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TODO.md

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TODO

Compatability

  • !!! Windows and the forward slash... :\

Cleanups

  • !!! Clean up the neurotransmitter table.
  • !!! Make sure all citations are correct: neurotransmitter citations are currently incomplete.

Data integration

  • !!! Add reading and writing to and from NWB format. Add that to the paper also.
  • !!! Write about csv/json integration.
  • !!! Add note section to each class. Add data_source (publication + location) from where data is taken in a note section.
  • !!! Redo the neuropeptide receptor connectivity. It has been redone in the git repo for the paper.
  • !! An adaptor connecting the CATMAID API directly into CeDNe objects.

New Classes

  • !!! Integrate behavioral components. Since there are limited behavioral outputs for the worm, having a framework for each might be useful.
  • !! Other graph elements (Map another graph to an object)
  • ! Mapping functions.

Core functions

  • !! Write down paths from one neuron to another at different levels of depth (direct, 1 path away, etc.)
  • !!! Formalizing connecting the StimResponse and Trial classes.

ML stuff

  • !!! Jax based optimization.
  • !!! Latin hypercube sampling for hyperparameter optimization.

Utility functions

  • !! Easy Loading functions for loading custom data.
  • !! Make movies for time series data.
  • !! Export graph for plotting elsewhere.
  • !! Dealing with missing (MISS), null (NOT) and alternative values (OR and AND) values for a given attribute.

Examples

  • !!! Run the neuropeptide example with the L4 connectivity.
  • !!! Example on Louvain modularity and structural analysis.
  • !!! Neurotransmitter check if paper uses connectivity information and do a shuffle to see correlation between connectivity and neurotransmitter identity.
  • !!! Example for gap junction subunits and check with Bhattacharya et al paper.
  • !!! Time series make movies.

Storage

  • ! HDF5 storage of data.
  • !! neo4j+json+hdf5 for data persistance instead of pickles. neo4j for storing relationships, json for metadata and hdf5 for large matrices.

Security

  • !! Pickle warning
  • ! Add some tests for sanitizing the pickle files

Issue tracking and support

Community involvement

  • !! Plugin development
  • !! Dataset uploads
  • !! Contribution guidelines
  • !! Evolving models framework (as a network): Setup for root models and submodels, etc.