Making Sense of Biological Systems:
Using Knowledge Mining to Improve and Validate Models of Living Systems
August 23-25, 2012, Department of Chemistry and Biochemistry, Bozeman Montana
Thursday, August 23rd:
2-5 pm: (Gaines Hall Room 346, MSU campus)
Katy Wolstencroft, University of Manchester; Sam Handelman, Ohio State University: Data Integration in Biology: Distributed tools and Workflows
Shuttle back to the Gran Tree Hotel at 5:30 pm for speakers6:30 pm: (Gran Tree Inn in Bozeman)
Dinner with keynote by Vincent E. Giuliano:
"Adventures of an Information Harvester and Integrator: Nrf2 and the death and rebirth of the oxidative damage theory of disease and aging as a case in point ”
Friday, August 24th (Byker Auditorium, Department of Chemistry and Biochemistry):
Shuttle from Hotel to MSU at 8:15 am
8:00 am – 10:00 am: Continental breakfast at the Byker Auditorium
9:00 am -1 pm: Session 1: How computers read biology (Chair: Anita de Waard)
9:00 am – 9:30: Ed Dratz, Anita de Waard: Welcome and Introduction
9:30 am – 10:15: Mark Wilkinson, University of British Columbia: Turning Bioinformatics into Biology.
10:15 am– 11:00 am Hagit Shatkay, University of Delaware: There is no such thing as Text-Mining: The things we do (and don't do) with biomedical text
1:00 pm – 2:00 pm: Lunch - Byker Atrium
2:00 pm – 5:30 pm: Session 2: What are some practical tools that can help make this happen? (Chair: Hagit Shatkay)
2:00 pm – 2:45 pm: Maryann Martone, UCSD/Neuroscience Informatics Framework: How do biocurators work, what current challenges are there?
2:45 pm – 3:30 pm: Dave DeRoure, Oxford eResearch Centre: Creating ‘Research Objects’ that contain collections of data, papers and research workflows
3:30 pm – 4:00 pm: Coffee Break
4:00 pm– 4:45 pm: Junichi Tsujii, Microsoft Asia: Text Annotation for Soliciting Knowledge for Text Mining from Biologists
4:45 pm – 5:30 pm, Panel discussion with the speakers, possible topics:
a) What initiatives are there to store, access, communicate data and workflows?
b) What are outstanding problems? Which of the problems can be solved by technology?
c) What data and article formats and tools would improve systems biology communications?
5:30 pm Hors d’oeuvres - Byker Atrium
6:00 Agilent Presentation - Agilent's GeneSpring Software for Multi-Omic Integration and Analysis
Shuttle from MSU to Emerson at 7:00 pm
Saturday, August 25th (Holiday Inn Hotel conference room - next door to GranTree)
9:00-12:00: Session 3: Knowledge modeling and sensemaking in biology and related disciplines (Chair: Dave DeRoure)
9:00 – 9:45: Anita de Waard, Elsevier Labs: Discourse Annotation and Sensemaking in Biology: Some Current Efforts
9:45 – 10:30: Catherine Blake, Urbana-Champaign: Claim Jumping: Bridging disciplinary boundaries using the Claim Framework
10:30 – 11:15: Gwen Jacobs, Montana State University: Eventually Perfect Data: The minimum requirements of scientific data management software
11:15 – 11:30: Coffee break
11:30 – 12:00 Panel discussion with the speakers; possible topics:
a) How can we best model biological knowledge?
b) What are outstanding problems?
c) Proposals for knowledge modeling that would improve multidisciplinary communications in systems biology.
12:00 – 12:30 pm: Wrap up & next steps
Edward Dratz, Montana State University; and Garry Handelman, UMass, Lowell.
Optional hikes etc - email Anita if you want to join a hike in the mountains!