About

About BioGPS

BioGPS is a gene portal built with two guiding principles in mind -- customizability and extensibility. Check out our BioGPS publication in Genome Biology!

First, although every scientist who visits a gene portal wants to view gene annotation, the specific reasons are different for every person. A geneticist may be here to find candidate genes in a genomic interval. A cell biologist may be here to view our Gene Atlas expression profiles. A molecular biologist may want to find information on protein domains. If everyone has their unique interests, gene portals should be adaptable to suit your individual needs. Therefore, BioGPS offers a customizable gene report layout, where you can control which pieces of data are displayed and how they're displayed. Select from our extensive plugin library only the sources that are relevant to you.

Second, are you tired of visiting a dozen different gene portals, each of which have 80% of the same data, for the 20% unique content? Or are you a web developer whose website doesn't quite have the visibility you think it deserves? We designed BioGPS to solve both of these problems by creating a simple plugin interface which allows anyone to add new plugins to BioGPS, completely autonomously. Our goal is to completely remove ourselves from the critical path of extending BioGPS. With other portals, you can beg and plead with the portal administrators to add new content. In BioGPS, if you see data that's missing (or have data that others would be interested in), you can do it all yourself. (Note that we're still finalizing this plugin architecture, so stay tuned!)

BioGPS is clearly a work in progress, but we think we've got a framework that's here to stay. Let us know if you've got suggestions, but otherwise, just dig in!

Cheers,

The BioGPS team

Contact Info

The core BioGPS team is currently composed of the following individuals:

Andrew Su
Camilo Orozco
Chunlei Wu
Marc Leglise
Ian MacLeod
GNF IT department

Past contributors:
James Goodale
Jason Boyer

Questions and comments can be sent to the BioGPS Google Group (biogps -at- googlegroups -dot- com). Private email to the developers can be sent to biogps -at- gnf -dot- org.

Funding

BioGPS is supported by research funds to GNF through the Novartis Research Foundation.

BioGPS is also supported by Award Number R01GM083924 from the National Institute Of General Medical Sciences. However, BioGPS does not necessarily represent the official views of NIGMS or the National Institutes of Health.

Technology

BioGPS was built following a three-tiered application model. The data tier was implemented using Oracle v11, and data tables were populated by importing gene annotations and relationships from common gene annotation databases (predominantly NCBI and Ensembl). The business logic tier was built using C# and the .NET Framework v3.5, utilizing the Windows Communication Foundation (WCF) to expose REST-based web services for querying and data retrieval. The presentation layer, which includes the plugin and layout management system, was built using the Django web framework and extensively uses the EXTJS JavaScript library.