Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / gyorilab/mira issues and pull requests

#396 - [BUG]: AMR ingest error caused by SKEMA bug

Issue - State: open - Opened by liunelson 11 days ago - 5 comments

#395 - Extend SBML distribution processing

Pull Request - State: closed - Opened by bgyori 21 days ago

#394 - Extend to more distributions from SBML

Issue - State: closed - Opened by bgyori 24 days ago

#393 - Process distributions from SBML models

Pull Request - State: closed - Opened by bgyori 25 days ago

#392 - Propagate concept descriptions

Pull Request - State: closed - Opened by nanglo123 about 1 month ago

#391 - Add model parameters to safe parse of distribution parameters

Issue - State: closed - Opened by djinnome about 1 month ago - 2 comments

#390 - Add model parameters to safe parse of distribution parameters

Pull Request - State: closed - Opened by djinnome about 1 month ago - 1 comment

#388 - Gamma is a reserved word in sympy

Issue - State: closed - Opened by djinnome about 1 month ago - 1 comment

#387 - Update utils.py

Pull Request - State: closed - Opened by djinnome about 1 month ago - 1 comment

#386 - Update URLs for DKG service

Pull Request - State: closed - Opened by bgyori about 1 month ago

#385 - Explicitly filter excluded controllers when considering cartesian product

Pull Request - State: closed - Opened by bgyori about 1 month ago

#384 - [BUG] Duplicate template generated when `cartesian_control = True`

Issue - State: closed - Opened by liunelson about 1 month ago - 1 comment

#383 - Speed up model composition by referring a singleton refinement closure

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#382 - Generalize SBML initial condition extraction

Pull Request - State: closed - Opened by bgyori about 2 months ago

#381 - Fix unit processing for model ingestion

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#381 - Fix unit processing for model ingestion

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#380 - Add "rdfs:subclassof" as a refinement relation

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#380 - Add "rdfs:subclassof" as a refinement relation

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#379 - Update util.py

Pull Request - State: closed - Opened by djinnome about 2 months ago - 1 comment

#379 - Update util.py

Pull Request - State: closed - Opened by djinnome about 2 months ago - 1 comment

#378 - AMR no longer loads in new version of mira

Issue - State: closed - Opened by djinnome about 2 months ago - 1 comment

#375 - Add all geonames admin2 regions

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#375 - Add all geonames admin2 regions

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#374 - SBML initialAmount is not supported, but initialConcentration is

Issue - State: closed - Opened by djinnome about 2 months ago - 2 comments

#373 - Only filter cities by minimum population

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#373 - Only filter cities by minimum population

Pull Request - State: closed - Opened by nanglo123 about 2 months ago

#370 - [BUG] The EPI DKG seems to be missing a few `geonames` nodes

Issue - State: closed - Opened by liunelson 2 months ago - 1 comment

#370 - [BUG] The EPI DKG seems to be missing a few `geonames` nodes

Issue - State: closed - Opened by liunelson 2 months ago - 1 comment

#368 - Fix sbml amr export

Pull Request - State: closed - Opened by nanglo123 2 months ago

#368 - Fix sbml amr export

Pull Request - State: closed - Opened by nanglo123 2 months ago

#367 - Add obo pickled graphs to docker build

Pull Request - State: closed - Opened by nanglo123 2 months ago

#367 - Add obo pickled graphs to docker build

Pull Request - State: closed - Opened by nanglo123 2 months ago

#366 - failed to convert mira model to AMR

Issue - State: closed - Opened by djinnome 2 months ago - 1 comment

#366 - failed to convert mira model to AMR

Issue - State: closed - Opened by djinnome 2 months ago - 1 comment

#365 - Update dkg links in notebooks

Pull Request - State: closed - Opened by nanglo123 2 months ago

#365 - Update dkg links in notebooks

Pull Request - State: closed - Opened by nanglo123 2 months ago

#364 - Implement adding observables by pattern

Pull Request - State: closed - Opened by bgyori 2 months ago

#364 - Implement adding observables by pattern

Pull Request - State: closed - Opened by bgyori 2 months ago

#363 - Addition of ontology terms and subtree terms

Pull Request - State: closed - Opened by nanglo123 2 months ago

#363 - Addition of ontology terms and subtree terms

Pull Request - State: closed - Opened by nanglo123 2 months ago

#362 - Add add_observable function with a concept pattern

Issue - State: closed - Opened by bgyori 2 months ago - 2 comments

#360 - Update code to be compatible with Pydantic2

Pull Request - State: closed - Opened by nanglo123 2 months ago

#360 - Update code to be compatible with Pydantic2

Pull Request - State: closed - Opened by nanglo123 2 months ago

#359 - Update code to be compatible with Pydantic2

Pull Request - State: closed - Opened by nanglo123 2 months ago

#359 - Update code to be compatible with Pydantic2

Pull Request - State: closed - Opened by nanglo123 2 months ago

#358 - Support expressions in parameters of distributions

Pull Request - State: closed - Opened by bgyori 2 months ago

#358 - Support expressions in parameters of distributions

Pull Request - State: closed - Opened by bgyori 2 months ago

#357 - Pydantic version conflict when installing MIRA with `biomodels` package

Issue - State: closed - Opened by liunelson 3 months ago - 1 comment

#357 - Pydantic version conflict when installing MIRA with `biomodels` package

Issue - State: closed - Opened by liunelson 3 months ago - 1 comment

#354 - Add parameter id to amr export if parameter display name doesn't exist

Pull Request - State: closed - Opened by nanglo123 3 months ago - 1 comment

#354 - Add parameter id to amr export if parameter display name doesn't exist

Pull Request - State: closed - Opened by nanglo123 3 months ago - 1 comment

#351 - Inconsistency in the structure of `param_dict`

Issue - State: open - Opened by liunelson 3 months ago - 2 comments

#351 - Inconsistency in the structure of `param_dict`

Issue - State: open - Opened by liunelson 3 months ago - 2 comments

#350 - Add updated notebooks and exports for 2024.08 scenarios

Pull Request - State: closed - Opened by bgyori 4 months ago

#350 - Add updated notebooks and exports for 2024.08 scenarios

Pull Request - State: closed - Opened by bgyori 4 months ago

#349 - Change new transition naming upon stratification

Pull Request - State: closed - Opened by bgyori 4 months ago

#349 - Change new transition naming upon stratification

Pull Request - State: closed - Opened by bgyori 4 months ago

#348 - Duplicated template names after stratification

Issue - State: closed - Opened by mwdchang 4 months ago

#348 - Duplicated template names after stratification

Issue - State: closed - Opened by mwdchang 4 months ago

#347 - Implement new templates to model metabolism

Pull Request - State: closed - Opened by bgyori 4 months ago

#347 - Implement new templates to model metabolism

Pull Request - State: closed - Opened by bgyori 4 months ago

#346 - grouped natural conversion class and test and schema

Pull Request - State: closed - Opened by augeorge 4 months ago - 5 comments

#346 - grouped natural conversion class and test and schema

Pull Request - State: closed - Opened by augeorge 4 months ago - 5 comments

#345 - Feature request: GroupedNaturalConversion

Issue - State: closed - Opened by djinnome 4 months ago

#344 - Add resources to dkg

Pull Request - State: closed - Opened by nanglo123 4 months ago

#344 - Add resources to dkg

Pull Request - State: closed - Opened by nanglo123 4 months ago

#343 - Adjust test that are affected by the sympy 1.13 update

Pull Request - State: closed - Opened by nanglo123 5 months ago

#343 - Adjust test that are affected by the sympy 1.13 update

Pull Request - State: closed - Opened by nanglo123 5 months ago

#342 - Extend DKG Instance

Pull Request - State: closed - Opened by nanglo123 5 months ago

#342 - Extend DKG Instance

Pull Request - State: closed - Opened by nanglo123 5 months ago

#341 - [BUG]: Some annotations are missed by `template_model_from_amr_json`

Issue - State: closed - Opened by liunelson 5 months ago - 1 comment

#341 - [BUG]: Some annotations are missed by `template_model_from_amr_json`

Issue - State: closed - Opened by liunelson 5 months ago - 1 comment

#340 - Fix serialization for datetime

Pull Request - State: closed - Opened by nanglo123 5 months ago

#340 - Fix serialization for datetime

Pull Request - State: closed - Opened by nanglo123 5 months ago

#338 - Rename templates during stratification

Pull Request - State: closed - Opened by bgyori 5 months ago

#338 - Rename templates during stratification

Pull Request - State: closed - Opened by bgyori 5 months ago

#337 - Change link for budyko-sellers decapode example

Pull Request - State: closed - Opened by nanglo123 6 months ago