Human 1.12 #396
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Human 1.12 #396
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…ication on MAM00097
…onversion to MNXref
…60 (instead of previous erroneous MAM01656 dehydrodolichol)
…to CHEBI:28542 (2-deoxy-D-ribofuranose 1-phosphate)
fix: remove gpr for MAR04840 resolves #342
* added metabolites MAM01639n and MAM01686n * changed MAR07160 and MAR07163 * added MAR13084 and MAR13085
- add RNA in nucleus - add reaction MAR13086, transport of RNA from nucleus to cytoplasm - add compartmentalised metabolite RNA[n] (MAM02847n) - change reaction MAR07161 (RNA creation) from cytoplasm to nucleus - add transport reaction of RNA from the nucleus to cytoplasm (MAR13086) - move gene rule of reaction MAR08639 to reaction MAR13086, as it represents the nuclear pore complex - swap the direction of reaction MAR07162, as explained in issue #354 - remove the reaction of DNA transport between the nucleus and cytoplasm MAR08639, since DNA shouldn't go out of the nucleus and the reaction's gene rule is no longer needed - delete reaction MAR08639 and add reaction MAR13086 - add deleted reaction MAR08639 to deprecatedReactions.tsv - score of reaction MAR13086 changed to 2
MAM01614 corticosterone, remapped to CHEBI:16827
MAM01631 remapped to CHEBI:83739
doing modifications on the file as asked by Jonathan in #358 (comment) #358 (comment) #358 (comment)
(re) example of correction to apply in order to avoid conflict during MNXref conversion
…nto-MAR04474 refactor: merge MAR08973 into MAR04474
doc: tINIT rename 'exchange metabolites' to 'boundary metabolites'
feat: add reaction names from KEGG
Fix: flag reactions MAR05127, MAR08749, MAR08750 as spontaneous
…ed legacy. This makes the pull requests in RAVEN and Human-GEM independent. Let's fix this at some later point.
…ious version of tINIT.
- the previous way relies on specific reaction feature, which may not exist in some models. Now subsystem and equation can be properly loaded regardless of the presence of certain slots reaction features
feat: ftINIT helpers
refactor: turn `importYaml` into a more generic function
…lSpeed # Conflicts: # code/io/importYaml.m
refactor: speed up writing model fields
haowang-bioinfo
approved these changes
Jun 19, 2022
JonathanRob
approved these changes
Jun 19, 2022
The merge from |
|
Ok, thanks, @haowang-bioinfo. It's weird, I was trying to view the new release instructions on the wiki recently and it wasn't loading properly, but now it seems to work. |
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will just merge this and move things forward |
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Main improvements in this PR:
importYamlin loading model fieldsimportYamlinto a more generic function #392):importYamlinto a more generic functionxlsxtotxtannotateGEMinto a more generic function Convert `annotateGEM` into a more generic function #380getINITModel2MAR04840as spontaneous