SASSIE 3.0 Contrast Suite Task List - madscatt/zazzie GitHub Wiki

New contrast suite and final polish of SASSIE-web, i.e, new GUI design and implementation, documentation and cleanup, to transfer the torch.

  • Write the new multi-component analysis module
    • Match Point analysis
      • write in SASSIE 3.0 API
      • add docstrings
      • polynomial fit to obtain initial match point guess
    • Stuhrmann and Parallel Axis analysis
      • refactor to SASSIE 3.0 API
      • add docstrings
      • SAXS inputs (enhancement)
    • Stoichiometry analysis
      • write in SASSIE 3.0 API
      • add docstrings
      • error analysis
      • SAXS inputs (enhancement)
    • Decomposition analysis
      • refactor to SASSIE 3.0 API
      • add docstrings
    • Multi-species analysis (future)
    • module tests
    • GUI design (in progress)
      • SASSIE 3.0 GUI with autofill (in progress) and plotting (prototype working)
    • GUI testing (in progress)
    • docs pages (keeping MD school in mind) (in progress)
  • Refactor data interpolation module (in progress)
    • module tests
    • GUI design (in progress)
    • SASSIE 3.0 GUI with plotting (prototype working)
    • GUI testing
    • revise docs pages
  • Refactor contrast calculator module
    • additional outputs for use by Multi-component Analysis module
    • add incoherent scattering prediction from experimental measurements (in progress)
    • SAXS contrast variation (enhancement)
    • module tests
    • GUI design
      • SASSIE 3.0 GUI with plotting
    • GUI testing
    • revise docs pages
  • Refactor chi-square filter module
    • inputs for multiple contrasts
    • global chi-square
    • module tests
    • GUI design
      • SASSIE 3.0 GUI with autofill and plotting
    • GUI testing
    • revise docs pages
  • Refactor sascalc as the new Contrast Explorer module
    • new file format (hdf5 through netCDF)?
      • has implications for other SASSIE modules
      • maintain compatibility with legacy file format
    • "VMD-like" syntax
      • consistent between modules
      • separate docs page
    • add incoherent scattering prediction from experimental measurements (in progress)
    • include total number of exchangeable H atoms in the output file
    • support explicit deuteration
    • add noise for aid in experiment planning
    • additional outputs for use by Multi-component Analysis module
    • calculate P(r)
      • FT done automatically
      • "atomic" P(r) as an advanced option
    • explicit solvent (future)
      • refactor capriqorn (currently alpha)?
    • convergence
      • automatic
    • clustering (after convergence)
      • advanced option?
    • calculate Rg of each component and distances between their centers of mass
      • for comparison to Sturhmann and parallel axis theorem results
      • advanced option (for two-component system)? OR does this belong elsewhere?
    • SAXS contrast variation (enhancement)
    • module tests
    • GUI design
      • SASSIE 3.0 GUI with autofill and plotting
    • GUI testing
    • revise docs pages
  • Write contrast suite paper
    • outline the paper
    • write the paper
      • description of new multi-component analysis module (in progress)
      • description of workflows (in progress)
        • experiment planning
        • data analysis
      • best practices for global chi-square filtering and ensemble analysis
        • readdress convergence, clustering, etc.
  • Prepare/hold contrast-specific SASSIE/MD school and/or tutorial
    • rewrite of entire SASSIE/MD school
      • add examples of contrast variation workflows (in progress)
        • protein-protein complex (in progress)
        • protein-DNA complex
        • protein-surfactant complex (in progress)
  • Plots in new GUI via Plotly
    • determine default configuration for plots
      • plot testing (in progress)
  • Final polish in new GUI
    • GenApp designer