federatedcloud / douglasmetabolicmodels Goto Github PK
View Code? Open in Web Editor NEWContainers, data, and software for the Douglas use case; private repo
License: Mozilla Public License 2.0
Containers, data, and software for the Douglas use case; private repo
License: Mozilla Public License 2.0
Re run prior analysis used for poster, and also integrate Cindy's analyses (depends on #4)
This should probably be done after #11 is implemented and use FunFlow to cache results.
Currently quite slow; could be improved if made parallel (importantly steadycom/gurobi does not seem to be using more than one cpu in these cases).
The main issue seems to be our memoized function call, which we are also using to save time, takes place in a parfor
loop. Replicating the memoized function between worker threads is likely the ideal way to handle this. If it doesn't work, then likely disabling memoization altogether would still be better than the current situation.
See here
Could try mcc
first, the though pipes might be easier.
As for the controlling language, use something with good support for recursion. PureScript native is an option, but Idris native might be better thanks to totality checking. See andyarvanitis/idris-cplusplus#1
Check the below as they are completed (we can discuss which ones are not needed):
$ find ./ -name '*.mat'
./iNA855.mat
./._model9.mat
./022118_iNA660.L.brev.mat
./022118_iNA755.A.pom.mat
./022118_iNA875.L.plan.mat
./iAF1260.mat
./iJN739.mat
./iNA854_argKO.mat
./iNA854_hisKO.mat
./L.brev.mat
./models/061518_iNA857.A.trop.mat
./models/061518_iNA875.L.plan.mat
./models/072618_iNA755.A.pom.mat
./models/073018_iNA751.A.fab.dsw54.mat
./models/080118_iNA671.L.brev.mat
./models/5.models.040318/040318_A.dsw54.mat
./models/5.models.040318/040318_A.pom.mat
./models/5.models.040318/040318_A.trop.mat
./models/5.models.040318/040318_L.brev.mat
./models/5.models.040318/040318_L.plan.mat
./vmh_xml/matlab.mat
./vmh_xml/vmh_models.mat
Let's try this:
https://www.mathworks.com/help/matlab/function-based-unit-tests.html
For now we have a prototype at https://github.com/federatedcloud/DouglasMetabolicModels/blob/master/Tests/testMultiModelSingleton.m that can be converted.
More tests for core functionality should be added.
Tests should be run at least before each code commit.
Make new function from here down:
https://github.com/federatedcloud/DouglasMetabolicModels/blob/master/Utils/makeMultiModel.m#L26
https://github.com/tweag/funflow
git diff
or similarIn this commit, I notice changes were added to some scripts. For instance, in ecoli_basicTest.m it looks like a rather large section was added to the script, but it doesn't seem to run for me.
Let's try to understand what happened, or if not, revert the change so that it is working again.
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