Mario’s Entangled Bank

Traditionally the day-to-day activities of academic research has been a closed endeavor where research note books are usually only available to people in the lab. Open Notebook Science (ONS), in contrast, represents a revolutionary concept going against the grain of these traditions where research notebook are available online as they are written. Although it might take a while to turn the tide and make ONS an accepted and established practice there are many advantages to it. The ONS lab of Rosania Research Group summarizes it nicely,

Open Notebook Science is ideally suited for community-wide collaborative research projects involving mathematical modeling and computer simulation work, as it allows researchers to document model development in a step-by-step fashion, then link model prediction to experiments that test the model, and in turn, use feeback from experiments to evolve the model. By making our laboratory notebooks public, the evolutionary process of a model can be followed in its totality by the interested reader. Researchers from laboratories around the world can now follow the progress of our research day-to-day, borrow models at various stages of development, comment or advice on model developments, discuss experiments, ask questions, provide feedback, or otherwise contribute to the progress of science in any manner possible.

Ever since seeing Jean-Claude Bradley and Garrett Lisi’s Open Notebook Science endeavors at SciFoo a few months back I have been toying with the idea of starting a similar enterprise. Although Jean-Claude and Garrett practice ONS, their individual approaches to research could not be more different, as a result their online research notebooks are very different animals. Jean-Claude is running a rather typical academic lab (i.e. a PI + a band of postdocs and students) in experimental chemistry and utilizes a combination of a wiki and blog hosted by Wikispace and Blogger for his UsefulChem project. In contrast, Garrett Lisi runs a one-man band as an independent researcher in theoretical physics and uses TiddlyWiki for his Deferential Geometry research notebook.

Largely due to the inspirational efforts of Jean-Claude and Garrett’s I have been pondering of starting my own little ONS research projects. Initially it would consist only of the notebook from one of my solo projects. Trying an ONS approach on a project involving collaborators (particularly when one is not the PI) is tricky and beyond my means currently.

As a spin off from the GillepieSSA package that I developed I have embarked on a more ambitious project for developing stochastic simulation algorithms aimed specifically at ecological and evolutionary models (see the last project on my research page, i.e. computational algorithms for statistical simulations of ecological and evolutionary processes). As I am thinking of how to set this up I realized that there are specific requirement that I need the online notebook to have, e.g. support, an interface to an source control management system (e.g. Subversion or Git), a client side tool would be preferable, and it needs to be easy to back it up. So far the candidates are,

• TiddlyWiki, pros: supports , nice non-linear approach where arbitrary posts (aka tiddlers) can be viewed and edited simultaneously, client side (doers not require web access), simple “installation” since the TiddlyWiki code and the contents reside in a single text file, simple hosting (no CGI required) cons: it is not clear how well the performance of the application scales for large projects, there does not appear to be an interface (in the form of a plug-in) to a source control management system, need to host it on a server.
• OpenWetware, pros: acts as a sort of glue for the Open Science community with the potential benefit of getting more exposure, aimed at academic research labs, the web hosting is taken care of, cons: servers side service (i.e. web access required), no interface to a source control management system, no obvious capabilities (?).
• Trac, pros: interfaces with Subversion, cons: limited capabilities, server side application with complex set up requiring CGI capabilities.

Currently I am leaning towards Trac, although it complex to set it up (relative to the other options) I have used it for many years and are comfortable with it and really like the integration between the wiki and Subversion. Neil Saunders has a post on his blog What You’re Doing Is Rather Desperate about using Trac for managing research projects and using it as an open notebook system. With the proper plugin Trac might even be able to render .

This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta.