DAS workshop 2008 - day 1

Today was the first day of the DAS workshop 2008 that I visited on behalf of the Bioclipse project. It was held at EBI and had some interesting presentations and discussions. Apart from introducing the Distributed Annotation System (DAS), the first day consisted of presentations of many client implementations. DAS is basically a set of Web services for annotation of biological sequences with the goal to split data and presentation. This means that a DAS client can request info from many DAS servers and integrate the info in a single view or analysis. The technology behind is simple HTTP requests that return XML responses. Uniprot is the reference server and provides the sequences.

Jim Procter presented Jalview and VAMSAS, an exchange format to combine Topali, Jalview, and AstexViewer.

Rob Finn talked about the new Pfam website with nice feature visualization that incorporated DAS. He talked about their REST web services and how they are superior to SOAP-based implementations for resource-providers like themselves.

Rafael Jimenez demonstrated Dasty2, which is a DAS web-client using AJAX.

Thomas Down talked about Dastard and the problem of firewalls. He also interestingly brought up the question weather DAS clients should be Web-based. He himself preferred desktop apps to get better interaction with other local programs (excel etc). He also recommended the Java database Derby over HSQLDB.

Andreas Prlic talked about DAS registries and the SPICE viewer for connecting genomes with structural data and visualize SNPs and multiple alignments on 3D.

Asja Grzibovska described the DAS Writeback project that extends read-only DAS model by adding possibilities to write data back to the server.

Hagen Blankenburg described molecular interactions with DAS, called DASMI. They have extended DAS servers with support for protein-protein interactions. He also showed the DASMIweb client which is able to integrate a lot of data from interaction databases. I wonder why people keep calling it molecular interactions instead of protein-protein interaction?

Jose Ramon Macias talked about their extension of DAS to cope with 3D Electron Microscopy, called 3D-EM DAS. They had built a client, Pepper, but as they required more responsive functionality they were discussing building yet another client for DAS based on the Netbeans Rich Client Platform. He was familiar with Bioclipse but had decided to use Netbeans because he was familiar with it. Let's hope they'll honor MVC to full extent!

Syed Haider presented Biomart which basically is a convenient way of joining databases together by visualizing original tables and generating the SQL for the mart construction. They are close to having an incremental-update function. We really should build a Biomart plugin for Bioclipse!

Several people mentioned OpenID for single sign-in. This is maybe something that we should consider for Bioclipse in the long run.

Well, this ends day 1. Tomorrow we will get hands-on instructions for coding a DAS client, but first it's dinner in Cambridge.