Steve's Corner
Happy New Year from Bio::Neos! We hope that you have begun to settle back in to your research routine by now and that the start of a new year has brought you new and interesting research ideas. (and budgets!)
If you haven't already, now is a great time to start thinking about a data management system to help you efficiently organize and analyze your data. Whether or not you already have a data management system, I urge you to consider the Genboree Discovery System developed by the Bioinformatics Research Laboratory (BRL) under the direction of Dr. Aleksander Milosavljevic at the Baylor College of Medicine. Although this solution is currently maintained and managed onsite at Baylor, I would like to announce the upcoming arrival of Genboree.com, a new service of IP Genesis, Inc. IP Genesis has licensed the Genboree technology from Baylor and will begin providing access to the genomic research community as a whole, starting March 1st, 2008. IP Genesis is currently seeking 7 to 10 interested researchers to participate as early adopters of the system, so contact them soon.
The following description of Genboree is summarized from the BRL website:
Genboree is a turnkey software system for genomic research. While it can be configured to support almost any genome-centric discovery process, a number of configurations already exist for specific applications. Current focus is on enabling studies of genome variation, including array CGH studies, PCR-based resequencing, genome resequencing using comparative sequence assembly, genome remapping using paired-end tags and sequences, genome analysis and annotation, multi-genome comparison and pattern discovery via genome self-comparison.
Genboree database and visualization settings, tools, and user roles are configurable to fit the needs of specific discovery processes. Private permanent project-specific databases can be accessed in a controlled way by collaborators via the Internet. Project-specific data is integrated with relevant data from public sources such as genome browsers and genomic databases. Data processing tools are integrated using a plug-in model. Genboree is extensible via flexible data-exchange formats to accommodate project specific tools and processing steps.
As of early 2007, the number of registered Genboree users exceeds 600. Contact IP Genesis soon to get started with this exceptional system.
Free Gene Browser - Release 1.1.0 Now Available!
That's right, Bio::Neos has just released a new version of the free gene-centric browser called GANT (Gene and Annotation Navigation Tool). Version 1.1.0 of GANT has been released and is available for download.
GANT allows you to visualize and interact with a gene, its associated annotation and design primers for your regions of interest with just a few clicks of the mouse. GANT has many useful features and it's free! Visit http://gant.bioneos.com now to try it out!
Be Heard!
Did you set a 2008 New Years resolution related to your research?
Yes, and I'm still on track!
Yes, but it's already been broken!
No way, I don't like to set myself up for failure.
What? It's 2008 already?
The Pubs
Recommended readings from the Bio::Neos team:
- Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. by Coarfa C et al. Pac Symp Biocomput. 2008;:102-13. (PMID: 18229679)
- Direct selection of human genomic loci by microarray hybridization. by Albert TJ et al. Nat Methods. 2007 Nov;4(11):903-5. (PMID: 17934467)
- Microarray-based genomic selection for high-throughput resequencing. by Okou DT et al. Nat Methods. 2007 Nov;4(11):907-9. (PMID: 17934469)
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