Workshop notes 2018

Notes from the Web Lab workshop 2018

• Rename 'result' and 'experiment' to 'prediction' in data model
• Dataset gets used for Prediction, experimental data, inferred parameters
  • Though Prediction extends this with Model & Protocol (version) links
  • Experimental data also has a Protocol (version) link
    • We might want to make this update-able? Only if fits haven't been run yet? Because you don't want to have to upload data again whenever you tweak the protocol to match it better...
  • Inferred parameters link to the fitting spec, and hence to the model, experimental data, and protocol
• Need to store (and be able to specify) RNG seed
• Fitting
  • A fitting spec is NOT just a special protocol
  • Needs a reference to a Dataset (and via that a Protocol) and a Model
  • Use actual pints code (more or less) as the spec, but create simple cases from GUI
  • Need to think about the guided GUI, e.g. how to select relevant data/proto, which parameters to fit, how to fit params that might not be annotated normally
  • The dataset used should be able to set model (& protocol?) parameters directly if their values were measured
    • This might reduce the need to have many different variations on protocols, e.g. different pacing frequencies. The downside is that you couldn't then use these naturally to compare forward simulations of a model.
  • Given a previous fitting, want to be able to apply the same process to a new model / dataset -> taking you to the guided GUI with most things preset
  • From a fitting result, want to be able to create clone(s) of the model with parameters drawn from the distribution
  • Prioritise designing & implementing these based on concrete use cases
• Entity View changes
  • When viewing a protocol we still want the 'Fittings' button, to see fittings that used that protocol
  • Want to be able to clone an existing model/protocol
    • Perhaps by default the matrix view should not show these clones? But can hover/right click to get an option to show clones for a single entity, similarly to showing multiple versions of an entity.
    • Keep a reference to the original in the clone's DB model (and list of clones on the original)
• Displaying data
  • The 'default' matrix shouldn't show data or fitting results, just forward simulations as now
  • We should be able to get from a protocol to see datasets linked to it
  • We should be able to compare simulation results against relevant data easily
  • How to let the user choose these appropriately is still an open question!
• Annotation
  • The RDF pulled from Dataset, Model, etc. should be used to show a link to the reference paper in the entity view
  • Will have separate triple store that Django can talk to, possibly Virtuoso (PMR uses this)
    • Need to be careful with configuration
    • Could also look at Neo4J, or rdflib can use postgres as store
  • Use datacite ontology to make citing things in Web Lab easier
  • Use identifiers.org; also FMA, OPB
• Ontology design
  • Probably do need to make our own, in OBO or OWL format
  • is or isVersionOf are reasonable ways to annotate; can also look at hasProperty and isProperty