Human Quantitative Dynamics Workshop

December 1 & 2, 2015

Bethesda MD

Human Quantitative Dynamics Workshop

Human Quantitative Dynamics Workshop; Dec 1-2, 2015

Discussion Forum Questions

Day 1

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?

Day 2

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