Scientific Computing Seminar

Date:
Friday, March 18, 2005
Time:
1:00pm-2:00pm
Location:
50A-5132
Seminar Speaker:
Nikos Kyrpides and Natalia Ivanova
Microbial Genome Analysis Program
Joint Genome Institute

Victor M. Markowitz
Biological Data Management and Technology Center
Lawrence Berkeley National Laboratory

http://crd.lbl.gov/html/BDMTC/index.html

Title:
The Integrated Microbial Genomes (IMG) System: A Case Study in Developing Biological Data Management Systems in an Academic Setting
Abstract:
Biological data management involves data generation and acquisition, data modeling, data integration, and data analysis. Data management challenges are posed by increasing amounts of experimental data generated by life science applications, difficulty of qualifying data generated using inherently imprecise tools and techniques, and complexity of integrating data residing in diverse and poorly correlated repositories. The employment of rapid prototyping techniques often compounds these challenges for biological data management systems developed in academic settings, whereby expediency in developing these systems comes at the expense of overall system comprehensibility, maintenance, and evolution. In this seminar, we will present the Integrated Microbial Genomes (IMG) system developed at the Joint Genome Institute (JGI) as a case study for developing biological data management systems in academic settings. IMG is the result of a collaboration between JGI’s Microbial Genome Analysis Program and LBNL’s Biological Data Management and Technology Center. IMG provides support for comparative analysis of genomes sequenced by JGI, and facilitates the visualization and exploration of genomes from a functional and evolutionary perspective. IMG aims at providing high levels of data diversity in terms of the number of integrated genomes, data coherence in terms of gene annotation quality, data completeness in terms of breadth of functional annotations, and system comprehensibility in terms of documenting its structural and operational semantics.
Sponsor of Seminar:
Horst Simon
Scientific Computing

Contact Esmond G. Ng EGNg@lbl.gov