WELCOME TO THE PITCHFORK PARTY This post comes in the context of a series of healthy discussion pieces on authoring scientific content for the web:[1] - LaTeX was not built for the Web by Alberto and Nate from Authorea. - LaTeX Something Something Darkside by Peter Krautzberger from MathJaX. - A Scholarly MarkDown discussion on Hacker News (see the comments) In this text, I will try to elaborate on the merits and deficiencies of using a pre-web authoring syntax, LaTeX, for writing modern publications in 2015 as active web documents. My stance is evolutionary – we should adapt our existing tools to the new environment and in the process gain insights for what the next generation of tools ought to be. If you are a working scientist who authors in LaTeX, I will suggest how to gradually adapt your existing toolchain, while making your first steps towards the future of publishing. If you don’t find the technical details interesting, you can skip to my suggestion in Section [sec:conclusion]. If you are a developer, I will argue with you that the next generation has not fully arrived yet. We’re not going to start a fire Feelings can burn strong when the words “LaTeX” and “Web” appear together. Debates over tool superiority, especially when online, tend to quickly become heated and destructive. My best guess is that the personal experiences with our tools over time evolve into full-blown relationships, with all associated pros and cons of that status. Maybe you truly love your tool, and that is great, please go ahead and nourish that feeling. Meanwhile, I will step back into more abstract territory and try to poke some applications with a stick and see when they bite. You’re welcome to tag along, but there’s no need for extra venom. [1] The author has his own torch in hand: I am a core contributor to LaTeXML and an enthusiastic developer at Authorea. So keep that bias in mind while reading on.

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

Today I merged a pull request for which introduced the following setup for equation editing, as an alpha feature for our RichText editor: 1. The “status quo” renderer, displaying the mathematics on all “read-mode” article components. 2. A new renderer, specifically loaded in the iframe of our editor widget. Why? Because loading MathJax twice is too slow for our show, but we still want our displayed richtext equations to be, well, rich. 3. An additional math renderer, part of our equation-specific editing widget, so that authors can also INPUT formulas in an appealing richtext flow.[1] See the great demos by for examples. You read that correctly - not one, not two, but THREE SEPARATE MATH RENDERERS ON THE SAME HTML PAGE, each of which different due to balancing on the trade-offs of performance, coverage and visualization. I hear you cry: – Well, this is clearly horrible design, simplify and streamline it! Indeed! My thoughts exactly. But the GREAT SOLUTION, the one that solves this problem not only for me, but for the ENTIRE MATH-ON-THE-WEB DEVELOPER ECOSYSTEM, is not for me or my team to implement. This renderer medley can be traced to a single root cause - the absence of ubiquitous support in modern browsers. If you are not familiar with MathML, it is a W3C and ISO standard and a core part of HTML5. MathML does a great job of providing a single language for representing mathematics in structured documents, especially web pages. But while we have that great language, we lack major browser implementations – in fact only Firefox has GREAT MathML support, and has long been the browser-lead in math support. A different perspective tells us that we are just two browsers short of having the tide turn overwhelmingly towards native rendering. I am referring specifically to and . Having native support would allow us – the mortal developers interested in providing exciting and powerful math-enabled web applications – to sleep calmly at night and work proudly at day. And hence my sincere plea to all major browser vendors: ------------------------------------------------------------------------ PLEASE, DO THE MATH. ------------------------------------------------------------------------ P.S. How is the native MathML solution better? - BEST. PERFORMANCE. POSSIBLE. Your browser will be capable to render MathML the moment it loads, just as it can CSS. No extra load times needed. - THE DOM WILL SET YOU FREE As math-on-the-web developers, we need to select into and manipulate mathematical objects, just as all web developers need to manipulate forms and input fields. I want my cool math interactivity widget to be an easy drop-in for any webpage, just the same way that a jQuery widget is. And we can’t have that without equations being a proper participant in the HTML DOM – CSS would have never taken off if say <div> and <span> elements only existed for sites that had first loaded a third-party css.js library. - OUT-OF-THE-BOX ACCESSIBILITY Exposing the MathML source of an equation directly in its web page[2] will be the default state of any HTML5 web page. Math-to-speech and Braille adaptors can then simply use the raw HTML as-is. P.P.S. If you are interested in showing your personal support for adding native MathML, add your vote and voice to the public issues: - Edge MathML support: https://wpdev.uservoice.com/forums/257854-microsoft-edge-developer/suggestions/6508572-mathml - Chrome MathML support: https://code.google.com/p/chromium/issues/detail?id=152430 Personally, I have joined an effort to promote MathML publicly and to remind developers of its many strong suits and far-reaching benefits to the web develpment ecosystem. You can visit our MathML Association website, or follow us on Twitter at @mathml3. [1] We also have an upcoming equation button palette to put the WYSIWYG cherry on our cake. [2] which you can also do today if you manage to carefully jump through the right JavaScript hoops

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.

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.

Research: the process by which we understand the world, ourselves, and other phenomena ranging from the alpha helix of a protein to the societal movements in politics is what life is.  That may be a bit too grandiose, but research is an integral part of advancing humankind forward.Said differently, research is the engine by which progress occurs.  Yet, performing successful research is something that is not easy. Unlocking the secrets of life is a laborious task and it requires cooperation amongst people in real time as well as those that came before us.  Key to this progress is clarity, completeness, and access.  One might guess that this is the what defines the research publishing community.  One might be wrong.Scholarly research is for the most part locked behind expensive paywalls in forms that resemble more of something like a trophy than a document used for conveying important of pieces of research in the best manner possible.  While there are lots of things occurring in scholarly research that don't make sense, one blatant one stands out.  We charge researchers to access other researchers documents-- not in the name of sustainability, but in the name of profit.  In fact, we had to invent a word to describe a publication process that is conducive to research: open access.  What is #OpenAccess and what is it good for?  Absolutely everything, as far as research is concerned.

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.

This is a story of _semantics-by-convention_ gone wrong that hit us at Authorea last week.

Write, edit, submit, revise, resubmit, resubmit, resubmit, resubmit.... Okay, you get the point: we send our manuscripts to lots of journals. The time formatting and reformatting manuscripts is a pain and it is one we are working to ease.  Your valuable time should be spent on your research, not tiresome formatting.  Today, we've added 8,249 article templates to Authorea! With the addition of these templates we now make it easy for you to write your article for just about any journal out there. We hope you won't submit to all 8,000+ different journals but at least you now have the power to do so!  We've also made it easy for users to create their own templates, so if you see a template missing, please feel free to create one.So...How does it work? It couldn't be any simpler. Just browse our template section for inspiration. Don't start from scratch. Our templates give you a mold that you can shape to your liking. Working feverishly on a research paper, grant proposal, university thesis or a class project? We do them all. Focus on your writing on the web, and enjoy Authorea's single streamlined web view of scholarly text. Once finished, you're truly finished - forget about formatting issues. With just a couple of clicks through our Export flow, you're ready to send in that submission!  Authorea's journal templates follow correct citations guidelines outlined by the journals, at no extra effort for our authors.We're really just getting started. If you need to send a printout to a colleague in draft shape, line-numbered and double-spaced, it's a selection away. Different journal? Same breeze. Your text, data, visuals, and citations will be updated automatically behind the scenes. In the unlikely event you hit a hurdle, our 24/7 support team will be happy to quality control your article and quickly get it back on the fast track to getting published.This is the first step towards making the writing and publication process as seamless as possible but we've got lot's more coming. We hope you'll join us so that we can make scholarly writing and publishing more effective and more enjoyable. Happy writing!

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WELCOME TO LLAMAPUN! The Cornell preprint contains roughly a million scientific papers, making it a treasure trove for natural language processing (NLP) experiments. However, a big difference from mainstream NLP corpora is the presence of mathematical formulas, citations and other language modalities specific to scientific discourse. A second, and in practice just as significant challenge is that the majority of documents are authored in LaTeX, making them very irregular for naive automated mining. At the research group at Jacobs University we have invested a lot of work in trying to regularize the dataset and make it available for NLP research, which is a large topic in its own right. I wrote an entry-level blog post about that effort here. In this blog post, I want to briefly introduce the newest incarnation of the NLP library for scientific documents, backed up by a running example of word tokenization on an average preprint from the dataset.

INTRODUCTION LaTeX is typesetting software that is widely used by mathematicians and physicists because it is so good at typesetting equations. It is also completely programmable, so it can be configured to produce documents with almost any desired formatting, and to automatically number equations, figures, endnotes, and so on. To prepare manuscripts for the American Journal of Physics (AJP), you should use the REVTeX 4.1 format for Physical Review B preprints, as indicated in the documentclass line at the top of this article’s source file. (If you’re already familiar with LaTeX and have used other LaTeX formats, please resist the temptation to use them, or to otherwise override REVTeX’s formatting conventions, in manuscripts that you prepare for AJP.) This sample article is intended as a tutorial, template, and reference for AJP authors, illustrating most of the LaTeX and REVTeX features that authors will need. For a more comprehensive introduction to LaTeX, numerous books and online references are available. Documentation for the REVTeX package can be found on the APS web site. LaTeX is free software, available for Unix/Linux, Mac OS X, and Windows operating systems. For downloading and installation instructions, follow the links from the LaTeX web site. It is most convenient to install a “complete TeX distribution,” which will include LaTeX, the underlying TeX engine, macro packages such as REVTeX, a large collection of fonts, and GUI tools for editing and viewing your documents. To test your installation, try to process this sample article.

Abstract goes here.

Let’s try: testing here. Here is an attempt: testing 1 + 2 = 3 here.

Still writing your own documents? That’s so 3200 BCE! At Authorea, we take digital publishing so seriously, we want to WRITE YOUR PAPER FOR YOU! Partnering with SCIGEN (who we briefly profiled last week), writing, submitting and disseminating your research will never again require a keyboard. Scholarly research and writing have never been easier. By stitching together a home-brewed soup of technical lingo, a cursory glance at your paper will yield resounding “Oh, hum, yes?”s — we guarantee! Concerned your manuscript won’t get accepted for publication? SCIgen has a proven record that _many_ of their randomly generated manuscripts have made it in to “peer reviewed” journals. And don’t worry, this is only horrifying if you aren’t in on it! Best of all, you can use a private article on Authorea to keep unwanted questions and comments out of the equation. Open and honest peer review is after all too dangerous an experiment, when we have venues ready and capable of accepting your SCIgen derived piece of utter genius. Happy Writing! ;)

TFS FILE FORMAT TFS is a an acronym for the “Table File System”. TFS files have been used in the LEP control system. The program knows only coded TFS files. The TFS format has been chosen for all table output of . TFS formatted tables can be read back into , and may then be further processed.

CONVENTIONS

This is the abstract. Change test. This wordshould be surrounded by double quotes.