comb through the auxiliary folder

[zoltuz]

Goal: finding the files that are not used by the code base anymore.

Action list:

1. run a string search on all the files against the code base,
2. delete the ones with any usage in the source code.
3. run the examples to test the code

[zoltuz]

Keep as it is

• [OK] herrorbar and hverrorbar are used by the mcmc_simbio
• [OK] stdshade is widely used
• [OK] findStringInAList part of the core functions
• [OK] strjoin used by txtl_addreaction

mcmc_simbio

• [OK] globalize_params is used the transcription and mcmc_simbio
• [OK] twofactors used by mcmc_simbio
• [ACTION] plotCustomSpecies and plotCustomSpecies2 are widly used (try to consolidate them)
• [OK] createFrateRules is used by mcmc_simbio
• [OK] createKdRules is used by mcmc_simbio
• [OK] getparam is used by createFrateRules
• [OK] setparam is used by mcmc_simbio

Parameter estimation

DECIDE whether to delete the whole paramest package I wrote, since Vipul uses another one

• convertIDsToNames belongs to exportForParameterEst
• exportForParameterEst = uses built in functions (probably can stay with some documentation)
• parseGetEqOutput is unused
• WriteODEFunction_externalParameters used by export for parameter estimation

Data importer for the ACS synbio paper

DECIDE whether to keep the data importer or remove it into a different package (e.g. publish it with the ACS SynBio TXTL data)

• csvimport is used by importwholeexp file (probably part of the paramest package)
• data_importer is to device specific, used on by mcmc folders, but seems also unused there
• expression_endtime is used by wholeExpfileReader
• expression_rate is used by wholeExpfileReader
• [DEL] expression_rate_peak is unused
• getDefaultMergedExpFileStruct is used by mergeWholeExpFile
• getStdMean is used by mergeWholeExpFile
• integrateMGData is used by mergeWholeExpFile
• mergeWholeExpFile is unused (traces of useage in mcmc_simbio)
• processMGData and processProteinData are used by mergeWholeExpFile
• [DEL] replaceMissingData is unused
• wholeExpfileReader is part of the documentation, but no example is given

[vipulsinghal02]

1. Yes delete the paramest package (just check once more that none of the functions are used. I do not recall using anything from there.)
2. For data importer, I think some of the functions get used to extract the data for the core parameter inference example within the mcmc_simbio package. I think any function that is not used can just be removed. But none of this needs to be documented, because the user will usually provide their own data, and does not particularly care how this data is extracted from the underlying database file.

[vipulsinghal02]

@zoltuz all yours!