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Blogging for the 21st Century

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Covid virus 3d

Alberto Pepe

and 4 more

We're in a crisis We are in the midst of an unprecedented global crisis. Just weeks since its outbreak, the Coronavirus pandemic (COVID-19) has already affected, and will continue to affect, our daily lives, around the globe, for the foreseeable future. The answers and the solutions to this crisis will come from science. But the crisis affects science, too.It affects students, educators, and researchers; not just their day-to-day lives, social ties, and work routines, but also their ability to actively collaborate, convene in face-to-face meetings, attend academic conferences, teach and learn in an open university setting, pay a visit to the library, work overnight at the laboratory, and so on.But the thing is: science cannot stop. Scientific progress must go on. For each one of the challenges that scientists face in this time of crisis, there is, or there will be, a solution. We believe that the solution is not to be found in a single technological tool, product, framework, institution, funding agency, or company. It is the global cyber-infrastructure of scientific collaboration, built on scientific rigor, intellectual curiosity, and cooperation, that will enable science to advance in such difficult times. The power of scientific collaborationAs scientists, publishers, science communicators and technologists, we believe that: a. Science is the solution to the ongoing crisis. Now more than ever, reliance on the scientific method, rigor and clarity of scientific communication, transparency, reproducibility, and seamless sharing of all research data (including negative results), are fundamental to solving this health crisis and advancing human progress.b. Global collaboration and cooperation, beyond and above national and economic interests, is necessary not only at the scientific level, but also at the political and societal level. We're more interconnected and interdependent today than ever. And such interconnectedness extends to the ecological ecosystem in which we live. A crisis of such scale requires global solidarity, bipartisan political action, civic participation, and long-term thinking.
Einstein ligo2
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.
Screen shot 2020 05 04 at 4.02.46 pm

Josh Nicholson

and 1 more

Hello, and welcome to Authorea!👋  We're happy to have you join us on this journey towards making writing and publishing smoother, data-driven, interactive, open, and simply awesome. This document is a short guide on how to get started with Authorea, specifically how to take advantage of some of our powerful tools. Of course, feedback and questions are not only welcome, but encouraged--just hit the comment icon at the top of the document 💬and join the conversation.The BasicsAuthorea is a document editing and publishing system built primarily for researchers. It allows you to collaborate on documents and publish them easily. Each Authorea document can include data, interactive figures, and code. But first, let's get started! 1. Sign up.If you're not already signed up, do so at authorea.com/signup.  Tip: if you are part of an organization, sign up with your organizational email.  2. First stepsDuring the signup process you will be asked a few questions: your location, your title, etc. You will be also prompted to join a group. Groups are awesome! They allow you to become part of a shared document workspace. Tip: during signup, join a group or create a new one for your team. Overall, we suggest you fill out your profile information to get the best possible Authorea experience and to see if any of your friends are already on the platform. If you don't do it initially during sign up, don't worry; you can always edit your user information in your settings later on.Once you've landed on your profile page (see below). There are a few things you should immediately do:Add a profile picture. You've got a great face, show it to the world :) For reference, please see Pete, our chief dog officer (CDO), below. Add personal and group information. If you haven't added any personal information, like a bio, a group affiliation, your ORCID, or your location, do it! You might find some people at your organization already part of Authorea, plus it is a great way to build your online footprint, which is always good for getting jobs.
Upgoer
“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)
Blog image

Josh Nicholson

and 3 more

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 
Aacr

Josh Nicholson

and 2 more

BROOKLYN, NY, August 28 2017 – Authorea, the online document editor for researchers, has partnered with the American Association for Cancer Research (AACR), the world’s first and largest cancer research organization.  By working with the AACR, Authorea aims to help researchers more easily format and submit their papers by offering one-click submission to journals published by the AACR.The AACR, founded in 1907, publishes some of the world’s most important discoveries in cancer research and is comprised of over 37,000 members in 108 countries. Christine Rullo, Publisher and Vice President, Scientific Publications at the AACR, says, “We’re excited to partner with Authorea for a more seamless submission option for researchers writing on Authorea.”Josh Nicholson, Chief Research Officer at Authorea, adds: “Our association with the AACR will help to advance research writing and editing for clinicians and scientists who work in all aspects of cancer research.  Authorea aims to bring document editing into the 21st century while supporting authors in meeting their professional goals.”Launched in 2014 and used by over 100,000 researchers from all disciplines in academia as well as leading private research companies, Authorea allows researchers to collaborate in real-time for an easier and more seamless writing and publishing experience. The journal templates below assist authors in structuring their manuscript as appropriate for each of the AACR journals. Templates• Cancer Research: https://www.authorea.com/templates/cancer_research • Cancer Immunology Research: https://www.authorea.com/templates/cancer_immunology_research• Cancer Prevention Research: https://www.authorea.com/templates/cancer_prevention_research• Molecular Cancer Research: https://www.authorea.com/templates/molecular_cancer_research• Molecular Cancer Therapeutics: https://www.authorea.com/templates/molecular_cancer_therapeutics• Cancer Discovery: https://www.authorea.com/templates/cancer_discovery_research_article • Clinical Cancer Research: https://www.authorea.com/templates/clinical_cancer_research• Cancer Epidemiology, Biomarkers and Prevention: https://www.authorea.com/templates/cancer_epidemiology_biomarkers_and_preventionPress 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.About the American Association for Cancer ResearchFounded in 1907, the American Association for Cancer Research (AACR) is the world’s first and largest professional organization dedicated to advancing cancer research and its mission to prevent and cure cancer. AACR membership includes more than 37,000 laboratory, translational, and clinical researchers; population scientists; other health care professionals; and patient advocates residing in 108 countries. The AACR marshals the full spectrum of expertise of the cancer community to accelerate progress in the prevention, biology, diagnosis, and treatment of cancer by annually convening more than 30 conferences and educational workshops, the largest of which is the AACR Annual Meeting with more than 21,900 attendees. In addition, the AACR publishes eight prestigious, peer-reviewed scientific journals and a magazine for cancer survivors, patients, and their caregivers. The AACR funds meritorious research directly as well as in cooperation with numerous cancer organizations. As the Scientific Partner of Stand Up To Cancer, the AACR provides expert peer review, grants administration, and scientific oversight of team science and individual investigator grants in cancer research that have the potential for near-term patient benefit. The AACR actively communicates with legislators and other policymakers about the value of cancer research and related biomedical science in saving lives from cancer. For more information about the AACR, visit www.AACR.org.
9d34ea56f103db66ac428b5489365f89 400x400

Josh Nicholson

and 4 more

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.
Ssrn

Josh Nicholson

and 4 more

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.
Export 613

Josh Nicholson

and 1 more

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. 
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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 beloweNeuroeNeuro title pageThe Journal of NeurosciencePress 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.
Fundingawardsuccessrate rpg

Matteo Cantiello

and 2 more

AbstractPreprints 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 preprintingBelow 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 discoveryWith 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).  
Sample article 1000

Alberto Pepe

and 1 more

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.
Rockerfelleruniv2010

Josh Nicholson

and 2 more

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 ContactAdyam Ghebre, Outreach, Authorea+1 (646) 598-9285About AuthoreaAuthorea 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.
Agu logo

Josh Nicholson

and 1 more

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• Radio Science• Reviews of Geophysics• Space Weather• TectonicsAuthorea 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 ContactAdyam Ghebre, Outreach, Authorea+1 (646) 598-9285About AuthoreaAuthorea 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.
Preprints

Josh Nicholson

and 2 more

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.
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 AtlanticWe 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.Analysis of ground-level ozone formation and its correlation with concentration of other pollutants and weather elementsVision Zero Crash Data AnalysisWe 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.  
Statistics (1)

Josh Nicholson

and 1 more

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 researchWhile 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 full color horizontal

Josh Nicholson

and 1 more

CAMBRIDGE, UK, Friday, January 13, 2017 -- Authorea, the leading online editor for writing and publishing research documents, is integrating eLife into its submission system to give authors more options for direct submission to journals.eLife, the non-profit initiative backed by leading research funding organizations and led by scientists, operates a platform for research communication that recognizes and encourages responsible practices in science. eLife is now working with Authorea to allow authors to write and submit research directly to the journal as quickly and easily as possible.eLife’s partnership with Authorea aims to reduce the burden of submission on authors. A new document editor for researchers, Authorea makes it easy to write research documents and to host these online or submit them to journals for publication.Authorea gives authors the ability to write in multiple markup languages and host documents directly as standalone preprints. There are also hundreds of export styles for these documents, and Authorea’s recent integration with EJournalPress (EJPress) provides a direct link to eLife, simplifying the journal submission process.Josh Nicholson, Chief Research Officer at Authorea, says: "We're excited to partner with eLife, a major innovator in research publishing. eLife is an ideal submission destination for the tens of thousands of researchers who use Authorea to write groundbreaking research, and we look forward to partnering with eLife to help scientists gain great exposure for their discoveries."Melissa Harrison, Head of Production Operations at eLife, adds: “We’re delighted to be working with Authorea to make the submission process easier for authors. We hope to see this and other partnerships continue over the coming months, so that we can provide our authors with the best possible writing and publishing tools available to them.”For more information, please contact:Emily Packer, Press Officer, eLifee.packer@elifesciences.org01223 855373Adyam Ghebre, Outreach, Authoreaadyam@authorea.com+1 (646) 598-9285About eLifeeLife is a unique collaboration between the funders and practitioners of research to improve the way important research is selected, presented, and shared. eLife publishes outstanding works across the life sciences and biomedicine -- from basic biological research to applied, translational, and clinical studies. All papers are selected by active scientists in the research community. Responses are consolidated by the Reviewing Editor into a single, clear set of instructions for authors, removing the need for laborious cycles of revision and allowing authors to publish their findings quickly. eLife is supported by the Howard Hughes Medical Institute, the Max Planck Society, and the Wellcome Trust. Learn more at elifesciences.org.About AuthoreaAuthorea 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.

Josh Nicholson

and 1 more

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. For more information, please visit: 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    felix.evert@sampleofscience.comAuthorea 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    Adyam Ghebre    Phone +1 646 598-9285    adyam@authorea.com
Artboard

Josh Nicholson

and 1 more

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."##

Josh Nicholson

and 1 more

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.

michaeljdklein

and 1 more

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_
8249
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 access

Josh Nicholson

and 5 more

14   copy

Lucy Chen

and 1 more

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 Buffer, content 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.
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 <div> and <span> 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
Einstein ligo2

Matteo Cantiello

and 1 more

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.
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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.

Jace Harker

and 3 more

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. ABOUT AUTHOREA: 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_ - Danny Park: dpark@broadinstitute.org
Pfos
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).

Jace Harker

and 4 more

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 , 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.”

Deyan Ginev

and 3 more

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{}
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Matteo Cantiello

and 1 more

Scientists are busy people. We have deadlines to meet, meetings to attend, lectures to give. And OF COURSE WE NEED TO WRITE PAPERS, not only because we are excited to share our findings, but also because scientific papers are the currency of the academic world. Authorea was created by scientists and for scientists. The idea: improving the process of writing and sharing the results of research. While Authorea has big plans for the paper of the future, in this post I want to focus on the here and now. This is because when I talk about the platform with my colleagues, by far the most common question I get is “Why should I use Authorea to write my paper?” GREAT QUESTION! Here some highlights that should make you curious: 1. With Authorea, your paper is accessible from any computer anywhere in the world. 2. You can write it from your browser, no installations required. 3. You can write in rich text (wysiwyg) LaTeX or in markdown. 4. Your paper is also a beautiful web page. 5. Collaboration is made easy. Managing your co-authors is straightforward. 6. Authorea is version controlled. Again, no installations required. 7. Adding citations has never been easier. Believe me, you will never wanna go back. 8. You can include data and code in your paper. This allows for transparency and reproducibility of results. 9. Export to any journal format with just one click. 10. Powerful commenting system. For internal or even external review. Ok, If you got this far you deserve more than a list of fancy features, so here’s my personal experience and why I think you should start using Authorea. I switched to writing papers with Authorea about a year ago and I noticed a number of immediate improvements: first of all MY PAPERS GET WRITTEN FASTER. Then I noticed that I have NO NEED TO EXCHANGE EMAILS WITH COLLABORATORS concerning the paper. This is fantastic. All the action happens (and it’s logged) on Authorea, including discussions about revisions and suggestions for improvements. This said, I didn’t really expect the most important upturn. By getting rid of the overhead I previously considered necessary, unavoidable parts of the scientific writing process, something remarkable happened. I actually STARTED ENJOYING WRITING MORE! And I do not mean just publishing; I had experienced that joy before. The difference is I now cherish the time I spend putting my science into words. It might sound crazy, but Authorea did something amazing: it made me DISCOVER THE PLEASURE OF WRITING SCIENCE TOGETHER with my collaborators.
Screenshot 2014 10 17 at 3.22.27 pm
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 . 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.
_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.
Wren

Matteo Cantiello

and 3 more

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 .
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?
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.
Paracelsustheeman
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:
Latex is dead1
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] - LaTeX was not built for the Web by Alberto and Nate from Authorea. - LaTeX Something Something Darkside by Peter Krautzberger from MathJaX. - A Scholarly MarkDown discussion on Hacker News (see the comments) 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.
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 . 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!
Friday, an op-ed piece _actually_ titled “Academic Science Isn’t Sexist” went up on the _New York Times_ blog (a version appeared in the Sunday Review). It was about academic research and the lack of sexism therein. The two editorialists are co-authors on a recently released analysis on the subject (it _is_ beautifully open access, and much of the raw data is available). The piece and the paper claim sexism has largely waned in academic research, the result of shifts from a previously sexist, male-dominated academy. Further, that any remaining incongruities between male and female enrollment, advancement, and achievement are artifacts and anecdotal. Academic research is completely gender-blind now. Any differences are largely the product of society-at-large and earlier life decisions (like the choice to play with dolls/cute animals versus trucks/destructive robots). Huh. The response from the science blogging community and Twittersphere was immediate and is still on-going. Jonathan Eisen responded Halloween night, soon after the piece was posted. His immediate critique was of the acknowledgement of reports of “physical aggression” in the op-ed piece, without ever addressing these in their data or analysis (even the 60+ page research paper is short on coverage). The assumption: they are also anecdotal? So everything is actually fine? Probably not (<- this article details accounts of _sexual misconduct in field work_ involving biology, anthropology, and other social sciences, disciplines the authors above highlight as _largely welcoming and open to women_). Emily Willingham provides excellent analysis of the data presented in the paper and in the broader debate at hand. It turns out there are numerous discrepancies and avoided topics of analysis (e.g. salary figures often had statistically significant differences by gender; women more often reported lack of inclusion; more details in her impeccable post). Likewise, Matthew Francis covered the story, emphasizing the need to actively address these still-existent problems and not ignore them: the importance of even a little explicit encouragement of female students in the face of implicit discouragement (like he sees in his native field of physics) is often all that’s needed. The ever-emphatic PZ Myers rounds out the debate by breaking down the major reasoning and assumptions in the original paper, with characteristic gusto. So what exactly were the original authors thinking? A handful of distributed scientists were able to challenge the key arguments of their paper, using their data and citations, in free time over the weekend. Talk about peer-review. Seriously though, what were they thinking? I would _like to think_ that this was actually a brilliantly orchestrated publicity stunt to get more attention on this critical issue. AFTER ALL, WHO IS GOING TO BLOG/TWEET/COUNTER-OP-ED “ACADEMIC SCIENCE IS SLIGHTLY LESS SEXIST THAN WHEN MALE ACADEMICS COULD STILL SMOKE IN THEIR OFFICES”? Because when you look at the data, the background on this issue, and the immediate response from the community, it’s obvious academic research isn’t now some utopian meritocracy brimming with equality. There is still institutional and systemic biases. Whether its gender, race, sexual-preference, or need related, or tied up in the archaic publishing system that is all too easily gamed, we have a long way to go before things can be considered “fair”. What might a fair system even look like?
Setihome
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.
Sabinvaccinebox3
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.
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 . 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
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!
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Ferdinando Pucci

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HOW IS ACADEMIC RESEARCH EVALUATED? There are many different ways to determine the impact of scientific research. One of the oldest and best established measures is to look at the Impact Factor (IF) of the academic journal where the research has been published. The IF is simply the average number of citations to recent articles published in such an academic journal. The IF is important because the reputation of a journal is also used as a proxy to evaluate the relevance of past research performed by a scientist when s/he is applying to a new position or for funding. So, if you are a scientist who publishes in high-impact journals (the big names) you are more likely to get tenure or a research grant. Several criticisms have been made to the use and misuse of the IF. One of these is the policies that academic journal editors adopt to boost the IF of their journal (and get more ads), to the detriment of readers, writers and science at large. Unfortunately, these policies promote the publication of sensational claims by researchers who are in turn rewarded by funding agencies for publishing in high IF journals. This effect is broadly recognized by the scientific community and represents a conflict of interests, that in the long run increases public distrust in published data and slows down scientific discoveries. Scientific discoveries should instead foster new findings through the sharing of high quality scientific data, which feeds back into increasing the pace of scientific breakthroughs. It is apparent that the IF is a crucially deviated player in this situation. To resolve the conflict of interest, it is thus fundamental that funding agents (a major driving force in science) start complementing the IF with a better proxy for the relevance of publishing venues and, in turn, scientists’ work. RESEARCH IMPACT IN THE ERA OF FORKING. A number of alternative metrics for evaluating academic impact are emerging. These include metrics to give scholars credit for sharing of raw science (like datasets and code), semantic publishing, and social media contribution, based not solely on citation but also on usage, social bookmarking, conversations. We, at Authorea, strongly believe that these alternative metrics should and will be a fundamental ingredient of how scholars are evaluated for funding in the future. In fact, Authorea already welcomes data, code, and raw science materials alongside its articles, and is built on an infrastructure (Git) that naturally poses as a framework for distributing, versioning, and tracking those materials. Git is a versioning control platform currently employed by developers for collaborating on source code, and its features perfectly fit the needs of most scientists as well. A versioning system, such as Authorea and GitHub, empowers FORKING of peer-reviewed research data, allowing a colleague of yours to further develop it in a new direction. Forking inherits the history of the work and preserves the value chain of science (i.e., who did what). In other words, forking in science means _standing on the shoulder of giants_ (or soon to be giants) and is equivalent to citing someone else’s work but in a functional manner. Whether it is a “negative” result (we like to call it non-confirmatory result) or not, publishing your peer reviewed research in Authorea will promote forking of your data. (To learn how we plan to implement peer review in the system, please stay tuned for future posts on this blog.) MORE FORKING, MORE IMPACT, HIGHER QUALITY SCIENCE. Obviously, the more of your research data are published, the higher are your chances that they will be forked and used as a basis for groundbreaking work, and in turn, the higher the interest in your work and your academic impact. Whether your projects are data-driven peer reviewed articles on Authorea discussing a new finding, raw datasets detailing some novel findings on Zenodo or Figshare, source code repositories hosted on Github presenting a new statistical package, every bit of your work that can be reused, will be forked and will give you credit. Do you want to do a favor to science? Publish also non-confirmatory results and help your scientific community to quickly spot bad science by publishing a dead end fork (Figure 1).
Open access costs
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!
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Academic pyramid
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?
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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.)
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_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.