Issue Solution Action - Sage Commons Congress
Transcript of Issue Solution Action - Sage Commons Congress
Issue Solution Action
Which model should be used for what application?
Individuals with different modeling approaches to develop framework for describing models and applications
Eric Schadt, David Haussler, Dexter Pratt, Gaurav Pandey on the hook for writing a paper to map network modeling approaches to applications
What are models and how can we make them inter-operable?
Develop semantic framework to describe models
Barend Mons Spyro Mousses to convene working group to develop this framework
How do we compare modeling approaches
Need reference datasets for comparing different approaches and their ability to predict features
Sage to look into “Network Challenge” on such datasets to engage community in contributing modeling apporaches
Main issues Problem: Lack of understanding of rules to be followed to use
platform Solution: Pay attention to governance rules and rules of
engagement in putting a platform together (e.g., can we use data as we please, do we need to include providers on papers, etc.)
Problem: How do a general class of modelers get connected to those with data and those who can aid in interpreting results
Solution: Platform needs to facilitate such matching, connecting those with data to those wanting to process data, with appropriate attributions worked in
Main issues Problem: Reproducible science Solution: Platform enforces information tracking, produces a
graph that details every dataset, changes to datasets, code applied, etc. relating to a set of results
Problem: How will I interact with the platform Solution: Need well defined APIs; need private workspaces to
work out models and associated code and then ability to “publish” when ready
Issue: Shouldn't use the term validation as it implies some context of absolute truth that is unattainable. Rather we are striving for levels of accuracy or more important "usefulness". Experimental important here not just computational validation.
Solution: Should use 1) Usefulness; 2) Predictiveness; 3) Generalizability (less important) NOT validation
Issue: Phenotypes are the weak link in much of the data. Need better intermediate/endo phenotypes. Being able to link to intermediate phenotypes powerful for thinking about validation where things like survival hard to attain
Solution: nothing specific here!
Issue: How to engage experimentalists? Solution: Prize-based out-sourcing solutions should be tried; open up access to validation tools (SGC efforts; tapping pharma compound collections?); FNIH Biomarker consortium effort; validation tool kits - zn-finger libraries, etc.
Issue: How do we target networks? Solution: Need to think beyond single gene/node targeting. Screen for activities based on network state. Use "connectivity map" to come up with POC.
Issue: How should we use model organisms? Solution: Need to consider how to match "network states" across organisms to convince that models are good molecular reflection of human disease state.