Todd's Corner
Happy holiday season from Bio::Neos! As always, we've included references to resources that we use, and that we hope will be useful to you. These include a selection of resources from programmatic guides to repositories of data. Also, be sure to check out our free gene browser called GANT, it has a great interface for oligo design.
I'd like to take this opportunity to reflect on the bigger picture of bioinformatics. Bioinformatics is at the intersection of the life-sciences and computational-sciences. While data analysis is the traditional focus of bioinformatics, an often overlooked aspect is data acquisition. Collected data must meet strict quality control requirements, else any derivative analysis is potentially flawed. Nothing is more frustrating than collecting months or years worth of data to find that your procedures were incomplete, incompatible, or inadvertently biased. In addition, data may be required in many different modalities - e.g., clinical, molecular and image. And from a regulatory stance, HIPAA requires particular care in the management of PHI (protected health information). Comprehensive solutions to these issues are similar to, but often beyond the scope of, electronic medical records. We understand that these are serious issues, and have experience in developing data acquisition systems tailored to our customers' needs.
Whether you are formulating a novel research project, or building upon an existing one, please keep Bio::Neos in mind for all of your software development needs. We have the experience and expertise to create secure, user-friendly applications to meet those needs. If you have an idea for a system to improve your research, give Bio::Neos a call, and we will work with you to turn that idea into a reality.
Free Gene Browser Released by Bio::Neos, Inc.!
That's right, Bio::Neos is now offering a free gene-centric browser called GANT (Gene and Annotation Navigation Tool). Version 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!
Conference Schedule
Our 2007 conference schedule has come to a close...and we thank all of you who visited us this year!
If you didn't get a change to visit us, don't worry, there will be more opportunities in 2008. In fact, we have already started planning our 2008 schedule, just visit our news page to see our up-to-date schedule!
Also, you may contact us to set up a seminar or meeting at your institution.
Be Heard!
What technology are you using to design primers?
Primer3, non-graphical
Graphical interface to Primer3
Online Tools
Other
What are primers?
Resources
Here is a list of some data repositories and programmatic resources that we have used at Bio::Neos as of late. If any of these resources pique your interest, don't hesitate to contact us! We will be happy to discuss how we can enable your research to utilize them.
Data Repositories
- Gene Expression Omnibus (GEO) - http://www.ncbi.nlm.nih.gov/geo/ - A gene expression data repository that is an online resource for browsing, querying and retrieving gene expression data.
- The GeneNetwork - http://www.genenetwork.org - A set of linked resources for systems genetics that is "designed for multiscale integration of networks of genes, transcripts, and traits such as toxicity, cancer susceptibility, and behavior."
- The Gene Ontology (GO) - http://www.geneontology.org - A project that provides a controlled vocabulary to describe gene and gene product attributes in any organism.
Programmatic Resources
- Drupal - http://drupal.org - An open source content management system
- dcm4che - http://www.dcm4che.org/ - A Java API for the Digital Imaging and Communications in Medicine (DICOM) standard
The Pubs
Recommended readings from the Bio::Neos team:
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project by Birney, E. et al Nature 2007 Jun 14; (PMID: 17571346)
- New Approaches to the Treatment of Dense Deposit Disease by Smith RJ et al. J Am Soc Nephrol 2007 Sep;18(9):2447-56. (PMID: 17675665)
- Epigenomics: mapping the methylome by Wilson IM et al. Cell Cycle. 2006 Jan;5(2):155-8. (PMID: 16397413)
Contact Us!
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