Researchers in the cloud

Screen Shot 2014-07-28 at 2.28.48 PMI have just published, a short Science & Society article in Trends in Biochemical Sciences (TIBS) about the emergence of online tools for researchers using cloud-based technologies. This is part of a TBIS series of articles on “Research 2.0” with topics ranging from open access and crowd-funding, to new digital tools for researchers.

With a similar approach to what I am doing with Connected Researchers, this article lists tools that are changing (or have the potential of changing) the way researchers do and communicate their work. Because this article is published in a journal non-tech-savvy researchers read, I am particularly hopeful that it will bring more researchers to the digital tool adopter side.

Find the article here: available for free until Sept 14th 2014
Paywall access here: Science Direct

Penflip, the writer-friendly GitHub

Screen Shot 2014-06-28 at 4.04.52 PMThe average number of authors per research papers has been steadily increasing over the past few decades. Naturally, writing papers became more collaborative, each researcher contributing to their area of expertise. But collaborating on a document is not always easy. Multiple Word documents sent back and forth by email,  text highlighted in all the colors of the rainbow to track who changed what in the text… Lucky for us researchers, over the past few years, a number of online tools have been developed to make collaborative writing a pain-free experience.

Inspired by the GitHub platform that allows programmers from around the world to collaborate on software code, Loren Burton developed Penflip. Penflip provides a web-based text editor that includes basic formatting options (bold, italic, lists, links..). You will not find advanced formatting options commonly found in other editing software such as Word or Google docs. But Penpile’s strong point lies somewhere else:  its advanced version control system.

In GitHub, large chucks of code can be extracted from a program, edited, then accepted back into the program while keeping track, line per line, of changes made. Github could in principle be used for text editing, but the whole platform has been designed for coders, with technical jargon that will scare many away. A writer-friendly version of GitHub was needed: Penflip.

Here is what the interface looks like. Pure and simple.

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After each modifications, additions are marked in green, and subtracted text is crossed out.

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Penflip offers many interesting features such as:

  • The ability to integrate mathematical formulas using MathJax.
  • Chapter management that allows to create chapters that can be easily drag & dropped to reorder.
  • Inline comments to discuss specific pieces of the text.
  • Discussion tools to share ideas and comments.

The free version of the tools is limited to public documents, meaning anyone could access your articles. A $8/month fee will give you access to private documents and premium support.

Note: another GitHub for writer is SciGit. The service is on hold for the moment, but keep an eye out for its return.

Roll the dice! PIpredictor calculates your likelihood of becoming a PI

qubodup_Ugly_non-perspective_cartoony_fort_fortress_stronghold_or_castle-1Academia is like a middle age fortress under siege, set in stone by traditions and habits, and ever so hard to get into. Whether academic life is a good choice for you or not is one question. But even if you want to be a Principal Investigator (PI), only between 0.45% and ~20% of PhD students end up in a tenure track position or similar. So you might think your odds are not great.

Well, now there is a tool to actually calculate those odds. Lucas Carey (Pompeu Fabra University) and his coworkers used machine learning to extract a set of laws that determines your chances of becoming a PI. This was achieved by looking at the careers and publication records of over 25,000 scientists in the PubMed biomedical literature database. They found that access to PI positions is highly predictable based on publication records and other parameters such as gender.

The study was recently published in Current Biology and a web-based tool, named PIPredictor, allows anyone to calculate their likelihood of becoming a PI. Any PI wannabe, should indicate their name, gender and a list of publication. The tool is free, but requires your publications to be referenced in PubMed.

PiPredictor allows anyone to calculate the likelihood of becoming a PI based on his/her publication record.

PiPredictor allows anyone to calculate the likelihood of becoming a PI based on his/her publication record.

A fun tool indeed! But beyond the amusing aspect of this study, the predictability achieved here is a reminder of the rigidity of academic institutions. In particular, the conservative approach to recruiting by many universities and research agencies. Lets (naïvely) hope this will be changes with the newer generations of academics.


Helpful link: Editage Insights

Screen Shot 2014-05-26 at 5.49.11 PMI have just added a link to Editage Insights on the blog roll to the right of the front page. This is not quite an online tool as I define it, but definitely a useful ressource for researchers. This is how Editage describes this relatively new platform:

Editage Insights is a dynamic blog designed to educate authors, connect journal editors with authors and vice versa, and allow people to engage in discussion about key developments in the academic publishing industry. It is available in English, Simplified Chinese, Japanese, and Korean, and thus has a wide reach, especially in East Asia, an emerging research hub. Some of the key highlights Editage Insights offers are interviews with journal editors and industry experts, a Q&A forum for authors seeking advice on the publication process, and updates on training programs conducted by Editage.

The service is an initiative from Editage, a editing service specialized in scientific publishing.

Writefull: using Google to help you write

Screen Shot 2014-05-08 at 11.49.58 PMIt seems there is no limit to the usefulness of Google’s services. Writers around the globe use Google Search to verify the spelling or mere existence of words or phrases. Google’s spelling corrector is extremely accurate and the number of search results is a great indication of how correct the query is. Strong of millions of webpages referenced by Google, this crowdsourcing methods is useful, but it is not practical and slow.

This is where Writefull comes in. Writefull is a free application for MacOS and Windows that uses the immense collection of words and phrases referenced by Google Books or Google Web Search to help you spell correctly and write more elegantly.

Writefull works as a small popover that can be activated on top of any application. With a simple keyboard command, a small window appears on top of your word document, web browser or email software.

A Writefull popup can appear on top of any application.

A Writefull pop-up can appear on top of any application.

Three options allow you to:

  • Know how often your selected text is found in the database.
  • Enter two chunks and directly compare their number of results.
  • See how the selected text is used in context (shows examples of your selected text in the database).
  • To fill a gap in your phrase (shows which words are used most often in a context you have selected).
  • To know if there is a more appropriate word for you to use in a particular context (provides a list of the most frequently used synonyms).

The application is a great idea and has a lot going for it. It is small, rapidly accessed, and usable with any text editing application. A free version works for up to 5 words per query and is based on the Google Books database. Using phrases found in books guaranties that your query is compared to phrases written in proper english, however the queries are limited in size due to technical limitations of the database. For a fee, Writefull can be upgraded to the web version. You then pay for every word queried and unlock access to the millions of websites referenced by Google. However, be aware that incorrect english is often published online. For example, “buetiful” returns 64,800 results. Also note that only the two first functionalities are activated when using the web version of Writefull for the time being.

This is a wonderful piece of software that I would love to see grow. On my wish-list for Writefull is a spelling corrector and an automatic suggestion option (“did you mean?“). This is because in case of incorrect spelling of the query, Writefull will find no results, which tells you something is wrong with your query, but without telling you what it is. On the other hand, Google Search is extremely good at guessing approximate spelling and it would be great to exploit this fully. It would also be nice to Writefull be able to replace text in my word processor and email application once I have found the right word or phrase.

A chrome extension for the “Lazy Scholar”

google-chrome-extensionsLazyScholar is a great Chrome extension that will save you time when looking for the full texts of scientific papers.

On his blog, Colby Vorland, developer of LazyScholar explains that he “got tired of highlight title-> ctrl+c -> open Google Scholar -> ctrl+p -> search every time [he] wants to check if Google Scholar has indexed the full text of a scientific abstract“. From this frustration is born LazyScholar, an extension that automatically searches the web for the full text version of the article abstract page currently viewed. The extension is available for free at the Chrome Web Store. Since the beginning of the development, features beyond the simple search for full text has been added to the extension. All features are there to help  streamline your literature search. Current features include:

  • Click the browser icon while on any scientific abstract and it will check Google Scholar for the full text.
  • Type “LS” in the address bar and quickly query Google Scholar. Type “LS” followed by “PM” to query PubMed.
  • Citation count (GScholar’s and Web of Science).
  • PubMed Commons & PubPeer comment count
  • Attempts to renames PDFs to a standard format (e.g. “year_first author_journal.pdf”). -Fast copying of citation to clipboard (currently: APA, MLA, Chicago formats, as well as a short citation for PowerPoint slides).
  • Fast save to Google Scholar Library. -Generated links to save citation to various reference managers (currently: EndNote, RefWorks, RefMan, BibTex).
  • Tag a press-release/news article with a link to the study discussed in the article by clicking the popup to save others the time searching for the link.
  • Highlight text on a page, right click, “Search Google Scholar” for fast searching.

Here is what the app looks like when Lazy Scholar finds a full text version of the paper. In this case I archived the article on my ResearchGate repository.

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 And here it is when the full test is not to be found.

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Cellkulture keeps a close eye on your cell culture

Screen Shot 2014-03-09 at 1.38.37 PMDigital solutions for lab notebooks have never been closer to becoming a reality. Cellkulture, is a web notebook dedicated to cell culture. A cloud-based and easy to use solution that allows you to document, archive and share your culture logs. The application is in a private alpha version, so development is in its very early phase.  Connected Researcher gives you a sneak peek at the functionalities you can expect from Cellkulture.

The virtual incubator

The virtual incubator

The application is divided into two sections: the Virtual Incubator, and the Cold Storage. The virtual incubator displays the flasks or plates that you are currently culturing. Clicking on a culture will bring you to another screen that allows you to enter details about your ongoing cell cultures. A set of parameters allows you to describe the state of the culture in a rather detailed way (passage number, color of the media, pictures of the cells…). On the right hand side, a summary of your previous culture media change, passage or freezing are displayed.

Input the information about your cell culture

Input the information about your cell culture

When it is time to freeze down your cultures to constitute a stock of cells, the stock vials can be placed in a virtual cold storage. This should help you keep track of stocks If you are careful to match your virtual and real-life cold storage. Still under development, but coming up soon, is a feature that allows frozen vials to start their own culture, with the information about the past of the culture.

The more long term goal of Cellkulture is to build a “github style version control tracking system for cell cultures that tracks each point at which cultures branch from the stock“, says Dave Pier, founder of Cellkulture. The app is clearly useful to record and archive this massive amount of information about cell cultures, but it can also be used in a more predictive way to help scientists. For example, “imagine a system that could alert you that your culture doubling time had reduced by 20% because the incubator was under heavy use and was not maintaining temperature, or a system that could highlight a rise in infection incidence after the stock of disinfectant was made up” says Dave.

This is definitely an interesting set of functionalities. The notebook and analytical aspects could serve cell culture intensive labs. While this could come as a great complement to more comprehensive solutions such as Labguru for less cell-culture intensive groups. Cellkulture is in private alpha release, meaning they have got a lot of ideas and improvements waiting to be implemented. You can register for private beta access by visiting their website.

Zappylab launches Protocols

Screen Shot 2014-02-18 at 11.14.43 PMA centralized location where all protocols could be described in detail and shared with the world. That is what Protocols from Zappylab (also creators of the PubChase literature search tool) is set to be. This could be an solution that researchers have been waiting for when faced with the often incomplete or incorrect protocols published in our favorite journals.

The website has gone live a few days ago, offering a simple interface to enter protocols. But Protocols is in Betra and more is to come. The launch is accompanied by a Kickstrater campaign to help get it started. Have a look!

Journal Guide helps you find, compare and rate journals

Screen Shot 2014-02-03 at 1.03.11 PMSo, after years at the bench, months fighting with your co-authors about the wording of the second phrase of the 5th paragraph, you are ready to publish! The question is, where should we publish the paper? With over 25,000 journals to choose from, the possibilities are plentiful and can be overwhelming. And for your paper to have impact, you must find your audience and thus find the journal that your audience reads…

Journal Guide is a platform that helps authors navigate through this profusion of scientific journals. It asks for your paper’s title and abstract, then extracts the important keyword and identifies a series of journals that seem to be a good fit.

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Example of search result in Journal Guide

The results are displayed in a table (see image above) with the search score, journal name, publisher and impact factor. For each journal, Journal Guide also identifies published articles that are related to your title and abstract. If others in your field have chosen a particular journal, you might want to consider it as well. Once you have chosen a couple of journals that seem appropriate, Journal Guide offers a tool to compare their characteristics side by side (see screen capture below).

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Comparison of three different journals

At any time during your search, clicking on the name of the journal will display another layer of information. There, one can learn about the journal’s aims and scope, costs and open access policies. But even more interesting is the ability of users to provide anonymous feedbacks about their personal experience with the journal. Information such as the speed of publication can be particularly useful.

Another online service provided by Edanz also helps authors decide on a journal by analyzing title and abstract. Journal Guide pushes the concept further by offering user accounts, side by side journal comparisons and journal rating. Although still in new and in beta version, Journal Guide has the potential to help create a more healthy competition between journals by making it easier to compare them and can already help young researchers better promote their research by choosing the right journal.

Out of curiosity, I have tested a few of my publications. Entering the title and abstract and looking down the list to see how the journal that I have selected are ranked by Journal Guide.  Some of my articles came up with the journal I published in as first choice. Others did not even show the journal they are published in. Perhaps this is a sign that the choice of journal can be quite irrational some times. Journal Guide could help us make more objective decision.

Journal Guide is a division of Research Square, a for profit organization also creators of AJE and Rubriq.

PubChase launches a career advice forum for researchers

Screen Shot 2014-01-12 at 3.00.46 PMPubChase has been busy these past few months. In addition to their literature recommendations search engine on desktop and mobile, they regularly invite researchers write assays on the story behind their latest publications. They now launched a new initiative that could have a strong impact by helping young scientists navigate in the sometimes troubled waters of academic life.

The new career advice forum is a semi-crowdsourced list of science career-related Q&A. PubChase has aligned a rather impressive panel of mentors that answer questions that anyone can ask. The motivation for the forum (as explained in this blog post) is to provide free and good quality mentoring for scientists and researchers. Too many young researchers are facing difficulties with their supervisors in part because academic scientific leaders often lack proper management training. PIs are also incredibly busy and giving career advice is often not on top of their list of priorities.

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List of questions and answers on the PubChase career advice forum

The forum gives you advice about what should you do if, for the past 3 years, your advisor has been asking for one “last experiment” before you publish? Or how should you react if your PI has simultaneously handed the same project to you and another student in the lab At the moment, one question is being answered every week, eventually buildup up to be a repository of career advise accessible to all. PubChase Career Advice Forum