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Sco-GEM 1.2.0 (#98)
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* fix: correct ec-models

- ecM1152_pool now accurately lacks the knocked-out genes
- ecM1152_33 is now no longer based on M145

* feat: create PCA and subsystem clustermaps

The script _analyze_random_samples.py_ can be used to create the
following plots
- subsystem clustermaps
- PCA plots of all the random samples
- PCA plots of the aggragate (e.g. mean) of the random samples

The subsystem clustermaps and the aggregated PCAs the reactions are
*summed* up to the normal reaction IDs (using function
*revert_GECKO_reactions*)

* feat: export current subsystem annotation

Adds a csv-file which will be used to curate the subsystem annotations
and the pytohon script used to generate the csv-file

* feat: pathway and subsystem annotation

I have used the KEGG and BioCyc annotations to extract pathway
information for each reaction. By using these automatic annotations and
the previous subsystem assignment from iMK1208/iKS1307 I have given
reactions a curated subsystem and pathway annotation. All reactions have
been given one (and only one) subsystem annotation, and 1964 of the 2552
reactions have been given one (and only one) pathway annotation. Where
no or multiple pathway annotations were present, adjacent reactions (in
terms of connectivity in the model) were used to determine the correct
annotation.

The following 16 set of subsystems were used:
- Amino acid metabolism
- Biomass and maintenance functions
- Biosynthesis of other secondary metabolites
- Carbohydrate metabolism
- Energy metabolism
- Exchange
- Glycan biosynthesis and metabolism
- Inorganic Ion Transport and metabolism
- Lipid metabolism
- Membrane transport
- Metabolism of cofactors and vitamins
- Metabolism of other amino acids
- Metabolism of terpenoids and polyketides
- Nitrogen metabolism
- Nucleotide metabolism
- Xenobiotics biodegradation and metabolism

128 different pathways were used. Note that some of these pathways are
slightly overlapping, and I've tried to be specific where detailed
information is known. These are the 128:
- 2-methylisoborneol synthase
- 3-hydroxyquinaldate biosynthesis
- Actinorhodin Biosynthesis
- Alanine, aspartate and glutamate metabolism
- Albaflavenol biosynthesis
- Alternate Carbon metabolism
- Amino sugar and nucleotide sugar metabolism
- Aminobacteriohopanetriol synthase
- Aminobenzoate degradation
- Arginine and Proline metabolism
- Arginine and proline metabolism
- Arginine biosynthesis
- Aromatic compound degradation
- Arsenate detoxification
- Ascorbate and aldarate metabolism
- Atrazine degradation
- Benzoate degradation
- Betaine biosynthesis
- Betalain biosynthesis
- Biflaviolin synthase
- Biosynthesis of siderophore group nonribosomal peptides
- Biosynthesis of type II polyketide backbone
- Biotin metabolism
- Bis-Molybdopterin metabolism
- Bisphenol degradation
- Butanoate metabolism
- C5-Branched dibasic acid metabolism
- Calcium-Dependent Antibiotics Biosynthesis
- Caprolactam degradation
- Carbon fixation pathways in prokaryotes
- Carnitine metabolism
- Carotenoid biosynthesis
- Chloroalkane and chloroalkene degradation
- Chloroaromatic Compound Degradation
- Chlorocyclohexane and chlorobenzene degradation
- Citric Acid Cycle
- Cpk biosynthesis
- Cysteine and methionine metabolism
- Cysteine metabolism
- D-Alanine metabolism
- D-Arginine and D-ornithine metabolism
- D-Glutamine and D-glutamate metabolism
- Desferrioxamine biosynthesis
- Ergothioneine biosynthesis
- FERI metabolism
- Fatty acid biosynthesis
- Fatty acid degradation
- Folate biosynthesis
- Folate metabolism
- Fructose and mannose metabolism
- Galactose metabolism
- Gamma-butyrolactones biosynthesis
- Geosmin synthase
- Geranial biosynthesis
- Geraniol degradation
- Germicidin Biosynthesis
- Glutathione metabolism
- Glycerolipid metabolism
- Glycerophospholipid metabolism
- Glycine, serine and threonine metabolism
- Glycogen metabolism
- Glycolysis/Gluconeogenesis
- Glyoxylate and dicarboxylate metabolism
- Histidine metabolism
- Inositol Phosphate metabolism
- Inositol phosphate metabolism
- L-Arabinose-Degradation
- Limonene and pinene degradation
- Lipoic acid metabolism
- Lipopolysaccharide biosynthesis
- Methane metabolism
- Methionine metabolism
- Methylenomycin biosynthesis
- Murein Biosynthesis
- Murein Recycling
- Murein recycling
- Mycothiol biosynthesis
- N-Glycan biosynthesis
- NADH repair
- Nicotinate and nicotinamide metabolism
- Nicotine degradation
- Nitrogen metabolism
- Norspermidine synthase
- Novobiocin biosynthesis
- One carbon pool by folate
- Oxidative phosphorylation
- Pantothenate and CoA biosynthesis
- Penicillin and cephalosporin biosynthesis
- Pentalenalactone biosynthesis
- Pentose and glucuronate interconversions
- Pentose phosphate pathway
- Peptidoglycan biosynthesis
- Phenylalanine metabolism
- Phenylalanine, tyrosine and tryptophan biosynthesis
- Phenylpropanoid biosynthesis
- Phosphonate and phosphinate metabolism
- Polyketide sugar unit biosynthesis
- Polysaccharid degradation
- Porphyrin and chlorophyll metabolism
- Propanoate metabolism
- Purine metabolism
- Pyrimidine metabolism
- Pyruvate metabolism
- Riboflavin metabolism
- Sesquiterpenoid and triterpenoid biosynthesis
- Starch and sucrose metabolism
- Steroid degradation
- Streptomycin biosynthesis
- Styrene degradation
- Sulfur metabolism
- Taurine and hypotaurine metabolism
- Terpenoid backbone biosynthesis
- Tetracycline biosynthesis
- Thiamine metabolism
- Threonine and Lysine metabolism
- Toluene degradation
- Tryptophan metabolism
- Tungsten bispterin metabolism
- Tyrosine metabolism
- Ubiquinone and other terpenoid-quinone biosynthesis
- Undecylprodigiosin Biosynthesis
- Valine, leucine and isoleucine biosynthesis
- Valine, leucine and isoleucine degradation
- Valine, leucine and isoleucine metabolism
- Vitamin B6 metabolism
- Xylene degradation
- beta-Alanine metabolism
- tRNA Charging

* docs: updated script information header

* fix: annotation bug

Remove one wrong subsystem annotation

* fix: remove double correction of mmy id

Previously, the ID was swapped (wrongly) in fix_iKS1317_issues.py, and
then this was corrected again in fix_issue33_annotation_bugs.py

I've now removed both corrections.

* chore: add initial .travis.yml

* feat/chore: add deploy.sh and .travis.yml

Hopefully this will get it going
Made small modifications, i.e. changed repo name and location of
deploy.sh

* chore: add encrypted GitHub access token

* fix: update memote.ini with new repo name (Sco-GEM)

* fix: add travis.yml content from rhto-GEM

* refactor: paths in reconstruct - script

Some paths in reconstruct_scoGEM.py were relative to the working
directory, which is inconvenient. Now, all paths are relative to the
directory of the file reconstruct_scoGEM.py

* docs: downgrade cobrapy to 0.13.4

Seems to be an issue in cobraby 0.14.2 with changing ids of metabolites.
Therfore, until this is fixed we need to use 0.13.4 to get the
reconstruct_scoGEM.py to work

* fix/refactor: mmy metabolite name issue

Because of some issue with the propagation of the metabolite ids with
optlang and gurobipy (https://github.com/opencobra/cobrapy/issues/819)
the reconstruct_scoGEM.py doesn't work with gurobi as the solver.
Therefore, glpk is used as solver in the reconstruction of ScoGEM, these
changes are incorporated into reconstruct_scoGEM.py

Additionally, this revealed an issue that was adressed but not solved properly in
fix_ikS1317_issues.py, but solved in fix_issue33_annotation_bugs.py.
This was very confusing. Thus, this issue is now sorted out completely
in fix_iKS1317_issues.py, and removed from
fix_issue33_annotation_bugs.py.

Finally, I've upgraded cobrapy to 0.14.2 in the requirements, as this
was wrongly suggested to cause the issued described above (see also PR
 #73)

* feat: print subsystem per model origin

Adds a function which prints out the count of the subsystems for each of
the model origins: iKS1317, Sco4 and iAA1259

* chore: change source branch to chore/travis for testing

* chore: update travis and deploy scripts

* chore: changed deploy script

* chore: added token to env var, and now it's working

* docs: name update and tags

* chore:travis deploy script

* chore: change .travis.yml

* chore: add snapshot report

* chore: only build on master branch

Travis is now working (history-report still looks bad), and I've now
updated the .travis.yml file to only build the report on the master
branch.

* chore: correct end-of-line characters

- run `dos2unix`

* ⬆️ update gecko submodule

* feat: random sampling of ecSco-GEM with protein pool

* feat: add files for random sampling and subsequent analysis

These files should have been added a month ago.
The random_sampling.py and batch_random_sampling.py, were used to create
random samples, which are analyzed using analyze_random_samples.py
The analyze_random_samples2.py is used to analyze the random samples
provided by Eduard Kerkhoven, and generated usen the Raven Toolbox.

* feat: add script for plotting time-series

Plot time-series of fluxes, expression levels or protein abundance

* feat: export gene-pathway table

* fix: capitalization bug in pathway annotation

For three pathways there were differences in capitalization leading to
duplicates when exporting pathways for different genes. Also, a few
transport reactions were annotated to a particular pathway.

Note that the model is not updated, only the spreadsheet.

* fix: change pathway name from cpk to coelimycin

Changed the pathway name for the CPK-ebcoded reactions from cpk
biosynthesis to Coelimycin biosynthesis

* fix: deleted genes without annotation

Deleted reactions mentioned in #82
All growth tests are identical

* fix: reaction bounds of atp-reactions and two cpk-reactions

Change reaction bounds according to table and text in issue #54.
Changed the bounds of 38 ATP-driven reactions, and CPKS4a and CPKS4b

* :arrow_up: update gecko submodule

* feat: create PCA and subsystem clustermaps

The script _analyze_random_samples.py_ can be used to create the
following plots
- subsystem clustermaps
- PCA plots of all the random samples
- PCA plots of the aggragate (e.g. mean) of the random samples

The subsystem clustermaps and the aggregated PCAs the reactions are
*summed* up to the normal reaction IDs (using function
*revert_GECKO_reactions*)

* feat: add files for random sampling and subsequent analysis

These files should have been added a month ago.
The random_sampling.py and batch_random_sampling.py, were used to create
random samples, which are analyzed using analyze_random_samples.py
The analyze_random_samples2.py is used to analyze the random samples
provided by Eduard Kerkhoven, and generated usen the Raven Toolbox.

* feat: add script for plotting time-series

Plot time-series of fluxes, expression levels or protein abundance

* :arrow_up: update gecko submodule

* feat: organizeSolutions does not necessarily combine

* fix: construct_ecScoGEM remove SCP genes

* feat: integrateProteomics allow 95% growth rate fit

* fix: prepareProteomics bug in protein normalization

- line 31 was commented out by mistake.

* feat: run with new scoGEM version

https://github.com/SysBioChalmers/Sco-GEM/pull/84

* feat: add function to test models only

Also changed objective to BIOMASS_SCO_tRNA and added lower bound to
ATPM.

* fix: reorganize solutions from protein_pool models

* fix: write full table of protein pool random sampling result

* fix: reorganize solutions from proteomics integrated models

* feat: n=500 samples of proteomics model

* fix: add exchange raction for cpk / coelimycin

Solves issue #85.
Adds an exchange reaction with lower bound of 0 for the metabolite
ycpk_e. This pathway was added from iAA1259, and the function adding
this pathway was therefore including in that script.

* feat: randomSampling n=5000 proteomics integrated models

- also, max bounds are Inf/-Inf for both M1152 and M145
- with cpk exchange reaction

* feat: proteomics integrated ecmodels

* feat: randomsampling n=5000 protein_pool models

* feat: improved and added plots used in manuscript or supporting material

* feat: merge fix/transporters into devel

This includes addtion of:
- 24 new transport reactions of existing metabolites
- 20 new transport reactions of new metabolites
- 39 reactions with updated gene association
- 28 new exchange reactions
- 48 new metabolites
- 186 new genes

Current stats is:
Reactions:  2612
Metabolites:  2071
Genes:  1799

Squashed commit of the following:

commit 86f28e56096c2329f19c0d2fa8d7531d5b7f8641
Merge: 1197c86 1e041eb
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:38:20 2019 +0200

    Merge branch 'devel' into fix/transporters

commit 1197c866a270676dbc55b184be11a654e8ab6019
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:20:45 2019 +0200

    chore: move scoGEM.yml to correct folder

commit d65d4f926898004313d0e626e697fe85adf145cc
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:14:07 2019 +0200

    chore: delete unnecessary csv files

    These two lists are not needed:
    - sinks are not added
    - Exchange reactions are added for all new extracellular metabolites

commit a1539fb1bd7e70f288abf77e13a0097414267b5d
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:10:38 2019 +0200

    chore: delete growth data files

    This is performed by the pytests already added to the repo

commit 0b5b5e3e5d797a6d888447fa1bd4bce4693638b4
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:08:17 2019 +0200

    chore: delete unnecessary model files

    These files are not used anymore

commit 47c87054f5a1444e5aea99d2d110d2580372e974
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:02:30 2019 +0200

    chore: delete unnecessary files

    These files are no longer needed to incroporate changes from the
    transport reaction curation, becuse they are replaced by
    fix_transporters.py.

commit 82434e45ac5017971fd0be8e06ec689cb499d7be
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 13:17:54 2019 +0200

    feat: script to add transport reactions

    This script incorporate all changes related to transport reactions:
    modification of existing reactions and addition of new. The script reads
    data from the csv-files:
     - newTransportRxns.csv
     - updated_grRules.csv
     - newTransportRxns_newMets.csv
     - new_mets_annotation.csv

    The script is incoporated into reconstruct_scoGEM.py, which first was
    updated from devel branch to ease later merging of branches

commit 463c19a58aa423c2e11ed8eefc96fbb0022e546a
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 09:54:41 2019 +0200

    fix/feat: clean tables and fix transport errors

    Made the following changes:
     - Converted G_SCOXXXX to SCOXXXX for readability
     - Added susbsystem annotation
     - Added column with reaction names for new reactions
     - Changed id of a few reactions to abbreviations more similar to the
     transported metabolite
     - Two ABC-transport reactions for melibiose were merged into one,
     concatenating gene reaction rule by "or", i.e. (SCO0290 and SCO7165) or
     SCO1707
     - Moved ammonium transport from "newTransportRxns.csv" to
     "updated_grRules.csv" as this reaction is already present in the model
     - Moved LPS transport to "NewTransportRxns_newMets.csv" as this metabolite is not in the model and added metabolite to "new_mets_annotation.csv"
     - Moved MEMYt (methylenomycin transport) from "NewTransportRxns_newMets.csv" to "newTransportRxns.csv" and changed the reaction into two separate reactions transporting out mmyA and mmyB
     - removed cobal from new_mets_annotation, because it's not used in any
     new reaction
     - corrected a few chemical formulas
     - corrected name of L-ascorbate to ascb__L
     - Moved CATECHOLt to "newTransportRxns.csv" because catechol is already
     present in model
     - Removed thmpp fromnew metabolite sheet, because it is present in
     model
     - Removed UACGAMpts from "NewTransportRxns.csv" because the suggested
     product metabolite couldn't be identified (uacgam6p)

commit 2e874fd936687d172d271400a5bd67c0336aa6ee
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 08:36:47 2019 +0200

    chore: update model file from devel branch

commit fdeed34a115da767ceda0ba4d15ff40c2a6fdfc1
Author: Snorre Sulheim <[email protected]>
Date:   Thu Sep 12 16:31:23 2019 +0200

    style: delete and rename redundant spreadsheets

    There were multiple files related to new transport reactions that were
    just different versions of each other. I have deleted the old versions
    and renamed the most recent version by removing any date/version suffix.

commit 76bf3b675fda5123d62ad5ef94e8073b7b5eff8a
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:40:21 2019 +0200

    updated_new_mets

    Table updated in correspondance with NewTransportRxns__newMets

commit 1419aaf6d397c7eca434baf0a40b310c9e0e073e
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:38:15 2019 +0200

    updated_newTransportRxns

    Addiitonal column(H) on annotation of transporters added adn somem double rxns removed.

commit 75de38645de875114f98be06722134c60d309126
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:37:07 2019 +0200

    updated_NewTransportRxns_with_newMets

    Additonal column  (H) on annotation of transporters added as well as double rxns removed.

commit dbebd92b209558b3dd939930c357af69673bcb25
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:35:32 2019 +0200

    updated_grRules

    Additional column(H) on annotation of grRules added as well as some minore changes to grRules and double rxns removal.

commit de097ec8c54416a401772076ceaca00f4647c9c1
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:30:44 2019 +0200

    updated_new_mets_annotation

    Updated table with resapect to NewTransportRxns_newMets,

commit f0056d38c5ff3148d91e2a9f57e8e38c26dac876
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:28:12 2019 +0200

    update_newTransportRxns

    Addiitonal column(H) on annotation for transporters have been aded as well as double reactions have been removed.

commit 90580904ece4006ada38313a6ac697d8263d93ca
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:26:29 2019 +0200

    update_newTransportRxns_with_newMets

    Additional column(H) on annotation of transporters has been added and double reactions have been removed.

commit 250aa6a9f18d1772fb33ba64889cce15a7275f7f
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:23:49 2019 +0200

    update_grRules

    Additional table has been added (H) on anotation for grRules. Additional correctiions(extrract double reactions has been added and some minor corrections to grRules for some reactions),

commit cf9c19a6d68cbdd36abc577d4043b9bc9f0b2e90
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:35:56 2019 +0200

    Add files via upload

commit 5712b3e08ca55c891ff7b1d0601c2eab0de4620c
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:35:09 2019 +0200

    Add files via upload

    updated table (add additional thiamine pyrophosphate)

commit 1e221076793296106ea46dd8b8f3c8766ae3bbc5
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:33:42 2019 +0200

    Add files via upload

    updated table witht the column on annotation of the transporters

commit bf0187fa24979b145a903547da3b57a3627fc53b
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:32:39 2019 +0200

    Add files via upload

    updated table of additional metabolites in added new transport reactions

commit 97b74a2f75158f23fe91b4d1654c4da22cee4b73
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:31:05 2019 +0200

    Add files via upload

    table updated with additional column on annotation of grRules

commit b8a7cb625b69e95eb27afce281634436ad73ae7c
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:29:42 2019 +0200

    Add files via upload

    updating table with the column on annotation for transporters and do the editing (extract double rxns)

commit 9a1b84ad1b49d2d68ed165b6e200298c30e3cb52
Author: Snorre Sulheim <[email protected]>
Date:   Mon Jul 8 17:06:11 2019 +0200

    chore: formatting transport tables

    Changed G_SCOXXXX to SCOXXXX in all tables to ease readability and
    implementation.
    Fixes typo: CELLabc -> CELLBabc

commit 0956834b1c617c66b3f02d943847348874acb537
Author: Snorre Sulheim <[email protected]>
Date:   Mon Jul 8 16:35:37 2019 +0200

    fix: update model file from devel

    The model file (scoGEM.xml) was updated from the devel branch to make the
    following implementation of the transport reactions less painful

commit 79ad56c30b496a2e6fb383d70837c99292282684
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 2 11:38:18 2019 +0200

    scoGEM_added_transporters_SBO_terms_remoe_sink_transport_rxns

    scoGEM file after adding transporters and added SBO terms and added gene rxn names. In addition, sink reactions for the new metabolites, involved in transport reactions are extracted.

commit ab958a17806f9653bdd143cf4bff5d7983e936f3
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 2 09:04:44 2019 +0200

    Add files via upload

commit 1974cfb8b9aaa31b08f1c4d1cfa4df184d872d60
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 21:12:06 2019 +0200

    Add files via upload

commit 84dcb2405466ef52bd46758b5bfc14a26c363866
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 21:04:50 2019 +0200

    Add files via upload

commit 2ce26914b42ac04b3701217b4682ec0af1dc542a
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 20:54:58 2019 +0200

    Add files via upload

commit 3148b747f1e387d95e36e0d75c49844279be96b8
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 20:54:24 2019 +0200

    Add files via upload

commit 48f405d5a4023142c000c850d61af69caabdde9b
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 20:53:44 2019 +0200

    Add files via upload

commit 4fe1f7084e3fc843825a5c69be77f1ad760139cd
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 20:53:00 2019 +0200

    Add files via upload

commit d942cd58b35ceb22e4487814d9cb29a437053ccf
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 20:52:18 2019 +0200

    Add files via upload

commit 939df94eb674ca7824cdccb00b8a42d8dfb5f75c
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 19:45:31 2019 +0200

    Add files via upload

commit 58856a5b4028c1cadc0058a2b0a42a7b8c2e8048
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 19:44:26 2019 +0200

    Add files via upload

commit 570ee5d5b03a650c54ef81d424f1322fe196593e
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 19:10:34 2019 +0200

    Add files via upload

    Added additional annotations for new metabolites ( KEGG, METANETX, ByoCyc)

commit 5917e97f88eb0d66a2f9eec9eeab064369caee31
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 19:09:00 2019 +0200

    Add files via upload

    New transport rxns with exisitng metabolites added to the scoGEM model.

commit 1a98318b3902164d579d1fa2723e1c9f9f5e7ee2
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 19:07:35 2019 +0200

    Add files via upload

    Added new transport rxns, involving new metabolites, not present in the initial scoGEM model.

commit e03adf117e7b802341667bf3d3796f22760f9227
Author: tjasakumelj <[email protected]>
Date:   Mon Jul 1 19:05:37 2019 +0200

    updated_grRules_for_transporters

    for the transporters in the table, only the gene rules have been updated, compared to the initial scoGEM model.

commit 0e6fbea4b74eaa481a82ca79de4feaccba282efd
Author: tjasakumelj <[email protected]>
Date:   Fri May 24 17:45:57 2019 +0200

    Update Create_yml.py

commit 3aec27d554aaa6dec8d337d7ecb6a5c966baeece
Author: tjasakumelj <[email protected]>
Date:   Fri May 24 17:32:02 2019 +0200

    scoGEM_added_transporters_added_SBO_terms_edited_gene_rxn_names

    Updated scoGEM model (scoGEM model with added transporters) with SBO terms, corrections of gene names and rxns names, where necessary, duplicates deleted.

commit 01adaea9623f0fd42f206fe47d1e07d802ca64d1
Author: tjasakumelj <[email protected]>
Date:   Fri May 24 17:30:32 2019 +0200

    scoGEM model in yml format after adding the transporters, SBO terms, gene and rxns names editing where necessary

    scoGEM model in yml format, from /xml/scoGEM.xml via Create_vml.py script uploaded in ComplementaryScripts

commit 7c6f792182e195aee24cc8a9ce86f58eabd3b147
Author: tjasakumelj <[email protected]>
Date:   Fri May 24 15:42:59 2019 +0200

    scoGEM model in yml format after adding the transporters, SBO terms, gene and rxn names aditing, where necessary

    scoGEM.yml (yml format created from /xml/scoGEM.xml with Create_yml.py, uploaded in Complementary Scripts.

commit dcafb49e1c3e1eeb57f58754766df8dce8fdd42a
Author: tjasakumelj <[email protected]>
Date:   Fri May 24 15:38:58 2019 +0200

    scoGEM_added_transporters_added_SBO_terms_edited_gene_rxn_names

    Updated scoGEM model (scoGEM model with added transporters) with SBO terms, corrections of gene names and rxns names, where necessary, duplicates deleted.

commit 029c78b9ca093f72c5f8333cf233e75fa5506527
Author: tjasakumelj <[email protected]>
Date:   Fri May 24 13:19:28 2019 +0200

    Update Create_yml.py

commit 9cca24ab956bce67bb271e3c5f4dff3f8d35c2a3
Author: tjasakumelj <[email protected]>
Date:   Fri May 24 13:16:11 2019 +0200

    scoGEM model in yml format after adding the transporters (converted from /xml/scoGEM.xml model)

    scoGEM.yml (the model after addition of transporters in yml format, created from scoGEM.xml model with Create_yml.py script, uploade in ComplementaryScripts)

commit f84e069bfda229dc69aaaee31ac6f2ab1e6476d7
Author: tjasakumelj <[email protected]>
Date:   Tue May 14 18:24:35 2019 +0200

    scoGEM model in yml format after adding the transporters (converted from /xml/scoGEM.xml model

    scoGEM.yml (the model after addition of transporters in yml format, created from scoGEM.xml model with Create_yml.py script, uploade in ComplementaryScripts)

commit fc363c2961c1c153c0557e3ca72adeaa23cd2436
Author: tjasakumelj <[email protected]>
Date:   Tue May 14 18:19:10 2019 +0200

    Add files via upload

commit aabae5447fdd7ac07e7bd53a7e1f87de1bcef075
Author: tjasakumelj <[email protected]>
Date:   Tue May 14 18:10:23 2019 +0200

    Create_yml_from_xml_format

    From scoGEM.xml ( the model after new transporters have been integrated), the script Create_yml, creates scoGEM.yml. Transformation from xml to yml format.

commit 0fc5092030811cdab8a7a65cdf689c16b4fe73e5
Author: tjasakumelj <[email protected]>
Date:   Sun May 5 18:40:03 2019 +0200

    lines_for_calling_matlab_script_into_python_script

commit c24c6d0f41b4c8cb229ae3f3f98e52076ca29fda
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:09:08 2019 +0100

    Delete updated_grRules.csv

    Files that were renamed and updated are deleted.

commit 1b46f4c50e33a24234c2509934aab23d4ce844b9
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:07:02 2019 +0100

    Delete newTransportRxns_newMets.csv

    Files that were renamed and updated are deleted.

commit 9ec56089dc34f41ecfc433f7ae0ae065b32cabf3
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:06:50 2019 +0100

    Delete newTransportRxns.csv

    Files that were renamed and updated are deleted.

commit d5973fe531918d27bcdc36a2fd7b50dd9adf08df
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:06:33 2019 +0100

    Delete SinkTransportRxns.csv

    Files that were renamed and updated are deleted.

commit ac8e012521e69fec818256e24bd827b49e2b8829
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:06:22 2019 +0100

    Delete ExTransportRxns.csv

    Files that were renamed and updated are deleted.

commit 8d63b70c83d538cbdc6cd93e339dc85e4186eb5d
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:05:47 2019 +0100

    Delete Table3_newTransportRxns_newMetabolites_280119_300119_3.csv

    Files that were enamed and updated are deleted.

commit d5e005462a62db720138a90d5444844bf060ab17
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:05:27 2019 +0100

    Delete Table2_newTransportRxns_280119_300119_3.csv

    Files that were enamed and updated are deleted.

commit 384344c2b3333cbdcbd94f3d71eb0f7c8707c15b
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:05:15 2019 +0100

    Delete Sink_Rxns_scoGEM_Transporters_300119_3.xlsx

    Files that were enamed and updated are deleted.

commit 050e98c1f73e986beadf0c2758674197f5b25117
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:04:58 2019 +0100

    Delete Table1_updated_grRules_280119_300119_6.csv

    Files that were enamed and updated are deleted.

commit 8beb1e41e571aa3a031ae14ff9dcb8d38db9f933
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:04:27 2019 +0100

    Delete ExRxns_added_Transporters_300119_3.xlsx

    Files that were enamed and updated are deleted.

commit 6f73fba8fdea596a476f5a15ec6038bd12fa25f9
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:03:34 2019 +0100

    TransportRxns

    Sink reactions with respect to the new metabolites in the new transport reactions, were integrated into the scoGEM model

commit b45551f53a4cea33625bb494871dad97773e1fc9
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:01:55 2019 +0100

    Add files via upload

    Exchange reactions, related to new metabolites in the new transporters, integrated into the scoGEM model.

commit 58e2ee3abb51f7d0f98e4989d5bc2a5072bb5dc8
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 19:00:35 2019 +0100

    TransportRxns

    New transport reactions with new metabolites integrated into the scoGEM model.

commit 0706e2ee7ce522029ac47262d87ca2ae3a1ff678
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:59:25 2019 +0100

    newTransportRxns

    New transport rxns integrated into scoGEM model.

commit cae57575bf06ba8510f55c336dfba1758dee112d
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:51:21 2019 +0100

    Update updated_grRules.csv

    The folder transport reactions involves 5 csv files, related to updated gene association to exisiting transport rxns, new transport rxns and new transport rxns with new metabolites as well as exchange reactions and sink reactions with respect to new metabolites.

commit 5a071c43b48e280668386bf563c545204cc2720e
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:51:11 2019 +0100

    Delete transport_reactions

    delete a file and create a folder under the same name

commit 4cb44ac1a79223851a66526a16fea8757291c2e7
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:45:00 2019 +0100

    Delete ExRxns_added_Transporters_300119.csv

    Delete this file; ExRxns_added_Transporters_300119.csv, as updated file was uploadedand move to the curation/transport_reactions folder

commit c5f862fdf3d52b1b8c90d789950833705b88e114
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:42:33 2019 +0100

    SinkTransportRxns

    Sink reactions with respect to new metabolites, involved in the new transporters,  were integrated into the scoGEM model.

commit 0f47e1c4e9cfe4844f63ddc1d1f1a44adad4a27c
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:41:23 2019 +0100

    Ex_TransportRxns

    Exchange reactions with respect to new metabolites, involved in the new transporters,  were integrated into the scoGEM model.

commit ba3769693957ec13b7824f8cb2df1dc00269c7d1
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:38:59 2019 +0100

    new_transport_rxns_new_mets

    New transport rxns with new metabolites were integrated into the scoGEM model.

commit 1dce146d925cdfd4cb7cc6282e7e930132415909
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:37:46 2019 +0100

    new_transport_rxns

    New transport reactions integrated into the scoGEM model.

commit 34d23c695b57f2ba6c38134d46c6e12b118c6c99
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:36:49 2019 +0100

    updated_gene_association

    updated gene association for exisitng transporters

commit 1b2b49c7f4bf47c22312a4fd428408dfd58e2bfb
Author: tjasakumelj <[email protected]>
Date:   Thu Mar 7 18:20:35 2019 +0100

    Create transport_reactions

    In this folder, there are five csv files; namely csv file that include updated gene association on exisitng transport reactions in the  scoGEM model and csv file that include new transport reactions and csv file that include new transport reactions with new metabolites. Consequently, sink reactions and exchange reactions for those new metabolites, were integrated into scoGEM model.

commit 6b8b8344f43e5da8234dc58543dd97a9724c15fa
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 16:42:05 2019 +0100

    Delete scoGEM.yml

commit 9206c249ecd0a27408892ce9a315a0c80f3e174b
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 16:31:20 2019 +0100

    adding_transporters

    script for automatically adding transporters to consensus scoGEM model. In addition directionality of rxns from reversibility to irreversibility for rxns with rxnIDs: VALTA, LEUTA, ILETA was changed.

commit fc40ff5ce42026722336ed6b83a0b4b23d699b4b
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:39:16 2019 +0100

    Delete Sink_Rxns_scoGEM_Transporters_300119_3.csv

    Copied to curration

commit e12328de7c31998a13cd6d9fb253aec106765fd0
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:37:33 2019 +0100

    Delete Sink_Rxns_scoGEM_Transporters.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit 1e086a840970f07179c6f8876113c18d14ef433b
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:37:05 2019 +0100

    Delete Sink_Rxns_scoGEM_Transporters_300119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit c78751d03f043aa2b918f6b00d7dec379cdcc713
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:36:13 2019 +0100

    sink_rxns_with_respect_to_new_mets

    Sink reactions added to consensus scoGEM model, with respect to new metabolites, present in new added transport reactions to the scoGEM model.

commit 501ae749d72e9c08ea016665245e12b2b468a698
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:32:33 2019 +0100

    Delete EX_Rxn_scoGEM_Transporters.csv

    All the tables that are not taken up by the script (automatically adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit 64a901f3f8f6540d35a78aabf743b0bb585af2b7
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:31:48 2019 +0100

    Delete ExRxns_added_Transporters_300119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters) for scoGEM model modification on transporters are deleted.

commit 93f215c14173b62983501124f262f68cf589732b
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:30:28 2019 +0100

    Delete Table3_newTransportRxns_newMetabolites_280119_300119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git)  for scoGEM model modification on transporters are deleted.

commit ccb04c545318cf040fec56f1250ad634a3a4cb53
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:29:41 2019 +0100

    Delete Table3_newTransportRxns_newMetabolites_280119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters) for scoGEM model modification on transporters are deleted.

commit 186e5c28d69e39c1671670b605c09f4b38a56289
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:28:46 2019 +0100

    Delete Table2_newTransportRxns_280119_300119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit b94362d2d946b5d17e5ae18234d521e06f8fb673
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:28:11 2019 +0100

    Delete Table2_newTransportRxns_280119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit 36c034373dc11c6f233e744528bf785b60c8a478
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:27:28 2019 +0100

    Delete Table1_updated_grRules_existing_transportrRxns_280119_300119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit 88148634ff74cc87fbdf6feb98e4544dddc78ac3
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:26:20 2019 +0100

    Delete Table1_updated_grRules_existing_transportrRxns_280119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit eeba2c8b8ddf258cfeb35d211914341b81167109
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:23:29 2019 +0100

    Delete TransportDB-main_UPDATED_281118.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit 0d92f43c00235745e2f4e6613914d43addc602c6
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:21:47 2019 +0100

    Delete Table_3_120119_updated_210119_240119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit 0d448827a05794e920bbaa52fcc50194da822751
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:21:07 2019 +0100

    Delete Table_3_120119.csv

    All the tables that are not taken up by the script (automatically_adding_transporters_git) for scoGEM model modification on transporters are deleted.

commit 1ea6c43bbaffbbc99739fdff343d86ac888318b9
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:20:17 2019 +0100

    Delete Table_2_120119_updated_210119_240119.csv

    All the tables that are not taken up by the script for scoGEM model modification on transporters are deleted.

commit f26d16590cbb1729ae8f311835fc522135928a48
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:19:43 2019 +0100

    Delete Table_2_120119_updated_210119.csv

    All the tables that are not taken up by the script for scoGEM model modification on transporters are deleted.

commit 77378246039c754051b1989b03613523ffae98e7
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:19:24 2019 +0100

    Delete Table_2_120119.csv

    All the tables that are not taken up by the script for scoGEM model modification on transporters are deleted.

commit 41b097b5387826336da646a3346ea347004b8727
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:19:02 2019 +0100

    Delete Table_1_120119_updated_210119_240119.csv

    All the tables that are not taken up by the script for scoGEM model modification on transporters are deleted.

commit a65d029839e07d1fcd8f43a85a76001a6de1d9d6
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:18:48 2019 +0100

    Delete Table_1_120119_updated_210119.csv

    All the tables that are not taken up by the script for scoGEM model modification on transporters are deleted.

commit b178e7f9b44768816adb4c5221b8a9dc038ad9a7
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 15:18:26 2019 +0100

    Delete Table_1_120119.csv

    All the tables that are not taken up by the script for scoGEM model modification on transporters are deleted.

commit 38985610cbed476b79992250c3c89c064ba56e72
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 11:49:02 2019 +0100

    Add files via upload

    Script for automatically added transporters. In addition, directionality of three reactions; VALTA, LEUTA, ILETA was changed from reversible to ireversible in a specific direction.  Output: scoGEM.xml

commit 97f82b82d49cf93930000e68eef5ca2357e7b30b
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 11:43:47 2019 +0100

    adding_transporters

    Script for automatically adding transporters, exchange rxns and sink reactions with respect to those transporters. In addition, directionality of the reactions with RxnIDs: VALTA, LEUTA, ILETA, was changed from reversible to ireversible in specific direction.

commit 4f49725ca7681035e1943a7ea65dfccb94e35615
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 11:26:12 2019 +0100

    scoGEM_model_versions

    consensus scoGEM model before addition of transporters, but after update of the thermodynamics (directionality of the reactions), in mat format-

commit e81352c76cb3b004552c315ea349960fa0615587
Author: tjasakumelj <[email protected]>
Date:   Fri Mar 1 10:54:09 2019 +0100

    scoGEM_model_before addition_of_transporters

    scoGEM model before additon of transporters, but this concensus scoGEM model already includes updated thermodynamics of the reactions (directionality of the reaactions),

commit b2eb727ab903fbae75d203eb1d14ef632688f708
Author: tjasakumelj <[email protected]>
Date:   Thu Feb 28 19:53:54 2019 +0100

    Delete scoGEM_model_added_transporters_cdir.xml

    scoGEM model with added transporters (scoGEM_model_added_transporters_cdir.xml) was renamed as scoGEM. So now scoGEM model on this branch include all the added transporters. Previous scoGEM_model_added_transporters_cdir.xml is deleted.

commit 2d1d264ae846ee2aac1ac918261672b3a2b46e5b
Author: tjasakumelj <[email protected]>
Date:   Thu Feb 28 19:39:27 2019 +0100

    scoGEM_added_transporters

    To scoGEM model, transport rxns were addedm with existing metabolites already in scoGEM model and with new metbaolites, for which sink and exchange rxns were added. In the scoGEM model for each of the transpor rxns, RxnID, RxnFormula, Gene Association, and lower and upper bound were integrated. Corresponding tables describing the integrated transporters are uploaded and integrated in the uploaded script.

    1. Table1_updated_grRules_280119_300119_6.csv (updated gene association on existing transport rxns)
    2. Table2_newTransportRxns_280119_300119_3.csv (new transporters with existing metabolites)
    3. Table3_newTransportRxns_newMetabolites_280119_300119_3.csv (new transporters with new transporters)
    4. ExRxns_added_Transporters_300119_3.csv (added exchange rxns with respect to new metabolites)
    5. Sink_Rxns_scoGEM_Transporters_300119_3.csv (added sink rxns with respect to new metabolites)

    In addition reversibility  rxns with RxnID: VALTA, LEUTA, ILETA was changed to irreversible.

commit a1759c63b588f582577c211f4cbf6080620457e5
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:24:05 2019 +0100

    exchange_rxns_added_scoGEM

    Exchange rxns of new metabolites, corresponding to new transport rxns added to scoGEM model.

commit f37cc94edc3a026bb4ba46536e240ecf2105055c
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:21:32 2019 +0100

    sink_rxns_corresponding_to_transport_rxns

    Sink rxns for new metabolites, corresponding to new transport rxns, were added to the scoGEM model

commit 5130037807778d67b08c0a3d2e73fa6d65dbe5f2
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:19:46 2019 +0100

    new_transport_rxns_with_new_metabolites

    New transport rxns with new metabolites were added to scoGEM model. For those new metabolites corresponding exchange rxns and sink reactions were added to the model.

commit 147c49cf21b9f1a7f9715fe666a59b27a491b977
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:17:48 2019 +0100

    new_transport_rxns_scoGEM

    New transport rxns added to the model, with reactionName, reactionFormula, geneRule, lowerBound, upperBound.

commit 7870a0bf5931181512ca6c2c7bea27b3c979f4e1
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:16:07 2019 +0100

    existing_transport_rxns_updated_geneRules

    Table includes existing transport rxns in scoGEM model, with updated/changed geneRules

commit 4a7aba38a1ad9d9d77d7516bb6ded4d964cebb59
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:13:35 2019 +0100

    Delete Table2_newTransportRxns_280119_300119_3.xlsx

commit ac9260e5a5a34228ba4e2fce258d329f4c3bd551
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:13:14 2019 +0100

    Delete Table1_updated_grRules_280119_300119_6.xlsx

commit 9e72fd8e04d83b5d7b5d91b3a51da73eaa284c78
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:11:48 2019 +0100

    new_transport_rxns_with_new_metabolites

    New transport rxns were added to the scoGEM model with reactionName, reactionFormula, geneRule, lowerBound, upperBound. For new metabolites corresponding exchange rxns and sink rxns were added.

commit d3a116a7b46453c2ce386dc1a38086b444dbb393
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:08:37 2019 +0100

    new_transport_rxns

    New transport rxns added to the scoGEM model, where reactionName, reactionFormula, geneRule, lowerBound, upperBound were added to scoGEM model.

commit 8233e2781b04668e37f47215fb72f82e47d305ce
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 18:06:22 2019 +0100

    updated_gene_association

    Gene association was updated for existing transport rxns in scoGEM model

commit cf7d3f049f2c4c196a65ca4582d836e079e401a8
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 17:53:33 2019 +0100

    mutant_growth_rates_scoGEM

    Table includes growth rates for certain knockouts in specific environment as demonstrated. Growth rates predicted by the model are compared to iKS1317 growth rates, iMK1208 growth rates and in vivo growth rates.

commit 203fbd6e3d2bf136a6e55c6a7775ce2fe6202b5f
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 17:51:20 2019 +0100

    wt_growth_rates_N_sources_scoGEM

    Table includes growth rates for the wild type with uptake of D-glucose of -1 mmol/gDW-hr as C source and uptake of each N source, iterating through all N sources in the model. Growth rates predicted by the model are compared to iKS1317 growth rates, iMK1208 growth rates and in vivo growth rates.

commit 8070077e0af865e1dd8a9878ed3ddce926b091ab
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 17:47:57 2019 +0100

    wt_growth_C_sources_scoGEM

    Table inlcudes growth rates for the wild type with uptake of nh4 of -1 mmol/gDW-hr as amonium source and uptake of C sources, iterating through C-sources in the model. Growth rates, predicted by the model are compared to iKS1317 growth rates, iMK1208 growth rates and in vivo growth rates.

commit 5ee410785ec0506e8c91ae67674dd49eb673d1f3
Author: tjasakumelj <[email protected]>
Date:   Tue Feb 12 17:38:07 2019 +0100

    integration_transp_rev_scoGEM

    In the scoGEM, I have integrated the transport rxns, as well as exchange rxns and sink rxns with respect tp transport rxns. Transport rxns were devided into 3 tables with prefix Table1, Table1, Table3, inlcuding existing transport rxns with updated/changed gene association (prefix Table1), new transport rxns (prefix Table2), and new transport rxns with new metabolites(prefix Table3), Rxns that include exchnage and sink rxns are in uploaded in tables with prefix Table4 and Table5, In addition to adding the transporters, rxns with rxnIDs of VALTA, LEUTA and ILETA were changed from reversible to ireversible in order to satisfy in vivo growth data on knockout (SCO4089) with L-leucine, L-valine, L-isoleucine  as N-source and D-glucose as C source. This final scoGEM model has ben evaluated  with respect to wild type growth on all carbon sources and  all nitrogen sources in the model and for knockout growth and compared to qualitative in vivo data, growth data on the model iKS1317 and growth data on iMK1208.

commit 62304f93bb896c7b27aaafe4708f6ed451716ab8
Author: tjasakumelj <[email protected]>
Date:   Sat Feb 9 18:20:12 2019 +0100

    Delete scoGEM_model_added_transporters.xml

commit 2ac6aa4e5767ca6c9c9f918ab4b1af9f09f1293a
Author: tjasakumelj <[email protected]>
Date:   Fri Feb 8 15:43:21 2019 +0100

    Add files via upload

commit 377e976b471c29db26dcb00cb90c16feffd56629
Author: tjasakumelj <[email protected]>
Date:   Wed Jan 30 20:35:27 2019 +0100

    Add files via upload

    Exchange rxns, corresponding to missing metabolites in scoGEM model.

commit bb22acfbd0cd26b4b8a84daa06e6c797d4b54bfd
Author: tjasakumelj <[email protected]>
Date:   Wed Jan 30 20:33:50 2019 +0100

    Add files via upload

    Updated sink rxns, corresponding to missing metabolites in scoGEM model,

commit 567c7f5c50fbaaec547a6838a398ac71e54c494d
Author: tjasakumelj <[email protected]>
Date:   Wed Jan 30 20:32:49 2019 +0100

    Add files via upload

    Updated ExchangeRxns, correesponding to the missing metabolites in scoGEM model.

commit 8e871be0a55059ec325b7772d7cfe6d358123e41
Author: tjasakumelj <[email protected]>
Date:   Wed Jan 30 20:31:29 2019 +0100

    Add files via upload

    Updated table with additional columns on Lower and UpperBound on new Transport Rxns with non-existing Mets in scoGEM model, for whcih exchange and sink rxns will be added to the scoGEM model.

commit 1dd3532d996e49e76264ca9444f37ac4ab189aef
Author: tjasakumelj <[email protected]>
Date:   Wed Jan 30 20:29:35 2019 +0100

    Add files via upload

    Updated with additional columns on LowerBound and UpperBound on new Transport Rxns that will be added to scoGEM model

commit 190d2de2e3e57c2f7e194ff8f6f1f8ce4fadb32b
Author: tjasakumelj <[email protected]>
Date:   Wed Jan 30 20:28:06 2019 +0100

    Add files via upload

    Updated with additional columns(lowerBound, upperBound) on TransportRxns already existing in scoGEM model, but now with updated gene association

commit c1a9e88264f5a78188a1adb66c85f64c7578e97d
Author: tjasakumelj <[email protected]>
Date:   Mon Jan 28 12:38:58 2019 +0100

    Add files via upload

    New Transport Reactions with substrates that are not further  metabolised in the consensus scoGEM model, therefore the sink rxns need to be integrated into the consensus scoGEM model for those metabolites. RxnsID, GeneAssociation and RxnFormula are shown in the table.

commit 7f812f604b47e0c3a4d12f38c2a4c46ca5eeab5c
Author: tjasakumelj <[email protected]>
Date:   Mon Jan 28 12:35:18 2019 +0100

    Add files via upload

    New transport reactions with RxnID, GeneAssociation and RxnFormula (i.e not existing in present consensus scoGEM model).

commit eb75de249d763959386acef54fce8df2055e0a76
Author: tjasakumelj <[email protected]>
Date:   Mon Jan 28 12:32:12 2019 +0100

    Add files via upload

    Gene associations are re-defined for transport reactions that are already existing in scoGEM model

commit cbdf134a280999673ca39efa57f417b1d42d5bfe
Author: tjasakumelj <[email protected]>
Date:   Thu Jan 24 17:48:37 2019 +0100

    Add files via upload

commit fc69a31e1061eba08928c770f3357bb9c79d6fa3
Author: tjasakumelj <[email protected]>
Date:   Thu Jan 24 17:48:02 2019 +0100

    Add files via upload

commit fa6fde89644b7e629f611ef86076a28d2f44ef1c
Author: tjasakumelj <[email protected]>
Date:   Thu Jan 24 17:47:30 2019 +0100

    Add files via upload

commit ab8017012bd9bd8ff13fcc099350289748b4b9c8
Author: tjasakumelj <[email protected]>
Date:   Mon Jan 21 09:55:05 2019 +0100

    Add files via upload

commit d958b7219408e2115ab550d533df4b54ee74e3b8
Author: tjasakumelj <[email protected]>
Date:   Mon Jan 21 09:54:31 2019 +0100

    Add files via upload

commit 67de53748d815447b6b5f35fad2d5e27c23a373d
Author: tjasakumelj <[email protected]>
Date:   Sun Jan 13 18:43:39 2019 +0100

    Add files via upload

commit b36060c23687c3bd6a86505e49b709916e11cc3b
Author: tjasakumelj <[email protected]>
Date:   Sun Jan 13 18:42:45 2019 +0100

    Add files via upload

commit 813027052bd77548867285bc90688e53d5e46191
Author: tjasakumelj <[email protected]>
Date:   Sat Jan 12 14:21:50 2019 +0100

    Add files via upload

commit 73cdaad2260928d562b771ed14a1554e50403192
Author: tjasakumelj <[email protected]>
Date:   Sat Jan 12 14:21:20 2019 +0100

    Add files via upload

commit 10e0315779b87538f8f44e84f54a66bc3fdd52a5
Author: tjasakumelj <[email protected]>
Date:   Sat Jan 12 14:20:30 2019 +0100

    Add files via upload

commit 93825e1bac93fb3eb5f00f110419a4a4898e35f0
Author: tjasakumelj <[email protected]>
Date:   Thu Nov 29 18:56:29 2018 +0100

    Add files via upload

* Merge pull request #70 from fix/transporters

This includes addtion of:
- 24 new transport reactions of existing metabolites
- 20 new transport reactions of new metabolites
- 39 reactions with updated gene association
- 28 new exchange reactions
- 48 new metabolites
- 186 new genes

Current stats is:
Reactions:  2612
Metabolites:  2071
Genes:  1799

Squashed commit of the following:

commit 86f28e56096c2329f19c0d2fa8d7531d5b7f8641
Merge: 1197c86 1e041eb
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:38:20 2019 +0200

    Merge branch 'devel' into fix/transporters

commit 1197c866a270676dbc55b184be11a654e8ab6019
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:20:45 2019 +0200

    chore: move scoGEM.yml to correct folder

commit d65d4f926898004313d0e626e697fe85adf145cc
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:14:07 2019 +0200

    chore: delete unnecessary csv files

    These two lists are not needed:
    - sinks are not added
    - Exchange reactions are added for all new extracellular metabolites

commit a1539fb1bd7e70f288abf77e13a0097414267b5d
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:10:38 2019 +0200

    chore: delete growth data files

    This is performed by the pytests already added to the repo

commit 0b5b5e3e5d797a6d888447fa1bd4bce4693638b4
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:08:17 2019 +0200

    chore: delete unnecessary model files

    These files are not used anymore

commit 47c87054f5a1444e5aea99d2d110d2580372e974
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 14:02:30 2019 +0200

    chore: delete unnecessary files

    These files are no longer needed to incroporate changes from the
    transport reaction curation, becuse they are replaced by
    fix_transporters.py.

commit 82434e45ac5017971fd0be8e06ec689cb499d7be
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 13:17:54 2019 +0200

    feat: script to add transport reactions

    This script incorporate all changes related to transport reactions:
    modification of existing reactions and addition of new. The script reads
    data from the csv-files:
     - newTransportRxns.csv
     - updated_grRules.csv
     - newTransportRxns_newMets.csv
     - new_mets_annotation.csv

    The script is incoporated into reconstruct_scoGEM.py, which first was
    updated from devel branch to ease later merging of branches

commit 463c19a58aa423c2e11ed8eefc96fbb0022e546a
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 09:54:41 2019 +0200

    fix/feat: clean tables and fix transport errors

    Made the following changes:
     - Converted G_SCOXXXX to SCOXXXX for readability
     - Added susbsystem annotation
     - Added column with reaction names for new reactions
     - Changed id of a few reactions to abbreviations more similar to the
     transported metabolite
     - Two ABC-transport reactions for melibiose were merged into one,
     concatenating gene reaction rule by "or", i.e. (SCO0290 and SCO7165) or
     SCO1707
     - Moved ammonium transport from "newTransportRxns.csv" to
     "updated_grRules.csv" as this reaction is already present in the model
     - Moved LPS transport to "NewTransportRxns_newMets.csv" as this metabolite is not in the model and added metabolite to "new_mets_annotation.csv"
     - Moved MEMYt (methylenomycin transport) from "NewTransportRxns_newMets.csv" to "newTransportRxns.csv" and changed the reaction into two separate reactions transporting out mmyA and mmyB
     - removed cobal from new_mets_annotation, because it's not used in any
     new reaction
     - corrected a few chemical formulas
     - corrected name of L-ascorbate to ascb__L
     - Moved CATECHOLt to "newTransportRxns.csv" because catechol is already
     present in model
     - Removed thmpp fromnew metabolite sheet, because it is present in
     model
     - Removed UACGAMpts from "NewTransportRxns.csv" because the suggested
     product metabolite couldn't be identified (uacgam6p)

commit 2e874fd936687d172d271400a5bd67c0336aa6ee
Author: Snorre Sulheim <[email protected]>
Date:   Fri Sep 13 08:36:47 2019 +0200

    chore: update model file from devel branch

commit fdeed34a115da767ceda0ba4d15ff40c2a6fdfc1
Author: Snorre Sulheim <[email protected]>
Date:   Thu Sep 12 16:31:23 2019 +0200

    style: delete and rename redundant spreadsheets

    There were multiple files related to new transport reactions that were
    just different versions of each other. I have deleted the old versions
    and renamed the most recent version by removing any date/version suffix.

commit 76bf3b675fda5123d62ad5ef94e8073b7b5eff8a
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:40:21 2019 +0200

    updated_new_mets

    Table updated in correspondance with NewTransportRxns__newMets

commit 1419aaf6d397c7eca434baf0a40b310c9e0e073e
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:38:15 2019 +0200

    updated_newTransportRxns

    Addiitonal column(H) on annotation of transporters added adn somem double rxns removed.

commit 75de38645de875114f98be06722134c60d309126
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:37:07 2019 +0200

    updated_NewTransportRxns_with_newMets

    Additonal column  (H) on annotation of transporters added as well as double rxns removed.

commit dbebd92b209558b3dd939930c357af69673bcb25
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:35:32 2019 +0200

    updated_grRules

    Additional column(H) on annotation of grRules added as well as some minore changes to grRules and double rxns removal.

commit de097ec8c54416a401772076ceaca00f4647c9c1
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:30:44 2019 +0200

    updated_new_mets_annotation

    Updated table with resapect to NewTransportRxns_newMets,

commit f0056d38c5ff3148d91e2a9f57e8e38c26dac876
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:28:12 2019 +0200

    update_newTransportRxns

    Addiitonal column(H) on annotation for transporters have been aded as well as double reactions have been removed.

commit 90580904ece4006ada38313a6ac697d8263d93ca
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:26:29 2019 +0200

    update_newTransportRxns_with_newMets

    Additional column(H) on annotation of transporters has been added and double reactions have been removed.

commit 250aa6a9f18d1772fb33ba64889cce15a7275f7f
Author: tjasakumelj <[email protected]>
Date:   Wed Jul 10 09:23:49 2019 +0200

    update_grRules

    Additional table has been added (H) on anotation for grRules. Additional correctiions(extrract double reactions has been added and some minor corrections to grRules for some reactions),

commit cf9c19a6d68cbdd36abc577d4043b9bc9f0b2e90
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:35:56 2019 +0200

    Add files via upload

commit 5712b3e08ca55c891ff7b1d0601c2eab0de4620c
Author: tjasakumelj <[email protected]>
Date:   Tue Jul 9 19:35:09 2019 +0200

    Add files via upload

    updated table (add addi…
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20 changes: 20 additions & 0 deletions .travis.yml
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@@ -0,0 +1,20 @@
language: python
sudo: true
python: 3.5
cache:
pip: true
git:
depth: false

branches:
- devel
before_install:
- pip install --upgrade pip setuptools wheel
install:
- pip install --upgrade memote

script:
# - memote run --skip-unchanged
- git checkout "${TRAVIS_BRANCH}"
- chmod +x ./ComplementaryScripts/*deploy.sh
- ./ComplementaryScripts/travis_deploy.sh
8 changes: 4 additions & 4 deletions ComplementaryData/README.md
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@@ -1,4 +1,4 @@
# ComplementaryData
The ComplementaryData folder is where data is stored that is used for curation, model testing, etc. Data should be stored as delimited text format (CSV) in their appropriate subfolder.

*Please do not remove this file*
# ComplementaryData
The ComplementaryData folder is where data is stored that is used for curation, model testing, etc. Data should be stored as delimited text format (CSV) in their appropriate subfolder.

*Please do not remove this file*
2 changes: 1 addition & 1 deletion ComplementaryData/annotations/genes.csv
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@@ -1,4 +1,4 @@
SCO_ID;Uniprot_Entry;Uniprot_Name;UniProt_Protein_names;Length;EC_number;Mass;Gene_ontology;GO_ID;RefSeq;BioCyc;Pfam;PANTHER;Protein_Sequence
SCO_ID;Uniprot_Entry;Uniprot_Name;UniProt_Protein_names;Length;EC_number;Mass;Gene_ontology;GO_ID;RefSeq;BioCyc;Pfam;PANTHER;Protein_Sequence
Data sheet 2 - List of metabolites in the model, to use with COBRA remove this line.;;;;;;;;;;;;;
SCO0006;Q9FBV7;Q9FBV7_STRCO;Putative ATP/GTP-binding protein;368;;38860;;;"NP_631869.1;NP_733755.1;WP_011026769.1;";;"PF05621;";;MNASPGTSDTPAGGSPSTAHRPPSAAASTDGDAPDAQPQAVATWDGFQAFATTPAAAPPPPGTPHRSLEERLAYHSRFVTVRTPAIDALAKNVRTLMILGRHQAVTARPSLIVTGPAGAGKTTALLQVGRACHLAHTRRHGAAATAGQAPVAYVLVPPAASAKTLAIEFARYLGIPVTAGMSQAQITGAVCHTYTAARVQLVMIDEIHRLNPRTTTGAQSADLIKDLTERIGATFVYAGIDVTTTPLFTGVRGAQLAGRASLIDCAAFPSRLGDQEPFRDLITAMESALDLRHHRPGTLPRLAPYLHERTAGRIGSLARLIRQAAITALLDGTERITKTTLDAIRLDHLAEQHYQPRARPRSRNTSTP
SCO0015;Q9S1X8;NHAA1_STRCO;Na(+)/H(+) antiporter NhaA 1/4 (Sodium/proton antiporter NhaA 1);410;;41975;"integral component of membrane [GO:0016021]; plasma membrane [GO:0005886]; antiporter activity [GO:0015297]; regulation of pH [GO:0006885]; sodium ion transport [GO:0006814]";"GO:0005886; GO:0006814; GO:0006885; GO:0015297; GO:0016021";"NP_624376.1;NP_631860.1;WP_011026778.1;";;"PF06965;";"PTHR30341;";MSAPSRITAALRSDAVGGSLLIGAAVIALIWANSPLSHSYEALRSFTFGPSALHLNLSVETWAADGLLAVFFFIVGNELKQELVHGELRDPRRAALPIAAALGGVAVPALVFLAFTLGSGGEAAGGWGIPMATGIAFAVAVLAVVGRHLPTPLRTFLLTLATVDDMSAVLVIAVACTSGINFTALALAAVGLAVFGYLQNGSGRAVARVRAMVPAWLLFVPLAAVVWALMHACGVHATIAGVVMGLLMRTRPQGAERVSPSHRAEEVLRPFSAGIALPLFALMSAGVSLAGAGGFVTSAITWNVLAGLLVGKVVGIFGGTWPTSRLTSAHLNPLLGWADIAGIAVLGGIGFTVSLPIAELSSTSQAHLTDAKGAILLASTTAALLAALLLGRRSRHHQRLARQAAQQATT
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330 changes: 165 additions & 165 deletions ComplementaryData/biomass/biomass_scaled.txt

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56 changes: 28 additions & 28 deletions ComplementaryData/biomass/prosthetic_groups_mets.txt
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@@ -1,28 +1,28 @@
mets coeffs
lipopb_c 4.228099e-05
ca2_c 5.413579e-06
cobalt2_c 4.776994e-06
cu2_c 3.510029e-05
fad_c 1.576062e-04
fmn_c 2.102677e-05
fmnh2_c 1.370829e-05
fe2_c 8.494727e-05
k_c 4.163981e-05
mg2_c 6.760645e-04
mn2_c 1.383008e-04
mocogdp_c 2.915914e-05
nad_c 3.866086e-05
nh4_c
ni2_c 1.674219e-05
zn2_c 3.156188e-04
2fe2s_c 2.579519e-05
4fe4s_c 1.660319e-04
adocbl_c 7.581754e-06
btn_c 1.648628e-05
hemeA_c 9.283915e-05
pheme_c 3.422161e-05
pydx5p_c 1.779235e-04
pyr_c 1.020737e-06
thmpp_c 2.255546e-05
hemeO_c
bmocogdp_c
mets coeffs
lipopb_c 4.228099e-05
ca2_c 5.413579e-06
cobalt2_c 4.776994e-06
cu2_c 3.510029e-05
fad_c 1.576062e-04
fmn_c 2.102677e-05
fmnh2_c 1.370829e-05
fe2_c 8.494727e-05
k_c 4.163981e-05
mg2_c 6.760645e-04
mn2_c 1.383008e-04
mocogdp_c 2.915914e-05
nad_c 3.866086e-05
nh4_c
ni2_c 1.674219e-05
zn2_c 3.156188e-04
2fe2s_c 2.579519e-05
4fe4s_c 1.660319e-04
adocbl_c 7.581754e-06
btn_c 1.648628e-05
hemeA_c 9.283915e-05
pheme_c 3.422161e-05
pydx5p_c 1.779235e-04
pyr_c 1.020737e-06
thmpp_c 2.255546e-05
hemeO_c
bmocogdp_c
846 changes: 423 additions & 423 deletions ComplementaryData/biomass/prosthetic_groups_uniProt.txt

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330 changes: 165 additions & 165 deletions ComplementaryData/biomass/standard_biomass.txt

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2 changes: 1 addition & 1 deletion ComplementaryData/curation/added_sco4_metabolites.csv
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Metabolite ID;Name;New ID;KEGG;BIGG;MNX
Metabolite ID;Name;New ID;KEGG;BIGG;MNX
CPD-16467_c;3-[(1-carboxyvinyl)oxy]benzoate;3ovobenz;C20772;;MNXM145735
5-AMINO-2-OXOPENTANOATE_c;5-amino-2-oxopentanoate;5a2opntn;C01110;5a2opntn;MNXM1714
L-GULONO-1-4-LACTONE_c;L-gulono-1,4-lactone;gullac;C01040;gullac;MNXM928
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2 changes: 1 addition & 1 deletion ComplementaryData/curation/added_sco4_reactions.csv
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Reaction ID;Fixed ID;Reaction name;KEGG annotation;metanetx;bigg;New ID
Reaction ID;Fixed ID;Reaction name;KEGG annotation;metanetx;bigg;New ID
1__46__1__46__1__46__127__45__RXN;1.1.1.127-RXN;"2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase;2,5-didehydro-3-deoxy-L-galactonate 5-reductase;2-keto-3-deoxy-D-gluconate dehydrogenase";R01542;MNXR107048;;2D3DGLUCDH
1__46__14__46__12__46__1__45__RXN_NADH;1.14.12.1-RXN_NADH;anthranilate dioxygenase (NADH);R00825;MNXR106707;;ANTDIO_NADH
1__46__14__46__12__46__1__45__RXN_NADPH;1.14.12.1-RXN_NADPH;anthranilate dioxygenase (NADPH);R00825;;;ANTDIO_NADPH
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