Biomolecular Networks Initiative

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Biomolecular Networks Initiative Bioinformatics Activities at the Pacific Northwest National Laboratory Ronald Taylor, Ph.D. Computational BioSciences Group Biological Sciences Division Pacific Northwest National Laboratory (PNNL) Richland, Washington Email: ronald.taylor@.pnl.gov Phone: 509- 372-6568 Group web site: http://www.emsl.pnl.gov:2080/docs/cbbb/ 1/2/2019

The Biomolecular Systems Initiative (BSI) The Biomolecular Systems Initiative (BSI). An umbrella organization, focused on understanding cellular networks. Interrogative Cell Signaling Group (EGF-receptor system as model). Bioinformatics tools: CCE, visualization, network reconstruction, integrated databases. Leaders: Steve Wiley, George Michaels. http://www.biomolecular.org, http://www.sysbio.org DOE Genomes to Life (GTL) program, designed to catalyze systems biology. PNNL is bidding for Facility II on global proteomics. http://www.doegenomestolife.org/ . GTL Goal 1 collab with ORNL to id and characterize protein complexes. A Pilot Proteomics Facility, tied to this PNNL/ORNL Center for Molecular and Cellular Systems, is being created with the infrastructure needed for high throughput isolation of complexes. Huge bioinformatics challenges for Goal 1 and later. www.ornl.gov/sci/GenomestoLife Environmental Molecular Sciences Laboratory (EMSL). 15+ mass spectrometers and NMR. Free use, after peer review. PRISM storage system for mass spec data. HP 2000-node supercomputer running 11.8 teraflops. Also, SGI 128-node supercomputer. Molecular modeling, computational chemistry. www.emsl.pnl.gov NIH proteomics resource center. Dick Smith’s group. $10.2 milllion 5 year grant awarded in Oct 2003 for creation of the center. PNNL is a proteomics world leader. Microbial Cell Dynamics Lab – cell imaging, metabolite characterization. Shewanella Federation. PNNL leads a cross-institution consortium working on a systems level understanding of how this bacterium senses and responds to its environment.

PNNL sees systems biology / computational biology as lead growth area PNNL sees systems biology / computational biology as lead growth area. BSI management goal is 30 new hires over 5 yrs. http://jobs.pnl.gov/, http://jobs.pnl.gov/WorldLocation/worldlocation.asp DOE encourages collaborations and has an educational mission. DOE Science Undergraduate Lab Internship (SULI) program. Year-round. Duration: 10 wks summer, 12-16 wks in fall or spring. $400/week + housing; http://science-ed.pnl.gov/undergrad/erulf.stm. Manager: Karen Wieda – karen.wieda@pnl.gov, (509) 375-3811. Of ~200 applications specifying PNNL as 1st round choice, 50 offers made. Summer term is the most competitive. DOE pays most of cost. PNNL Office of Fellowship Programs. Undergrad, grad, visiting scientists, sabbaticals. $400-750/week, 5 months max. http://science-ed.pnl.gov/studentops.stm, http://www.biomolecular.org/ students/index.html. Manager: Rebecca Janosky – rebecca.janosky@pnl.gov, (509) 375-2302. About 900-1000 applications/yr, of which 250 get an offer. Completed applications posted to central site. Mentor/host pays the cost, plus 18% overhead. Limited Term Employees (LTEs). Posted and competed for. 33% lab overhead to host scientist. June 7-8, 2004 Symposium on Systems Biology at PNNL. Speakers: Lee Hood, Len Peters. http://www.sysbio.org/resources/workshops/index.stm