Much has been said about (and blamed upon) communication problems between biologists and computer scientists. But after attending a meeting with biologists and computer scientists this week, I am starting to suspect that the problem isn’t just communication.
We are currently exploring various strategies to encourage people to let us know when they find errors or omissions in UniProt, or even to contribute data as they publish their research, rather than waiting for a curator to pick up their results from a publication.
After having meetings and discussions that dragged on for more than an year, we are now finally distributing our data under a Creative Commons license.
Brief review of Data and Reality by William Kent. This book was written in 1978, but is still remarkably relevant in many ways.
It looks like our initiative to port all of our code to a more compact and efficient language didn’t get very far. So what next?
From a recent review article in Nature Genetics:
[...] current ad hoc IR systems are not able to retrieve our example sentence when they are given the query ‘yeast cell cycle’. Instead, this could be achieved by realizing that ‘yeast’ is a synonym for S. cerevisiae, that ‘cell cycle’ is a Gene Ontology term, that the word ‘Cdc28′ refers to an S. cerevisiae protein and finally, by looking up the Gene Ontology terms that relate to Cdc28 to connect it to the yeast cell cycle. Although this will not be easy, we see this form of query expansion as the next logical step for ad hoc IR.
Brief review of Emotional Design. Donald Norman uses this book to expand a bit on the well-known The Design of Everyday Things. In particular, the new book discusses some of the non-rational aspects of design that the previous book ignores.
Brief review of Information Visualization by Colin Ware. This is a textbook with a great amount of detail on the physics, biology and psychology behind visual perception.
Nature reports about a study showing that users may be deciding on whether or not they like a site within a fraction of a second.
Here are some notes on the book Producing Open Source Software. The book does an excellent job of explaining how open source projects work and how they deal with typical problems.