17 years of IBEST (©2010, james a. foster)

17 years of sustained high performance interdisciplinarity (IBEST)

James A. FosterUniversity of Idaho

foster@uidaho.edu

1 October 2010

17 years of IBEST (©2010, james a. foster)

1993: In the beginning...

Good colleagues, good science

17 years of IBEST (©2010, james a. foster)

1993: Reading Group

Still meet weekly after 17 years

Books read•Third chimpanzee•Blind watchmaker•Hyperspace•Getting to “yes”•7 Habits•Bell Curve•(“etc”?)

17 years of IBEST (©2010, james a. foster)

1995: First Publication

Factoids•Lead author: undergraduate•Built tool for later collaboration•Combined: modeling, computation, molecular biology•Major journal

James E. Clough, James A. Foster, Michael Barnett, Holly A. Wichman (1996) “Computer simulations of transposable element evolution: random template and strict master models.” J. Mol. Evol. 42(1):52-58. DOI: 10.1007/BF00163211

17 years of IBEST (©2010, james a. foster)

1996-2001: funding begins

NIH Fellowship (Foster, 2y)•Support computer scientist (Foster) to do experimental evolution with phage in a biologist’s (Wichman) lab

NSF Program Project (1y)•NSF EPSCoR (Foster): $500,000 to build core, classroom, begin research projects

NIH Program Project (5y)•NIH COBRE (Forney): $10M to build computing and sequencing cores•begin collaborative research projects leading to PI independence•Included statisticians, mathematicians, chemist

17 years of IBEST (©2010, james a. foster)

2002: Core & classroom

Factoids•Core built/programmed by students•Classroom used by multiple colleges

17 years of IBEST (©2010, james a. foster)

2003: Graduate program

Bioinformatics & Computational Biology

Organization/Curricula•Integrated research/classes in Math/Stat, Computation, and Biology•Interdisciplinary thesis committees•Faculty have self-identified specialties•Home departments/colleges get “credit”•Managed by IBEST

Factoids•Postdocs/faculty positions at top schools (Yale, Florida State, Cornell, University of Michigan, etc.) •One of first Ph.D. bioinformatics programs in the USA•Faculty in 9 departments, 5 colleges•First graduate in 2005

“Graduates of the BCB program will be the vanguard who create the bioinformatics and computational biology of the future.” -BCB homepage

17 years of IBEST (©2010, james a. foster)

2003-now: Core expansion

Bioinformatics Core•300+ years workstation-equivalent computation on over 700 processors, 1.4 TB•$600K/yr operating expenses•Staff of 3.25•All current support staff are/were undergraduates at UI

Genetics/Genomics Core•Roche 454 GS FLX Titanium•Illumina BeadExpress•Multiple ABI capillary sequencers•Staff of 3 (one a former BCB student)•Projects: glacial soil, women’s health, genetics of stress, and more

17 years of IBEST (©2010, james a. foster)

2009: national consortia (BEACON)

BEACON: Evolution in Action

•5 yr NSF STC ($25M)•5 institutions•Emphasis on cross-institutional, cross-disciplinary research

17 years of IBEST (©2010, james a. foster)

2009+: Sustaining IBEST

Plans•Increase individual project funding•Shift cores to “service center” model•Fund core staff on state lines•Help departments make strategic hires•Expand program project activity•Expand national consortia involvement

17 years of IBEST (©2010, james a. foster)

A time line

1993: beginnings 1993: “Computational biology seminar” 1995: first publication 1999: Funding (NSF, NIH) 2001: graduate program 2002: first core facility and classroom 2003: entered exponential growth phase 2005+: expansion of cores 2009+: national consortia (BEACON, HMP) 2010+: entered sustainability phase

17 years of IBEST (©2010, james a. foster)

How to do what we did

Start with the right people• Passionate about scholarship and education• Enjoy each others’ company• Risk takers with disciplinary strengths

Focus on what YOU can do• Not on administrative mandates, program projects

Eat (and drink) together (go outside) Be patient Keep it real

• do good work, recognizable by external peers• insist on the highest quality research/education• Involve students if that’s your mission

IBEST is about “having fun by doing good science with good colleagues”

17 years of IBEST (©2010, james a. foster)

Acknowledgements

Thanks to all current and past IBEST-ians and BCB-ers

Especially Holly Wichman, Larry Forney and Paul Joyce

Thanks to NSF and NIH for funding, especially• BRIN/INBRE (Laskowski/Bohach) NIH P20 RR016454• NSF “Evolution in Action” (Goodman) STC DBI

0939454 • COBRE (Forney) NIH P20 RR16448• NSF EPSCOR (Foster) EPS 80935• NIH (Foster) F33 GM20122• Follow-on awards to IBEST PIs