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MyersResearchGroup / iBioSim

iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
http://www.async.ece.utah.edu/ibiosim
Apache License 2.0
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CHANGE: add preferences for consistency checking #48

Open buggsley opened 7 years ago

buggsley commented 7 years ago

Add preferences for consistency checking. For example, do you we want to check consistency after flattening? Which errors should be reported back in this case? Etc.

Chris

buggsley commented 7 years ago

There are several non-fatal errors reported by check consistency especially due to the arrays package. Check consistency should filter these out and not display them to the user. If this is done, check consistency can be reenabled in flattenBioModel.

buggsley commented 7 years ago

Need to check validity before saving a hierarchical model to make sure that it is valid after flattening. However, only errors should be reported that are serious problems that would affect simulation. Warnings should not be reported unless save and check is called.

buggsley commented 7 years ago

Add preferences about when to run validation, and what actually is to be checked.