to describe a publication process that is conducive to research: open access. What is #OpenAccess and what is it good for? Absolutely everything, as far as research is concerned. Scholarly Publishing: Unnecessarily Slow in the Modern Era. and 3 collaborators Scholarly publishing is slow, really slow. The time from submission to publication takes on average one year, likely an underestimate considering the fact that many authors are forced to submit to multiple publishers. What Really Happened: Fleming's Penicillin Discovery Penicillin: medicine's greatest discovery. The super-substance became the world's first antibiotic and made many lethal bacterial infections a thing of the past. The man credited with its discovery is Alexander Fleming, who received the Nobel prize (among numerous other honors and distinctions) for his work. What started as an accident--spores floating in through an open window-- turned into a revolution, completely changing the nature of medicine. Incredible. But is that really what happened? What Really Happened: Darwin's Finches Finches are often thought to be the key to Charles Darwin's theory on evolution. These birds were present on the Galapagos Islands when Darwin visited. They varied in size and (perhaps most memorably to grade school evolutionary biology enthusiasts and textbooks) beak shape--seemingly different species of finches appeared on the different islands. Often credited with the inspiration for Darwin's idea of descent with modification, finches are a famous example of Darwin's theories in action... But how much credit do they really deserve? Dear Social Media, Get DNA Chirality *Right* and 1 collaborator DNA stands for Deoxyribonucleic Acid. It is the molecule of life and it is being abused. Abused not by PCR machines and sloppy grad student's in labs but by journalists, designers, and many others on social media. How is it being misrepresented? Like people, DNA has a handedness (right handed vs left handed), or in scientific jargon chirality. DNA is right-handed, meaning it twists up and to the right. It may not be obvious from just looking at the double helix but it's all in the twist. See image below. What Really Happened: Benjamin Franklin's Kite Experiment Ben Franklin, his kite, and lighting. Likely, you've seen or heard about Ben Franklin's Kite experiment somewhere--a stamp, a textbook, or a popular science magazine. It's nearly as famous as the apple that fell on Sir Isaac Newton's head, but did he really conduct the experiment? If so, was he the first? The first report of extracting energy from lightning was published in May 1752 from Thomas Dailbard and his group in France. They used a forty foot tall iron structure, not a kite. A few months later Jacques De Roma, described his proposal to use "a child's toy" to test if electricity could be captured from the clouds. It was not until August of that year that Franklin published his own description. Although typically a man of detail, Franklin wrote how one could use a kite to capture electricity from the clouds during a storm. He described how easy it would be to conduct the experiment, as if to convince readers to try. In fact, a few months after his publication he published a call to his readers for their own experiences with different materials, maybe the first example of #citizenscience? All great truths begin as blasphemies: In Defense of "Silly" Research and 1 collaborator ## "Research is intended to solve life's mysteries." The Decline of Accuracy in Science Communication: Who is to Blame? and 1 collaborator Proper science reporting can take a while. And it should, as daily science news stories—new treatments, tests, products, and procedures—have a huge impact on consumers. While Americans' trust in the media is at an all-time historical low, still 4 in 10 Americans trust mass media. Many journalists are accused of cutting corners, sacrificing accuracy in an attempt to push interesting (and often false) scientific findings at vulnerable readers.In Kill or cure?, Paul Battley lists Daily Mail’s "ongoing effort to classify every inanimate object into those that cause cancer and those that prevent it." Below, we've included the list of articles associated with Aspirin, which apparently both causes and prevents cancer. Authorea User Spotlight: Jenna Morgan Lang and 2 collaborators # What is the main takeaway from your current research and why is it important? Nope! 8 Rejected Papers That Won the Nobel Prize Nobel prize winning ideas are not always accepted by the community. By definition, they are paradigm shifting, revolutionary. Accordingly, many breakthroughs that are in our textbooks today were initially rejected, if not ridiculed, by the scientific community. Howard Temin proposed a reversal of the central dogma, wherein RNA could create DNA. It was called "ludicrous" and his Nobel "came after a lonely battle to overcome derisive criticism from scientific leaders who refused to believe in his theory that some viruses carry their genetic information in the form of RNA, which is then copied into DNA in infected cell." Similarly, Werner Arber, the scientist who discovered restriction enzymes worked, "in a climate of almost total indifference, notably that of the committees and organizations tasked with allocating funds for research" Jacob 1998.Here we outline 8 Nobel prize papers that were initially rejected by anonymous pre-publication peer review and ask, "What Nobel ideas are we rejecting and/or delaying today?" Interdisciplinarity: Working Together Takes Work Cell asked its 40 Under 40 what they thought was the biggest problem facing young scientists today. Todd P. Coleman, associate professor at UCSD stated: A big challenge, but one that I enjoy, is that the important—many of the most societally relevant—problems can no longer be just solved with physics like for the transistor or biology like the for Polio vaccine. It is increasingly the case that we need to bring different groups of people together from very different disciplines to partner and tackle important problems. It is like the analogy that we can no longer act like golf or tennis players—we have to now think in terms of baseball or football. A baseball team will not be successful if it is full of shortstops. Top 3 Social Media Tools Every Researcher & Scholar Needs # Hootsuite Data Visualization: Create Powerful Infographics and 1 collaborator Data visualization helps scientists communicate complex information both effectively and engagingly because being able to visualize information helps brains digest and retain. Thus, infographics are not only impactful, but using them can increase research visibility as they are more easily shared online—like through Twitter! However, not all visualizations are created equally. Wrong presentation—chart type, typography, colors, etc.—can diminish impact and even misrepresent data entirely. Here are our top tips for making quality infographics. 7 Crazy Things You Didn't Know About DNA # 1. There is enough DNA in an average person’s body to stretch 10 billion miles. That's approximately the distance from the Earth to Pluto and back! Secure Research Funding With Visuals and 1 collaborator Among the many challenges scientists face today, a major headache is securing funding. Generally, scientists receive funding based on how much attention their research is estimated to generate. The more popular the topic, the more likely it is to receive funding. For instance, research on cancer gene BRCA2 is more likely to gain traction than frog copulation processes... for now. Fishing in a smaller pool of money means that scientists need a competitive edge to get a bite. Fear not! There are ways to increase attention and discussion of the research for popular and nonpopular topics alike. Infographics and interactive data allow researchers to communicate more effectively and engage readers in a refreshing way. Content with visuals get 94% more total views and is 40x more likely to get shared on social media (Lee). Thus, visualized data can be the path to funding. Essay Contest: How has social media enhanced your research? and 6 collaborators Social media is generally discouraged in science today. A recent article, "I'm a serious academic, not a professional Instagrammer" castigated scholars with active online social lives. Most advisors won't ask you to "tweet out our paper" or "write a blog post about our findings" and it's likely that you'd close Twitter or Reddit if your colleague or advisor walked by. Some conferences have taken it so far as to enforce a "no tweeting" policy. But social networking is here to stay and will likely become even more integrated into our lives and research. Authorea Spotlight: Viputheshwar Sitaraman (Draw Science) Who is the youngest person in the U.S. to ever raise venture capital funding? Vip Sitaraman. Vip—no relation to Very Important Person, although he is pretty damn cool—is a 3-time entrepreneur, scientist, and designer extraordinaire. He is at the helm of GMTRY (parent company of Draw ScienceRXN, and Explica), an open access publishing platform that turns academic papers into infographics. Did we mention he's 18 years old? Data Visualization: Tools for Creating Infographics We weren't all born with the eye-for-design or abe to afford a graphic designer for every need. Luckily, there are many high-quality and free online resources out there to help—did I mention free? Here's a list of my top favorites plus a few points of differentiation for each. Happy designing! When the Obstacle is the Course: Job Security in Academia This post is part of the series called OBSTACLES IN ACADEMIA, which aims to highlight the many challenges young scientists face today. Data Visualization: Intro to Infographics and 1 collaborator Today, science & R&D social media channels have become just as cluttered as consumer social media channels. For academic researchers, trying to get the word out on your research paper has come to parallel digital and online marketing. It’s as if communicating research main points effectively wasn’t hard enough. Now, even trying to stay afloat on Twitter—much less going viral—is a challenge. This is where data visualizations come in to play. Visualized data, such as charts, infographics, and interactive figures can represent extensive amounts of complicated data more coherently. It's significantly faster to analyze information in graphical format (versus in spreadsheets). Consequently, scientists, government bodies, and businesses are able to spot correlations, patterns, trends, outliers, etc. with greater ease. Data visualization also makes communication possible, effective, and interesting. Getting over the subject-specific learning curve (e.g. jargon) often makes sharing findings to the general public hard--even with other researchers! Using visually impactful representations of data gets the message across quickly, engages new audiences, encourages sharing and visibility, and opens the floor to new research opportunities. Click here to read about How the Scientific Community Reacts to Newly Submitted Preprints. According to Buffercontent with visuals get 94% more total views and visual content is more than 40X more likely to get shared on social media than other types of content. In fact, infographics are liked and shared on social media 3X more than other any other type of content. (MassPlanner) So here are a few common types of data visualizations to help the writer to explain and reader to explore large quantities of data. Authorea Partners with Italian Doctoral Association and 1 collaborator June 14, 2016. We're pleased to announce a new partnership with the Italian national association of research doctoral students and graduates, ADI (Associazione dottorandi e dottori di ricerca italiani). The partnership will begin with the Rome-area Chapter of ADI. ADI Roma members will now have access to a free personal Premium plan and to a dedicated research group page on Authorea. Since the number of users who will be able to take advantage of the partnership is limited, ADI is asking all its members (as well as prospective members) to submit an application form. Find more information (in English and Italian) and apply using by clicking this link. ADI represents and protects PhD students and postdocs. It aims to increase grants, help in position search and security, and enhance the overall value of the PhD. Through this collaboration, we hope to make writing for academics easier and accelerate the scientific research process. Happy writing! Authorea Joins Microsoft 365 Education Solutions and 1 collaborator Thursday, June 2 2016. We are excited to announce that Authorea is officially part of Microsoft's Office 365 Education Solutions program! O365 single sign-on allows schools and universities to provision solutions to students and teachers. Over 250 million educators can now easily access Authorea through Microsoft’s App Backpack. MathML on the Web -- Please! Today I merged a pull request for which introduced the following setup for equation editing, as an alpha feature for our RichText editor: 1. The “status quo” renderer, displaying the mathematics on all “read-mode” article components. 2. A new renderer, specifically loaded in the iframe of our editor widget. Why? Because loading MathJax twice is too slow for our show, but we still want our displayed richtext equations to be, well, rich. 3. An additional math renderer, part of our equation-specific editing widget, so that authors can also INPUT formulas in an appealing richtext flow.[1] See the great demos by for examples. You read that correctly - not one, not two, but THREE SEPARATE MATH RENDERERS ON THE SAME HTML PAGE, each of which different due to balancing on the trade-offs of performance, coverage and visualization. I hear you cry: – Well, this is clearly horrible design, simplify and streamline it! Indeed! My thoughts exactly. But the GREAT SOLUTION, the one that solves this problem not only for me, but for the ENTIRE MATH-ON-THE-WEB DEVELOPER ECOSYSTEM, is not for me or my team to implement. This renderer medley can be traced to a single root cause - the absence of ubiquitous support in modern browsers. If you are not familiar with MathML, it is a W3C and ISO standard and a core part of HTML5. MathML does a great job of providing a single language for representing mathematics in structured documents, especially web pages. But while we have that great language, we lack major browser implementations – in fact only Firefox has GREAT MathML support, and has long been the browser-lead in math support. A different perspective tells us that we are just two browsers short of having the tide turn overwhelmingly towards native rendering. I am referring specifically to and . Having native support would allow us – the mortal developers interested in providing exciting and powerful math-enabled web applications – to sleep calmly at night and work proudly at day. And hence my sincere plea to all major browser vendors: ------------------------------------------------------------------------ PLEASE, DO THE MATH. ------------------------------------------------------------------------ P.S. How is the native MathML solution better? - BEST. PERFORMANCE. POSSIBLE. Your browser will be capable to render MathML the moment it loads, just as it can CSS. No extra load times needed. - THE DOM WILL SET YOU FREE As math-on-the-web developers, we need to select into and manipulate mathematical objects, just as all web developers need to manipulate forms and input fields. I want my cool math interactivity widget to be an easy drop-in for any webpage, just the same way that a jQuery widget is. And we can’t have that without equations being a proper participant in the HTML DOM – CSS would have never taken off if say and elements only existed for sites that had first loaded a third-party css.js library. - OUT-OF-THE-BOX ACCESSIBILITY Exposing the MathML source of an equation directly in its web page[2] will be the default state of any HTML5 web page. Math-to-speech and Braille adaptors can then simply use the raw HTML as-is. P.P.S. If you are interested in showing your personal support for adding native MathML, add your vote and voice to the public issues: - Edge MathML support: https://wpdev.uservoice.com/forums/257854-microsoft-edge-developer/suggestions/6508572-mathml - Chrome MathML support: https://code.google.com/p/chromium/issues/detail?id=152430 Personally, I have joined an effort to promote MathML publicly and to remind developers of its many strong suits and far-reaching benefits to the web develpment ecosystem. You can visit our MathML Association website, or follow us on Twitter at @mathml3. [1] We also have an upcoming equation button palette to put the WYSIWYG cherry on our cake. [2] which you can also do today if you manage to carefully jump through the right JavaScript hoops NY Open Science Meetup with Brian Nosek and 1 collaborator Hello Everyone, we're hosting our next NY Open Science Meetup with Brian Nosek on Friday, May 13th, 2016 at 6:00pm at the Authorea HQ, 43 West 23rd Street, 2nd Floor. New York, NY 10010. Authorea User Spotlight - Casey Law and 2 collaborators When did you know you wanted to become a scientist? I took physics as a senior in high school and found it thrilling. It excited me to find a subject that tries to tackle the most fundamental laws of the universe. When I realized I could study that full time in college, I didn't hesitate to declare my major. Can you summarize the main focus of your research? My current research focuses on data intensive uses of radio interferometers. Interferometers have a rather peculiar way of seeing (Fourier transforms abound!) and there are a wide range of algorithms that can be applied to get at the underlying signal. I am tackling projects to perform large surveys, real-time data analysis, and high-speed imaging. Gravitational Waves and the Death of the PDF and 1 collaborator Einstein published in 1916 a paper containing the prediction of the existence of gravitational waves. It has just one author (A.E. himself) and consists of a few pages of text and equations \citep{1916SPAW.......688E}. Fast forward exactly 100 years, the LIGO collaboration announced in a paper that they observed what Einstein had predicted. The paper has more than 1000 co-authors and it condenses, in just a few pages of text, equations and figures, an enormous amount of technical information \citep{PhysRevLett.116.061102}. How is Authorea different from ShareLaTeX and Overleaf? and 4 collaborators Deciding between ShareLaTeX and Overleaf? Choosing the right editor for your LaTeX manuscript is not easy. Here are some key comparison points that showcase how Authorea is different. How many scholarly articles are written in LaTeX? How many people use the typesetting language LaTeX? This is obviously a hard question. However, another way to look at it is to calculate the percentage of published scholarly articles written in LaTeX. Open Science Meetup on April 1 with computational biologist Holly Bik and 3 collaborators We're excited to invite you to our THIRD NY Open Science Meetup hosted at our new location in the Rise Labs in the Flatiron District. Our guest speaker is Holly Bik, an awesome Project Scientist at the Center for Genomics and Systems Biology at NYU. Her work uses environmental DNA sequencing to track changes and patterns in microbial communities, such as the impact of the Deepwater Horizon oil spill on marine microbes in the Gulf of Mexico. She is also heavily involved in software development projects, including Phinch, an open source data visualization framework for large genomics datasets. Holly will talk about her experience as an interdisciplinary computational biologist and how she contributes to the Open Access movement (check out her ImpactStory profile). Don't be an April fool; come geek out with Holly and Authorea in our new office space instead! Wine and light bites will be offered. When: Friday April 1 at 6pm How might libraries serve 21st century information needs? Authorea's proposal. and 3 collaborators This document summarizes Authorea's submission entry to the Knight Foundation's open call for ideas focused on advancing libraries to better serve individuals and communities in the 21st century. Here is the call for proposals. From Einstein to LIGO: 100 years of Science and 1 collaborator Einstein published in 1916 the paper containing the prediction of the existence of gravitational waves. It has just one author (A.E. himself) and consists of a few pages of text and equations . Fast forward exactly 100 years, the LIGO collaboration announced in a paper that they observed what Einstein had predicted. The paper has more than 1000 co-authors and it condenses, in just a few pages of text, equations and figures, an enormous amount of technical information . THE EINSTEIN AND LIGO PAPERS THAT, RESPECTIVELY, PREDICTED AND OBSERVED GRAVITATIONAL WAVES ARE VERY SIMILAR IN FORMAT. SO MUCH HAS CHANGED IN 100 YEARS OF SCIENCE. SO LITTLE HAS CHANGED IN 100 YEARS OF SCIENTIFIC PUBLISHING. The complexity of the LIGO experiment is astounding, as well as the details of what scientists needed to do to reach this milestone. Measuring a change in length equivalent to 1/1000 the diameter of a proton is not an easy endeavor. And yet, the sheer technological and intellectual progress that we witnessed in the last century, with the rise of the internet and large scale computing, is not reflected in the methods we use to write up our science. Little has changed since the time of Einstein. Actually not much has changed since the time of Galileo either! Galileo is one of the founding fathers of the scientific method and one of the first people to ever publish a scientific paper in 1610. That’s 400+ years of scientific advancement and we’re still disseminating papers in paper format (or PDF, which is, really, just paper). Why has scientific publishing changed so little? Scientific papers represent the de-facto currency of academia. Scholars need to publish in journals to get tenure, and in turn publishers have become the “banks” of the academic world. But the paper of the future should encapsulate all the exciting technological progress we have made. It should be interactive, multilayered and contain all the data and code required for the science described to be carefully reproduced. The LIGO group, together with some Open Science advocates, prepared and shared an amazing interactive document where everyone can play with the real data and pipeline used by the scientists to reach their final conclusions. However, this was not part of the original publication, the reason being that the format of the published article does not allow for such integration. We created Authorea to address specifically this challenge. Authorea lives in the cloud and is meant to allow large collaborations to write science and easily integrate data, code and all the material needed to reproduce (and discuss) results. Authorea can allow the long-awaited leap that will move the scientific paper in the 21st century. Authorea goes to Paris and 1 collaborator Great news! We're happy to announce that Authorea is one of the winners of the NYC-Paris Business Exchange competition. We'll be opening an Authorea office in Paris in March 2016. C'est génial! Introducing real time chat for user support and 1 collaborator Do you have a question, problem, idea, bug report or feedback about your Authorea experience? To provide better and faster support for all our users, we recently added a real time chat feature. Go to any document (yes, this one included) and just look for the help chat icon (the speech bubble in the lower right corner), click on it and start a conversation with one of our experts. Ask them anything, they solve problems! The Surfer's Guide to Gravitational Waves In a nutshell: Gravitational waves are ripples in the fabric of space time produced by violent events, like merging together two black holes or the explosion of a massive star. Unlike light (electromagnetic waves) gravitational waves are not absorbed or altered by intervening material, so they are very clean proxies of the physical process that produced them. They are expected to travel at the speed of light and, if detected, they could give precious information about the cataclysmic processes that originated them and the very nature of gravity. That’s why the direct detection of gravitational waves is such an important endeavor. Definitely worthy of a Nobel prize in physics. Gravitational Waves: The First Swell! A BIG DISCOVERY On 14 September 2015 at 4:50:45 AM Eastern standard time, the LIGO experiment detected for the first time the passage of gravitational waves. Scientists saw a very specific pattern of stretching and compression of space-time called a “chirp”. The detection was done independently at the two locations of the experiment, one in Hanford (Washington) and the other one in Livingstone (Louisiana). This amazing discovery has occurred almost exactly 100 years after Albert Einstein published his General Theory of Relativy , and represents the last verification of this beautiful theory of gravity. How did the waves look like? Glassy and double-overhead! Authorea Raises a new round of funding to Advance Open, Reproducible, Data-Driven Research Hi friends! We're happy to announce today that we raised another round of funding to make Authorea better and advance Open, data-driven science and scholarship. This financing round is led by Lux Capital, a VC firm with an incredible track record and reputation in the scientific and academic fields. They recently referred to Scientists as the new rebels! Among the new investors, we also welcome on board Knight Foundation which supports transformational ideas that promote quality journalism, advance media innovation, engage communities and foster the art. Awesome! The full Press Release of the announcement is included below. (Oh, and we're hiring!) Press Release. (Link) NEW YORK --- Authorea, the fastest growing science collaboration and publishing platform, today announced that it has closed a$1.5 million financing to deliver valuable new tools and capabilities to scholars and researchers across the world. The financing was led by Lux Capital, a venture firm that invests specifically in counter-conventional science & technology companies, along with the John S. and James L. Knight Foundation, a non-profit foundation dedicated to supporting transformational ideas that foster informed and engaged communities. Earlier seed investors ff Venture Capital and New York Angels also participated in the round.

Authorea.com is the leading collaboration platform to write, share, and discuss research – all in real-time. It was created in 2013 by Dr. Alberto Pepe, a Harvard astrophysicist, and Dr. Nathan Jenkins, a UC Berkeley physicist, who met while working at CERN and were disappointed by the slow, inefficient, and obsolete ways by which research papers are written and disseminated.

Authorea is currently used by more than 80,000 scholars across 70 countries, in fields as diverse as physics, astronomy and computer science. The company offers users a collaborative online editing platform tailored for academic and technical writing – a word processor, which makes adding citations and equations and formatting references incredibly simple. Authorea is built on a Github-style model and every document created is a Git repository. This allows users to track changes in documents in a very granular way and to easily integrate data into documents.

“We’re extremely excited to welcome Lux Capital and Knight Foundation as new investors,” said Authorea co-founder Dr. Pepe. “Both have strong reputations and excellent track records in backing transformational companies in science and technology.”

Authorea allows researchers and academics of all kinds to share findings, lessons and data, creating richer, more quality information," said Ben Wirz, Knight Foundation director for venture investments. “By enabling collaboration, it can serve as a building block for more knowledgable communities and drive new discoveries and innovations."

"All economic growth depends on new discoveries, which depend on science,” said Adam Goulburn, PhD, Partner at Lux Capital and Authorea Board member. “Authorea is taking on the science of science itself – how it's researched, reviewed, produced, and published. Whether taking on the crisis of reproducibility or shortening the time from discovery to market, Authorea is an indispensable tool spanning breakthroughs from the cosmos to cancer."

"The future of science rests on powerful methods for collaborating on open and reproducible research – Authorea is leading the way to make this happen,” said Sam Arbesman, PhD, Scientist in Residence at Lux. “What Github did for software developers, Authorea is doing for scientists. Forget stale research stuck in static journals, Authorea catalyzes real-time collaborations and sparks curiosity and creativity in the scientific method. Whether powerfully handling formulas, figures, comments, research results or references – it is a game-changer and competitive edge for any scientist.”

Authorea is rapidly growing in fields outside of the hard sciences, such as genomics, environmental science, and computational biology. For example, in June 2015, a dedicated global team of epidemiology researchers began an ambitious project to track the Ebola virus using large-scale genome sequencing. Their groundbreaking research, written on Authorea, was published in the journal Cell and covered by the New York Times. The Authorea version of their article is the only place where readers can peruse the history, workflows, and research data connected with the study. Authorea is poised to shake up the stale academic publishing industry via an online platform that encourages data sharing, and a more open and transparent dissemination of research results complete with all the data sources necessary to reproduce them. Authorea plans to use the proceeds of this funding to encourage more open, data-driven research of this kind.

Concinnitas: The Art of the Equation

and 3 collaborators

San Francisco, CA – On view at Crown Point Press is an exhibition of etchings by scientists and mathematicians, September 4 - October 27, 2015.

We came across this set of beautiful etchings on Artsy depicting mathematical equations. We decided to reproduce them on Authorea, using our equation editor and some LaTeX. Here’s the result.

Library of Words

This blog post describes the rationale and motivation behind the Library of Words, a digital collection of pages filled with every possible combination of 320 words.

Physicists can code

So this happened. At a startup pitch event in Santa Monica last week, one investor asked us: how did you guys manage to build the codebase for Authorea since you're all physicists?The answer is that physicists write code too. Ha! And as a matter of fact, it is not only physicists. Also most computational biologists and medical researchers and virtually any scholar who works with data, in some way, will learn to code. Yes, even psychologists, social scientists, and digital humanists.

Measuring Open Science

and 4 collaborators

# Open Science

“Open science commonly refers to efforts to make the output of publicly funded research more widely accessible in digital format to the scientific community, the business sector, or society more generally” writes the Organisation for Economic Cooperation and Development (OECD) in its newly released study “Making Open Science a Reality”.

In the digital age the role of tools like Authorea is to increase the efficiency of research as well of its diffusion. The benefits of open science identified by the OECD are multiple:

1. Reducing duplication costs in collecting, creating, transferring and reusing data and scientific material; allowing more research from the same data; and multiplying opportunities for domestic and global participation in the research process.

2. The greater scrutiny offered by open science allows a more accurate verification of research results.

3. Increased access to research results (in the forms of both publications and data) can foster spillovers not only to scientific systems but also innovation systems more broadly. (Firms and individuals may use and reuse scientific outputs to produce new products and services.)

4. Open science also allows the closer involvement and participation of citizens.

Authorea on Xconomy

An article about Authorea was recently published in the online magazine Xconomy. The piece, titled Collaboration Platform Authorea Helps Ebola Virus Researchers, Others by João-Pierre S. Ruth discusses Authorea's vision to become a platform for open science collaboration.

Hello, moon

A document by Alberto Pepe, written on Authorea.

How to import documents from arXiv, Overleaf, and ShareLaTeX

and 1 collaborator

and 1 collaborator

Watch this paper in real time at authorea.com/nytm

Authorea demos new Rich Text editor at the NY Tech Meetup

and 1 collaborator

We’re pleased to announce that Authorea will do the first public demo of our new Rich Text editor – Authorea for Word users! – at the New York Tech Meetup tomorrow, September 9, at 7pm.

You can buy a ticket here: http://www.meetup.com/ny-tech/events/220016163/

The presentation will feature our co-founders Nate and Alberto and chief scientific officer Matteo all together on stage, with the Authorea team cheering in the audience. If you live in NYC and want to meet the folks behind Authorea, this is a great opportunity!

The Meetup is held at the NYU Skirball Center for the Performing Arts.

A Tufte-styled scientific article.

A central problem in convex algebra is the extension of left-smooth functions. Let  be a combinatorially right-multiplicative, ordered, standard function. We show that ℓI, Λ ∋ 𝒴U, 𝔳 and that there exists a Taylor and positive definite sub-algebraically projective triangle. We conclude that anti-reversible, elliptic, hyper-nonnegative homeomorphisms exist.

A Moral Imperative: Open Science in the Ebola Crisis

and 3 collaborators

Last June, a dedicated global team of Ebola researchers began an ambitious project to track the virus using large-scale genome sequencing. Their research, published June 18 in Cell, reveals critical information about how the virus traveled and spread over seven months of the recent Ebola outbreak.

The team, which included researchers from over a dozen institutions, made a conscious decision to pursue Open Science practices for this project.

One choice they made was to write their paper on Authorea, a new science editing and publishing website.

The full working version of the paper is now available to the public on Authorea. By using the “History” feature, readers can get a behind-the-scenes look at how the research came together, including every edit and change from the writing process.

“When we were kicking off the study, we discussed how much we would open up what we’re doing,” said co-lead author Danny Park. “Our team comes out of the Human Genome Project, so culturally we come from the open science ’put everything out there’ background. And especially in this kind of emergency situation there’s a moral imperative” to publish the data openly and quickly, he said.

The team chose Authorea in order to make the writing process transparent. Authorea’s History feature allows the public to view every change made during the writing process. Because key technical sentences were revised and words chosen carefully over time, the evolution of the document can be educational, said Dr. Park.

Authorea was just one of many tools used by the research team to publish their work as quickly and openly as possible. The team:

• Published their raw genome data to the GenBank database and Virological.org online forum as soon as it was collected, so that other research teams could use and discuss the data immediately

• Released demographic and clinical metadata on a special website to enable other researchers to spot important trends

• Set up a new website to gather and visualize data from multiple research groups

• Published a Comment in Nature strongly advocating open sharing of data during this and future outbreaks

• Chose Authorea as a platform to write and edit their draft manuscript, allowing readers to view the writing process with full transparency

• Published their article as fully Open Access in Cell

“One of the most rewarding aspects of working in this outbreak response is the connections we have made with so many extraordinary individuals through open data sharing”, said senior author Pardis Sabeti.

The goal of Open Science principles is to produce stronger, more reproducible, transparent scientific results as quickly as possible. It’s a virtuous circle: openness begets collaboration begets more openness. And in a serious outbreak like the recent Ebola epidemic, more open research can quite literally save lives.

Authorea is an online word processor that makes research writing and publishing faster and easier. Created by scientists, for scientists, Authorea encourages and supports Open Science, transparency, and collaboration.

With over 41000 users and a weekly growth rate that has doubled in the past nine months, Authorea is currently the fastest-growing science publishing platform in the world.

Other Resources

Authorea contacts

• Alberto Pepe, co-founder and CEO, Authorea: alberto@authorea.com, +1 (310) 600-3929

• Jace Harker, Growth and Community: jace@authorea.com, +1 585-737-6459

• Tanya Anderson, Outreach: tanya@authorea.com

Key author contacts

Authorea Newsletter - July 2015: Full LaTeX, Templates, and Ebola on Authorea

and 1 collaborator

Keep up the good work! Best regards,

The Authorea Team

New York Open Science Meetup: Are we alone in the Universe?

and 1 collaborator

There is on average one planet orbiting every star in the Universe. Our Galaxy (the Milky Way) is an immense disk of gas and stars with a diameter of about 100 000 light years, hosting about 100 billion stars and, therefore, also about 100 billion planets. Take a deep breath. Now, it turns out the Milky Way is just one of 100 billion galaxies that populate our Universe, a colossal expanding stretch of spacetime with an age of 13.7 billion years. The math is trivial: There are about 10 000 000 000 000 000 000 000 = 1022 planets out there. This number is extremely large. Apparently larger than the number of grains of sand found in every beach and every desert on Earth. But how many of these planets host life? And in particular, how many planets host intelligent life we might be able to communicate with?

RSVP and join us for our second official New York Open Science Meetup. Check this blog post series if you wanna know more.

This event is supported by Authorea.com, Minds.com and the Bitcoin Center NYC.

Public-Friendly Open Science

PREVIOUS “A “MODERN SCIENTIST” MANIFESTO” In the 21st century science is growing more technical and complex, as we gaze further and further while standing on the shoulders of many generations of giants. The public has often a hard time understanding research and its relevance to society. One of the reasons for this is that scientists do not spend enough time communicating their findings outside their own scientific community. Obviously there are some exceptions, but THE RULE IS THAT SCIENTISTS WRITE CONTENT FOR SCIENTISTS. Academia is often perceived as an ivory tower, and when new findings are shared with the outside world, this is not done by scientists, but by the media or even the political class. The problem is that these external agents do not have the necessary background to digest and properly communicate this knowledge with the rest of society. They often misunderstand, over-hype and in some case even distort the results and views of the scientific community. IT’S IRONIC AND SOMEWHAT FRIGHTENING THAT THE DISCOVERIES AND RECOMMENDATIONS FOR WHICH SOCIETY INVESTS SUBSTANTIAL ECONOMIC AND HUMAN CAPITAL, ARE NOT DIRECTLY DISSEMINATED BY THE PEOPLE WHO REALLY UNDERSTAND THEM. At the same time transparency and reproducibility are at stake in the increasingly complex world of research, which is still using old-fashioned tools when packaging and sharing content. This is not only a big problem for research itself, but can give science a bad name in front of the public opinion, which increasingly does not understand and trust the work of scientists. To the average tax-payer science is often cryptic, with most recently published papers behind a pay-wall and the majority of research virtually inscrutable. In this scenario it is hard for the public to access and capture the relevance of scientists’ work. I strongly believe that a society that does not trust its scientists is set on a dangerous course. ACTION ITEMS. To improve the situation 21st century scientists need to: 1. Learn to efficiently share and communicate their research with the public at large. 2. Make their research more transparent and reproducible, so that it can be trusted and better understood by their peers and the public at large. 21st century scientists need to produce “PUBLIC-FRIENDLY OPEN SCIENCE” (PFOS).

Understanding a Dataset: arXiv.org

WELCOME TO ARXMLIV! The arXMLiv project by the KWARC research group at Jacobs University Bremen has been ongoing for almost a decade, dating back to 2006. I was lucky enough to enroll as a bachelor student at Jacobs during that same year, and got personally involved with arXMLiv in 2007. The goal of arXMLiv is to transform the sources of ≈1 million scientific papers from arXiv starting with the author-friendly syntax of TeX/LaTeX and ending with highly processible, machine-friendly, XHTML/HTML5 documents. Over the years we have become partners with the LaTeXML converter, which ambitiously aims at translating any TeX document into as good as possible web equivalent.

A “Modern Scientist” Manifesto

THE TIMES THEY ARE A-CHANGIN Science is going through a rapid phase of transformation. Two important trends are emerging: 1. Research is becoming more complex, requiring larger collaborations and bigger experiments. 2. Science and technology increasingly affect modern society. The first trend is easy to understand. Let’s think of the cumulative knowledge of humankind as a sphere. Scientists work at the surface and try to “push the boundary”. Discovery increases the volume of knowledge. As the sphere’s volume grows, so does its surface area. Therefore an ever increasing number of researchers is required to tessellate the expanding cutting-edge of science. Moreover, contrary to a few hundred years ago when the sphere of knowledge was so small that a single polymath could master large chunks of it, nowadays no human can understand the details of more than a few research topics. To capture the bigger picture and understand very complex research questions, collaborative efforts combining together a number of highly specific expertises are required.

Sharing and Caring. In the Open.

and 3 collaborators

Friday June 26, 2016.

Today is a great day for human rights.

The Supreme Court of the United States has ruled that the Constitution guarantees a right to same-sex marriage. This decision reflects a shift in American public opinion: according to recent polls, 60% of Americans now support same-sex marriage.

As a company devoted to promoting openness and collaboration, Authorea feels strongly this is an important step in the right direction.

Obviously, sharing the ups and downs of life with another person is an immensely more important and complex task than writing a collaborative paper. Yet if we can draw a parallel, we might say that a useful measure of the progress of a society, and humankind in general, is its ability to share and care openly, together.

That’s the way to unlock society’s true potential, and foster creativity and love.

Happy writing.
Happy loving.
Authorea

Open Science Takes Major Leap Forward: Authorea Releases Unprecedented Details of Ebola Study.

and 4 collaborators

NEW YORK – Last June, a dedicated global team of Ebola researchers began an ambitious project to track the virus using large-scale genome sequencing. Their research, which was written on the research platform Authorea and published June 18 in the journal Cell \cite{26091036}, reveals critical information about how the virus traveled and mutated over seven months of the recent Ebola outbreak.

Today Authorea is pleased to announce that the working draft, data, workflows, and full edit history of the paper are available to the public for free on Authorea.

This is the first time that such complete details have ever been released for a scientific paper. This release provides unprecedented transparency and detail, empowering students and researchers to review every change and edit to every word during the writing of this landmark research paper, using Authorea’s “History” feature.

“When we planned this study, our team decided to make our work as open and transparent as possible, and writing the paper on Authorea is part of that,” said co-lead author Daniel Park. “We felt a moral imperative to put everything out there, especially in this kind of emergency situation.”

“Authorea was founded to make researchers’ day-to-day tasks easier,” says Authorea co-founder and Harvard Research Associate Alberto Pepe. “We realized we were wasting time emailing around documents and data. So we built a website where everyone could write and edit in the same place.”

But Authorea also supports a bigger goal: making science more open. The platform is free to use for open research. “We encourage scientists to publish their entire research process: writing, data, and discussion,” said Dr. Pepe. “The default stance is often to be closed, and we encourage more openness and transparency.”

Researchers in life sciences and other fields often withhold their raw data for months before and even after publishing, according to recent surveys. This practice has questionable utility, as it slows the pace of research, makes it less reproducible, and erodes public trust in science.

“Open access saves lives,” said Professor Peter Suber from the Harvard Office for Scholarly Communication and the Harvard Open Access Project, which were not involved with the Cell Ebola study. “Research saves lives, and when access is unaffordable or delayed, the access barriers put lives at risk. This is especially true in a crisis like Ebola where time is of the essence.”

From academia to founding a startup: five tips.

_Thinking of leaving academia to become an entrepreneur? Here’s five tips to improve your chances to succeed._

The statistical likelihood of Steph Curry's ridiculous shooting streak

The best 3-point shooters in the NBA hit around 40% of their attempts with Kyle Korver leading the way at nearly 50%. An oft-forgotten detail is that these numbers occur against NBA level defenses. What would these guys shoot under little or no pressure, ie what would they shoot in practice?

Live Mathematics on Authorea A Case for Transparency in Science

and 1 collaborator

Authorea is a collaborative platform for writing in research and education, with a focus on web-first, high quality scientific documents.

We offer a tour through our integration of technologies that evolve math-rich papers into transparent, active objects. To enumerate, we currently employ Pandoc and LaTeXML (for authoring), MathJax (for math rendering and clipboard), D3.js (data visualization), iPython (computation), Flotchart and Bokeh (interactive plots).

This paper presents the challenges and rewards of integrating active web components for mathematics, while preserving backwards-compatibility with classic publishing formats. We conclude with an outlook to the next-to-come mathematics enhancements on Authorea, and a technology wishlist for the coming year.

How To Write Advanced LaTeX (LaTeX for Power Users)

and 3 collaborators

QUICK INTRODUCTION (TL;DR) Authorea Beta supports LaTeX writing. In order to insert LaTeX: CLICK ON THE INSERT BUTTON IN THE TOOLBAR AND THEN SELECT LATEX FROM THE DROPDOWN. A LaTeX label shows next to the LaTeX block in which you can write LaTeX notation. Some tips for writing LaTeX in Authorea 1. Click anywhere outside of the LaTeX block to render it. 2. Hover on Preview to see a Preview of the rendered content. 3. Do not paste an entire LaTeX article! Instead import documents from your homepage. 4. Only type LaTeX content in a LaTeX block, i.e. everything you would write after . 5. Do not type preamble (e.g. documentclass), frontmatter, macros or figures. 6. To add macros (newcommands) and packages, click Settings → Edit Macros 7. Use the Insert Figure button to insert images (and data). 8. Use math mode for equations, e.g. $\mathcal L_{EM}=-\frac14F^{\mu\nu}F_{\mu\nu}$. 9. Try the citation tool (click cite) to find and add citations, or use \cite{}. 10. To insert more LaTeX blocks click Insert → LaTeX. 11. You can use sectioning commands like \section{},\subsection{},\subsubsection{} to add headings.[1] BACKGROUND has deployed a new backend for its input language, teaming up with the ambitious project, which strives to offer a full reimplementation of TeX with targeted generation of web-first manuscripts, supporting HTML5 and ePub. Note: is the default engine for rendering TeX in Authorea Beta articles. If you bump into any problems, make sure to visit your article settings and select your LaTeX renderer to . In this article you can find an overview of some of our new high-impact authoring features. NOTE: THIS ARTICLE DOES NOT COVER MATHEMATICAL NOTATION. CHECK OUT THIS CHEATSHEET AND THESE EXAMPLES TO SEE HOW LATEX CAN BE USED TO WRITE ADVANCED MATHEMATICS. [1] You can toggle heading numbering on/off from the article settings. This footnote is generated via \footnote{}

How To Create Complex Data Tables (Advanced)

and 3 collaborators

This post showcases some complex tables created using LaTeX. In Authorea Beta, select INSERT → LATEX and use the source code added after each table.

Deluxe Tables with Authorea

Example of an “astronomer friendly” deluxe table formatted with Authorea. This is the example posted by Jess K on astrobetter in How to Make Awesome Latex Tables. For this table we are using the LaTeXML engine, have a look at this quick tutorial if you are a prospective Authorea power LaTeX user. cccccccc 1/3 Bright & & 4.24 ⋅ 10−4 & 6.19 && 96.97 & & & [0.3,3] & & & 1.77 & & 96.7 & 1.9σ 2/3 Dim & & 4.26 ⋅ 10−4 & 4.48 & & 52.77

Interactive Drake Equation

In order to estimate the number of technological civilizations that might exist among the stars, in 1961 Frank Drake proposed a simple equation. Below you can play with an interactive plot showing the number N of communicative civilizations in the Galaxy as function of their average longevity L. You can change the values of the various parameters using the sliders.

Are we alone in the Universe?

In this short post series I try to tackle one of the biggest questions out there: Are we alone? The reasoning leads to some radical implications for the very near future of humankind. Read till the end and feel free to comment as you go. Hopefully this will spark interesting discussions.

1. Habitable Planets How many habitable planets exist in the Universe?

2. The Drake Equation How to estimate the number of technological civilizations in our Galaxy?

3. Astrobiology Is biological life common in the Universe?

4. The Fermi Paradox Is intelligent life common in the Universe? And if yes, does it last?

5. Interactive Drake Equation Use your own intuition to calculate the chance of being alone or not

Are we alone in the Universe? The Fermi Paradox

Previous “Astrobiology” – Next “Interactive Drake Equation”
With an estimated diameter of 93 billion light years and age of 13.7 billion years, our Universe is an astonishingly big place that’s been around for a very long time. When you look up, you only get a short glimpse at a fraction of the hundreds of billions of stars that populate our Galaxy (which in turn is one of hundreds of billions in the cosmos), but it’s enough to make you wonder: “Are we alone?” In the previous post we discussed the likelihood of the emergence of (intelligent) extraterrestrial life. Starting from the famous Drake Equation and using recent findings in astrophysics and some astrobiology arguments, we obtained a simple way to estimate N, the number of communicative civilizations in our Galaxy. This reduces to the product of the chance of emergence of intelligent life fi and the longevity L (in years) of a civilization’s communicative phase:

$$\label{eq:Drake_simplified} N \approx \, \frac{1}{4}\, f_i \, L \,.$$

Are we alone in the Universe? The emergence of life

Previous “Drake Equation” – Next “Fermi Paradox
We are thinking creatures living on a planet orbiting a pretty common star in a pretty common galaxy. Our home planet has been around for about 4.5 billion years, while the Universe is about 13.7 billion years old. We just learned that there are about 1 000 000 000 000 000 000 000 = 1021 planets potentially similar to the Earth in the cosmos, a number larger than the amount of grains of sand found on every beach and every desert on Earth. Are we alone? To answer this question in 1961 scientist Frank Drake formulated his famous equation, which I discussed in the previous post of this series. The Drake equation calculates the number N of communicative civilizations in our Galaxy. In its 2015 form it reads:

N ≈ 2 flfifcL

Academia: a view from the bottom

This post is part of a series called Is Academia Broken? It relates the experiences of Jeff, Authorea’s Community coordinator, and weighing the options on pursuing a PhD. Be sure to check out Alberto’s first blog post, on the perils of early career interdisciplinary research, and his second, on the overabundance of PhDs and dearth of academic positions.

Why should I use Authorea to write my paper?

and 1 collaborator

High Impact Research in Lower Impact Packages

In recent coverage of a massive meta-analysis of the Google Scholar archives, the top-ten “elite” journals are compared to “the rest” in several broad disciplines.

For papers published from 1995 to 2013, there was a 64% average increase of top-1000 cited papers coming out of non-elite journals (here, “elite” = top-ten most-cited journals for a given category; “non-elite” = the rest). Lest you worry these represent the only cited articles in non-elite journals: the total share of citations going to non-elite articles rose from 27% to 47% over the same period.

Part of the reason for this sudden shift is digitization. In the conclusion to the paper the team responsible for Google Scholar (released 10 years ago in November 2014) state:

Now that finding and reading relevant articles in non-elite journals is about as easy as finding and reading articles in elite journals, researchers are increasingly building on and citing work published everywhere.

With the introduction of exactingly searchable databases, the playing field is indeed leveling for access and awareness of all tiers of journals, splashy-high-impact or otherwise. This naturally leads to faster and more efficient scientific endeavors. (Imagine getting even closer, accessing new developments and discoveries in near-real-time. If you think the rate of progress in science is dizzying now...)

Not mentioned, however, is the fact fields have grown more specialized, and publishers have responded by producing more specialty-specific journals. This may in part account for the increased share of non-elite citations: the publication of a groundbreaking article in a lower impact specialty journal will become a necessary citation in many subsequent papers in that and related fields. Another interesting point to consider in future studies is how open access journals measure up in citation rate.
It has also been documented that high impact, elite journals have higher rates of retraction \cite{Fang_2011}. Do the high impact works from non-elite journals show comparable rates of retraction? Given their high impact, many of the same explanations high impact journals give for higher retraction rates should still apply (i.e. increased exposure and thus increased scrutiny).

Regardless, it is clear that new considerations must be made and changes are underway with respect to academic publications. Hopefully scientists return to their roots of open discourse and dissemination of their data so we can get further, faster, together.

Are we alone in the Universe? The Drake Equation

Previous “Habitable Planets” – Next “Astrobiology
There is on average one planet orbiting every star in the Universe \citep{2013ApJ...764..105S, 2012Natur.481..167C}. If this sounds exciting, you might wanna read the previous post in this series. Our Galaxy (the Milky Way) is an immense disk of gas and stars with a diameter of about 100 000 light years, hosting about 100 billion stars and, therefore, also about 100 billion planets. Take a deep breath. Now, it turns out the Milky Way is just one of 100 billion galaxies that populate our Universe, a colossal expanding stretch of spacetime with an age of 13.7 billion years. The math is trivial: There are about 10 000 000 000 000 000 000 000 = 1022 planets out there. This number is extremely large. Apparently larger than the number of grains of sand found in every beach and every desert on Earth.

But how many of these planets host life? And in particular, how many planets host intelligent life we might be able to communicate with?

In order to estimate the number of technological civilizations that might exist among the stars, in 1961 Frank Drake proposed the following simple equation:

Disseminate Better

SO YOU ACTUALLY WANT YOUR RESEARCH READ... Every year in science, tech, and medicine, on the order of 2 MILLION PAPERS are published. That’s a lot of papers. To remain current with their field, physicians must read about 20 PAPERS A DAY. Given the growing “scourge” of cross-disciplinary science and the interconnectivity of life, our world, and everything, 20 papers honestly seems low. How, then, is an average journal article only read by 10 people, or only 20% of _cited_ papers actually read? Maybe it has to do with the overextension of researchers (see Alberto’s post above for massive discipline-spanning course lists). Or maybe it has to do with the way papers are presented. They’re long, in archaic formats, and only accessible with a background in the given discipline (and, critically, freedom from paywalls). Why can’t we - scientists/communicators of knowledge/sharers of discoveries - agree to write clearly, concisely, and for broad impact and appeal? Many universities and other research institutions have press offices that interface with the public for just this reason. This is critical, as institutions’ research and resources help attract more funding and, nobly, should be shared with the world. The problem? You, as the person who did the research, probably know it better! And you (hopefully) won’t oversell it!

Working on a Ph.D.? There may not be an academic job for you at the end of the tunnel.

This blog post is part of a series called IS ACADEMIA BROKEN? This is the second in the series and it discusses the overabundance of PhDs compared to the number of available academic openings. The first blog post, on the perils of doing interdisciplinary research early in your career, can be found here.

Lessons on Sharing from Bacteria

A recent article in Nature Communications \cite{Benomar_2015} is extremely informative.
Like many good studies, it takes assumed fixtures or mainstays of a field (in this case isolated culturing in microbiology), flips them in some way, and arrives at novel observations and conclusions.

Bacteria have usually been studied in single culture in rich media or in specific starvation conditions. These studies have contributed to understanding and characterizing their metabolism. However, they coexist in nature with other microorganisms and form consortia in which they interact to build an advanced society that drives key biogeochemical cycles.

Briefly, the authors showed co-cultured bacteria (i.e. two different species from the same environment were grown together) formed physical connections with each other to allow one species to harness the other’s unique metabolic chemistry when the former could not survive under the given starvation conditions. In turn, the donor species growth was elevated compared to isolation due to accessing it’s partners’ own metabolites.

The researchers got some great pictures.

Esther Lederberg: _Techniques and Tools Spanning Generations

_BEYOND MARIE CURIE_ Marie Curie. Maybe Rosalind Franklin. These are two of the main names that come to mind when one thinks “women in science.” The reasons more female contributors to science aren’t a larger part of our collective consciousness are many and unjust and unfounded. Better coverage of these issues abound, and the tides are _very_ slowly turning, but MANY MAJOR SCIENTIFIC ADVANCES, OFTEN BY WOMEN, ARE STILL NOT WELL-KNOWN. That’s why I wanted to give Dr. Esther Lederberg a mention. She was a microbiologist at the forefront of 20th century discoveries (lambda virus, gene transfer, fertility factor F, etc.) in bacterial genetics that are now ushering in 21st century revolutions in biotechnology. What’s unfortunately not revolutionary, however, was the overshadowing of her career by that of her (ex-)husband, Nobel Prize winner Joshua Lederberg. Besides making major contributions to his Nobel-winning work, she developed innovative tools and methods that allowed better study of the incredibly small. It goes without saying, but lacking the edge these techniques provided, her husband’s laureateship may have been at risk. One of these tools was remarkably simple, but nevertheless incredibly powerful. This was REPLICA PLATING. A piece of velvet is held taut in the shape of a petri dish, a dish with isolated bacterial colonies on it transfers an identical pattern of the colonies to the velvet. This creates a “stamp” for the colonies, allowing the re-creation of the same species’ colonies in the same pattern on any type of plate a researcher would want (e.g. with or without a critical nutrient to see the effect on the bacteria). Then, researchers can test differentially affected colonies and probe what makes them distinct. Later in her career, Lederberg headed the Plasmid Research Center, a now-defunct institute at Stanford. Here, she oversaw the study, cataloging, and distribution of countless newly discovered bacterial plasmids (circular pieces of DNA) that contained resistance-contributing genes and many others that are now hallmarks of microbiology labs across the world. Beyond the gender bias in science, Esther Lederberg serves as another example of bias: that of a researcher who makes ENORMOUS AND IMPACTFUL CONTRIBUTIONS that don’t get big splashy headlines. That don’t get Nobels (fun fact: she and her husband were the first team to share a microbiology prize a mere two years before he received the Nobel). That don’t necessarily get you a place in popular memory. Why is this? Tens of thousands of researchers everyday must use plasmids of genes she first systematically studied. How can we better ensure tool makers, information sharers, disseminators, and distributors get fair credit? BY SHARING THEIR STORIES BIT BY BIT AND BASE BY BASE.

Open Peer Review with Authorea

and 3 collaborators

The peer review process is a pillar of modern research, verifying and validating the ever-increasing output of academia. While the academic community agrees that some process of review is necessary to ensure the quality of published research, not everybody agrees on the best approach. In particular, doubts have been cast on the current peer review process: most journals select and assign one anonymous referee (few journals assign two or more) who is in charge of reviewing the manuscript and recommending it for publication or rejection. The argument is that the current peer review system is becoming inadequate. Here’s an incomplete list of issues: - Research is increasingly collaborative, complex, and specialized. Thus, it is less likely that one or a few referees can have the necessary expertise (and time) to properly handle many modern articles. Simply put, THE AVERAGE NUMBER OF AUTHORS PER PAPER HAS BEEN STEADILY INCREASING IN THE LAST FEW DECADES, WHILE THE NUMBER OF REFEREES PER PAPER HAS NOT. - “Publication pressure” means there is a growing number of papers to referee. This need can not be easily matched since scholars, who need to constantly publish and engage in the “funding race”, HAVE LESS TIME TO BE DEDICATED TO COMMUNITY SERVICE (in a “single referee” system the review process is very time consuming). - Given the anonymous nature of peer reviewing manuscripts, RESEARCHERS WHO VOLUNTEER THEIR VALUABLE TIME AND KNOWLEDGE DON’T GET RECOGNITION for contributing. - Cases of peer-review scams, mostly from predatory open access publishers, have grown in number over recent years. A number of journals, exploiting the publication pressure climate, accept and publish articles with LITTLE OR NO PEER REVIEW. - Similarly, there are reports of fraud in which authors review their own or close friends’ manuscripts to give favorable reviews .

Authorea launches Open Science Meetup in New York City

We’re happy to announce today the launch of an Open Science group which will meet monthly in New York City and discuss Open Science, data-driven science, scientific transparency and reproducibility and the future of scholarly writing and publishing.

New York Open Science Meetup

P.s. There will be PIZZA.

A Git History and Philosophy of Science

On the left, you’ll see a little clock icon - this opens the article’s History: a Git-based log of updates and edits authors have applied to the article. This post should hopefully only have one entry as it’s short and typed in one sitting (edit: this is never the case), but we all make mistakes.

Two interesting ideas to meditate on, w.r.t. science and scholarly communication:
1.) What would a Git history look like for an entire piece of research, or even just the many iterations of a single experimental procedure? GitHub does this for software development of course (we can integrate your articles with your GitHub repos by the way), but there’s a whole untapped academic ecosystem - how do thoughts mature and develop in other fields?
2.) If you had a Git History of Science, there would be so many re-additions and re-deletions and entire huge sections removed (phlogiston, anyone?), Compare views would be a wash of green and red. How many “mistakes” have been made and re-made over time? What could we learn from the trends and developments of knowledge?

Science is really a process and a way of thinking. Why aren’t we keeping better track of the thought process and showing errors made along the way? It would help us build or fork better off each others’ works for one thing. Less redundancies and unnecessary pitfalls as well. Plus “mistakes” are a helpful and fateful force in the scientific process itself. Think about any great thinker, writer, artist, maker. I bet any of their rough drafts would seem pretty valuable now.

In what other ways might we benefits from having detailed histories of inventive, creative, and thoughtful processes?

Peer/Pure Fabrication _what can the academic community do to combat misconduct in peer review?

Perhaps you have heard of the peer review fraud scandals rocking several big journals. Rings of researchers’ quid pro quo favorable reviews; PIs reviewing their own work unbeknownst to editors; probably other bad things that we haven’t found out about yet. Or perhaps you remember prank paper generator SCIgen: it has produced many nonsensical manuscripts that were “peer reviewed”, accepted, and later and embarrassingly retracted. To combat the systemic problem these jokes expose, Springer designed SciDetect to do the job a “peer” should be able to do in the first place – spot blatantly obvious bullshit. Maybe you even know of “soft fraud” – knowing that editors have sympathies or vested interests in a sub-discipline at _Journal X_; reaching out to an old colleague likely to review your manuscript; frequently collaborating with big name PIs whose brand has more clout than carefully done and clearly communicated science likely ever could. WHAT CAN WE DO?! That is the question. Certainly _Nature_ charging authors for faster peer review is not an intended answer . At Authorea, we think all levels of the scientific process would benefit from some openness and transparency. While different researchers might draw different lines, experimenting with open peer review seems like a good place to start (its kind of astounding that post-publication open review isn’t widely practiced yet). Open up your work to the light of day and get some honest open feedback that makes it better – what if adding more eyes brought about changes that got your manuscript accepted to a higher tier journal than you hoped? If that’s a solidly achievable best case, what’s the worst case? “BUT WHAT IF I GET SCOOPED?” This is always meant as the inevitable and terrible outcome of open access. To ensure speed, maybe you specify a time frame. To ensure security, maybe you specify no anonymous viewing or commenting. But really, that won’t change much. Without any data (open or paywalled), I’m pretty confident the majority of “scooping” incidents are the result of many players shooting for the same goals, smart people working hard, and good old-fashioned word of mouth. Maybe if we shared more we’d all get so much further! That’s the thing: as scientists we are proud of our work. We publish to show the world, so why not show it off sooner? Get credit faster? Get more feedback and make more useful connections? These represent some major features of the Internet that researchers are still chronically under-utilizing, and it was invented for us! THIS IS THE 21ST CENTURY. WE SHOULD SCIENCE LIKE IT.

Paracelsus: Prince of Physicians, King of Chemists _Original Rockstar of Science

Philippus Aureolus Theophrastus Bombastus von Hohenheim, self-styled as PARACELSUS, was a Swiss-German polymath and occultist active in the early 1500s. Notable among his many contributions (including the designation “father of toxicology”) was his emphasis on observation when knowledge from the past held in highest regard. This belief, admittedly revolutionary at the time, was further reflected in his personal motto: _alterius non sit qui suus esse potest_ (“let no man belong to another who can belong to himself”). He refused to follow centuries-old schools of thought, relying on his own wits to understand the world around him. Paracelsus’s defiant independence naturally clashed with authorities, only serving to stoke his ego (see quote below). His challenges to traditional medicine, advocacy for observation as the path to knowledge, and use of common language for scholarly communication (learned individuals only lectured in Latin) all reflect changes society still struggles with today. WHAT CAN WE LEARN ABOUT SCIENCE FROM A 16TH CENTURY MYSTIC? Science, compared to other fields like math or art or finance, is formally a recent development. The first text to resemble a modern journal article - Galileo’s _Starry Messenger_ - like Paracelsus and his philosophy, is prophetic of open science and data. Paracelsus believed knowledge and the information behind it should be wide-spread (e.g. even physicians of his time were comparably educated with barbers and butchers ) as well as rigorously examined and questioned. He also thought he was incredibly smart:

An Arctic Journey: Chasing the Solar Eclipse

and 2 collaborators

FABIO, WHEN DID YOU DECIDE TO GO WATCH AN ECLIPSE IN THE ARCTIC? I’ve been feeling this urge to visit the northernmost parts of Earth for a while now. My PhD in Stockholm gave me the opportunity to explore the Norwegian coastline and Lapland, but the Arctic was a different story. A sort of forbidden dream. Then last year I started a postdoc at Yale, in the research group led by John Wettlaufer, who’s an expert on sea ice and the Arctic. When I heard there was gonna be a total solar eclipse at Svalbard I knew I had to go. WHERE IS SVALBARD, EXACTLY? Svalbard is an archipelago situated about half way between continental Norway and the North Pole, and it is an outpost for research and arctic exploration. In Longyearbyen, a little city of about 2000 people, and Svalbard’s capital, there is the world’s northernmost institution for higher education and research: the University Center in Svalbard.

Want to get tenure? Stay away from interdisciplinary research.

This blog post is part of a series called IS ACADEMIA BROKEN? This is the first in the series and it discusses the perils of doing interdisciplinary research for early career academics. You can find the second blog post of the series here.

LaTeX is Dead (long live LaTeX) Typesetting in the Digital Age

# Welcome to the Pitchfork Party

This post comes in the context of a series of healthy discussion pieces on authoring scientific content for the web:1

In this text, I will try to elaborate on the merits and deficiencies of using a pre-web authoring syntax, LaTeX, for writing modern publications in 2015 as active web documents. My stance is evolutionary – we should adapt our existing tools to the new environment and in the process gain insights for what the next generation of tools ought to be.

If you are a working scientist who authors in LaTeX, I will suggest how to gradually adapt your existing toolchain, while making your first steps towards the future of publishing. If you don’t find the technical details interesting, you can skip to my suggestion in Section [sec:conclusion].

If you are a developer, I will argue with you that the next generation has not fully arrived yet.

## We’re not going to start a fire

Feelings can burn strong when the words “LaTeX” and “Web” appear together.

Debates over tool superiority, especially when online, tend to quickly become heated and destructive. My best guess is that the personal experiences with our tools over time evolve into full-blown relationships, with all associated pros and cons of that status. Maybe you truly love your tool, and that is great, please go ahead and nourish that feeling. Meanwhile, I will step back into more abstract territory and try to poke some applications with a stick and see when they bite. You’re welcome to tag along, but there’s no need for extra venom.

1. The author has his own torch in hand: I am a core contributor to LaTeXML and an enthusiastic developer at Authorea. So keep that bias in mind while reading on.

Open Review on an ApJ-submitted Pre publication

and 3 collaborators

A recent article titled The spin rate of pre-collapse stellar cores: wave driven angular momentum transport in massive stars was written on Authorea and submitted to the Astrophysical Journal (ApJ) and to the arXiv as a pre-print. While waiting on peer review from the ApJ, the authors want to test Authorea as a platform for OPEN PEER-REVIEW. By going to the document’s page, you can comment on a section, figure, observation, sentence, or the whole piece. The authors and other commenters can respond and further the discussion. And it’s all out in the open, just how science was meant to be. But it doesn’t stop there. You can also view full-size, high-resolution versions of the paper’s figures, as well as easily follow links in the References at the bottom of the page. In the paper, show for the first time how internal gravity waves, excited in the turbulent layers of stars at least ten times larger than the Sun, can radically change their internal rotation rate. In particular, these waves – somewhat analogous to ocean waves – can determine how rapidly the stellar core spins around its axis when the star is about to die and become a supernova. The spin of a pre-supernova core is important because it deeply affects the stellar explosion and determines the rotation rate of the stellar remnant (neutron star or black hole).

The Uncomfortable Calculations of Publisher-Library Relations

# The System as It Stands

A study published in July 2014 used the Freedom of Information Act to request access to contracts between academic publishers and 55 university and 12 consortia of libraries \cite{Bergstrom_2014}. 360 contracts were received, documenting prices and bundling of deals from 9 major publishers (including Elsevier, Springer, Wiley, ACS, and Oxford University Press).

The contracts show the result of opaque sales practices, manipulation, and varying degrees of negotiation skill: publishers can charge vastly different prices for the same products and services. Keep in mind they are selling to nonprofit institutions whose members

• conduct groundbreaking and lifesaving research (often taxpayer-funded)

• volunteer their time and talent to the publishers’ peer review process

• pay for the submission of articles published in journals

• and are now buying it all back.

Also keep in mind that top publishers have profit margins on the order 30% or more.

In the mid 1990s, with the shift from print-only to digital distribution, economic formulations changed. No longer would a research university need to subscribe to multiple copies of in-demand journals. No longer would storage space play a significant role in decisions (e.g. storage and maintenance costs for a 2500 page journal volume range from $300-1000). No longer would impact be a limiting factor for purchased titles, or as it’s now emerging, should it even be. And publishers could now offer their whole catalog of journals at one discounted “Big Deal” price. In the words of Derk Haank, then Elsevier and current Springer CEO: But what it [electronic publishing] does do is to dramatically lower the marginal costs of allowing access.... [The cost for each new users] is virtually nil and that means that we should be more creative in the business model.... where we make a deal with the university, the consortia or the whole country, where we say for this amount we will allow all your people to use our material, unlimited, 24 hours per day. And, basically the price then depends on a rough estimate of how useful is that product for you; and we can adjust it over time. [emphasis added] Here, “adjust it over time” means mandate an average 5-6% price increase annually. Bergstrom, et al calculate: “A bundle whose price increased by 5.5% per year would double its price between 1999 and 2012, whereas over the same period the US consumer price index rose by 38%.” [emphasis added] What’s more, such “creative” business models force library administrators to try to quantify abstractions like the value of information. Information, however, is context dependent. The difference of opinion on a paper’s importance could range from “meaningless” to a critical insight for unraveling a disease pathway. At the end of the day, an all-inclusive “Big Deal” bundle may be easiest – if funds are available. When cost limits access, however, researchers may rely on e-mailed PDFs from helpful colleagues at better-equipped campuses. Another solution, when access is out of reach or publication slow (e.g. a year from initial acceptance to publication is common for some Statistics journals), is pre-print repositories like arXiv. Unfortunately, the articles aren’t peer-reviewed, a reason big publishers can charge so much. This is also a reason we think researchers (and journals!) might want to try their own pilot study of Authorea-as-interactive-repository or submission platform. This is the 21st Century, scientists should be writing and disseminating like it! Have thoughts about this? Let us know in the Comments or follow us to get updates! SOLVE, four days that could change the world and 1 collaborator Tens of thousands of innovators met in Austin, Texas last week to discuss emerging tech, science, and innovation. It was the Interactive portion of South by Southwest (SxSW). Authorea was there. Among many great events, the MIT Media Lab presented “SOLVE”, an initiative set to bring together the most gifted researchers and innovators to identify and tackle challenges where new thinking and emerging technologies have the potential to make the world a better place. SOLVE identified four main themes: Learn, Cure, Fuel, Make. Authorea's APS Travel Grant Winners and 1 collaborator Today we are proud to announce the winners of our travel grant for European student attendees of the APS March meeting in San Antonio, TX. WHY DID AUTHOREA SPONSOR THESE TRAVEL GRANTS? At Authorea, we want to build bridges between scholars, disciplines, and cultures in order to form a collaborative scholarly community at a global scale. Sometimes, _face-to-face meetings are the best catalysts for sharing and creating new connections_. Two of us at Authorea - Alberto and Matteo - are from Italy. They have benefited from academic careers abroad (postdocs at Harvard and University of California, Santa Barbara, respectively) also thanks to important connections they made at international conferences in the early stages of their academic career. Our winners for the March Meeting are ALBERTO DE LA TORRE and JUAN TRASTOY QUINTELA, both from Spain. We hope that the connections they made at the March Meeting will bring fruitful collaborations. Joys of Pi: A test server and monitor host for the startup developer and 2 collaborators I work at a startup. We get things done on a budget. This is a summary of how I got: - A new test server for my local dev machine - An extra monitor for my dev setup - Tons of FUN! And all for less than$100.

Authorea at SxSW 2015

Who’s going to be at SxSW this weekend? Matteo and Alberto will be there as part of an event called ffMassive. If you are going to be in Austin, TX on Sunday March 15, stop by for drinks, life size jenga, and to learn more about music, tech, and science, of course. Here’s the RSVP link: https://ffmassive2015.eventbrite.com/

We have a couple of VIP tickets left for the after party (invite-only). Interested? Just let us know at hi@authorea.com

How To Import EndNote

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Thomson Reuters’s reference management system ENDNOTE makes it easy to store, share, annotate and export your citations in selected formats. FIRST TIME SETUP IN ENDNOTE Adding references from EndNote is easy. You’ll need to do a little one-time prep work first. STEP 1 Download the BibTeX output style from the EndNote homepage. STEP 2 Add the BibTeX output style to your EndNote Styles folder. STEP 3 Open EndNote and through the Edit drop-down menu, go to Output Styles > Open Style Manager...

How To Import Mendeley References into Authorea documents

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To import Mendeley references into your Authorea writing environment follow these simple steps (more here). IN MENDELEY First, make sure you set the Mendeley default export format to BibTeX. Follow the steps below:

How To Import Zotero references to Authorea

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To import Zotero references into your Authorea writing environment follow these simple two steps (more here) IN ZOTERO First, make sure you set the Zotero default export format to BibTeX. Navigate to Preferences, Export and select BibTeX as the default format.

Authorea Australia Tour 2015

G’day- Authorea’s Australia Tour (Au♥Au) starts next week! Our co-founders, Nate and Alberto, will be down in Oz for the Research Bazaar conference at the University of Melbourne. We’re so very excited to hang out with our friends at UniMelb and make some new friends in the Melbourne area (and beyond!).

We’re working on completing our schedule of speaking engagements. Below is a rough schedule of events/talks/demos that will take place during the tour. We will be updating it as we go along.

Authorea sponsors student travel grants for APS conferences

We’re very happy to announce a special TRAVEL GRANT for European FGSA and FIP members attending the AMERICAN PHYSICAL SOCIETY APS MARCH MEETING 2015, in San Antonio, Texas. Authorea is committed to helping the advancement of scientific collaboration and this travel grant aims to foster the interexchange between young EU and US members, helping students and postdoc to integrate in the international APS community and to share their different experiences. These travel grant will be recognized at the Student and FIP Receptions, during the March Meeting 2015. For more information on the travel grant and application instructions please visit http://www.aps.org/units/fgsa/travel/ and http://www.aps.org/units/fip/awards/travel-grant.cfm.

Authorea HQ moves to Gramercy Park area, NYC.

Goodbye Soho, hello Gramercy! Today we move Authorea’s HQ to a new office in the Gramercy Park area of New York City. We’re excited to move to a bigger, brand new office (with windows!) in this “exclusive neighborhood boasting cute shops, cool taverns, and one very special members-only park” (yep, this is how Airbnb depicts Gramercy Park). Update your address book and come say hi.

Authorea

120 E 23rd Street

5th Floor

New York, New York 10017

Authorea launches #institutions

We’re launching #Institutions today! Since the beginning of Authorea, it’s been our mission to work closely with universities, departments, research labs, and libraries to help them manage and curate scholarly content.

So, what’s new? You can now:

1. Browse institutions and find yours! If it’s missing, let us know and we’ll add it.

3. Let your librarian or PI know about #institutions at Authorea, so that they can claim and manage their institutional page.

How To Comment

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Authorea has a new powerful commenting framework built into the editor. Each document has comment bubbles to the right of the text that may be toggled to leave or view comments. HOW TO COMMENT To insert a comment anywhere on the document, click on the comment icon that appears on the right margin of your document

Authorea supports GIFs!

Use a fancy GIF in your next scholarly paper!

Bill Gates on the Future Wall-Free College in Your Pocket _no books or 8am class, just learning

Bill Gates has some thoughts about education. Specifically, how its future might look. He recently visited Arizona, where Rio Salado College and University of Phoenix are broadening access to education. improvements include: 1. LOW COSTS (compare Rio Salado’s $84/credit-hour vs the 2011 average$250/credit-hour for in-state, public tuition); 2. FLEXIBILITY (many classes start new sections every week); 3. online and MOBILE INTEGRATION (U of Phoenix offers an app for studying and course management from anywhere, anytime). These innovative offerings help solve practical problems for modern education. Given the 40% college dropout rate, ever-rising costs of tuition, associated increases in post-college debt, the need to stay competitive, and the desire to explore new areas of knowledge, anything that lowers friction is certainly welcome. Given that these two institutions alone serve over 350k students, you also can’t argue with demand that’s clearly there.

Are we alone in the Universe? Habitable planets

A revolution has occurred in the last two decades in the world of astrophysics. It all started in the mid ’90s with the first discovery of new worlds around other stars. The term “Extrasolar planet” (or Exoplanet) became widely used to identify planets orbiting a star other than the Sun. A planet is a celestial body massive enough to be bounded by its self gravity (unlike a rock or an asteroid, that are kept together by electromagnetic forces), but not massive enough to produce energy through nuclear fusion (as stars do). Planetary scientists have confirmed the existence of more than 1500 exoplanets and have identified a few thousand exoplanet candidates that require more investigation before they can join the planet club (see exoplanets.org for the most recent figures). The most remarkable discoveries came only in the last couple of years thanks to the Kepler space telescope. This amazing instrument has been patiently looking for the extremely tiny dimming induced by the passage of a planet in front of its host star. The wealth of data provided by Kepler has revealed an astonishing fact: “When you wish upon a star, you are wishing upon a star with planets” (W. Borucki). There is on average one planet orbiting every star in the Universe \citep{2013ApJ...764..105S, 2012Natur.481..167C}. Just in our Galaxy this means we have 100 billion planets. Since we have about 100 billion galaxies in the Universe, there are about 10,000,000,000,000,000,000,000 = 1022 planets out there.

ASU and the New American University

In this week’s Nature, a special issue on the evolution of modern academic institutions, Arizona State University (ASU) President Michael Crow and his vision of the New American University are profiled. Appointed President in 2002, previously Executive Vice Provost at Columbia University, Crow began restructuring ASU. His goal: to shape it into a hub of multidisciplinary research, entrepreneurship, and innovation.

12 years into Crow’s tenure, ASU has expanded its campus, forming and constructing new research institutes like the Biodesign Institute, School of Earth and Space Exploration, and the School of Human Evolution and Social Change. The University’s growth in funding and collaboration are also remarkable. From the Nature piece:

ASU’s funding numbers show that grant-givers find the cross-disciplinary approach attractive. From 2003 to 2012, the university’s federally financed research portfolio grew by 162%, vastly outpacing the average increase seen at 15 similar public institutions. ... The number of funded projects with principal investigators in two or more departments rose by 75% between 2003 and 2014.

While the article further notes that ASU’s publication rate has more than doubled, it asserts its scientific profile has hardly been raised. Citing largely unchanged proportions of publications in high-profile journals or with high numbers of citations, this analysis doesn’t account for some important factors.

1. Since ASU’s funding at present has more than doubled, one should expect an explosive BOOM in publications and citations over the next few years;

2. Collaborating, whether in the same institution or across the world is fraught with challenges, so pace may lag;

3. The research from ASU’s new institutes and far-reaching collaborations is inherently different (innovation is, by definition); like Crow said, “We don’t want to ask the same questions as other institutions,” so there aren’t yet large circles to cite these early works;

4. Building off the above point, it can take years for journal articles to accumulate even a portion of their lifetime citations (an argument against impact factor);

Even without these caveats, ASU’s progression and the essence of Crow’s New American University model presciently anticipated recent developments in the modern university. Observing ASU’s emphasis on cross-disciplinary entrepreneurship and innovation (E&I) through research, one notes similar trends at top-tier universities across the world. With job markets in flux, a rapidly changing economy, and an ever-increasing focus on science and technology, schools attract students and build connections to business through E&I hubs, an explicit goal of Crow’s vision for ASU.

Rethinking and reimagining research and education at academic institutions is critical for universities and their students to remain competitive. Best of all, science and society will both benefit. Here’s to hoping the New American University expands beyond Phoenix, Arizona.

Racist Polio Vaccines and Scientific Credit

Who gave summer back to children of the 50s and 60s?
Yesterday was Dr. Jonas Salk’s 100th birthday. The Google Doodle celebrating it was profiled in The Guardian, which acknowledged:

The story of Salk’s search for a vaccine isn’t one that should be told in isolation, stopping with the elimination of polio in the US. Instead, it sits within a rich tapestry of stories about scientific discovery and progress.

Except that Salk’s treatment wasn’t responsible for eradicating polio in the US. His treatment was too expensive for millions of Americans at a time when children were kept indoors during summer to prevent infection. Despite the oft-repeated Salkian quote, “There is no patent. Could you patent the sun?”, adminstrative powers above Salk (his involvement is unclear) determined they could not legally patent the vaccine, given previous works. Still, three vaccine shots and a booster priced polio protection only within the reach of middle class Americans and above.

So infection rates dropped among demographics that could afford the Salk vaccine, while rates expanded in lower income communities, especially among under-served minority groups. This was an economic as well as access problem: pediatricians could command higher prices as there was high demand for the multi-course regimen. Dr. Albert Sabin, another polio researcher, knew that Salk’s vaccine was not the best possible solution or even sufficiently safe. His arguments for impartiality and caution were largely ignored by the council backing Salk’s vaccine (see link below), yet Sabin labored on. He developed a single orally-dosed drug that allowed low-cost, wide-scale distribution of this life-saving treatment.

As described in the aptly titled review, The Myth of Jonas Salk, Sabin’s treatment was truly responsible for ending polio in the US (and is currently the one in use to eradicate polio across the globe):

Beginning in January 1962, pediatricians in two Arizona counties ... conducted separate but similar voluntary mass immunizations using Sabin’s vaccine. “Previous programs using the Salk vaccine had failed to bring polio immunization to a satisfactory level,” they reported a year later in the Journal of the American Medical Association.... More than 700,000 people were immunized – 75 percent of the total population in both counties. The vaccine was given at the cost of 25 cents, for those who could pay. It was given to population groups that were socially, racially, and culturally diverse, on Indian reservations and military posts and in urban and rural areas. The program became a model for subsequent U.S. mass-immunization programs. By the mid-1960s, Sabin’s vaccine was the only one in use in the United States. It was the Sabin vaccine that closed the immunity gap and effectively put an end to polio in the States.

Of course aspects of Sabin’s work were built off the work of Salk - all of science is inherently iterative. But we as a community and society at large need to have systems in place to ensure credit is given where credit is due. Thanks to a half-century of good PR and first-mover advantage, Dr. Salk is heralded as the vanquisher of polio, while it was Sabin’s dogged persistence at achieving a better solution that tipped the scales (not to mention countered an economically and racially-biased course of treatment).

There is an entire subset of scientists who passed through history largely undetected, while making tremendous impacts. Female scientists have made up a disproportionate amount of this subset, routinely discouraged from research (e.g. see comments in this post). For every triumphant Salk, there is almost always a Sabin (or Rosalind Franklin, et al) who deserves equal if not more recognition. Hopefully with improved access and documentation, the scientific community can better allocate credit, resources, support, and realize improvements faster.

Share this on Facebook to extend Salk’s celebration to Sabin (and the other researchers who contributed to the polio vaccine), and to serve as a reminder of the less-than-famous scientists who are giants in their own right.

Interview: Long-time LaTeX User

# Introducing...

Christina Laternser has a B.S. and M.S. in Mathematics and an M.S. in Economics. An experienced LaTeX user, she wrote her thesis on hyperbolic geometry using it, as well as her economics thesis. She has worked in data analytics, application development, and lectured in mathematics. She finds some time to do academic research as well.
While Christina has developed and managed global intra-company team collaboration tools over LAN, effectively a stripped-down version of Authorea, this is her first introduction to the collaborative platform for research.

Network models to evaluate reproducibility in biomedical research _or, The Future of Science

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The traditional way to publish scientific work is to write a narrative describing the performed experiments and related conclusions. Nowadays, the pressures for funding and journal impact factor generate a vicious circle promoting, at the very least, an increase in the minimum number of relevant findings required for publication and the over-stretching of claims. As a consequence, the problem of reproducibility in science has surged to the attention of the media, including The New York Times and The Wall Street Journal.

Mysterious Particle Discovered

In 1937, just one year before suddenly disappearing under mysterious circumstances, a brilliant italian physicist named ETTORE MAJORANA predicted the existence of a very peculiar particle. Having the exciting property of being its own antiparticle (that is it simultaneosly behaves as matter and anti-matter) the elusive “MAJORANA PARTICLE” has been finally observed by a group of scientists at Princeton University . To achieve the important result they used a two-story-tall microscope to observe the end of a superconducting wire.

EU's Breakthrough in Clinical Trial Transparency

In a breakthrough victory for open access, the EU’s European Medicines Agency (EMA) approved a system last week that provides researchers and the public with the vast majority of data from clinical trials. While generally resistant to such developments, some pharmaceutical companies are already opening up their data to scrutiny. In the US, NIH’s clinicaltrials.gov hosts a similar database for voluntary submission of public and private clinical trial results. By January 1, 2015, however, all companies in the EU will be required by law to submit trial data for newly approved drugs. FDA is considering adopting such a policy, with safety and efficacy data-mining projects in mind.

As the analysis from ScienceInsider notes:

Published journal articles often contain the main outcomes, . . . but lack detailed data and information about study design, efficacy, and safety analysis, which might shed a different light on the results when analyzed by others; moreover, some trials aren’t published at all. The AllTrials campaign has argued that the details of every trial should be publicly available for anyone to study.

Traditional publication formats disconnected from modern needs? A move toward data-rich scientific content? Opening up the process of verification and analysis to a wider audience? It’s as if science was always meant to be open, or something.

Naturally, there are caveats to the ruling. Only identified researchers can download searchable trial results and data, while registered public users can only view results on-screen. Further, certain types of commercially relevant data may be redacted by companies, with the EMA providing an 18 month window before completed trial results are finalized and posted. Still, however, this represents a huge step forward for widespread access to and synthesis of information that could be critical for improving patient outcomes.

Long-sought by many researchers, the beneficial network effects of open trial data have been lauded in the literature, with comparisons made to successes in the open-source community \cite{Dunn_2012}. In one example, data-sharing led to rapid analysis and determination of treatment for a deadly e coli outbreak in 2011. By broadly applying standard protocols to ease the access and use of clinical trial information, researchers contend we will see huge health care improvements. Results include learning what treatments are best in which circumstances, determining contraindications faster, and increasing adoption and innovation rates in treatments.

Here’s to hoping EMA’s actions are successful, FDA approves similar measures, and science in aggregate opens up to take advantage of these synergetic network effects.

EMA Q&A release

How Can Authorea Help University Students and Professors Writing and Reviewing Papers?

Simple, mundane tasks can take huge tolls on our productivity. A growing body of research is quantitatively demonstrating the existence of willpower depletion, so don’t be a statistic. Authorea helps cut out friction associated with academic writing and editing, so you can get back to doing what you love instead of just writing about it.

Here’s the situation:

You’ve spent months (or even years) running and reproducing experiments, keeping meticulous notes, collecting and annotating data, writing code, writing grant applications, presenting your progress and, occasionally, sleeping. All for that slam-dunk publication. Which, finally, you are writing up.

But there are some problems.

From stylistic preferences and building consensus with your colleagues, to back-up paranoia, to re-re-re-formatting your article for the reach, next best, achievable, journal of last resort, Authorea has you covered.

An Authorea-tative Difference

As the recent over 200-author CERN paper demonstrates, Authorea can really kill it when it comes to collaborating, on any scale. This is particularly powerful, given the well-feared notion that communication complexity increases as the square of the number of people on a project. Regardless of your level of distribution (worldwide or just down the hall), with Authorea, everyone you care to include can view, edit, comment, commit, and even upload and review data, code, and figures.

Let’s consider that last point for a minute. No longer will you have to fumble for flash drives, attach and contextualize via email, or compile, edit, and view in separate programs. All the data and code associated with your figures is online in the upper left-hand folder for your collaborators to play with. Further, if your document is public, members from the wider Authorea community can comment, verify, and even fork it - increasing your FF and contribution to science. Pretty sweet.

Authorea, given the oft-made comparisons to GitHub and Google Docs, also helps with versioning updates and the distributed editing of your manuscript. Let’s say your PI isn’t thrilled with your phrasing or explanation in the Discussion. With Authorea, you can: lock the section while you edit it (i.e. no one is looking over your shoulder, judging); commit the update for all to see (oh, how they will marvel); get real-time feedback through additional comments and edits; and, when your PI has a change of heart, you can easily revert back to the section’s previous version (by clicking on that handy “History” clock icon).

So, Authorea provides a platform for collaborative writing and review of your manuscript, an easy and automated citation mechanism, a one-stop repository for all your figures’ data, code, and editing, and even lets you get pre-publication feedback from your peers. What’s more, Authorea will also format your manuscript for the journal of your choice - text, figures, bibliography and all - at a click of a button.

Two questions:

1. Why wouldn’t you use Authorea for your next collaborative publication?

2. What would you do with the time saved when you’d otherwise be emailing around drafts and data, sharing and modifying code, clarifying, citing, and formatting?

Let us know in the comments!

First evidence of Quantum Gravity? Ask the dust

Rise and fall of the biggest discovery of the century highlights the importance of open, collaborative science.

On 17 March 2014 BICEP2, a South Pole based experiment aimed at studying the very first moments of the universe, made a sensational announcement. They claimed to have detected for the first time the signature of an extremely rapid expansion of space that occurred right after the universe’s birth. This expansion, also called inflation, is believed to be responsible for the existence of large-scale structures like clusters of galaxies, as well as to explain why the properties of the universe appear to be the same for all observers. If confirmed, the existence of inflation would represent the first evidence of a fundamental connection between gravity (general relativity) and quantum physics.

Authorea raises a seed round of investment.

We are very excited to announce that Authorea has recently raised its first round of funding for a total of \$610k with a joint investment by ff Venture Capital and NY Angels!

ffVC is an institutional venture capital investor in seed-stage companies based in New York City. NY Angels is the largest and most active technology-focused angel investment organization on the East Coast.

This investment is important for Authorea on many levels.

First of all, we are solidifying and growing our team. We're hiring! If you are interested in making science better, you will enjoy working with us. Drop us a line.

A bigger team means that Authorea will get better faster.
We will keep working toward our mission to accelerate science, to improve dissemination and quality of research results and to promote Open Science. We look forward to making Authorea your platform of choice for scholarly writing, research collaboration, and data sharing.

We are also thrilled to announce that our brand new Board of Directors will welcome John Frankel, CEO of ff Venture Capital, and Brian Cohen, Chairman of NY Angels. Together with John and Brian, the board will also be composed of Matteo Cantiello (formerly Authorea's Scientific Advisor) and us, the two co-founders, Nathan and Alberto. We will be announcing our full team and advisory board in the next few weeks.

Happy writing!

---Nathan and Alberto

The Fork Factor: an academic impact factor based on reuse.

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Authorea awarded with the Digital Science Catalyst Grant

We're a bit late with this blog post, but we're happy to announce that at the end of last year Authorea was awarded with the Digital Science Catalyst Grant and that we recently ended the program. Hooray! WHAT IS DIGITAL SCIENCE? Digital Science is an innnovative technology company, based in London UK, serving the needs of scientific research. Some software products developed at Digital Science include Figshare and Readcube. WHAT IS THE CATALYST GRANT PROGRAM? Digital Science offers every year grants to help researchers and scientists take ideas from concept to prototype. Think of the program as an incubator for early stage ideas. Along with funding, Digital Science also offers the opportunity to work with their team to refine and develop the innovation. The program runs for six months and funds can be used for any purpose that serves the project, including equipment purchases, software licensing, travel and reasonable living expenses. You can find out more on the grant homepage. WHAT DID AUTHOREA DO WITH THE CATALYST GRANT? Did you ever wish that a scientific article you are reading made available "the data behing a figure"? For example, you may be reading an article reporting data and predictions about the cost of publishing articles in open access journals and you may bump into the figure below (Beware, it's fictitious data!). Wouldn't it be nice if you could access the data associated with this figure as well as all the code that was utilized to make this graph? Yep, and luckily (thanks to the work we did under the Catalyst Grant) now you can!

Science was always meant to be open

Here’s my crux: I find myself criticizing over and over the way that scientific articles look today. I have said many times that scientists today write 21th-century research, using 20th-century tools, packaged in a 17th-century format. When I give talks, I often use 400-year-old-articles to demonstrate that they look and feel similar to the articles we publish today. But the scientific article of the 1600’s looked that way for a reason. This forthcoming article by \citet{ploscomp} explains:

In the early 1600s, Galileo Galilei turned a telescope toward Jupiter. In his log book each night, he drew to-scale schematic diagrams of Jupiter and some oddly-moving points of light near it. Galileo labeled each drawing with the date. Eventually he used his observations to conclude that the Earth orbits the Sun, just as the four Galilean moons orbit Jupiter. History shows Galileo to be much more than an astronomical hero, though. His clear and careful record keeping and publication style not only let Galileo understand the Solar System, it continues to let anyone understand how Galileo did it. Galileo’s notes directly integrated his data (drawings of Jupiter and its moons), key metadata (timing of each observation, weather, telescope properties), and text (descriptions of methods, analysis, and conclusions). Critically, when Galileo included the information from those notes in Siderius Nuncius, this integration of text, data and metadata was preserved:

How is Authorea different from Google Docs?

Are you comparing Google Docs vs Authorea?Choosing the right word processor for your documents is very important. While Google Docs and Authorea are similar in some ways, Google Docs is a great tool for writing general purpose drafts whereas Authorea is more appropriate if you are writing a scholarly manuscript, a student essay, a math heavy manuscript, a technical blog post, or a data-driven document. We listed here a few key comparison points that show how Google Docs and Authorea are different.

More and more scholars are leaving their academic posts (see [1] [2] [3]). As it turns out, it’s not possible to fully leave academia unless you write a detailed blog post about it. So, here’s mine.

I resigned from my postdoctoral position at Harvard two months ago. My academic career was fairly typical. I spent the last twelve years doing research. After college, I worked at CERN for a few years, then pursued a Ph.D. at UCLA and a 3-year Postdoc at Harvard. During my Ph.D. and Postdoc I did not even apply to a single tenure-track job. Why? My research background is very (maybe, way too) interdisciplinary: B.Sc. in Astronomy, M.Sc. in Computer Science, at CERN I did Data Science (basically working in Tim Berners-Lee former group), my Ph.D. is in Information Science, and my Postdoc in Astrophysics. Who the hell is going to hire me? While many praise academic interdisciplinarity as an asset, at the end of the day to get tenured you need to be able to teach core classes in one discipline. So, even though I was working in an amazing research group and my publication record was just fine, I decided to leave.

Leaving a postdoc at a top institution was a hard and risky decision to make. Yet, with so many PhDs and postdocs leaving academia today, I certainly don’t feel alone. But, how common (or rare) is it to leave academia? Last week I attended the ScienceOnline conference and in a session called Alternative careers in science, Eva Amsen discussed the infographic below.

LaTeX was not built for the web

One of the questions we get more often from our users at Authorea is: Why is my LaTeX command not working? The SHORT ANSWER to that is: Because that LaTeX command was not intended for a webpage; it was intended for the printer. :( THE LONGER ANSWER. Authorea understands and renders markup languages such as Markdown, and LaTeX. But it does not rely on a compiler which takes TeX and spits out PDF. All the content created on Authorea is web-native. As we create more and more content on the web, we think that SCHOLARLY ARTICLES, TOO, SHOULD LIVE ON THE WEB. That said, we do enjoy and use LaTeX frequently at Authorea. This post for example, was written in LaTeX! Want to see? Let’s grab a pre-baked equation, for example this Fourier transform and render it below: a \Leftrightarrow 2\pi a\sum^\infty {\delta (\omega + 2\pi k)} ,( - \infty < n < \infty ) a \Leftrightarrow 2\pi a\sum^\infty {\delta (\omega + 2\pi k)} ,( - \infty < n < \infty ) We decided to support LaTeX from the very beginning, as it is the document preparation toolkit of choice for many (most?) researchers in the hard sciences. We think LaTeX is still the best programming language to tell a computer how to place text on a page. But the TeX project started pre-web, in 1978, and its scope and function are tightly linked to the PRINTED PAGE, not the WEBPAGE. Take, as an example a table definiton that begins with [ht]. This table command instructs TeX to put the table in the page, here, where the table is declared (h) AND at the top of the page (t). The list of examples could go on and on — think of minipage environments, page margins, text width parameters... all LaTeX notation that does really not make sense for a webpage. IS CSS THE NEXT LATEX?. What does the future hold for academic writing? We like to think that a few years from now we will format our research papers with the web version in mind, rather than the printed PDF. And we are not alone! LaTeX will very likely be used many years from now, but, we think, in a much more stripped-down, web-friendly incarnation, like the subset that Authorea currently supports. (We use some amazing tools like Pandoc and MathJax to convert between formats and render equations). Or maybe someday we will just format papers using CSS stylesheets?

Research collaboration in the Cloud: Plotly and Authorea

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# Introduction

We are happy to announce a partnership between Plotly and Authorea that gives you a free suite of powerful, collaborative tools for doing your analysis, graphing, coding, and publication. Authorea and Plotly, together, can power your research collaboration.

Want to insert a Plot.ly graph in your own documents? Follow these instructions

Example Article: Geoscientific Visualization in Authorea with iPython Notebooks

INTRODUCTION Ok, I can’t stand to try it out and test Authorea with a visualization I made for a former lab report. Let’s go. Create Notebook File At first, we have to create a Notebook file. I took the data and Python script that I made for the lab report and put it in a local folder called ipython. Using the terminal, I switched into this folder and called ipython notebook %matplotlib inline. The latter argument is used to have my plot show up in ipython itself underneath the code cell that runs the plot. I also splitted up the code in smaller chunks and converted some of my code comments into Markdown cells. That makes it nice to read the Notebook and structures the code. Afterwards I ran every code cell from top to bottom using the Shift + Enter keys. The plot the plot appearing under the last cell was then saved to the folder containing the Notebook file. Upload to Authorea Ok, now I have some files containing my code (the Notebook file), the rendered plot image, and the raw data in an Excel Sheet. To use the image in Authorea, I just need to upload it and reference it inside my latex document. But as a scientist standing for open research, I also want my colleagues and readers to be able to access the raw data and algorithms used to produce the plot, so I upload them, too. So I created a folder inside my document structure in Authorea called depth-plot and put all files in it. Inside my structure.md file I referenced the image with the relative path and now it shows up at the corresponding position of the document structure (below this text). Because the image and the Notebook file are in the same folder, hovering over the image shows a “launch ipython” button, that anybody can use to open the Notebook inside the browser and play around with it. Nice, isn’t it? (At the moment, Notebook sessions opened inside the browser get killed automatically after 5 minutes. I think that’s due to the fact that Authorea is still quite new and should be seen as Beta software. If you want to have a closer look at the Notebooks, you still can download it and play around locally.)

Linking Visualization and Understanding in Astronomy

This post accompanies a talk by the same name and author, presented at the 223rd Meeting of the American Astronomical Society, at 11:40 AM on January 6, 2014. Talk slides will be online after noon on January 6 at http://projects.iq.harvard.edu/seamlessastronomy/presentations.

# Abstract

In 1610, when Galileo pointed his small telescope at Jupiter, he drew sketches to record what he saw. After just a few nights of observing, he understood his sketches to be showing moons orbiting Jupiter. It was the visualization of Galileo's observations that led to his understanding of a clearly Sun-centered solar system, and to the revolution this understanding then caused. Similar stories can be found throughout the history of Astronomy, but visualization has never been so essential as it is today, when we find ourselves blessed with a larger wealth and diversity of data, per astronomer, than ever in the past.
In this talk, I will focus on how modern tools for interactive “linked-view” visualization can be used to gain insight. Linked views, which dynamically update all open graphical displays of a data set (e.g. multiple graphs, tables and/or images) in response to user selection, are particularly important in dealing with so-called “high-dimensional data.” These dimensions need not be spatial, even though, e.g. in the case of radio spectral-line cubes or optical IFU data), they often are. Instead, “dimensions” should be thought of as any measured attribute of an observation or a simulation (e.g. time, intensity, velocity, temperature, etc.). The best linked-view visualization tools allow users to explore relationships amongst all the dimensions of their data, and to weave statistical and algorithmic approaches into the visualization process in real time.
Particular tools and services will be highlighted in this talk, including: Glue (glueviz.org), the ADS All Sky Survey (adsass.org), WorldWide Telescope (worldwidetelescope.org), yt (yt-project.org), d3po (d3po.org), and a host of tools that can be interconnected via the SAMP message-passing architecture.
The talk will conclude with a discussion of future challenges, including the need to educate astronomers about the value of visualization and its relationship to astrostatistics, and the need for new technologies to enable humans to interact more effectively with large, high-dimensional data sets.

Data-driven, interactive science, with d3.js plots and IPython Notebooks

and 1 collaborator

JAVASCRIPT, D3.JS, AND D3PO.JS Javascipt offers many ways to create data-driven graphics. A popular solution is D3.js, a JavaScript library to create and control web-based dynamic and interactive graphical forms. A gallery of some beautiful d3.js plots can be found here. Authorea now supports most Javascript-based data visualization solutions. The example below - Figure [fig:1] - is a plot generated using D3po.js which is a javascript extension of d3.js. D3po allows anyone with no special data visualization skills, to make an interactive, publication-quality figure that has staged builds and linked brushing through scatter plots. What’s even cooler is that the plot below is based on actual data (astrophysics data, yay!). The figure describes how metallicity affects color in cool stars. It is based on work of graduate student Elizabeth Newton and others . TRY CLICKING AND DRAGGING IN THE SCATTER PLOTS to understand the power of linked brushing in published figures. You should know that THIS ENTIRE VISUALIZATION IS RUNNING WITHIN AUTHOREA. The Javascript, HTML, CSS and ALL THE DATA associated with this image are all part of this blog post. They are individual files which can be found by clicking on the folder icon on the top left corner of this page.