DD-DeCaF simulations issues

DD-DeCaF / simulations

Model service which takes care of adjusting model according to incoming messages and returns information such as fluxes, theoretical maximum yields, etc

Apache License 2.0

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chore: bring staging changes to production

#160 BenjaSanchez opened 3 years ago
0
Refactor install

#159 Midnighter closed 4 years ago
0
Catch and forward reframed warnings

#158 kvikshaug closed 4 years ago
1
Active exchanges

#157 ChristianLieven closed 4 years ago
1
fix: ensure feasible simulations of ecModels

#156 BenjaSanchez closed 4 years ago
2
Feat: add pytfa metabolomics

#155 carrascomj opened 4 years ago
1
Implement minimal community modeling endpoint

#154 kvikshaug closed 4 years ago
1
Upgrade dependencies

#153 kvikshaug closed 4 years ago
1
test: simulate each method only once

#152 kvikshaug closed 4 years ago
1
feat: uptake/secretion rates in flexibilize_proteins

#151 BenjaSanchez closed 4 years ago
2
fix: bound assignment for reverse exchange rxns

#150 BenjaSanchez closed 4 years ago
6
refactor: implement exchange reaction logic as cobra helper function

#149 kvikshaug closed 4 years ago
1
Fix/exchange rxns ecModels

#148 BenjaSanchez closed 4 years ago
1
Feat/add gecko functions

#147 BenjaSanchez closed 4 years ago
3
Fix cobra models & upgrade cobrapy

#146 kvikshaug closed 5 years ago
2
Update data schema for warehouse

#145 kvikshaug closed 5 years ago
1
fix: create demand reaction, not exchange reaction

#144 kvikshaug closed 5 years ago
1
fix: store compartment id on exception instance

#143 kvikshaug closed 5 years ago
1
Abstract parsing bigg metabolite identifier to a function

#142 kvikshaug closed 5 years ago
1
More log details

#141 kvikshaug closed 5 years ago
1
Handle infeasability

#140 kvikshaug closed 5 years ago
1
Add and apply black

#139 kvikshaug closed 5 years ago
1
Fix compartments for added metabolites

#138 kvikshaug closed 5 years ago
0
Remove existing reaction

#137 kvikshaug closed 5 years ago
1
fix: parse compartment from metabolite if possible

#136 Midnighter closed 5 years ago
1
refactor: compare lower case gene names

#135 Midnighter closed 5 years ago
2
Fix local

#134 Midnighter closed 5 years ago
3
When adding genes, remove reaction id if it already exists

#133 kvikshaug closed 5 years ago
1
Fix driven test

#132 kvikshaug closed 5 years ago
1
fix: add reaction using cobra's reaction object

#131 annasirunian closed 5 years ago
1
Move scripts to `scripts` subdir

#130 kvikshaug closed 5 years ago
1
feat: limit cobra logs to warnings

#129 kvikshaug closed 5 years ago
1
Avoid network i/o in unit test

#128 kvikshaug closed 5 years ago
1
Various fixes in data adapters

#127 kvikshaug closed 5 years ago
1
Remove duplicate compounds to speed up metabolite lookup

#126 kvikshaug closed 5 years ago
4
Deserialize gnomic object at schema level

#125 kvikshaug closed 5 years ago
1
Remove unused endpoint

#124 kvikshaug closed 5 years ago
1
Add integration test for Prokaryomics MD120 BW25113 experiment

#123 kvikshaug closed 5 years ago
0
Adapter improvements

#122 kvikshaug closed 5 years ago
1
Updates to match other services

#121 kvikshaug closed 5 years ago
0
Remove "deltas" feature

#120 kvikshaug closed 5 years ago
1
Use sync gunicorn workers

#119 kvikshaug closed 5 years ago
1
Caffeine

#118 kvikshaug closed 5 years ago
0
Check for request context

#117 kvikshaug closed 5 years ago
1
Authorization handling

#116 kvikshaug closed 5 years ago
1
Don't return measured fluxes if the model is infeasible

#115 kvikshaug closed 6 years ago
1
docs: change expected identifier type to integer

#114 Midnighter closed 5 years ago
2
Create unknown metabolites

#113 kvikshaug closed 6 years ago
0
Handle insufficient permissions

#112 kvikshaug closed 6 years ago
1
Retrieve models from model storage

#111 kvikshaug closed 6 years ago
2