Cellkulture shut down, but code alive on Github

Screen Shot 2014-08-26 at 2.47.24 PMCellKuture, the digital lab notebook that helps you track and manage cell cultures, shut down 5 months ago. But although the project in not actively being developed, the code lives on, published on the Github repository, free for anyone to use.

Startup turnover is a very natural thing to happen in the new space of Digital Science. Entrepreneurs simply cannot have a perfectly clear vision of what the research ecosystem will look like in a few years. Startups are taking their chances by exploring new markets and testing the reactions of customers to new services. And in this context, it can be hard to gather enough users to really push your startup off the ground, especially when targeting a niche market (like cell culture experts).

A consequence of this high-risk environment, is the sense of responsibility we should expect from these digital science startups. They should think in advance of opt-out options for users changing providers or if the company goes under. This means providing ways to export the data in a reusable format, and in some cases, providing the code so that users can continue to use the platform. CellKuture is doing exactly that by providing a functional software for free with instructions to install and run it. On top of making CellKulture users happy, this move could attract new users, and most importantly inspire other developers to build upon this piece of work.

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.

Design and share DNA sequences with Benchling

Screen Shot 2013-10-17 at 10.16.30 PMCollaboration seems to have never been easier with the collection of online tools at our disposal. These tools take advantage of the cloud to store data accessible everywhere to anyone. The software is usually browser-based, which makes access simple and fast. As mentioned here several time before, online tools aiming at enhancing collaboration between researchers have flourished over the past few years (see GitHub, Authorea or SciGit for example). Benchling has been named the GitHub for genetics, with it, anyone working with DNA can effortlessly design, analyze, and share sequence data. Benchling gathers into one platform most of the tools you will need to manipulate genetic sequences. Getting ready for cloning? Benchling will help you in the process with tools that identify restriction sites, suggests appropriate reaction buffers and can generate virtual gels to compare theoretical to experimental reaction products. Other bioinformatic tools offered by Benchling help you design primers, align multiple sequences or annotate sequences. The fruits of your hard work can then be tagged and store in the cloud, in an easily searchable format. Benchling also generates interactive sequence for easy visualization of constructs.

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The workspace can be divided into the sequence and the plasmid map. All most items are interactive. To the far right, tools to align sequences, annotate, design primers and more.

Benchling is also about collaboration. Users can grant access to their sequence libraries for download or editing by collaborators. Changes in the sequences can be tracked with the possibility to revert to a previous version. All the data is stored in one location, meaning no more exchanging emails that get lost or overlooked. Benchling was founded in August 2012, by Cory Li and Sajith Wickramasekara.