JJ's blog on bioinformatics

Personal Genomics

2009-05-21T21:16:00.000-07:00

Some one asked me what was the biggest impression on RECOMB2009. Well, the biggest impression was the desert with a lot of rain--it kept raining for two days. Ooh.. you mean my impression on the conference. That was, the game of personal genomics is really going on and rapidly evolving. Quite a few talks and posters are talking about next generation sequencing, personal genomics and personal medicine. The whole business session is about personal genomics. 23andme, Navigenetics, Complete Genomics and some other companies, who attended the panel discussion on the conference, are obviously eager to take a share in this immense market.

It seems that suddenly you have to get a copy of your own genome. Companies such as 23andMe and deCODEme offer cheap (sub-$1000) genome scans looking at between 500,000 and a million sites of common variation throughout the genome. Knome offers sequencing of all of your protein-coding genes for $24,500. Knome is even selling a DNA whole genome sequence experience on ebay for $68,000, and interestingly someone has bidden on it.

Memo on ID mapping and bridgedb (skyped with Martijn 04/30/09)

2009-05-01T08:24:00.000-07:00

ID mapper API needs to be redesigned, using bridgedb Xref.
ID mapper API should be generic, or independent of Cytoscape.
ID mapper API design V3 on the project wiki is preferred.
IDMapperRDB in ID mapping API would be a wrapped-up interface of GDB in bridgedb.
ID mapper makes use of bridgedb, but not the other way.
bridgedb can be adapted to the need to ID mapping.
Integrate web service in bridgedb.
Many people are thinking about ID mapping, so it's important to start coordinating.
I will focus on the following two things before May 23:
1. Refine ID mapper API with the team.
2. Design GUI according to bridgedb spec V & VI: make some GUI mockup and discuss with others.

GSoC, I'm back!

2009-05-01T08:19:00.001-07:00

After a long (2-week) anxious wait, I got accepted by GenMAPP as a GSoC student again this year. My project is to develop ID mapping plugin for Cytoscape. Dr. David States is my mentor for this project.

During the last summer, I developed the Advanced Network Merge plugin (mentored by Kei Ono). ID mapping based network merge was one of the features of that plugin. As a result, some preliminary work has been done in ANM. For instance, the ID mapping APIs have been designed, the file-based ID mapping has been implemented, and the ID mapping GUI has been designed.

In the following summer, I will work closely with my mentor Dr. States and the BridgeDb team. Our project aim is to provide the community with a set of ID mapping APIs and a ID mapping plugin for Cytoscape, using different ID mapping sources such as local/remote files, databases and web services.

More project progress will be blogged here...