Human Quantitative Dynamics Workshop
Human Quantitative Dynamics Workshop; Dec 1-2, 2015
Discussion Forum Questions
12:45 pm – 1:30 pm - Brenda Andrews
1. Will HQD, if successful, be useful for biomedical sciences? What would be the benchmarks for success?
2. Proteins, metabolites, and interactions in a specific cell type: how complete is complete?
3. There is very little incentive to perform high throughput biochemical studies now. How do we encourage high throughput technology development in biochemistry and cell biology to study dynamics?
5:40 pm – 6:20 pm - Salvatore Sechi,
Discussants: Mikko Taipale, Peter Sorger, Marc Birtwistle
1. What additional experimental technologies do we need to increase throughput?
2. Can we assess what is commercially available and determine how it might fit in?
3. How do we start thinking about QA/QC issues early on? Is technology the major bottleneck, or do we have to change how we deal with QA/QC?
4. How do we identify and classify metadata associated with different experimental technologies?
10:00 am – 10:45 am - Olga Troyanskaya
Discussants: Kara Dolinski, Marc Vidal, Shankar Subramaniam
1. How do we resolve qualitative vs. quantitative features of databases?
2. How do we annotate common and distinct features of data for different cell types?
3. Associating metadata and QA/QC with core HQD data
12:00 pm – 12:30 pm - Ravi Iyengar
Discussants: Theresa Fan, Anne-Claude Gingras, Bob Murphy, Mathias Ulhen, Joshua Coon
1. Can we use metabolite dynamics to infer enzyme activities and calculate Kms?
2. What about measuring post-translational modifications?
3. Do we need to explicitly measure enzymatic activities? Can we generate canonical guidelines for parameter assignment?
2:20 pm – 2:40 pm - Les Loew
Discussants: Chad Meyers, Olga Troyanskaya, Shankar Subramaniam
1. Data structure for statistical and graph theory models
2. Data structure for ODE models
3. How about other types of dynamical models, e.g., agent based models?
4:00 pm – 5:00 pm Sarah Dunsmore & Marian Walhout
Discussion: Olga Troyanskaya, Alex Hoffmann, Ravi Iyengar, Ajay Pillai, Salvator Sechi, David Balshaw
1. Reproducibility and applicability in differing contexts: Structuring large-scale projects for success, defining and constraining scope
2. Community engagement and how big projects can enable small projects
3. Path forward engaging various interested parties
4. Outline for Workshop Report