Archive for the ‘bergman lab’ Category

Preview of the Dmel-stock-keeping database “flystockdb”

Posted 09 Nov 2010 — by caseybergman
Category bergman lab, database, drosophila

We are in the process of developing a database for stock-keeping of Drosophila melanogaster (fruit fly) stocks; it is ingenuously named “flystockdb” and will eventually be publicly available and open to anyone.

Key features of flystockdb:

  • web-interface (HTML + JavaScript)
  • rights-management (publicly-, privately-shared stocks)
  • software aided entry of genotypes and genomic features

The central access-point to flystockdb is its web-interface, which permits users to conveniently connect to the centralised fly-stock keeping database from everywhere. There is no installation process necessary, whilst data safety is guaranteed via the secured and rights-managed flystockdb server.

A fine granularity rights-management allows for sharing stocks publicly with everyone else, sharing stocks with designated flystockdb-users, and to keep private non-shared stocks. “Groups” can be used to accumulate communal stock-collections, to serve as repositories for private stock-supplies, or anything in-between.

Automatic recognition and linkage of whole genotypes — but also of single genotypic features — via FlyBase simplifies and aides the entry of fly-stocks. Genes, alleles, balancers and even P-elements are sorted onto the right chromosomes by contextually aware algorithms that can decompose and analyse user-input on-the-fly.

A preview of flystockdb is available via a screencast:

We anticipate to go live mid-2011.

Welcome to the Bergman Lab Blog

Posted 09 Mar 2009 — by caseybergman
Category bergman lab

After getting bitten by the blogging bug about a year ago and following posts about evolution, genomics and bioinformatics from good citizens in the blogosphere, I’ve decided to enter the ring by developing a blog for tips and lessons in computational biology that people in my group have found useful.

I had previously tried to do this for a few hacks to port evolutionary genetics and bioinformatics code to OSX, which I’m reposting here for to get things rolling. I’m hoping that members of the lab might also join in as well, and we can use this forum as a to pass along our collective (in)experience to whomever might be reading along.