Alberto Pepe

and 1 more

Why are scientific ideas disseminated via "papers"? Is a paper the best way to share and publish research results today? The format and function of research communication has not changed much in the last 400 years. Take any paper published this week, download it, and compare it to a digitized version of a paper from the 1600s. The two papers may differ in page layout, color, and typeface, but they are essentially identical in format - a collection of text and figures. Indeed, the fact that we refer to the mainstream outlet of research communication as "paper" speaks volume of its boundness to print.While the published format has not changed in the last 400 years, the change in published content is astronomical: a proclamation of the success of science. The discovery of molecular structure of DNA \cite{WATSON_1953}, penicillin \cite{Fleming1980}, and the formulation of general relativity \cite{Einstein_1916} are some of the biggest and most splendid scientific discoveries of all time. They were all published in a two-dimensional paper format. Even more recently, the groundbreaking discovery of gravitational waves, which earned the 2017 Nobel Prize in Physics to the leads of the LIGO collaboration, was published with a traditional paper format \cite{Abbott_2016}. LIGO's groundbreaking was certainly not analyzed on a 2D piece of paper.So, how is it possible that scientists produce and write cutting-edge "21st-century research" and still publish it in a "17th-century format"? \cite{obsolete,Pepe}Obviously, the paper format, being so enduring and persistent, has served science well. But things have changed in the last three decades. The recent explosion of content digitalization, growing internet speed and connectivity, and reliance on data, code, and computational power are leading to an unprecedented and irreversible path to changing the way we publish and disseminate research ideas. A Gutenberg-style revolution in scholarly communication is upon us, and we believe it is being pioneered by the Open Science movement. The Open Science initiative aims to make scientific research and its dissemination accessible, reproducible, and transparent. In addition to encouraging publication of research as Open Access as early as possible (the availability of preprints in subject-based repositories has moved beyond  the realm of physics), for many computational domains Open Science translates into making code and data available to everyone, and into practicing "open notebook" science. In other words: readers and reviewers must be able to understand how the authors produced the computational results, which parameters were used for the analysis, and how manipulations to these parameters affect the results. Increasingly, journals and funding agencies are mandating that researchers share their code and data when reporting on computational results based on code and data. However, even when data and code are provided by authors, and published, they are oftentimes relegated to Supplementary Information or to entirely separate platforms, disconnected from the published "full text". Since code, data, and text are not linked on a deep level, readers and reviewers are faced with barriers that hinder their ability to understand and retrace how the authors achieved a specific result. In addition, while data and code may be available in repositories external to the corresponding article \cite{Antoniol_2002}, it takes readers and reviewers considerable effort to verify the software and re-run analyses with, say, changed parameters.The idea of a multimedia, multi-dimensional, scholarly publication that defies the limitations of the 2-dimensional paper format  is not new. The publication history of the first detection of gravitational waves by the LIGO collaboration is an example of how much this is needed in scientific publishing. The discovery was reported in a series of traditional articles \cite{Abbott_2016}\cite{Abbott_2016a} but with an associated and externally hosted supplemental Jupyter notebook \cite{losc-tutoriallosc_event_tutorialmaster}. The notebook allows readers to run and tweak the code, change parameters to alter the analysis, and, in its section dedicated to the signal processing of the gravitational waves into sound, it even allows readers to play the bloop of two black holes colliding. Yet, the notebook and the multimedia elements had to reside outside the article. Why?

Alberto Pepe

and 4 more

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

Authorea Help

and 3 more

WHAT IS LATEX? LaTeX is a programming language that can be used for writing and typesetting documents. It is especially useful to write mathematical notation such as equations and formulae. HOW TO USE LATEX TO WRITE MATHEMATICAL NOTATION There are three ways to enter “math mode” and present a mathematical expression in LaTeX: 1. _inline_ (in the middle of a text line) 2. as an _equation_, on a separate dedicated line 3. as a full-sized inline expression (_displaystyle_) _inline_ Inline expressions occur in the middle of a sentence. To produce an inline expression, place the math expression between dollar signs ($). For example, typing $E=mc^2$ yields E = mc². _equation_ Equations are mathematical expressions that are given their own line and are centered on the page. These are usually used for important equations that deserve to be showcased on their own line or for large equations that cannot fit inline. To produce an inline expression, place the mathematical expression between the symbols \[! and \verb!\]. Typing \[x=}{2a}\] yields \[x=}{2a}\] _displaystyle_ To get full-sized inline mathematical expressions use \displaystyle. Typing I want this $\displaystyle ^{\infty} {n}$, not this $^{\infty} {n}$. yields: I want this $\displaystyle ^{\infty}{n}$, not this $^{\infty}{n}.$ SYMBOLS (IN _MATH_ MODE) The basics As discussed above math mode in LaTeX happens inside the dollar signs ($...$), inside the square brackets \[...\] and inside equation and displaystyle environments. Here’s a cheatsheet showing what is possible in a math environment: -------------------------- ----------------- --------------- _description_ _command_ _output_ addition + + subtraction - − plus or minus \pm ± multiplication (times) \times × multiplication (dot) \cdot ⋅ division symbol \div ÷ division (slash) / / simple text text infinity \infty ∞ dots 1,2,3,\ldots 1, 2, 3, … dots 1+2+3+\cdots 1 + 2 + 3 + ⋯ fraction {b} ${b}$ square root $$ nth root \sqrt[n]{x} $\sqrt[n]{x}$ exponentiation a^b ab subscript a_b ab absolute value |x| |x| natural log \ln(x) ln(x) logarithms b logab exponential function e^x=\exp(x) ex = exp(x) deg \deg(f) deg(f) degree \degree $\degree$ arcmin ^\prime ′ arcsec ^{\prime\prime} ′′ circle plus \oplus ⊕ circle times \otimes ⊗ equal = = not equal \ne ≠ less than < < less than or equal to \le ≤ greater than or equal to \ge ≥ approximately equal to \approx ≈ -------------------------- ----------------- ---------------

Alberto Pepe

and 1 more

Hello, and welcome to Authorea!👋  We're happy to have you join us on this journey towards making writing and publishing smoother, data-driven, interactive, open, and simply awesome. This document is a short guide on how to get started with Authorea, specifically how to take advantage of some of our powerful tools. Of course, feedback and questions are not only welcome, but encouraged--just hit the comment icon to the right of this text 💬  (You can also highlight specific parts of the text to leave a comment on). (Ha. That's your first lesson!).The BasicsAuthorea is a collaborative document editor built primarily for researchers. It allows you to collaboratively write in real-time in normal text, LaTeX, and Markdown all within the same document. In addition to easily writing together, each article on Authorea is a git repository, which allows you to host data, interactive figures, and code. But first, let's get started! 1. Sign up.If you're not already signed up, do so at authorea.com/signup.  Tip: if you are part of an organization, sign up with your organizational email.  2. First stepsDuring the signup process you will be asked a few questions: your location, your title, etc. You will be also prompted to join a group. Groups are awesome! They allow you to become part of a shared document workspace. Tip: during signup, join a group or create a new one for your team. Overall, we suggest you fill out your profile information to get the best possible Authorea experience and to see if any of your friends are already on the platform. If you don't do it initially during sign up, don't worry; you can always edit your user information in your settings later on.Once you've landed on your profile page (see below). There are a few things you should immediately do:Add a profile picture. You've got a great face, show it to the world :) For reference, please see Pete, our chief dog officer (CDO), below. Add personal and group information. If you haven't added any personal information, like a bio, a group affiliation, or your location, do it! You might find some people at your organization already part of Authorea, plus it is a great way to build your online footprint, which is always good for getting jobs.Invite your colleagues. Click here to invite contacts from your Gmail. You'll get extra private documents in your account and you'll make Pete very happy!
Jingjing  Liang1*, Thomas W. Crowther2, Nicolas Picard3, Susan Wiser4, Mo Zhou1, Giorgio Alberti5, Ernst-Detlef Schulze6, A. David McGuire7, Fabio Bozzato8, Hans Pretzsch9, Sergio de-Miguel10,11, Alain Paquette12, Bruno Hérault13, Michael Scherer-Lorenzen14, Christopher B. Barrett15, Henry B. Glick16, Geerten M. Hengeveld17,17.5, Gert-Jan Nabuurs17,17.6, Sebastian Pfautsch18, Helder Viana19,20, Alexander C. Vibrans21, Christian Ammer22, Peter Schall22, David Verbyla23, Nadja Tchebakova24, Markus Fischer25,26, James V. Watson1, Han Y.H. Chen27, Xiangdong  Lei28, Mart-Jan Schelhaas17, Huicui Lu29, Damiano Gianelle30,31, Elena I. Parfenova24, Christian Salas32, Eungul Lee33, Boknam Lee34, Hyun Seok Kim34,35,36,37, Helge Bruelheide38,39, David A. Coomes40, Daniel Piotto41, Terry Sunderland42,43, Bernhard Schmid44, Sylvie Gourlet-Fleury45, Bonaventure Sonké46, Rebecca Tavani47, Jun Zhu48,49, Susanne Brandl9,49.5, Jordi Vayreda50,51, Fumiaki Kitahara52, Eric B. Searle27, Victor J. Neldner53, Michael R. Ngugi53, Christopher Baraloto54, Lorenzo Frizzera30, Radomir Bałazy55, Jacek Oleksyn56, Tomasz Zawiła-Niedźwiecki57, Olivier Bouriaud58,58.5, Filippo Bussotti59, Leena Finér60, Bogdan Jaroszewicz61, Tommaso Jucker40, Fernando Valladares62, Andrzej M. Jagodzinski56,63, Pablo L. Peri64,65,66, Christelle Gonmadje46,67,William Marthy68, Timothy O'Brien68, Emanuel H. Martin69, Andrew R. Marshall70,70.5, Francesco Rovero71, Robert  Bitariho72, Pascal A. Niklaus73,74, Patricia Alvarez-Loayza75, Nurdin Chamuya76, Renato Valencia77, Frédéric Mortier78, Verginia Wortel79, Nestor L. Engone-Obiang80, Leandro V. Ferreira81, David E. Odeke82, Rodolfo M. Vasquez83, Simon L. Lewis84,85, Peter B. Reich18,86

Alberto Pepe

and 1 more

INTRODUCTION 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, as shown in Figure 1. Galileo's work advanced the "Scientific Revolution," and his approach to observation and analysis contributed significantly to the shaping of today's modern "Scientific Method" . Today most research projects are considered complete when a journal article based on the analysis has been written and published. Trouble is, unlike Galileo's report in _Siderius Nuncius_, the amount of real data and data description in modern publications is almost never sufficient to repeat or even statistically verify a study being presented. Worse, researchers wishing to build upon and extend work presented in the literature often have trouble recovering data associated with an article after it has been published. More often than scientists would like to admit, they cannot even recover the data associated with their own published works. Complicating the modern situation, the words "data" and "analysis" have a wider variety of definitions today than at the time of Galileo. Theoretical investigations can create large "data" sets through simulations (e.g. The Millennium Simulation Project). Large scale data collection often takes place as a community-wide effort (e.g. The Human Genome project), which leads to gigantic online "databases" (organized collections of data). Computers are so essential in simulations, and in the processing of experimental and observational data, that it is also often hard to draw a dividing line between "data" and "analysis" (or "code") when discussing the care and feeding of "data." Sometimes, a copy of the code used to create or process data is so essential to the use of those data that the code should almost be thought of as part of the "metadata" description of the data. Other times, the code used in a scientific study is more separable from the data, but even then, many preservation and sharing principles apply to code just as well as they do to data. So how do we go about caring for and feeding data? Extra work, no doubt, is associated with nurturing your data, but care up front will save time and increase insight later. Even though a growing number of researchers, especially in large collaborations, know that conducting research with sharing and reuse in mind is essential, it still requires a paradigm shift. Most people are still motivated by piling up publications and by getting to the next one as soon as possible. But, the more we scientists find ourselves wishing we had access to extant but now unfindable data , the more we will realize why bad data management is bad for science. How can we improve? THIS ARTICLE OFFERS A SHORT GUIDE TO THE STEPS SCIENTISTS CAN TAKE TO ENSURE THAT THEIR DATA AND ASSOCIATED ANALYSES CONTINUE TO BE OF VALUE AND TO BE RECOGNIZED. In just the past few years, hundreds of scholarly papers and reports have been written on questions of data sharing, data provenance, research reproducibility, licensing, attribution, privacy, and more--but our goal here is _not_ to review that literature. Instead, we present a short guide intended for researchers who want to know why it is important to "care for and feed" data, with some practical advice on how to do that. The set of Appendices at the close of this work offer links to the types of services referred to throughout the text. BOLDFACE LETTERING below highlights actions one can take to follow the suggested rules.

Alyssa Goodman

and 10 more

ABSTRACT The very long, thin infrared dark cloud Nessie is even longer than had been previously claimed, and an analysis of its Galactic location suggests that it lies directly in the Milky Way’s mid-plane, tracing out a highly elongated bone-like feature within the prominent Scutum-Centaurus spiral arm. Re-analysis of mid-infrared imagery from the Spitzer Space Telescope shows that this IRDC is at least 2, and possibly as many as 8 times longer than had originally been claimed by Nessie’s discoverers, ; its aspect ratio is therefore at least 150:1, and possibly as large as 800:1. A careful accounting for both the Sun’s offset from the Galactic plane (∼25 pc) and the Galactic center’s offset from the (lII, bII)=(0, 0) position defined by the IAU in 1959 shows that the latitude of the true Galactic mid-plane at the 3.1 kpc distance to the Scutum-Centaurus Arm is not b = 0, but instead closer to b = −0.5, which is the latitude of Nessie to within a few pc. Apparently, Nessie lies _in_ the Galactic mid-plane. An analysis of the radial velocities of low-density (CO) and high-density (${\rm NH}_3$) gas associated with the Nessie dust feature suggests that Nessie runs along the Scutum-Centaurus Arm in position-position-velocity space, which means it likely forms a dense ‘spine’ of the arm in real space as well. No galaxy-scale simulation to date has the spatial resolution to predict a Nessie-like feature, but extant simulations do suggest that highly elongated over-dense filaments should be associated with a galaxy’s spiral arms. Nessie is situated in the closest major spiral arm to the Sun toward the inner Galaxy, and appears almost perpendicular to our line of sight, making it the easiest feature of its kind to detect from our location (a shadow of an Arm’s bone, illuminated by the Galaxy beyond). Although the Sun’s (∼25 pc) offset from the Galactic plane is not large in comparison with the half-thickness of the plane as traced by Population I objects such as GMCs and HII regions (∼200 pc; ), it may be significant compared with an extremely thin layer that might be traced out by Nessie-like “bones” of the Milky Way. Future high-resolution extinction and molecular line data may therefore allow us to exploit the Sun’s position above the plane to gain a (very foreshortened) view “from above" of dense gas in Milky Way’s disk and its structure.

Alyssa Goodman

and 10 more

Josh Nicholson

and 1 more

Research is really f**king important.  This statement is almost self-evident by the fact that you're reading this online.  From research has come the web, life-saving vaccines, pasteurization, and countless other advancements. In other words, you can look at cat gifs all day because of research, you're alive because of research, and you can safely add milk to your coffee or tea without contracting some disease, because of research. But how research is done today is being stymied by how it is being communicated.  Most research is locked behind expensive paywalls \cite{Bj_rk_2010}, is not communicated to the public or scientific community until months or years after the experiments are done \cite{trickydoi}, is biased in how it is reported - only "positive" results are typically published \cite{Ahmed_2012}, does not supply the underlying data to major studies \cite{Alsheikh_Ali_2011}, and has been found to be irreproducible at alarming rates \cite{Begley_2012}.Why is science communication so broken?Many would blame the fault of old profit-hungry publishers, like Elsevier, and in many respects, that blame is deserved. However, here's a different hypothesis: what is holding us back from a real shift in the research communication industry is not Elsevier, it's Microsoft Word. Yes, Word, the same application that introduced us to Clippy is the real impediment to effective communication in research.Today, researchers are judged by their publications, both in terms of quantity and prestige.  Accordingly, researchers write up their documents and send them to the most prestigious journals they think they can publish in.  The journals, owned by large multinational corporations, charge researchers to publish their work and then again charge institutions to subscribe to the content. Such subscriptions can run into the many millions of dollars per year per institution \cite{Lawson_2015} with individual access costing $30-60 per article.The system and process for publishing and disseminating research is inimical to scientific advancement and accordingly Open Access and Open Science movements have made big steps towards improving how research is disseminated. Recently, Germany, Peru, and Taiwan have boycotted subscriptions to Elsevier \cite{Schiermeier_2016} and an ongoing boycott to publish or review for certain publishers has accumulated the signatures of 16,493 researchers and counting.  New developments such as Sci-hub, have helped to make research accessible, albeit illegally.  While regarded as a victory by many, the Sci-hub approach is not the solution that researchers are hoping for as it is built on an illegal system of exchanging copyrighted content and bypassing publisher paywalls \cite{Priego}.  The most interesting technologist view of the matter is that the real culprit for keeping science closed isn't actually the oligopoly of publishers \cite{Larivi_re_2015}-- after all, they're for-profit companies trying to run businesses and they're entitled to do any legal thing that helps them deliver value to shareholders. We suggest that a concrete solution for true open access is already out there and it's 100% legal.What is the best solution to truly and legally open access to research?The solution is publishing preprints -- the last version of a paper that belongs to an author before it is submitted to a journal for peer review. Unlike other industries (e.g. literature, music, film, etc.), in research, the preprint version copyright is legally held by the author, even after publication of the work in a journal.Pre-prints are rapidly gaining adoption in the scientific community, with a couple of preprint servers (e.g. arXiv which is run by Cornell University and is primarily for physics papers, and bioRxiv which is similarly for biology papers) receiving thousands of preprints per month.Some of the multinationals are responding with threats against authors not to publish (or post) preprints. However they are being met with fierce opposition from the scientific community, and the tide seems to be turning. Multinationals are now under immense pressure not just from authors in the scientific community, but increasingly from the sources of public and private funding for the actual research. Some organizations are even mandating preprints as a condition of funding. But what is holding back preprints and in general a better way for Authors to have more control of their research?We think the inability for scientists to independently produce and disseminate their work is a major impediment and at the heart of that of that problem is how scientists write. How can Microsoft Word harm scientific communication?Whereas other industries, like the music industry, have been radically transformed and accelerated by providing creators with powerful tools like Youtube, there is no parallel in research.  Researchers are reliant upon publishers to get their ideas out and because of this, they are forced into an antiquated system that has remained largely stagnant since it's inception over 350 years ago.Whereas a minority of researchers in math-heavy disciplines write using typesetting formats like LaTeX, the large majority of researchers (~82%) write their documents in Microsoft Word \cite{brischoux2009don}. Word is easy to use for basic editing but is essentially incompatible with online publishing. Word was created for the personal computer: offline, single-author use. Also, it was not built with scientific research in mind - as such, it lacks support for complex objects like tables and math, data, and code. All in all, Word is extraordinarily feature-poor compared to what we can accomplish today with an online collaborative platform. Because publishers have traditionally accepted manuscripts formatted in Word, and because they consistently fail to truly innovate from a technological standpoint, millions of researchers find themselves using Word. In turn, the research they publish is non-discoverable on the web, data-less, non-actionable, not reusable and, most likely, behind a paywall.  What does the scientific communication ecosystem of the future look like?What is needed is a web-first solution. Research articles should be available on distinct web pages, Wikipedia style. Real data should live underneath the tables and figures. Research needs to finally be machine readable (instead of just tagged with keywords) so that it may be found and processed by search engines and machines. Modern research also deserves to have rich media enhancement -- visualizations, videos, and other forms of rich data in the document itself.All told, researchers need to be able to disseminate their ideas in a web first world, while playing the "Journal game" as long as it exists. Our particular dream (www.authorea.com) is to construct a democratic platform for scientific research -- a vast organizational space for scientists to read and contribute cutting edge science. There is a new class of startups out there doing similar things with the research cycle, and we feel like there is a real and urgent demand for solutions right now in research.