github.com/GeomScale/dingo issues | Ecosyste.ms: OpenCollective

Add mmcs method to sampling

akisschinas opened this pull request 3 months ago

Tutorial is outdated

KeShih opened this issue 4 months ago

Update documentation for PR #104

KeShih opened this pull request 4 months ago

Clustering and Graphs from steady-states correlation matrix

SotirisTouliopoulos opened this pull request 5 months ago

Add pyoptinterface_based_impl.py and integrate it

KeShih opened this pull request 5 months ago

Functions for correlation matrix, copula indicator and plotting

SotirisTouliopoulos opened this pull request 5 months ago

abandoned

KeShih opened this pull request 6 months ago

Add pulp_based_impl.py and pulp_impl_test.py

KeShih opened this pull request 6 months ago

PreProcess class for reactions removal

SotirisTouliopoulos opened this pull request 6 months ago

fix typo in slow_fba, and a bug in fast_fba

KeShih opened this pull request 8 months ago

new interface for samples and fba, fva solutions and workaround for #96

hariszaf opened this pull request 9 months ago

rename biomass_function to objective_function, fixes issue #82

hritikb opened this pull request 9 months ago

Error using fva after sampling

vfisikop opened this issue 9 months ago

Redundant methods in MetabolicNetwork

vfisikop opened this issue 9 months ago

Refactor mmcs algorithm

vfisikop opened this issue 10 months ago

Fix rounding test

vissarion opened this pull request 10 months ago

Update README installation instructions to be more user friendly #89

rkstu opened this pull request 10 months ago

solve issue #83: generate_steady_states fails when you edit a model's optimal percentage twice #83

rkstu opened this pull request 10 months ago

Update README installation instructions to be more user friendly

rkstu opened this issue 10 months ago

Build volestipy with lpsolve

vfisikop opened this pull request 11 months ago

Update dingo to use volesti develop instead of volesti4dingo branch

vfisikop opened this pull request 11 months ago

loopless sampling

hariszaf opened this issue 11 months ago

solve issue #83: generate_steady_states fails when you edit a model's optimal percentage twice #83

rkstu opened this pull request 11 months ago

Modernize LP solver interface

vissarion opened this issue 12 months ago

`generate_steady_states` fails when you edit a model's optimal percentage twice

hariszaf opened this issue about 1 year ago

Consider renaming `biomass_function` routine

hariszaf opened this issue about 1 year ago

Create redundant_facet_removal_backup.py

nitishmalang opened this pull request over 1 year ago

Create imp-16.py

nitishmalang opened this pull request over 1 year ago

Dockerfile is added to the codebase

ai-naymul opened this pull request over 1 year ago

Consider a docker image

hariszaf opened this issue over 1 year ago

Error in installation (incompatible versions of Python and numpy)

savvas-paragkamian opened this issue over 1 year ago

support of medium modification and cobra model loading

hariszaf opened this pull request over 1 year ago

alternative suffix for sbml models

hariszaf opened this issue over 1 year ago

Modify model's medium

TolisChal opened this issue over 1 year ago

Expose HMC walks with Gaussian and exponential distributions

stormaths opened this pull request over 1 year ago

rounding.py is excluded from github actions

TolisChal opened this issue over 1 year ago

Update README.md

nitishmalang opened this pull request over 1 year ago

Fix bug in retrieving samples

TolisChal opened this pull request over 1 year ago

Update README.md

nitishmalang opened this pull request over 1 year ago

Exposed two HMC walks with exponential and Gaussian sampling from Volesti

stormaths opened this pull request over 1 year ago

Sampling on the flux space of multiple metabolic networks

vissarion opened this issue over 1 year ago

non-uniqueness issue in dynamic FBA

hariszaf opened this issue over 1 year ago

sample asking for a min/max value of the objective function

hariszaf opened this issue over 1 year ago

Add volume computation support and motivation

vissarion opened this issue over 1 year ago

fix magic command denoter; issue #60

hariszaf opened this pull request almost 2 years ago

Fix poetry version 1.3.2 in actions.

vissarion opened this pull request almost 2 years ago

update colab; fix #60

hariszaf opened this pull request almost 2 years ago

Error importing MetabolicNetwork class from dingo package in Google Colab (GSoC 2023)

samadpls opened this issue almost 2 years ago

Adding CodeCov

bsarthak16 opened this pull request almost 2 years ago

Edits on copula illustration and export

hariszaf opened this pull request almost 2 years ago

Improve copula illustration and export

TolisChal opened this pull request almost 2 years ago

Bump future from 0.18.2 to 0.18.3

dependabot[bot] opened this pull request almost 2 years ago

Move the documentation to readme

TolisChal opened this pull request almost 2 years ago

Expose rounding methods

TolisChal opened this pull request about 2 years ago

implement copula illustration in dingo pipeline

TolisChal opened this pull request about 2 years ago

Add cobra package as a dependence.

vissarion opened this pull request about 2 years ago

Load models

hariszaf opened this pull request about 2 years ago

reorder sections and minor edits

hariszaf opened this pull request about 2 years ago

Update poetry installation CI command

vissarion opened this pull request about 2 years ago

segmentation fault when ESS low

hariszaf opened this issue over 2 years ago

Experiments

hariszaf opened this pull request over 2 years ago

include volume approximation

Patrickens opened this issue over 2 years ago

Expose uniform random walks

Kostas-Pallikaris opened this pull request over 2 years ago

Update mention of unit tests in main README

dymil opened this pull request over 2 years ago

Move updated tutorial to tutorials folder and copyedit

dymil opened this pull request over 2 years ago

Make changes to code style

dymil opened this pull request over 2 years ago

Copyedit main README + comments in volestipy.pyx

dymil opened this pull request over 2 years ago

Fix typo in tutorial README

dymil opened this pull request over 2 years ago

sampling using the maximum entropy probability distribution

hariszaf opened this issue almost 3 years ago

Support ellipsoid sampling methods

vissarion opened this issue almost 3 years ago

code coverage for dingo

vissarion opened this issue over 3 years ago

Add a boolean to control the preprocessing method

TolisChal opened this pull request over 3 years ago

For Begginer

nikdantani opened this issue over 3 years ago

Fix the bug in sample_from_polytope function

TolisChal opened this pull request over 3 years ago

Fix compile errors

TolisChal opened this pull request over 3 years ago

Improve preprocessing

TolisChal opened this pull request over 3 years ago

Read `.xml` models

hariszaf opened this issue over 3 years ago

Read `.mat` models

hariszaf opened this issue over 3 years ago

`NameError` when using the `sample_from_polytope` function

hariszaf opened this issue over 3 years ago

Compartments

hariszaf opened this issue over 3 years ago

Fix/json biomass index value

vissarion opened this pull request over 3 years ago

sampler does not converge with iLJ478 model

vissarion opened this issue over 3 years ago

fast_inner_ball computes negative radius

vissarion opened this issue over 3 years ago

Error with biomass index handling after parsing json files

vissarion opened this issue over 3 years ago

Sampling on the flux space of multiple metabolic networks

hariszaf opened this pull request over 3 years ago

dingo tutorial notebook

hariszaf opened this pull request over 3 years ago

dingo crashes with various metabolic models

vissarion opened this issue over 3 years ago

Add examples and use-cases

vissarion opened this issue over 3 years ago

Add Contribution guidelines

vissarion opened this issue over 3 years ago

Knock out a reaction flux

TolisChal opened this pull request over 3 years ago

Set Black code style

TolisChal opened this pull request over 3 years ago

Fix tests

TolisChal opened this pull request over 3 years ago

Add github actions

vissarion opened this pull request over 3 years ago

Improve Python code

TolisChal opened this pull request over 3 years ago

Update boost download link

vissarion opened this pull request over 3 years ago

Restructure of Python code

TolisChal opened this pull request over 3 years ago

Initialization of the default branch

TolisChal opened this pull request over 3 years ago

Computation of the right nullspace of the stoichiometric matrix

TolisChal opened this pull request almost 4 years ago

Computation of the maximum inscribed ball of a convex polytope

TolisChal opened this pull request almost 4 years ago

Implementation of FBA

TolisChal opened this pull request almost 4 years ago