Introduction to online markdownMarkdown is a markup language with a simple text formatting syntax. It is designed to provide basic formatting to text. Each piece of Markdown formatting has a corollary in HTML. This means that online Markdown is easy to write and maintain. Markdown was released in 2004 and is now one of the most popular markup languages on the web, powering GitHub (with Github-flavored Markdown or GFD) and many other sites.Advantages of online markdownOnline Markdown editors make it easy to write Markdown in the browser. Markdown can be integrated into apps for writing (as is the case with Authorea -- which supports inline Markdown). It can also be used as a standalone service for things like note-taking. Some of the most popular online markdown editors are:DillingerMinimalist Online Markdown EditorMarkableStackEditAuthoreaMarkdown for research writingAuthorea is an online document editor that has full Markdown support. Whether you want to write entirely in Markdown, or switch between markdown and richtext, you can do so in Authorea. If you're writing technical or scientific documents you'll find that Authorea can support your writing style. Authorea also renders the online Markdown environment beautifully to HTML5 in the browser. This makes documents into beautiful web pages.

The importance of collaborative writingCollaborative writing is on the rise in science \cite{Weeks_2004} due to the increase in complexity and scope of research projects.  A recent study of academic research communication demonstrated that most researchers write 60% to 100% of their manuscripts in collaboration \cite{Scheliga_2015}. As the number of co-authors and interdisciplinarity of research topics increases, so too will the need for better tools for collaborative writing. We built Authorea to fill this need and make collaborative writing easy and powerful for researchers.The majority of researchers write their manuscripts using the desktop word processor Microsoft Word \cite{Pepe_2016} and take the following approach: A single author starts writing the manuscriptThe manuscript is shared via email with another author or multiple authors.Different sections are written separately and then emails are again exchangedThis process is repeated over and over for copy-editing.Such an approach can creates obvious problems. Important edits can be overlooked, or saved to the wrong version. There are time delays as drafts are sent between individuals and reference libraries are mismatched. One author waits while the other works.How to write collaboratively, better.Advances in technology have made web-based document processing a reality and many people use Google Docs to achieve this. Such an approach is, however, very limiting for researchers. Authorea allows real-time collaborative editing with the full capabilities a researcher needs to write their articles. Edits are saved automatically and back-ups are easily accessible. Researchers can continue to write and edit while they wait for questions to be addressed. 

Introduction to online LaTeXLaTeX (pronounced lay-tech or lah-tech) is a Turing-complete markup language and typesetting framework used most often in the physical and mathematical sciences \cite{texentry}. LaTeX has history going back to 1985 -- and TeX, the progenitor of LaTeX, goes back to 1978 when it was introduced by computer scientist and mathematician Donald Knuth.LaTeX is first and foremost designed for typesetting mathematical notation on the printed page. LaTeX gives increased control for typesetting, enabling far stricter control of elements on a page -- from tables to specialized mathematical notation and so forth. LaTeX is widely used in the physical sciences and to this day LaTeX is used for typesetting journals, textbooks, and other structured texts.How to Write Mathematical Equations, Expressions, and Symbols with LaTeXIn recent years, several LaTeX software options have introduced online-only versions that bring the traditional LaTeX compiler to the cloud. These online LaTeX solutions come with advantages and disadvantages, however LaTeX on its own remains problematic for producing web-native content as it's extremely difficult to determine how text will look online if typeset using LaTeX.

Do you have a colleague who is a die-hard LaTeX writer?Welcome to the good life, Word user. Authorea is here to calm your Word-meets-LaTeX research writing woes. "BUT HOW?" You might ask. Well, it's simple: you don't have to learn how to write LaTeX and your LaTeX collaborator does not have to endure the pain of converting .tex files into a .docx format. Authorea brings writers from different platforms together by offering an interactive writing experience with tools familiar to both segments of writers. Gone are the days of frustrating multi-platform collaborative writing and editing. Here's how Authorea facilitates collaboration between Word and LaTeX writers. A Rich-Text Editor that looks like Word, but can render LaTeX tooAuthorea's standard rich-text editor is familiar to Word writers. The interface is clean and simple. Yet, it allows you to enter and format rich text as well as blocks of LaTeX code inside the same document. Your LaTeX collaborator will be able to write with the freedom and power to fully typeset and program their text. For example, typing this snippet of code in a LaTeX block, we were able to render equation (eq \ref{eq:ex}), below:

Most research today is not in Open Access JournalsThe majority of research today is published behind a paywall (figure \ref{420454}).  This is unlikely to be the case in the next few years. Particularly since new policies require research to be published in open access journals (figure \ref{420454}).  First coined in the early 90's, open access refers to content that is freely accessible and reusable under specific copyright agreements, such as the Creative Commons Attribution 4.0 license (CC-BY 4.0). What has lead to the rise of open access journals? How does Authorea, a collaborative authoring platform, fit within the landscape?

Introduction to LaTeX Software LaTeX (pronounced lay-tech or lah-tech) is a markup language and document typesetting system. Developed by Leslie Lamport and originally released in 1985, the software has proliferated greatly since its release. It is distributed under a free and open source license, but there are numerous paid LaTeX software offerings  \cite{tex}.Despite the lack of a unified style specification, LaTeX remains a standard for many academic publications. Especially those in areas like physics, astronomy, mathematics, and other technical fields. Despite the lack of a WYSIWYG interface (LaTeX source code is vastly different than rendered LaTeX), LaTeX remains popular for typesetting and publishing because of the professional outputs available via LaTeX software.All LaTeX software originates from TeXThe progenitor of LaTeX is TeX, a typesetting system first introduced by computer scientist and mathematician Donald Knuth in 1978. TeX software was designed to make it easy to translate nonstandard characters to the computer. Also, to ensure that the results would be the same no matter where the content was viewed.Now more than 30 years old, LaTeX remains one of the most popular tools out there for writing scientific and technical content. Authorea recently estimated that ~20% of scholarly articles are still written in LaTeX. This is surprising since LaTeX was developed in the pre-Internet era and was originally designed for a world in which document editors copied the paradigm of pen and paper. Today's leading document editors and LaTeX software are designed for a world in which content is shared and distributed on the web. As a result, the old model of page-based document editing is starting to look more and more obsolete.Most popular LaTeX softwareThe most popular LaTeX software options today are compilers that run locally on a user's machine. Some example are the following:TeXmakerTeXstudioTeXworksTeXliveLyXIssues with LaTeX softwareLaTeX was not created with the modern web in mind. It was created with physical pieces of paper in mind. Therefore, LaTeX software is suited to produce professional on-the-page results. It is ill-suited to produce professionally typeset web content. This has long been a frustration for many and there have been numerous attempts to convert LaTeX to HTML over the years. The future of LaTeX software on the webAuthorea provides the only web-based LaTeX environment that renders beautifully to HTML5 in the browser.Further ReadingMathML on the Web, Please!

Deciding between Overleaf and Authorea? Choosing the right editor for your LaTeX manuscript is simple. Here are some key comparisons to help you decide. 

LaTeX and Word users might ask where they can collaborate on single platform. Once upon a time, the answer to this question was They Can't! That is until Authorea came onto the scene. Ideas to foster collaboration between the two segments of users were often an exercise in frustration. While the Word writers would spend time learning LaTeX, the LaTeX users would have to convert their files into Word's proprietary format - a process with imperfect tooling and many painful points. LaTeX and Word co-authors often run into issues with editing and formatting documents, since it is difficult to complete these tasks while working on different platforms. Authorea solves this multi-platform issue and enables an easier and more interactive collaborative writing process, complete with support for commenting, reviewing and tracking changes. Here are four ways Authorea fosters writing relationships between LaTeX and Word users. Format AgnosticAuthorea's HTML editor is a true rich text WYSIWYG (what you see is what you get) editor, making it a natural home for Word authors, who don't encounter a learning curve. Word users do not require any knowledge of LaTeX or any other markup language in order to start writing. They find that the Authorea interface is clean, familiar, and simple to use.  LaTeX content is authored in a separate dedicated code editor, with advanced syntax highlighting and optional keybindings (e.g. EMacs and VIM shortcuts). This makes working across disciplines a breeze.Commenting SystemNo matter what writing system co-authors use for their research, communication is the key to a successful collaboration. Since Authorea is web-native, researchers will always see the most up-to-date version of their document, modified in real time. If a Word user logs in and finds that edits are required in a LaTeX-written section, they can simply use Authorea's powerful built-in comments framework to write a note for their co-author to revise that section. There is no need for them to do any technical writing.

Introduction to document editorsA document editor or word processor is a software application that helps write, edit, format, and publish documents. A document editor differs from a text editor in that it is purpose-built for creating human-readable documents -- rather than simply for modifying text or code snippets. If you look at virtually any industry -- education, research, business, and so on -- document editors are more or less ubiquitous. The most popular document editors globally are Microsoft Word and Google Docs, but it wasn't always that way.History of the document editor

Scientific writing is the art of communicating complex discoveries. In the current competitive publication environment, authors who cannot communicate effectively do not get past the editor's desk. A decade ago, some journals reviewed every submission. They worked with researchers who had excellent data, but poor writing skills. Today, journals receive far more manuscripts than they can process. A majority of submissions get only a cursory glance, or rejection without review. Skilled writers know how to manipulate conventions with powerful scientific writing. They present complex ideas efficiently and capture an editor's attention. Luckily, many common manuscript errors can be eliminated with the final edit. Here are three simple revisions you can make to improve your final draft: Identify when subjects and verbs are too far apartAvoid nominalizationsOptimize flow1. Subject & Verb DistanceDistant subject and verbs occur when the author puts too much information in one sentence, perhaps thinking this will avoid redundancy. Always prioritize clarity. To revise this, identify the main subject and verb of the sentence. If they are far apart, rephrase the sentence or break it into multiple sentences. Example: The assumptions that all sites evolve at one of two evolutionary rates, that these rates are uniform across the genome, that sites evolve independently conditional on whether they are in conserved or non-conserved regions, and that the phylogenetic models for conserved and non-conserved regions have the same branch-length proportions, base compositions, and substitution patterns, all represent over-simplifications of the complex process of sequence evolution.In this example, the subject is 'assumptions' and the verb is 'represent'. Let's revise this:Rewrite: Several key assumptions represent oversimplifications of sequence evolution. These include...2. Nominalizations Nominalizations are nouns created from adjectives or verbs. They often cause passive voice or require unnecessary words. These can dramatically slow the read of your paper. As you edit, go through and underline any nominalizations. Take a closer look and see if they should be changed to verbs. Example: We performed an analysis...Rewrite: We analyzed...3. Poor FlowFlow is critical to the introduction and discussion sections, which usually provide background or explanatory information. Information flows from one idea to another. The shift in the subject of each sentence should follow a logical order, known as the 'subject string'. Example: We searched the database to look for base pair repeats. A protein involved in the regulation of human methylation was identified by the search.In this example, flow can be improved when the subject that has already been introduced (a search) comes before a new idea (protein). The sentence can thus be re-written with protein as the object of the sentence:Rewrite: We searched the database of sequences to look for base pair repeats. The search identified a protein involved in the regulation of human methylation. In the final revision of your manuscript, highlight the subject of each sentence. Does the subject string follow a logical flow, pivoting only when you want to shift the topic or key point? Or does it jump around at random? Understanding flow takes practice, but once you have a feel for flow, the clarity of your writing will improve.Final wordToday, excellent research is being lost in the midst of poor scientific writing skills. Using these revision techniques, you can work towards  journal editors recognizing the significance of your findings. There are some great resources to help identify these common errors. For example, while writing on Authorea, we offer a Grammarly plug-in that will correct your grammar and spelling errors. Also check out the Hemmingway Editor, which allows you to copy paste chunks of text and highlight adverbs, nominalizations, passive voice, and more. For examples of flow, check out the Scientific Writing Resource from Duke University. 

Writing your thesis often comes after years of work and research. It is an exciting process that marks an important transition in your life and career as a student. If you are reading this, you are probably considering or starting writing a thesis... Congratulations! Theses can range from a few dozen pages to hundreds (see Fig \ref{974669}), depending upon discipline. While many students choose to write their thesis offline in Microsoft Word or in LaTeX, there is a growing number of student's choosing to write their thesis online, with tools like Authorea.

Writing research documents has not advanced much in the last few decades. Researchers, as a whole, still write their documents in Microsoft Word \cite{Pepe}, emailing different versions back and forth amongst each other. This workflow predates online document editors, making research collaboration and dissemination slower and more tedious than what is technically possible today in 2017.  This is why we built Authorea, a modern collaborative online document editor for researchers, to make research collaboration and dissemination seamless.  Below we highlight the benefits of writing research with an online document editor, like Authorea.What are the benefits of writing with an online document editor?1. Less emails in your inbox!

Research collaboration has not advanced much in the last few decades. Researchers, as a whole, still write their manuscripts in Microsoft Word \cite{Pepe_2016}, emailing different versions back and forth amongst each other. This workflow predates online text editors. As a result, collaboration is slower and more tedious than what is technically possible today in 2017.  This is why we built Authorea. It's a modern, collaborative online text editor for researchers that makes the process seamless.  Below we highlight the pro's of preparing research with an online text editor like Authorea.Why should researchers write their papers with an online text editor?1. Save your inbox from a deluge of unnecessary emails.On average people receive 121 emails per day. Collaboration across labs, continents, and markup languages can lead to a messy inbox like below. In contrast, researchers who write online save time and their inbox.

Software started in university aisles and, as such, a lot of software today is academic software. Software programs make researchers' work more efficient and competitive. Here are the five best software tools that can help academics especially in their data-based and authoring practices. Note that all these tools integrate with Authorea - the collaborative word processor for academics.1. GithubFourteen million software developers use Github to collaborate and maintain code repositories. Although originally designed for professional developers, Github has now expanded to the classroom. Authorea is also based on git, so integration between the two platforms is as easy as clicking a button.  This feature allows researchers to work offline and provides access to version controls via Github. Read more about Authorea Github Integration here: Syncing articles to GitHub2. PlotlyAcademics and researchers use Plotly to analyze and to visualize plots and graphs. Plotly generates graphs in a variety of formats. Many of these also have interactive online capabilities. Authorea integrated with Plotly so researchers can create and access interactive graphs.3. Jupyter Notebooks (IPython notebooks)Jupyter is a virtual lab environment that contains mathematics, plots, rich media, text, and code. Instructors across academia use Jupyter to conduct research and easily inspect rerun analyses. Authorea is integrated with Jupyter notebooks so that collaborators can create data-rich manuscripts. 4. AuthoreaAuthorea itself is one of the best tools to write academic papers in collaboration. You may think of it as a Google Docs for academia. Google Docs is the most widely used collaborative editor in the world. Despite its prevalence, it lacks many features for citation management, math, LaTeX, and version control. Authorea makes it easy to import any Google Doc directly into Authorea by simply copying and pasting the URL of the document you wish to import. 

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

Among the public, there are three potential population of foster care enablers, categorized by their commitment levels. One group is people who clearly want to be or have been foster parents. Another group is people who are on the fence of becoming one. The third group is people who do not want to be foster parents now, however, want to know more about the system. They are potential social recruiters who have been neglected by ACS and foster care agencies while would contribute greatly advocating foster care parenthood among the community.Based on how the website and information are distributed, ACS has only focused on the first group. By valuing the latter two groups, we can improve both the volume and the quality in the recruitment pool of foster parents. We documented our experiences as the third group when using ACS website and getting information to explain how we observe ACS is neglecting the latter two groups. Search info on ACS websiteWhen we entered ACS’s website, it didn’t address much on why someone should be a foster care parent, however it has clear steps on how to become one.When there’s little information on the benefit of becoming a foster care parent, ACS assumes that all website visitors have strong motivation and ACS does not need to encourage them more. This shows that ACS foster care website’s intended audience is only for the first group.When the second group (people on the fence) sees little info on why, the probability of advancing to the final step of the recruitment process goes down. And as the third group, we did not become more interested in the system and would less likely to recommend foster parenting to friends and communities.Request for more informationOn ACS site, besides the FAQ, there’s a link to request more information. This is a great feature for people wanting to learn more about foster care. Yet, when we clicked the link, we were redirected to Prospective Parent Recruitment Form. As social recruiters, we were overwhelmed by being titled as prospective parents and did not want to move forward to the next step, continuing asking for more information.

The majority of the world's population has not and will not ever publish a scientific paper. That fact is even more true for pets. Yes, dogs, cats, hamsters. Pets. Surprisingly, however, there are papers with pets as authors. Here's a selection of three articles coauthored by our furry friends.1. Hamster: Tisha 🐹 Do you have a paper with a Nobel laureate? No? Well... Hamster Tisha does! The pet hamster of the physics Nobel laureate Andrew Geim was co author on the publication "Detection of earth rotation with a diamagnetically levitating gyroscope" \cite{Geim_2001}. Go Tisha!

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