“If you can't explain it to a six year old, you don't understand it yourself.”

To enter, follow these steps:

1. Signup at authorea.com/signup to create an account.
2. Upon signup, select the group "Up-Goer Five" to join the challenge.
3. Describe your research using the ten hundred most common words with the Up-Goer five text editor. 
4. Copy and paste your entry into a public Authorea document.
5. Hit "Publish" on the toolbar to publish your document to the Up-Goer five group.
6. Assign a digital object identifier (DOI) to make it citable.
7. Share it socially and challenge your friends! (#upgoerfive)

Blogging as a place for correcting the scientific record

Blogging as a place for publishing "grey literature"

Blogging as a place of public outreach

Blogging as a way to advance your career

What is your mission?

What is the story behind Authorea?

Templates

Publishing needs to keep up with research writing

Most of the time submission is grueling for authors

Enter Authorea

What is the ArXiv?

How do ArXiv and Authorea compare?

1. A scholarly repository is more than a PDF dump

1. Hamster: Tisha 🐹 

The importance of citations in scholarship

What is version control?

"If people had deposited raw data and full protocols at the time of publication, we wouldn’t have to go back to the original authors," says Iorns. That would make it much easier for scientists to truly check each other’s work.- The Atlantic

• Analysis of ground-level ozone formation and its correlation with concentration of other pollutants and weather elements
• Vision Zero Crash Data Analysis

The Authorea Fitbit of research

• 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?

Authorea: our pitch.

A new era

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

A modern new look

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

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

• how to break the cycle of the individual in academia and squash the collective obsession with academic rankings; 
  
• how open science and open scholarship will positively shape the future of academic publishing and increase the rate of scientific discovery;
  
• introduce the 'paper of the future'; whereby a static paper is no longer viewed as an acceptable form of submission, rather a digital-born format that allows the reader to access and interact with the most important elements of a researcher's work: the data and code.
  

https://redd.it/52vtf7

"The Imagine Science Film Festival is a conversation between scientists, filmmakers, and artists to explore the latest scientific advances and theories in unique and thought-provoking ways." - Nate Dorr, Director of Programming

A big challenge, but one that I enjoy, is that the important—many of the most societally relevant—problems can no longer be just solved with physics like for the transistor or biology like the for Polio vaccine.  It is increasingly the case that we need to bring different groups of people together from very different disciplines to partner and tackle important problems. It is like the analogy that we can no longer act like golf or tennis players—we have to now think in terms of baseball or football. A baseball team will not be successful if it is full of shortstops.

Hootsuite

1. There is enough DNA in an average person’s body to stretch 10 billion miles. That's approximately the distance from the Earth to Pluto and back!

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 page² 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.

Deciding between ShareLaTeX and Overleaf? Choosing the right editor for your LaTeX manuscript is not easy. Here are some key comparison points that showcase how Authorea is different. 

1. Click on the 'Export' button on the top right of your page

We're excited to invite you to our THIRD NY Open Science Meetup hosted at our new location in the Rise Labs in the Flatiron District.

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 \citep{1916SPAW.......688E}. Fast forward exactly 100 years, the LIGO collaboration announced in a paper that they observed what Einstein had predicted. The paper has more than 1000 co-authors and it condenses, in just a few pages of text, equations and figures, an enormous amount of technical information \citep{PhysRevLett.116.061102}.

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.

Great news! We're happy to announce that Authorea is one of the winners of the NYC-Paris Business Exchange competition. We'll be opening an Authorea office in Paris in March 2016. C'est génial!       

In a nutshell: Gravitational waves are ripples in the fabric of space time produced by violent events, like merging together two black holes or the explosion of a massive star. Unlike light (electromagnetic waves) gravitational waves are not absorbed or altered by intervening material, so they are very clean proxies of the physical process that produced them. They are expected to travel at the speed of light and, if detected, they could give precious information about the cataclysmic processes that originated them and the very nature of gravity. That’s why the direct detection of gravitational waves is such an important endeavor. Definitely worthy of a Nobel prize in physics.

A Big Discovery

On 14 September 2015 at 4:50:45 AM Eastern standard time, the LIGO experiment detected for the first time the passage of gravitational waves. Scientists saw a very specific pattern of stretching and compression of space-time called a “chirp”. The detection was done independently at the two locations of the experiment, one in Hanford (Washington) and the other one in Livingstone (Louisiana). This amazing discovery has occurred almost exactly 100 years after Albert Einstein published his General Theory of Relativy \citep{1916AnP...354..769E}, and represents the last verification of this beautiful theory of gravity.

How did the waves look like? Glassy and double-overhead!

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.

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

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

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

Open Science

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

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

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

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

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

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

Do you write in LaTeX? At Authorea, importing from arXiv, ShareLaTeX, and Overleaf is now as simple as pasting your document’s URL.

By bringing your work to Authorea, you can take advantage of the power of Authorea for writing LaTeX natively on the web, Authorea’s powerful citation tool, one-click export to over 90 journal formats, and the ability to include live interactive figures in your articles.

Clicking on the Import button at the top right of your homepage will now give you three new import options:

• Import an arXiv.org document,

• Import your (public) ShareLaTeX document,

• Import your Overleaf document,

And as always, you can also import a LaTeX/BibTeX combo or a compressed LaTeX archive.

At Authorea, we’re excited to integrate with external academic services to make your writing experience as seamless as possible. We’re pleased to announce this improvement to our document importer. Now you can bring your work into Authorea from three very useful LaTeX-centered services – arXiv, ShareLaTeX and Overleaf – just by typing the document’s URL.

Remember: we hate vendor lock-in as much as you. You can export your documents (in full, including the git log) from Authorea at any time.

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

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

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

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

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

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

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

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

Welcome to arXMLiv!

The arXMLiv project by the KWARC research group at Jacobs University Bremen has been ongoing for almost a decade, dating back to 2006. I was lucky enough to enroll as a bachelor student at Jacobs during that same year, and got personally involved with arXMLiv in 2007.

The goal of arXMLiv \cite{Stamerjohanns_2010} is to transform the sources of ≈1 million scientific papers from arXiv starting with the author-friendly syntax of TeX/LaTeX and ending with highly processible, machine-friendly, XHTML/HTML5 documents. Over the years we have become partners with the LaTeXML converter, which ambitiously aims at translating any TeX document into as good as possible web equivalent.

The Times They Are a-Changin

Science is going through a rapid phase of transformation. Two important trends are emerging:

1. Research is becoming more complex, requiring larger collaborations and bigger experiments.

2. Science and technology increasingly affect modern society.

The first trend is easy to understand. Let’s think of the cumulative knowledge of humankind as a sphere. Scientists work at the surface and try to “push the boundary”. Discovery increases the volume of knowledge. As the sphere’s volume grows, so does its surface area. Therefore an ever increasing number of researchers is required to tessellate the expanding cutting-edge of science. Moreover, contrary to a few hundred years ago when the sphere of knowledge was so small that a single polymath could master large chunks of it, nowadays no human can understand the details of more than a few research topics. To capture the bigger picture and understand very complex research questions, collaborative efforts combining together a number of highly specific expertises are required.

Friday June 26, 2016.

Today is a great day for human rights.

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

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

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

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

Happy writing.
Happy loving.
Authorea

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

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

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

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

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

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

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

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

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

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

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

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

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

Example of an “astronomer friendly” deluxe table formatted with Authorea. This is the example posted by Jess K on astrobetter in How to Make Awesome Latex Tables. For this table we are using the LaTeXML engine, have a look at this quick tutorial if you are a prospective Authorea power LaTeX user.

cccccccc 1/3 Bright & & 4.24 ⋅ 10⁻⁴ & 6.19 && 96.97 & &
& [0.3,3] & & & 1.77 & & 96.7 & 1.9σ
2/3 Dim & & 4.26 ⋅ 10⁻⁴ & 4.48 & & 52.77

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

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

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

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

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

N ≈ 2 f_l f_i f_c L

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.

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

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

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

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

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

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

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

So you actually want your research read...

Every year in science, tech, and medicine, on the order of 2 million papers are published.

That’s a lot of papers.

To remain current with their field, physicians must read about 20 papers a day. Given the growing “scourge” of cross-disciplinary science and the interconnectivity of life, our world, and everything, 20 papers honestly seems low.

How, then, is an average journal article only read by 10 people, or only 20% of cited papers actually read?
Maybe it has to do with the overextension of researchers (see Alberto’s post above for massive discipline-spanning course lists).

Or maybe it has to do with the way papers are presented. They’re long, in archaic formats, and only accessible with a background in the given discipline (and, critically, freedom from paywalls).

Why can’t we - scientists/communicators of knowledge/sharers of discoveries - agree to write clearly, concisely, and for broad impact and appeal?

Many universities and other research institutions have press offices that interface with the public for just this reason. This is critical, as institutions’ research and resources help attract more funding and, nobly, should be shared with the world.

The problem?

You, as the person who did the research, probably know it better!
And you (hopefully) won’t oversell it!

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

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

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

The researchers got some great pictures.

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.

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 \cite{Ferguson_2014}.

In an effort to bring science outside of research labs, today Authorea is launching an exciting new line of fragrances and beauty products for scientists and scholars. The first product to hit shelves will be Acqua d’Autore. This unisex and cross-disciplinary fragrance is a light and elegant scent for the modern researcher. It begins with mild citrus notes followed by elegant notes of tobacco and vanilla. The scent finishes smoothly with wood notes, known to enhance scientific collaboration. Whether you’re stepping out of the lab or into your favorite shoe store, Acqua d’Autore is guaranteed to attract the gaze of your next coauthors. Authorea’s cofounder, Alberto Pepe, a life long supporter of the #scienceperfume movement comments: “Today marks the beginning of a new era that will see fashion and science finally joined, bringing scientific transparency, data, and good looks to one place”.

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 \cite{Cressey_2015}. 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.

Fabio, when did you decide to go watch an eclipse in the Arctic?
I’ve been feeling this urge to visit the northernmost parts of Earth for a while now. My PhD in Stockholm gave me the opportunity to explore the Norwegian coastline and Lapland, but the Arctic was a different story. A sort of forbidden dream. Then last year I started a postdoc at Yale, in the research group led by John Wettlaufer, who’s an expert on sea ice and the Arctic. When I heard there was gonna be a total solar eclipse at Svalbard I knew I had to go.

Where is Svalbard, exactly?
Svalbard is an archipelago situated about half way between continental Norway and the North Pole, and it is an outpost for research and arctic exploration. In Longyearbyen, a little city of about 2000 people, and Svalbard’s capital, there is the world’s northernmost institution for higher education and research: the University Center in Svalbard.

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.

A recent article titled The spin rate of pre-collapse stellar cores: wave driven angular momentum transport in massive stars was written on Authorea and submitted to the Astrophysical Journal (ApJ) and to the arXiv as a pre-print.

While waiting on peer review from the ApJ, the authors want to test Authorea as a platform for open peer-review. By going to the document’s page, you can comment on a section, figure, observation, sentence, or the whole piece. The authors and other commenters can respond and further the discussion. And it’s all out in the open, just how science was meant to be.

But it doesn’t stop there. You can also view full-size, high-resolution versions of the paper’s figures, as well as easily follow links in the References at the bottom of the page.

In the paper, \citet{fuller} show for the first time how internal gravity waves, excited in the turbulent layers of stars at least ten times larger than the Sun, can radically change their internal rotation rate. In particular, these waves – somewhat analogous to ocean waves – can determine how rapidly the stellar core spins around its axis when the star is about to die and become a supernova. The spin of a pre-supernova core is important because it deeply affects the stellar explosion and determines the rotation rate of the stellar remnant (neutron star or black hole).

The System as It Stands

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

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

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

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

• pay for the submission of articles published in journals

• and are now buying it all back.

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

In the mid 1990s, with the shift from print-only to digital distribution, economic formulations changed. No longer would a research university need to subscribe to multiple copies of in-demand journals. No longer would storage space play a significant role in decisions (e.g. storage and maintenance costs for a 2500 page journal volume range from $300-1000). No longer would impact be a limiting factor for purchased titles, or as it’s now emerging, should it even be. And publishers could now offer their whole catalog of journals at one discounted “Big Deal” price. In the words of Derk Haank, then Elsevier and current Springer CEO:

But what it [electronic publishing] does do is to dramatically lower the marginal costs of allowing access.... [The cost for each new users] is virtually nil and that means that we should be more creative in the business model.... where we make a deal with the university, the consortia or the whole country, where we say for this amount we will allow all your people to use our material, unlimited, 24 hours per day. And, basically the price then depends on a rough estimate of how useful is that product for you; and we can adjust it over time. [emphasis added]

Here, “adjust it over time” means mandate an average 5-6% price increase annually. Bergstrom, et al calculate:

“A bundle whose price increased by 5.5% per year would double its price between 1999 and 2012, whereas over the same period the US consumer price index rose by 38%.” [emphasis added]

What’s more, such “creative” business models force library administrators to try to quantify abstractions like the value of information. Information, however, is context dependent. The difference of opinion on a paper’s importance could range from “meaningless” to a critical insight for unraveling a disease pathway.

At the end of the day, an all-inclusive “Big Deal” bundle may be easiest – if funds are available. When cost limits access, however, researchers may rely on e-mailed PDFs from helpful colleagues at better-equipped campuses. Another solution, when access is out of reach or publication slow (e.g. a year from initial acceptance to publication is common for some Statistics journals), is pre-print repositories like arXiv. Unfortunately, the articles aren’t peer-reviewed, a reason big publishers can charge so much.
This is also a reason we think researchers (and journals!) might want to try their own pilot study of Authorea-as-interactive-repository or submission platform.

This is the 21st Century, scientists should be writing and disseminating like it!

Have thoughts about this? Let us know in the Comments or follow us to get updates!

Tens of thousands of innovators met in Austin, Texas last week to discuss emerging tech, science, and innovation. It was the Interactive portion of South by Southwest (SxSW). Authorea was there.

Among many great events, the MIT Media Lab presented “SOLVE”, an initiative set to bring together the most gifted researchers and innovators to identify and tackle challenges where new thinking and emerging technologies have the potential to make the world a better place. SOLVE identified four main themes: Learn, Cure, Fuel, Make.

I work at a startup. We get things done on a budget.

This is a summary of how I got:

• A new test server for my local dev machine

• An extra monitor for my dev setup

• Tons of fun!

And all for less than $100.

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

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

Thomson Reuters’s reference management system EndNote makes it easy to store, share, annotate and export your citations in selected formats.

First Time Setup in EndNote

Adding references from EndNote is easy. You’ll need to do a little one-time prep work first.

Step 1

Download the BibTeX output style from the EndNote homepage.

Step 2

Add the BibTeX output style to your EndNote Styles folder.

Step 3

Open EndNote and through the Edit drop-down menu, go to Output Styles > Open Style Manager...

To import Zotero references into your Authorea writing environment follow these simple two steps (more here)

In Zotero

First, make sure you set the Zotero default export format to BibTeX. Navigate to Preferences, Export and select BibTeX as the default format.

We’re very happy to announce a special Travel Grant for European FGSA and FIP members attending the American Physical Society APS March Meeting 2015, in San Antonio, Texas.

Authorea is committed to helping the advancement of scientific collaboration and this travel grant aims to foster the interexchange between young EU and US members, helping students and postdoc to integrate in the international APS community and to share their different experiences.

These travel grant will be recognized at the Student and FIP Receptions, during the March Meeting 2015.

For more information on the travel grant and application instructions please visit http://www.aps.org/units/fgsa/travel/ and http://www.aps.org/units/fip/awards/travel-grant.cfm.

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

Authorea’s new address is:

Authorea

120 E 23rd Street

5th Floor

New York, New York 10017

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

So, what’s new? You can now:

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

2. Add your affiliation(s) to your profile. Just log in and click on User Settings in your profile.

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

Authorea has a new powerful commenting framework built into the editor. Each document has comment bubbles to the right of the text that may be toggled to leave or view comments.

How to comment

To insert a comment anywhere on the document, click on the comment icon that appears on the right margin of your document

Whether you’re celebrating Thanksgiving today in the US or it’s just another day in the lab, it’s important to remember that there’s a lot to be thankful for, especially in regards to Open Access.

Increased Open Access

There’s no question that Open Access (OA) is the future, and each year the numbers clearly show its growth and the world’s approval and desire to learn. Here’s a collection of statistics compiled for OA Week in October. Some truly exciting numbers.

The Community

When people get together (in person or online) who believe there’s a right to access fundamental knowledge about the world, good things emerge. Ideas can be shared, developed, grown, and implemented instantly. Collaborations, contacts, and friendships are formed that will span careers. The OA Community is a rich, vibrant group with core beliefs that inherently make it a hot bed of acceptance, creativity, and productivity.

More Governments, Foundations, and Organizations Supporting OA

With the EU’s recent changes mandating clinical trial transparency and similar rules under consideration in the US, open access is really going prime time. Coupled with the recent announcement by the Gates Foundation of impressively stringent OA guidelines, there’s a clear trend towards more openess - a good thing for funding bodies, governments, researchers, and every citizen of the world.

Innovative Ways to Open Your Research

Every week, there’s some innovation, update, new service or framework that makes it easier to share your work. Whether its repositories for code and data, groups that give you an informal framework to talk about your research, organizations that advocate for OA, or places to get the word out generally about what your true passion is, we are all living in a moment filled to the brim with potential. We need to remember to be thankful for it and take advantage of every opportunity to make sure our world and our science are as open as possible.

Happy Thanksgiving,
The Authorea Team

P.S. And of course we’re thankful for all our users and followers on Twitter, Facebook, and Google+ ! :)

Bill Gates has some thoughts about education.
Specifically, how its future might look.

He recently visited Arizona, where Rio Salado College and University of Phoenix are broadening access to education.
improvements include:

1. Low costs (compare Rio Salado’s $84/credit-hour vs the 2011 average $250/credit-hour for in-state, public tuition);

2. flexibility (many classes start new sections every week);

3. online and mobile integration (U of Phoenix offers an app for studying and course management from anywhere, anytime).

These innovative offerings help solve practical problems for modern education. Given the 40% college dropout rate, ever-rising costs of tuition, associated increases in post-college debt, the need to stay competitive, and the desire to explore new areas of knowledge, anything that lowers friction is certainly welcome. Given that these two institutions alone serve over 350k students, you also can’t argue with demand that’s clearly there.

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?

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.

Introducing...

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

In 1937, just one year before suddenly disappearing under mysterious circumstances, a brilliant italian physicist named Ettore Majorana predicted the existence of a very peculiar particle. Having the exciting property of being its own antiparticle (that is it simultaneosly behaves as matter and anti-matter) the elusive “Majorana particle” has been finally observed by a group of scientists at Princeton University \cite{Nadj_Perge_2014}. To achieve the important result they used a two-story-tall microscope to observe the end of a superconducting wire.

Do you enjoy using Authorea?
Do you want to help spread it to your colleagues?
Do you want to learn more from a real person instead of a website?

Then drop us a line at hi@authorea.com and we can arrange a demo/presentation at your department, library, on-campus organization, group meeting, research laboratory. Whether it’s a Department of Astronomy, a Women in Science Club, a Physics library, a Molecular Biology lab, (or a Happy Hour!), we’ll be very happy to come and showcase Authorea.

You might be asking yourself,

What’s in it for me?

To that we say,

check out these benefits!

1. Get a first-hand introduction to Authorea

   Learn your way around the website, get your questions answered, your troubles shot, and hear more about Authorea’s vision.

2. Connect with like-minded people

   What do Albert Einstein, Ben Franklin, DARPA, Google, J.R.R. Tolkien, Socrates, Stanislaw Ulam, and The Super Friends have in common? They are all known to have established tight-knit communities of highly-skilled people with which to meet, discuss, bounce around ideas, create, and solve interesting problems. You can think of Authorea as a way to help such like-minded people document and iterate their thoughts. Maybe even produce something to publish.

3. Learn technical writing

   LaTeX and Markdown are powerful document preparation systems / markup languages that stress content over form. LaTeX is widely used for technical writing and for the formatting and publication of articles, especially in CS, math, and the physical sciences. If you or your colleagues want a brief tutorial while our representative is on-campus, we can get you started with the basics of document text and structure, image incorporation, and handling other elements in and outside the editor on Authorea.

4. Free Stuff!

   Not one to show up empty-handed, we’ll bring along some Authorea-style goodies, tips and tricks sheets, some refreshments to entice attendance, and a free 3-month organizational subscription!

Shoot us an email and say hi at hi@authorea.com if you want to meet up!

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!

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

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

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

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

This investment is important for Authorea on many levels.

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

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

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

Happy writing!

---Nathan and Alberto

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!

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

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

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.

Introduction

Wikipedia and Github host code and articles. The content is produced on collaborative, web-based platforms. As of January 9, 2014, Wikipedia reports having 4,420,275 articles. GitHub recently announced having 10 million public repositories.

Plotly and Authorea, together, now provide similar platforms; ours are for research content, data analysis, graphing, and scholarly publications. We are happy to announce a partnership between Plotly and Authorea that gives you a free suite of powerful, collaborative tools for doing your analysis, graphing, coding, and publication. Authorea and Plotly, together, can power your research collaboration.

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.)

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.