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iPG2P Modeling Tools Working Group

December 2, 2009 - 4pm EST

Attendees: Adam Kubach, Ann Stapleton, Chris Myers, Matt Vaughn, Melanie Correll, Steve Welch, Sanjoy Das, Jeff White, Karla Gendler

Action Items:

  1. Gendler will transform document into wiki
  2. Everyone should evaluate and comment on workflow
  3. Everyone should look at user profiles and comment
    1. White will add to biologically savvy grad student
    2. Das will add to mathematical/statistical scientist
  4. Offline discussion on moving forward on use case

Notes/Agenda:

  1. Review Action Items
    1. All: Provide list of modeling tools currently used
      1. Myers has put some notes up on the wiki. Welch has sent out his modeling workflow. Melanie Correll has started but needs to upload it. Ann Stapleton has sent along some tools in an email (Promote). Question arose as to what tools are and Myers responded that tools are software packages and types of methods used, maybe you end up writing that code yourself. What does this group construe as modeling? Das asked about model simulation and parameter estimation. Myers suggested to point out references and describe them in a list to post to the wiki.
      2. With Welch's document, a list of tools could be populated from what is written there and this would allow people to comment on the various tools.
    2. Talk with other working groups to see how modeling connects with use cases from steering committee
    3. Adam and Liya: look at SBML, BioModels.net, and OpenMI
      1. Kubach is just beginning to digest the SBML standard
    4. Gendler send out email with Confluence introduction, how organized, where to find meeting notes, etc
    5. Gendler send out poll to establish a regular meeting time
  2. Discussion on Modeling Workflow sent out yesterday
    1. Welch described the image presented on the first page of the document
    2. Questions
      1. Are we looking for computation tools to faciliate process (network inference)?
    3. Comments
      1. Myers commented that we want to show data in visual manner and to have tools for assiting interface between modeling and visualization.
      2. Myers asked if this captures the notion of canonical modeling workflow?
        1. Das stated that it is a very good workflow and captures all components. There are some small, minor modifications that are needed though. White added that it covers the overall layout but wondered with crop models, he would like to see it get to a point where there is a modular framework and asked how does modularity evolve out of this framework? Welch responded that right now there are major classes of models (whole plants, plant process phenomenon) that are in a lot in different languages. Cellular and molecular modeling done in different ways but focus on scripts and interpretive languages with SBML emerging though it is restrictive. He can see where things are going but not one framework that captures everything. Welch added that since crop modeling has been talking about using OpenMI, this would allow “composer” to work with models (see document).
    4. Myers suggested that to move forward on the document, that it be posted on the wiki for people to comment on. Welch added that there is a need to have more specifics and for people to pencil in where their questions are. Myers added that DI is missing from this diagram but yet, it kind of highlights it. Welch said that as we ID at each place the types of data that sets the target for the data integration group.
    5. What appears to be missing is model construction
  3. User Profiles (Ann Stapleton suggested piggybacking on StatInf group's profiles)
    1. Andres (the computational postdoc)
      1. Generates phenotypic data and wants to fully analyze all potential genotypic links for publication
    2. Biologically savvy graduate student
      1. Generates phenotypic data and just wants to find a list of genotypes that might influence the phenotype
    3. Mathematical or Statistical scientist
      1. Wants to access the data and computational resources to test their algorithm for genotype to phenotype linkage
      2. Would want the ability to insert new algorithms into the package for use
      3. Would want the ability to get performance measures on the computational time per test, etc
    4. Highschool or undergraduate lab student
      1. Might have a mapping population and do a phenotyping analysis in a lab course
      2. Would then want to be able to do the genotype to phenotype tests and get some generally informative answer
      3. Likely involve links to other modules
    5. Lab Instructor
      1. Ability to understand what their students are doing with the module
    6. White asked how do we broaden the reach of modeling to the larger community? Maybe add people who don’t know modeling but want to move forward and this could be subsumed by one of the personalities. Myers said that something useful would be to instill computational thinking in the people that are generating data. White added that it is important to realize that the majority of the biological scientists that are interested in modeling end up generating data. White will add a full bullet points under biologically savvy grad student. Das will edit mathematical/statistical scientist. White also asked about the real model end users? Welch suggested that the postdoc be folded into b and then add an end user category. Vaughn cautioned to not feel constrained by these personas and that maybe in the modeling group, maybe the prioritization is horizontal in representing diversity in people with expectations and experiences.
  4. Relationship between extant tools and tools that we might build
    1. What tools are useful in core infrastructure?
      1. Catalog of relevant tools, methods, and workflows
    2. Welch suggested that CM, JW, MC, and SW have an offline discussion to flesh out how to move forward
  5. Identify Action Items
    1. Gendler will transform document into wiki
    2. Everyone should evaluate and comment on workflow
    3. Everyone should look at user profiles and comment
      1. White will add to biologically savvy grad student
      2. Das will add to mathematical/statistical scientist
    4. Offline discussion on moving forward on use case