Support for various types of System History

[BrainAnnex]

As of the current version 1.0RC1, support for convenient history-keeping is provided by the UniformCompartment class, which facilitates the creation and management of 2 types of history:

1. time snapshots of (some of) the chemical concentrations : stored in the object variable self.history, of type CollectionTabular, and primarily created thru calls to the method add_snapshot()
2. time snapshots of the rates of each reaction : stored in the object variable self.rate_history, of type CollectionTabular, and created thru calls to self.rate_history.store()

Defaults:

• time snapshots of chemical concentrations are automatically saved whenever a concentration is set in UniformCompartment
• time snapshots of ALL chemical concentrations are automatically saved at each simulation step by the main function for reactions, single_compartment_react()
• similarly, time snapshots of the reaction rates for ALL reactions are automatically saved at each simulation step by that same main function, single_compartment_react()

Currently, there's no way to completely disable snapshots, other than to request a very high value for "frequency" in the dictionary passed as the argument snapshots to single_compartment_react()

By contrast, 1D systems (class BioSim1D) and 2D systems (class BioSim2D) currently provide no substantial support for automated history keeping. BioSim1D offers a method called add_snapshot(), but largely it is the user's responsibility to create and maintain any desired data snapshots.
Also, for any simulation of reaction/diffusion or reaction for 1D or 2D systems, no history support is provided by the lower-level class UniformCompartment, because the calls to it don't go thru the method single_compartment_react().

Considerations and Design Ideas:
Low-level support for the maintenance of tabular data, and data in other formats, is provided by the classes CollectionTabular, CollectionArray, and Collection. However, no general or standardized high-level support for the management of historical data is currently offered across Life123 : it's the responsibility of individual modules (best exemplified by UniformCompartment), or the user, to create and manage the desired data snapshots.
Possible future directions might involve a module or modules for high-level management of various types of histories. Support provided by them might include operations such as:

• Start/pause a particular history
• Specify the desired frequency (granularity) of any history
• Deal with different type of histories (eg., concentration, rate)
• Specify what is being saved (some/all concentrations, some/all reactions, some/all bins)
• Retrieval (complete or partial) of a desired history

Note: low-level diagnostic data (meant for debugging and development, rather than for general users) is a separate entity, and is currently supported by the class Diagnostics (but only for reaction data.)

[BrainAnnex]

The latest version, 1.0RC2, addresses heads-on most of the issues previously raised in this thread!

Low-level support for history keeping, of both tabular and non-tabular data, has long been available in Life123, provided by the python classes CollectionTabular, CollectionArray, and Collection.

And now, with the latest release, high-level support is also made available by means of the new python class History, and its 3 derived (children) classes: HistoryBinConcentration, HistoryReactionRate and HistoryUniformConcentration

Now, the various simulation modules, such as UniformCompartment, BioSim1D, BioSim2D, etc, can all get substantial support in the common aspects of high-level management of various types of histories. For example, operations such as:

• Start/pause a particular history
• Specify the desired frequency (granularity) of any history
• Deal with different type of histories (e.g., concentration, rate)
• Specify what is being saved (some/all concentrations, some/all reactions, some/all bins)
• Retrieval (complete or partial) of a desired history

The new high-level python classes for history keeping, typically for use by the various simulation modules rather than by the end user, are:

Class Name	Usage
HistoryBinConcentration	For the management of historical data for bin concentrations
HistoryReactionRate	For the management of historical reaction-rate data for Uniform Compartments
HistoryUniformConcentration	For the management of historical concentration data for Uniform Compartments

Reference Guide