Einstein published in 1916 a paper containing the prediction of the existence of gravitational waves. It has just one author (A.E. himself) and consists of a few pages of text and equations \citep{1916SPAW.......688E}. Fast forward exactly 100 years, the LIGO collaboration announced in a paper that they observed what Einstein had predicted. The paper has more than 1000 co-authors and it condenses, in just a few pages of text, equations and figures, an enormous amount of technical information \citep{PhysRevLett.116.061102}.

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.

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.

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.

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.

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

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

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

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

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.”

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.

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

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

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.

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

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

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

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.

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

New York Open Science Meetup

Please join us to keep posted about future events.

P.s. There will be PIZZA.

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?

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.

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.

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

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

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

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.

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

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.

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

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

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

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

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

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

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

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

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

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.

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

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

As the analysis from ScienceInsider notes:

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

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

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

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

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

EMA Q&A release

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

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

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

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

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.