General Requests and Enhancements

[hooman650]

Feature Request and enhancement

This is an attempt to track the enhancements and feature requests in BioModelChecker 🔉 🔬
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• If a model only contains Steady State constrains and no Trajectory, BioMC does not import its solutions properly (reported by JohnC)
• Import solutions from multiple folders
• Check the input json file and check whether length of Trajectory matches the number of entities
• Allow constraints for "rest" value of each node (decay)
• Match states in output trajectories to input (which states are added automatically by model checker?)
• Select SS1 or SS2 from competing models as MIS targets
• The tool does not run properly with its shortcut desktop version (e.g. path-issue)
• Parse K matrix to display truth tables for each node (e.g. Output a multivalued logical equation)
• Identify available node-steady states supported by a given parameter set (SS detection)
• Identify oscillatory attractors
• Identify failed constraints (specific causes of unsatisfiability)

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🚣 🚛

[hooman650]

@mcmrgh Find the latest release, in the release tab.

[mcmrgh]

It looks like solutions cannot be imported if the initial json didn't have a Tr field. This can be remedied by adding a "dummy" trajectory field to the json, but it's a little clumsy for processing solutions.

[mcmrgh]

Possible to estimate total search space size and keep track of progress? Complex models can take a long time to converge, and it would be useful to get a rough idea of how much search space remains at regular intervals.

[hooman650]

It looks like solutions cannot be imported if the initial json didn't have a Tr field. This can be remedied by adding a "dummy" trajectory field to the json, but it's a little clumsy for processing solutions.

@mcmrgh Thanks for letting me know. I will resolve this soon. Meanwhile, you will be able to import the solutions by selecting the "Pathlength" as the option from the main panel prior to the import.

[hooman650]

Possible to estimate total search space size and keep track of progress? Complex models can take a long time to converge, and it would be useful to get a rough idea of how much search space remains at regular intervals.

@mcmrgh Possible to estimate the search space but constraint solvers search the constraint space. I am afraid this is "solver" dependent, some solvers provide indications in regards to the process (e.g. traversal of the constraint graph) some don't. Besides as the problem is NP-hard and also multi-objective, there is no guarantee that an optimal solution would be found at all (If any).

[mcmrgh]

Solution db does not include steady states, though they can be extracted from text output.

[mcmrgh]

I ran MIS discovery on a set of 40 models for 3 hours each; it progressed well (with MIS identification and robustness checking) through the first 4 models but then hung. Log shows only that the Matlab parallel pool was shut down after an idle period.

[mcmrgh]

Is it possible to constrain trajectories that do not exist?
i.e. if a node is 0, there is no way for it to become 1 without external intervention, though decay from 1 to 0 is valid.

[mcmrgh]

Some metric for complexity of K values would be very helpful for assessing the quality of solutions-- when solving exhaustively, many "trivial" solutions are often generated by alteration of a K value which is seldom invoked.