Open lab book

An open lab book is just the ordinary lab-book, only in digital format and on-line. It has a lot of advantages over the traditional one:
  • You and your collaborators can access it from anywhere.
  • It is much safer than a regular lab book, whose fate is usually to get lost the next time you move to a new lab. The electronic lab book stays forever, both in your hard drive and on the internet.
  • Many people can contribute to the lab book simultaneously.
  • You can easily search for any content.
  • You can disclose it to the public, so that everyone can see the work behind your publications.
  • The date of each entry is saved automatically. Any later edition is saved with its date, and the older version remains available.

There are many ways to keep an electronic lab book. Unfortunately, most of them require a great deal of discipline and organization on your side. But there is a simple method, that I borrowed from Amanda Sorribes, which allows you to easily keep an electronic lab-book with no need of specialized software, and being as shabby as you would be with your paper notebook.

Summary of the method:
  • The lab book is stored in a blog, each entry in the lab book being a post.
  • The posts are not edited using the tools available online, but in MS Word 2007 (or later). Therefore, one has all the power of MS word, including the possibility of adding images just by copy-pasting them. Also, after publishing the post you can still save it in your hard drive, keeping a local copy.

Implementation of the method:

  • Create a blog in wordpress.com
  • Configure MS Word to communicate with it. It is very easy: you will only need to enter the address of your blog, your username and password. In MS Word 2007, go to "New Document" -> "New Blog Post", "Blog Post" -> "Manage Accounts" and follow the instructions.
  • You are done! You can then open a new blog post ("New Document" -> "New Blog Post"), and start editing! Once you are done, just click "Publish". Word will automatically upload the post, including all images.

Note to Matlab users:

Matlab has the option to publish the results of a script. The result is a document with the code, all comments of the script and the output (including figures) nicely arranged. You can use this tool to easily post your Matlab analysis in your lab book. To do it: (1) Publish your script in .doc format (type doc publish in Matlab's command window for help of how to do it. Recent versions of Matlab have direct shortcuts from the editor). (2) Open the .doc file in Word. In Word 2007 go to the Office button (roun button on the top-left corner) -> Publish -> Blog. Word will transform the document in a blog post that you can upload to Wordpress as described above.


My open lab books

Labbook 1: From February 2009 to December 2009. Among many other ideas, it contains work related to the following pulblications:
  • A. Pérez-Escudero, M. Rivera-Alba, G.G. de Polavieja (2009) Structure of deviations from optimality in biological systems. Proc Natl Acad Sci USA 106, 20544-20549 (pdf) (web) (Open Labbook) (Faculty of 1000)
  • A. Pérez-Escudero, C. Dorronsoro, S. Marcos (2010) Correlation between radius and asphericity in surfaces fitted by conics. JOSAA 27(7):1541-1548 (pdf) (web) (Open Labbook)

Labbook 2: From October 2009 to May 2014, also edited by Sara Arganda and Julián Vicente-Page. It contains work on Collective Behavior, especially regarding zebrafish experiments and tracking of multiple animals. Contains work related to the following publications:
  • A. Pérez-Escudero, G.G. de Polavieja (2011) Collective Animal Behavior from Bayesian Estimation and Probability Matching. PLoS Comput Biol 7(11): e1002282. doi:10.1371/journal.pc bi.1 002282 (pdf) (web) (journal cover)
  • S. Arganda, A. Pérez-Escudero & G. G: de Polavieja (2012) A common rule for decision-making in animal collectives across species, Proc Natl Acad Sci USA vol. 109 no. 50 20508-20513 (pdf) (web)
  • A. Pérez-Escudero, N. Miller, A.T. Hartnett, S. Garnier,I.D. Couzin, G.G. de Polavieja (2013) Estimation models describe well collective decisions among three options. Proc Natl Acad Sci USA vol. 110 no. 37 E3466-E3467 (pdf) (web)
  • A. Pérez-Escudero, J. Vicente-Page, R.C. Hinz, S. Arganda, G.G. de Polavieja. idTracker: Tracking individuals in a group by automatic identification of unmarked animals. Nature Methods (in press)