Monday, April 19, 2010

Abstract or concrete? It all depends on your point of view.

Our team is working with a number of task forces in bioinformatics. Each of those task forces was started to collaborate on the development of a platform for their sub-field: a set of software tools that work together to solve the problems that everyone in the field needs to solve. Developing the platform does not require any new bioinformatics developments: the purpose is to put existing tools together.

The advantage of having these platforms available is obvious:
  • to a biologist the advantage consist of having all the de facto standard tools available under the press of a button.
  • to a specialist bioinformatics researcher working on a new tool the advantage is that he does not have to deal with the intricacies of all the other tools, and is able to plug his new tool into the platform using well described protocols.
To get to the development of such a platform there is a bootstrapping problem. The situation is like a table with biologists sitting on one side, bioinformaticians at the other side. Above the table, a thick (volcanic?) fog. The layout of the platform is drawn in diagrams on the table: all the tools making up the common work flow, with all their relations. On the side of the bioinformaticians, the diagram shows the concrete tools. Through the fog, they can vaguely see the workflow on the other side of the table. For the biologists, the situation looks completely different: they have a clear view on the concrete workflow they need, but the tools are vague entities that are only visible through the thick fog.

Without good support from a project leader that can listen to people on both sides of the table, the bioinformaticians will try to solve the very concrete problems they encounter on their very concrete individual tools. A little optimization here, a better data storage facility there. None of this is visible for the biologists.

This is why we put project leaders from our engineering team into each of the task forces. They will direct the focus of the bioinformaticians towards more visible changes. Work on common data formats. Work on (common) user interfaces.

Getting things to work together will bootstrap the true collaborative advantages. It will blow away the fog. Suddenly the biologists will be able to see what is going on. They will be able to provide directed feedback. And the bioinformaticians will be able to see the workflow even from their side, and build upon it.

Image credit: Three views of three tables, by EJP Photo on Flickr.