Labfolder: a digital lab notebook

Screen Shot 2013-11-21 at 10.45.41 PMLabfolder is an online digital lab notebook. An online space where users can write, draw and assemble reports of their latest experiments, that they can then safely store in the cloud.

The digital lab notebook revolution has been announced for quite some time now. There are promises of digital notebooks accessible from anywhere that are data rich, searchable, sharable and never lost or damaged by spilled coffee.  But the path toward its full implementation in academic labs is long, partially because no alternatives really beats the old notebook and pencil when it comes to user friendliness. So in that respect, the challenges faced by Labfolder are significant.  But Labfolder proposes interesting functionalities and a nice, clean, fresh interface that may seduces more than one researcher.

The Labfolder experience start by creating a new folder (what a surprise) in your project tab. Under each folder, multiple entries can be added, corresponding to the pages of your traditional lab notebook. Within each entry, the users can create boxes containing text, images, links to files and hand-drawn (or should I say mouse drawn) sketches that can be useful to annotate images. These boxes can be easily resized or moved around and when satisfied with an arrangement, the entries can be saved and reused as templates. After the content is added, the final entries can then be save to the cloud, or downloaded as a pdf for sharing.

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Labfolder is completely free for individual use and for groups up to 3 users. A cloud space of 3 GB is offered to store all files. Forming a groups with other Labfolder users enables sharing entries and templates with collaborators.

Labfolder was started by two german PhD students from the MaxPlank Institute; Simon Bungers and Florian Hauer. They where surprised how digital tools were poorly used in research and decided to add their contribution by founding Labfolder. Labfolder is an ongoing venture, and encourage users to send their comments and ideas to them (contact@labfolder.net).

A look at Pubmed’s new commenting platform

Screen Shot 2013-11-04 at 10.00.50 AMPubmed is implementing a new function that enables researchers to share their thoughts about scientific publications. By allowing readers to comment and debate about specific papers publicly,  PubMed Commons is trying to extend the peer-review of manuscripts after their publication. If successful, PubMed Commons will become a platform for scientific discussions that could foster constructive criticism and eventually improve published papers and science. The service is currently in its pilot version which is restricted to recipients of NIH or Wellcome Trust funding. But I’ve put together a couple of screeenshots to give you a quick look at this interesting new feature.

Nothing much has changed from the familiar Pubmed abstract page. But notice that at the bottom of the page, a new “Reader Comments” section has appeared. Comments can be directly typed in the text box.

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Although comments of any length can be posted, it is recommended to keep it short and clear. Simple formatting options are offered, but need to be written as code in the text box.

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For example, links to other articles can be added by including the PMID number.  A direct link with author and year appears when published.

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All contributions are published under the Creative Commons Attribution 3.0 License and can be edited or deleted after publications. The comments are assigned a unique and permanent link so that they can be easily referred to. It is also not allowed to use anonymous pseudonyms to maximize accountability for comments. As of today about 200 articles have comments link to them, which is negligible compared to the 23 million referenced papers in Pubmed. But that will surely increase greatly with the service going live in the near future.

Similar initiatives such as Pubpeer and publishers such as Faculty of 1000, Frontiers and Plos already offer similar functionalities. However, the relatively small size of their user-communities and the lack of incentive for researchers to comment publicly on papers have limited their success up to now.  Pubmed Commons is starting off with a very large number of regular users, so perhaps this will be a different story. I believe that post-publication review will start being a serious alternative to the traditional post-publication peer review when at least two factors are combined:

  1. Commenting needs to happen on a centralized system, which is already familiar to researchers and that counts a certain critical mass of active users. Pubmed common has the potential to make that happen and Pubpeer’s talks about joining forces with Pubmed Commons could only help.
  2. Researchers need to accept that publications are not absolute truths, set in stone for eternity. Everyone should be allowed to make (honest) mistakes, if they are ready to accept constructive criticism. Publication should be dynamic documents, living with the evolution of knowledge. Papers are constantly being commented, criticized and applauded, but why keep these behind closed doors?