My colleagues regularly ask me if I couldn’t provide them with some graphic view of my code, looking at source code is so tedious etc. I’ve looked at various UML tools in the past, but never managed to get any truly useful visualization out of any of them. But maybe the problem with UML is that it’s so limited to two dimensions? Enter Relief, a tool that visualizes code in three dimensions!
Gave a brief talk about programmatic access to beta.uniprot.org at the EMBRACE workshop in Geneva today.
Here is a simple Greasemonkey script that adds a Clear button to Google search result pages.
In order to bulk-load RDF data into Oracle (Spatial) 11g, the data needs to be converted to N-Triples first. If the data set is large, this step can add quite a bit of overhead, which is why I decided to benchmark and compare several options.
The UniProt RDF distribution is over 5GB large. To help people retrieve the data more efficiently, we now mirror the data and provide a Metalink file that describes all the file locations.
The best choice of virtual machine is of course dependent both on the application and on the hardware the application is running on; here are the conclusions of a performance comparison with the latest batch of Java virtual machines for a web application that makes heavy use of BerkeleyDB and Lucene on an off-the-shelf Intel machine with 64-bit extensions.
The Google Gadgets API can be used to create small applications that people can add to their personalized Google home page. Here is a simple “gadget” for blasting protein sequences.
Google now allows you to create custom search engines. I used this to set up a search engine that searches in well know life sciences sites.
How do you concatenate two huge XML files efficiently without writing any code?
Google Subscribed Links provide a mechanism for adding information at the top of a Google search results page. I set up an example that can be used to see information from the Enzyme Nomenclature Database when searching for something like EC 1.2.3.4.