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tlubitz / parameter_balancing

Software tool for metabolic modelling in Systems Biology
http://www.parameterbalancing.net
MIT License
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SBtab format for `prior` files changed? #40

Open eladnoor opened 2 years ago

eladnoor commented 2 years ago

This example for a prior SBtab seems to not work with the current version of the code. Specifically, there is no !UseAsPriorInformation column which is required: https://github.com/tlubitz/parameter_balancing/blob/cb57d51548741a926fcc9ab1e7dfc80225f5de77/standalone_version/balancer.py#L246

eladnoor commented 2 years ago

In addition, the following columns are in the prior file but are not supported column types (in the PyPI version of the SBtab package): BiologicalElement, MathematicalType, PriorGeometricStd, PriorGeometricStd, PriorGeometricStd, UseAsPriorInformation, UseAsPriorInformation

tlubitz commented 2 years ago

All allowed columns are defined in the definitions.tsv and as far as I know it is on the most current status.

We can see here that the UserAsPriorInformation column is in place, but it belongs to TableType Quantity, while the prior table has the TableType QuantityInfo. Thus, we have a problem here. Also, this is the reason for the other columns that are not supported (they belong to Quantity, too).

In older versions of the prior files you can see that they used to have the TableType Quantity and everything was fine then. But apparently we switched this at some point in time and changed the prior TableType to QuantityInfo, without also applying these changes to the definitions file. Maybe you could check back with Wolf what the correct TableType should be, before we fix this.

eladnoor commented 2 years ago

Okay, we will discuss this together with other format issues in our meeting next week.