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NATIONAL CENTERS FOR BIOMEDICAL COMPUTING: Resources

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biomarkers & Medical Diagnostics, Cell Biology, Signaling & Cell Circuits, Computational Biology/Systems and Bioinformatics, FDA Regulatory Affairs, Genome Biology, Genomic Testing: Methodology for Diagnosis, Molecular Genetics & Pharmaceutical, Personalized and Precision Medicine & Genomic Research, Population Health Management, Genetics & Pharmaceutical, Proteomics, Scientist: Career considerations, Statistical Methods for Research Evaluation, Technology Transfer: Biotech and Pharmaceutical, tagged , , , , , , , , , , on September 20, 2012| Leave a Comment »

 

Reporter: Aviva Lev-Ari, PhD, RN

NATIONAL CENTERS FOR BIOMEDICAL COMPUTING

An overarching approach to several disciplines:
  • Other Genomics related subdisciplines:
  • The Biomedical Computing Space

An illustration of the systems approach to biology

http://en.wikipedia.org/wiki/Systems_biology

 

The National Centers for Biomedical Computing (NCBCs) are part of the U.S. NIH plan to develop and implement the core of a universal computing infrastructure that is urgently needed to speed progress in biomedical research. Their mission is to create innovative software programs and other tools that will enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease.

Biomedical Information Science and Technology Initiative (BISTI): Recognizing the potential benefits to human health that can be realized from applying and advancing the field of biomedical computing, the Biomedical Information Science and Technology Initiative (BISTI) was launched at the NIH in April 2000. This initiative is aimed at making optimal use of computer science and technology to address problems in biology and medicine. The full text of the original BISTI Report (June 1999) is available.

Current Centers

SimBioS
National Center for Simulation of Biological Structures (SimBioS) at Stanford University
MAGNet
National Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) at Columbia University
NA-MIC Logo
National Alliance for Medical Image Computing (NA-MIC) at Brigham and Women’s Hospital, Boston, MA
I2B2
Integrating Biology and the Bedside (I2B2) at Brigham and Women’s Hospital, Boston, MA
NCBO
National Center for Biomedical Ontology (NCBO) at Stanford University
IDASH
Integrate Data for Analysis, Anonymization, and Sharing (IDASH) at the University of California, San Diego

A Biositemap is a way for a biomedical research institution of organisation to show how biological information is distributed throughout their Information Technology systems and networks. This information may be shared with other organisations and researchers.

The Biositemap enables web browsers, crawlers and robots to easily access and process the information to use in other systems, media and computational formats. Biositemaps protocols provide clues for the Biositemap web harvesters, allowing them to find resources and content across the whole interlink of the Biositemap system. This means that human or machine users can access any relevant information on any topic across all organisations throughout the Biositemap system and bring it to their own systems for assimilation or analysis.

http://en.wikipedia.org/wiki/Biositemaps

http://www.ncbcs.org/

For

Genome and Genetics: Resources @Stanford, @MIT, @NIH’s NCBCS

go to

http://pharmaceuticalintelligence.com/2012/09/18/genome-and-genetics-resources/

 

Biomedical Computation Review (BCR) is a quarterly, open-access magazine funded by the National Institutes of Health and published by Simbios, one of the National Centers for Biomedical Computing located at Stanford University. First published in 2005, BCR covers such topics as molecular dynamics, genomics, proteomics, physics-based simulation, systems biology, and other research involvingcomputational biology. BCR’s articles are targeted to those with a general science or biology background, in order to build a community among biomedical computational researchers who come from a variety of disciplines.

http://en.wikipedia.org/wiki/Biomedical_Computation_Review

 

REFERENCES on BIOINFORMATICS

  1. ^ Biositemaps online editor
  2. ^ a b Dinov ID, Rubin D, Lorensen W, et al. (2008). “iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources”. PLoS ONE 3 (5): e2265. doi:10.1371/journal.pone.0002265. PMC 2386255. PMID 18509477.
  3. ^ M.L. Nelson, J.A. Smith, del Campo, H. Van de Sompel, X. Liu (2006). “Efficient, Automated Web Resource Harvesting”. WIDM’06.
  4. ^ Brandman O, Cho J, Garcia-Molina H, Shivakumar N (2000). “Crawler-friendly Web Servers”. ACM SIGMETRICS Performance Evaluation Review 28 (2). doi:10.1145/362883.362894.
  5. ^ Cannata N, Merelli E, Altman RB (December 2005). “Time to organize the bioinformatics resourceome”. PLoS Comput. Biol. 1 (7): e76.doi:10.1371/journal.pcbi.0010076. PMC 1323464. PMID 16738704.
  6. ^ Chen YB, Chattopadhyay A, Bergen P, Gadd C, Tannery N (January 2007). “The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System—a one-stop gateway to online bioinformatics databases and software tools”.Nucleic Acids Res. 35 (Database issue): D780–5. doi:10.1093/nar/gkl781. PMC 1669712. PMID 17108360.
 REFERENCES on GENOMICS

  1. ^ National Human Genome Research Institute (2010-11-08).“FAQ About Genetic and Genomic Science”. Genome.gov. Retrieved 2011-12-03.
  2. ^ EPA Interim Genomics Policy
  3. ^ [1]
  4. ^ Min Jou W, Haegeman G, Ysebaert M, Fiers W (1972). “Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein”. Nature 237 (5350): 82–88. Bibcode1972Natur.237…82J. doi:10.1038/237082a0.PMID 4555447.
  5. ^ Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M (1976). “Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene”. Nature 260 (5551): 500–507.Bibcode 1976Natur.260..500F. doi:10.1038/260500a0.PMID 1264203.
  6. ^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977). “Nucleotide sequence of bacteriophage phi X174 DNA”. Nature 265 (5596): 687–695. Bibcode 1977Natur.265..687S.doi:10.1038/265687a0. PMID 870828.
  7. ^ Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. (1995). “Whole-genome random sequencing and assembly of Haemophilus influenzae Rd”. Science 269 (5223): 496–512.Bibcode 1995Sci…269..496F. doi:10.1126/science.7542800.PMID 7542800.
  8. ^ “Complete genomes: Viruses”. NCBI. 2011-11-17. Retrieved 2011-11-18.
  9. ^ “Genome Project Statistics”. Entrez Genome Project. 2011-10-07. Retrieved 2011-11-18.
  10. ^ Hugenholtz, Philip (2002). “Exploring prokaryotic diversity in the genomic era”. Genome Biology 3 (2): reviews0003.1-reviews0003.8. ISSN 1465-6906.
  11. ^ BBC article Human gene number slashed from Wednesday, 20 October 2004
  12. ^ CBSE News, Thursday, 16 October 2003
  13. ^ National Human Genome Research Institute (2004-07-14).“Dog Genome Assembled: Canine Genome Now Available to Research Community Worldwide”. Genome.gov. Retrieved 2012-01-20.
  14. ^ McGrath S and van Sinderen D, ed. (2007). Bacteriophage: Genetics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 978-1-904455-14-1.
  15. ^ Herrero A and Flores E, ed. (2008). The Cyanobacteria: Molecular Biology, Genomics and Evolution (1st ed.). Caister Academic Press. ISBN 978-1-904455-15-8.
  16. ^ McElheny, Victor (2010). Drawing the map of life : inside the Human Genome Project. New York NY: Basic Books. ISBN 978-0-465-04333-0.
  17. ^ Hugenholz, P; Goebel BM, Pace NR (1 September 1998).“Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity”. J. Bacteriol 180 (18): 4765–74. PMC 107498. PMID 9733676.
  18. ^ Eisen, JA (2007). “Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes”. PLoS Biology 5 (3): e82.doi:10.1371/journal.pbio.0050082. PMC 1821061.PMID 17355177.
  19. ^ Marco, D, ed. (2010). Metagenomics: Theory, Methods and Applications. Caister Academic Press. ISBN 978-1-904455-54-7.
  20. ^ Marco, D, ed. (2011). Metagenomics: Current Innovations and Future Trends. Caister Academic Press. ISBN 978-1-904455-87-5.
  21. ^ Wang L (2010). “Pharmacogenomics: a systems approach”.Wiley Interdiscip Rev Syst Biol Med 2 (1): 3–22.doi:10.1002/wsbm.42. PMID 20836007.
  22. ^ Becquemont L (June 2009). “Pharmacogenomics of adverse drug reactions: practical applications and perspectives”.Pharmacogenomics 10 (6): 961–9. doi:10.2217/pgs.09.37.PMID 19530963.
  23. ^ “Guidance for Industry Pharmacogenomic Data Submissions” (PDF). U.S. Food and Drug Administration. March 2005. Retrieved 2008-08-27.
  24. ^ Squassina A, Manchia M, Manolopoulos VG, Artac M, Lappa-Manakou C, Karkabouna S, Mitropoulos K, Del Zompo M, Patrinos GP (August 2010). “Realities and expectations of pharmacogenomics and personalized medicine: impact of translating genetic knowledge into clinical practice”.Pharmacogenomics 11 (8): 1149–67. doi:10.2217/pgs.10.97.PMID 20712531.

http://en.wikipedia.org/wiki/Genomics

 

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