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whole-cell-tutors / whole-cell-reduced

the reduced model developed in salt lake city
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[Translation & ProteinDecay & Macromolecular Complexation] Submodel creation for set of protein identifiers #17

Open matthiaskoenig opened 9 years ago

matthiaskoenig commented 9 years ago

Create a submodel for a given set of protein identifiers. This should be a script, so that with a changing set of protein identifiers new submodels can be created for these identifiers.

In case of the multimers the macromolecular complexation group has to provide the submodel for the complexation and extend the list for the translation & ProteinDecay group.

For instance MG_453_TETRAMER -> MG_453_MONOMER MG_041_069_429_PENTAMER -> MG_041_MONOMER, MG_069_MONOMER, MG_0429_MONOMER

Example sets: S1: {MG_061_MONOMER} S2: {MG_453_TETRAMER, MG_111_DIMER, MG_041_069_429_PENTAMER, MG_053_TRIMER, MG_061_MONOMER} -- Complexation list extension --> {MG_453_MONOMER, MG_111_MONOMER, MG_041_MONOMER, MG_069_MONOMER, MG_429_MONOMER, MG_053_MONOMER, MG_061_MONOMER}

den2042 commented 9 years ago

The task is clear in general. But details of the input are not. Let's agree on the input. Mattias, can you please confirm that txt ProteinIDsubsetExample.txt file with one long line, IDs separated by commas (attached) would be OK? Or propose another input format

matthiaskoenig commented 9 years ago

Input format is okay. Proteincomplexation should work with the same inputs & outputs, i.e. take MG_453_TETRAMER, MG_111_DIMER, MG_041_069_429_PENTAMER, MG_053_TRIMER, MG_061_MONOMER create MG_453_MONOMER, MG_111_MONOMER, MG_041_MONOMER, MG_069_MONOMER, MG_429_MONOMER, MG_053_MONOMER, MG_061_MONOMER

matthiaskoenig commented 9 years ago

In the glycolysis submodel the following proteins are involved

MG_023_DIMER    fructose-1,6-bisphosphate aldolase, class II
MG_041_062_429_PENTAMER PTS system, fructose-specific
MG_041_069_429_PENTAMER PTS system, glucose-specific
MG_061_MONOMER  Mycoplasma MFS transporter
MG_063_DIMER    1-phosphofructokinase, putative
MG_111_DIMER    glucose-6-phosphate isomerase
MG_215_TETRAMER 6-phosphofructokinase
MG_216_TETRAMER pyruvate kinase
MG_300_MONOMER  phosphoglycerate kinase
MG_301_TETRAMER glyceraldehyde-3-phosphate dehydrogenase, type I
MG_407_DIMER    enolase
MG_410_411_412_PENTAMER phosphate ABC transporter
MG_430_MONOMER  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
MG_431_DIMER    triosephosphate isomerase

In input format

MG_023_DIMER, MG_041_062_429_PENTAMER PTS, MG_041_069_429_PENTAMER PTS, MG_061_MONOMER, MG_063_DIMER, MG_111_DIMER, MG_215_TETRAMER, MG_216_TETRAMER, MG_300_MONOMER, MG_301_TETRAMER, MG_407_DIMER, MG_410_411_412_PENTAMER, MG_430_MONOMER, MG_431_DIMER
den2042 commented 9 years ago

OK, got it. Working on subset in Translation / Protein Decay

den2042 commented 9 years ago

Of note, Translation/Decay operates with monomers only. But the input list is clear

den2042 commented 9 years ago

Translation subset xml is located in https://github.com/whole-cell-tutors/whole-cell-reduced/tree/master/Translation/subset New one can be generated by python translationSubset.py -subset ProteinIDsubsetExample.txt

den2042 commented 8 years ago

Protein decay subset xml is located in https://github.com/whole-cell-tutors/whole-cell-reduced/tree/master/ProteinDecay/subsetDecay New one can be generated by python proteindecaySubset.py -species ProteinIDsubsetExample.txt