San Francisco, 19-20 April 2013

"The Truth of Personalized Medicine: Our Commons Future"

Workgroup B – Map Building

(3 Sept 2011) Updates on the post-Congress Workgroup/Community of Interest activities are available in the Sage Bionetworks web site.

Strengthening the efforts of Map Builders
Leaders: Jonathan Derry & Eric Schadt

Brief Description of the Map Builders and Users Community
This community consists of the individuals that are generating datasets and/or developing tools for network modeling and integrative genomic analysis as well as the users of the maps and tools available in the Sage Commons. In this sense this set of individuals can be thought of as the data providers and data consumers, with the Platform Builders providing the infrastructure to access and analyze the data, maps and tools. The Map Users are a diverse group including basic research and translational scientists from academia and industry, as well as Disease Foundations with particular focused interests. This group will include scientists that use network modeling in their own research efforts, those that work at genome institutes or facilities where this type of data is generated and distributed, tool developers, model builders and consortium that are working to collectivize data generation, distribution and/or analysis. More broadly patient advocacy groups, regulators and publishers can be included in this community. The common interest that defines this community is a desire to see molecular maps of disease that enable rational development of new drug therapies for well defined patient populations.

Congress Workshop will include:
The workshop will be split into three sections that will discuss: Modeling approaches and applications; Needs for the modeling community; and Use cases and desires for the platform. We will have different formats for each of these three parts with a series of short presentations followed by open discussion (part 1); five breakout groups and a report back (part 2); and a group discussion (part 3). Overall as a group we are charged with identifying important issues that need solutions and proposing specific things that will be done in the coming year to tackle them – this will be our report out of our activities for Saturday morning to the whole congress group.

Workshop Schedule

Part 1: Modeling approaches and applications (1h)

The aim will be to come out of this part with a broad description of modeling approaches and how these can be applied to different types of biological problems such as: classification/prediction of disease state and drug response; mechanisms/pathways associated with disease or drug action; and identification of drug targets. Potentially this could be written up as a review piece, since to date there really aren’t many comprehensive review pieces that cover the different types of “network” modeling approaches that could be applied, strengths and weaknesses, what problems different methods are good for, etc.

Four different speakers will give brief (5 min) descriptions of approaches:

  • David Haussler – prediction and classification methods for patient stratification (disease subtypes, responder status, etc.)
  • Gaurav Pandey – classification and interaction detection (ensemble based classification to elucidate epistatic interactions)
  • Dexter Pratt – reconstructing causal models
  • Eric Schadt – integrated probabilistic causal networks

Part 2: What does the Model Building Community Need (1h 30 mins)
In this section we will take on five different topics as breakout groups of ~10. Each group will have a breakout leader, in parentheses. After 1h discussion each group will report back to the entire group specific issues, potential solutions to these issues with a plan for action. We will discuss as a group and finalize for the report out to the whole congress on Saturday morning.

Breakout Discussions:

  • Challenges to creating a platform-based analysis environment that people will use (Eric Schadt)
  • Standard for Models and Approaches to ranking models (David Haussler)
  • Incentives for people to share data, models and tools (Jason Bobe)
  • Validating models and predictions through prospective experimentation; how do we engage biologists? (Jonathan Derry)
  • Needs for pharma to incorporate network modeling into drug discovery/development (Paul Retjo)

Part 3: Use Cases and Desires for the Platform (1h)
We will have Dave Burdick from the Sage Bionetworks Platform team to hear feedback from this important constituency of users. The goal will be to have some specific recommendations for the platform team and identify individuals interested in helping to shape the development of the platform.

 

Outcomes from the Congress

Consensus set of important issues that need solutions for the Map Building Community including proposed solution and specific things that will be done in the coming year to tackle them.

Pre-Congress Materials:

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