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.

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 to the right of this text 💬  (You can also highlight specific parts of the text to leave a comment on). (Ha. That's your first lesson!).The BasicsAuthorea is a collaborative document editor built primarily for researchers. It allows you to collaboratively write in real-time in normal text, LaTeX, and Markdown all within the same document. In addition to easily writing together, each article on Authorea is a git repository, which allows you to host 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, 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.Invite your colleagues. Click here to invite contacts from your Gmail. You'll get extra private documents in your account and you'll make Pete very happy!

Moved to https://natejenkins.ch/steph-shooting-streak

The vast majority of academic researchers write their research in Microsoft Word \cite{Pepe_2016}. Word is easy to use due to its what-you-see-is-what-you-get (WYSIWYG) interface, however it is limited in many ways that are necessary for effectively communicating research. It necessitates the use of publishers (some of which have very antiquated models) and it limits the capability to collaborate and share data. Furthermore, it means that proper research publishing and indexing will always be costly as the conversion from Word to HTML and JATS XML (the gold standard of research articles) is an onerous process, often times manually performed "offshore". On Authorea we seek to marry the ease of writing on Word or Google Docs with the power of LaTeX, HTML, and Git.  By doing that we seek to combine the writing and publishing process so that writing is publishing. We believe that this paradigm can not only make communicating research quicker but can also make it drastically cheaper for authors and publishers.The power of LaTeX 💪LaTeX is a powerful markup language used primarily by those in the hard sciences--physicists, computer scientists, mathematicians etc. It is immensely powerful for controlling the presentation of documents, however it comes with a steep learning curve. Want to bold text? In LaTeX you need to write \textbf{bold}. Want to italicize text? Write \textit{italicize}.  In the eyes of some researchers that extra control and access to the underlying layer of markup is a benefit allowing the precise control of typesetting at a professional level.  On the converse, many, if not most, might see this as as being too cumbersome for editing and thus will never use it. At Authorea, we believe that there are strengths and weaknesses of LaTeX. We seek to provide a broad spectrum of LaTeX support so that whether you are Donald Knuth himself or someone who thinks LaTeX is a rubber, you can take advantage of Authorea and the power of LaTeX.  Below, we highlight how we are re-positioning and repurposing LaTeX in a way that is accessible to \textit{all researchers}. 🙃 Labeling and referencing figures and headingsLabeling figures and tables is something that is commonly done when writing a research article but how you do this depends upon how you write research articles. If you're writing in Word or Google Docs, you may refer to a figure or table like this:As seen in Figure 1.If you're writing in LaTeX, you will likely refer to a figure in a different way, like this:As seen in Figure \ref{527885}.While this is not a revolutionary change, it makes editing easier if you're working with multiple figures and you need to change the organization of the document around.  On Authorea, labeling and numbering is updated automatically whenever you add, remove, or move a figure or heading. Insert a new figure or move a figure around and they are automatically re-labelled.  This feature is expected in LaTeX (and commonly used) but is difficult to achieve and consequently use in Word.  We've made it easy for researchers that typically write in Word, as well as LaTeX writers, to label and reference any part of a document.More on labels and references here 👈Powerful document exportingResearchers who write in LaTeX not only write differently than most researchers, they also tend to publish and share their work differently.  Indeed, Figure \ref{527885} highlights the differences in pre-printing (self-publishing) between fields where LaTeX is the norm (arXiv) and where LaTeX is largely unheard of (Life sciences). Although there are many issues and reasons for the differences in preprint growth between disciplines, it can't be ignored that LaTeX helps facilitate preprints by allowing researchers to produce professionally typeset documents on their own.

If you find Authorea useful, please help support it: send us feedback, invite colleagues to sign up, or buy a subscription. Keep up the good work! Best regards, The Authorea Team

More and more scholars are leaving their academic posts (see [1] [2] [3]). As it turns out, it’s not possible to fully leave academia unless you write a detailed blog post about it. So, here’s mine. I resigned from my postdoctoral position at Harvard two months ago. My academic career was fairly typical. I spent the last twelve years doing research. After college, I worked at CERN for a few years, then pursued a Ph.D. at UCLA and a 3-year Postdoc at Harvard. During my Ph.D. and Postdoc I did not even apply to a single tenure-track job. Why? My research background is very (maybe, way too) interdisciplinary: B.Sc. in Astronomy, M.Sc. in Computer Science, at CERN I did Data Science (basically working in Tim Berners-Lee former group), my Ph.D. is in Information Science, and my Postdoc in Astrophysics. Who the hell is going to hire me? While many praise academic interdisciplinarity as an asset, at the end of the day TO GET TENURED YOU NEED TO BE ABLE TO TEACH CORE CLASSES IN ONE DISCIPLINE. So, even though I was working in an amazing research group and my publication record was just fine, I decided to leave. Leaving a postdoc at a top institution was a hard and risky decision to make. Yet, with so many PhDs and postdocs leaving academia today, I certainly don’t feel alone. But, HOW COMMON (OR RARE) IS IT TO LEAVE ACADEMIA? Last week I attended the ScienceOnline conference and in a session called _Alternative careers in science_, Eva Amsen discussed the infographic below.

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?

PREVIOUS “HABITABLE PLANETS” – NEXT “ASTROBIOLOGY” There is on average one planet orbiting every star in the Universe . If this sounds exciting, you might wanna read the previous post in this series. Our Galaxy (the Milky Way) is an immense disk of gas and stars with a diameter of about 100 000 light years, hosting about 100 billion stars and, therefore, also about 100 billion planets. Take a deep breath. Now, it turns out the Milky Way is just one of 100 billion galaxies that populate our Universe, a colossal expanding stretch of spacetime with an age of 13.7 billion years. The math is trivial: There are about 10 000 000 000 000 000 000 000 = 10²² planets out there. This number is extremely large. Apparently larger than the number of grains of sand found in every beach and every desert on Earth. But how many of these planets host life? And in particular, HOW MANY PLANETS HOST INTELLIGENT LIFE WE MIGHT BE ABLE TO COMMUNICATE WITH? In order to estimate the number of technological civilizations that might exist among the stars, in 1961 Frank Drake proposed the following simple equation:

Retraction Watch is a blog that tracks retractions in science -- and it's probably a site you never want your research to be on. To many, retracting your work means that you've committed fraud, and in most cases can be the end of a researcher's career. However, that's not always the case: in fact, retracting your work for the right reasons can even be good for your career and good for science (Lu 2013). Retraction Watch highlights cases where scientists did not retract their work due to fraud, but rather because it was "the right thing."  Here we take the opportunity to further highlight these pieces and the courageous scientists that did the right thing despite an enormous stigma.We believe the future of scholarly communication will be more dynamic than it is today. By definition, this will require more corrections and retractions.  Authorea was built to show the full history of a document, from creation to final publication. We allow annotations of the literature and believe that a more dynamic and robust form of communication is the future -- it's what we're building. Join us!

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:

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.  

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

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

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

In this short post series I try to tackle one of the biggest questions out there: ARE WE ALONE? The reasoning leads to some radical implications for the VERY NEAR FUTURE OF HUMANKIND. Read till the end and feel free to comment as you go. Hopefully this will spark interesting discussions. 1. Habitable Planets How many habitable planets exist in the Universe? 2. The Drake Equation How to estimate the number of technological civilizations in our Galaxy? 3. Astrobiology Is biological life common in the Universe? 4. The Fermi Paradox Is intelligent life common in the Universe? And if yes, does it last? 5. Interactive Drake Equation Use your own intuition to calculate the chance of being alone or not

Writing a thesis is a laborious process that takes months. Thesis writing marks the culmination of years of work for many students and is a process that can be both exciting and terrifying. Whether you are an undergraduate, a masters, or a doctoral student, writing your thesis or dissertation means work, and lots of it. Get ready and try to make the most out of the experience. While arduous, it can also be gratifying.How long is a thesis?The average length of a thesis varies depending upon discipline and the degree you are pursuing. However, most doctoral theses and dissertations are dozens, if not hundreds, of pages long (see Fig \ref{382478}). On average, the longest theses are found in history and anthropology (300 pages long) whereas the shortest ones are in mathematics and biostatistics (100 pages or less). 

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

Einstein published in 1916 a paper containing the prediction of the existence of gravitational waves. It has just one author (A.E. himself) and consists of a few pages of text and equations . 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 .