Ecosyste.ms: Issues

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

GitHub / matthiaskoenig/sbmlsim issues and pull requests

#165 - Bump postcss, css-loader and vue-loader in /reports/fit-report

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#164 - Bump bootstrap from 4.0.0-beta to 4.0.0-beta.2 in /reports/fit-report

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#163 - Bump tough-cookie, @vue/cli-plugin-typescript and node-sass in /reports/fit-report

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#162 - Bump minimist from 1.2.5 to 1.2.8 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#161 - Bump express from 4.17.1 to 4.18.2 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#160 - Update dependencies

Issue - State: open - Opened by matthiaskoenig almost 2 years ago

#159 - Update ray to 2.2.0

Issue - State: open - Opened by matthiaskoenig almost 2 years ago

#158 - Bump qs from 6.5.2 to 6.5.3 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#157 - Bump decode-uri-component from 0.2.0 to 0.2.2 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#156 - Bump loader-utils from 1.4.0 to 1.4.2 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#155 - Bump minimatch from 3.0.4 to 3.0.8 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#153 - Bump terser from 4.8.0 to 4.8.1 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#152 - Bump shell-quote from 1.7.2 to 1.7.3 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#151 - Better handling of figures and data

Issue - State: open - Opened by matthiaskoenig over 2 years ago

#150 - Problem in parameter fitting (pravastatin)

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: bug, parameter estimation

#149 - Switch on new LLVM in roadrunner

Issue - State: open - Opened by matthiaskoenig over 2 years ago

#148 - Segmentation fault with RoadRunnerSBMLModel

Issue - State: closed - Opened by matthiaskoenig over 2 years ago - 1 comment
Labels: bug

#147 - Refactor parameter estimation to be in line with PETab/SED-ML

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: parameter estimation

#145 - Update handling of events in simulations

Issue - State: open - Opened by matthiaskoenig over 2 years ago

#144 - Create and add logo

Issue - State: closed - Opened by matthiaskoenig over 2 years ago

#143 - Make new release (0.3.0)

Issue - State: open - Opened by matthiaskoenig over 2 years ago

#142 - Fix uncertainty calculation and visualization

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: bug

#141 - Fix failing tests

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: testing

#140 - Twitter integration

Issue - State: closed - Opened by matthiaskoenig over 2 years ago

#139 - Refactor tests

Issue - State: closed - Opened by matthiaskoenig over 2 years ago

#138 - Problems with sbmlsim/amici on MacOS

Issue - State: open - Opened by stemllb over 2 years ago - 4 comments
Labels: bug, documentation

#137 - Bump async from 2.6.3 to 2.6.4 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#136 - Update dependencies

Issue - State: closed - Opened by matthiaskoenig over 2 years ago

#135 - Rename master branch

Issue - State: closed - Opened by matthiaskoenig over 2 years ago

#134 - Bump minimist from 1.2.5 to 1.2.6 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#133 - Bump url-parse from 1.5.1 to 1.5.10 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#132 - Bump url-parse from 1.5.1 to 1.5.7 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#130 - Update libroadrunner version

Issue - State: closed - Opened by matthiaskoenig almost 3 years ago

#129 - Python 3.10 support

Issue - State: open - Opened by matthiaskoenig almost 3 years ago

#128 - Bump follow-redirects from 1.13.3 to 1.14.8 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#127 - Bump node-sass from 4.14.1 to 7.0.0 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#126 - Bump follow-redirects from 1.13.3 to 1.14.7 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#125 - Reduce timepoints to simulation timepoints in parameter fitting

Issue - State: open - Opened by matthiaskoenig about 3 years ago
Labels: parameter estimation

#124 - Remove duplicate timepoints in concatenated timecourses

Issue - State: closed - Opened by matthiaskoenig about 3 years ago - 1 comment

#123 - Tolerance settings not applied in parallel simulations

Issue - State: open - Opened by matthiaskoenig about 3 years ago
Labels: bug

#122 - Update sensitivity simulations for simvastatin

Issue - State: closed - Opened by matthiaskoenig about 3 years ago - 1 comment

#120 - Refactor KISAOS to use KISAO SBO instead of ontology

Issue - State: closed - Opened by matthiaskoenig about 3 years ago
Labels: bug

#119 - Fix failing omeprazole simulations

Issue - State: closed - Opened by matthiaskoenig about 3 years ago

#118 - Refactor log and console (rich support)

Issue - State: closed - Opened by matthiaskoenig about 3 years ago

#117 - Failing simulations with pancreas model

Issue - State: closed - Opened by matthiaskoenig about 3 years ago
Labels: bug

#116 - Possible unit conversion bug in ICG simulation (Meijjer)

Issue - State: open - Opened by matthiaskoenig about 3 years ago - 3 comments
Labels: bug, priority

#115 - Bump url-parse from 1.5.1 to 1.5.3 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#114 - Goodness of fit plot for parameter estimation

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: parameter estimation

#113 - Bump path-parse from 1.0.6 to 1.0.7 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#112 - Error after running `pip install -e . --upgrade`

Issue - State: closed - Opened by JBrandh over 3 years ago - 1 comment

#111 - Clamp model changes are not working

Issue - State: open - Opened by matthiaskoenig over 3 years ago

#110 - Check validity of fit mappings on executing simulation experiment

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: parameter estimation

#109 - Support for SED-ML/COMBINE validation

Issue - State: open - Opened by matthiaskoenig over 3 years ago

#108 - Bump dns-packet from 1.3.1 to 1.3.4 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#107 - Bump hosted-git-info from 2.8.8 to 2.8.9 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#106 - Bump ssri from 6.0.1 to 6.0.2 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 2 comments
Labels: dependencies

#105 - Support kisao via kisao library

Issue - State: open - Opened by matthiaskoenig over 3 years ago

#104 - Move legends outside of plot

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: visualization

#103 - Provide a simulator in biosimulators

Issue - State: open - Opened by matthiaskoenig over 3 years ago - 1 comment
Labels: feature, help wanted

#102 - Support generation of webgraphics from matplotlib backend (mpld3)

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: feature, visualization

#101 - Optimization fails with data with all NaN y-errors

Issue - State: closed - Opened by matthiaskoenig over 3 years ago
Labels: bug, parameter estimation

#100 - Add API documentation to docs

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: documentation

#99 - Implement loss function for parameter fitting

Issue - State: closed - Opened by matthiaskoenig over 3 years ago
Labels: feature, parameter estimation

#98 - Bump webpack-dev-server from 2.11.5 to 3.1.11 in /reports/fit-report

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment

#97 - Bug in normalization of SensitivityScan

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: bug

#96 - Updated parameter fitting results plot

Issue - State: closed - Opened by matthiaskoenig over 3 years ago
Labels: parameter estimation

#95 - Handle units consistently in JSON serialization

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: bug

#94 - Update xarray to v0.17.0

Issue - State: closed - Opened by matthiaskoenig over 3 years ago

#93 - Feature parameter fitting

Pull Request - State: closed - Opened by matthiaskoenig almost 4 years ago

#91 - Support Hex colors in plotting

Issue - State: closed - Opened by matthiaskoenig almost 4 years ago

#90 - Fix mypy issues

Issue - State: open - Opened by matthiaskoenig almost 4 years ago
Labels: testing

#89 - Fix flake8 issues

Issue - State: closed - Opened by matthiaskoenig almost 4 years ago
Labels: testing

#88 - Figures not closed in parameter fitting (consuming too much memory)

Issue - State: closed - Opened by matthiaskoenig almost 4 years ago - 1 comment
Labels: bug, parameter estimation

#85 - Fitting of individual parameters per experiment/ group of experiments

Issue - State: open - Opened by matthiaskoenig almost 4 years ago
Labels: parameter estimation

#84 - Save/export model with model changes

Issue - State: open - Opened by matthiaskoenig almost 4 years ago
Labels: feature

#79 - Implement RMSD report for parameter fitting / model simulations;

Issue - State: closed - Opened by matthiaskoenig almost 4 years ago
Labels: parameter estimation

#75 - Support python 3.9

Issue - State: closed - Opened by matthiaskoenig almost 4 years ago - 1 comment
Labels: feature

#74 - Implement relative simulation experiments in parameter fitting

Issue - State: closed - Opened by matthiaskoenig almost 4 years ago - 1 comment
Labels: wontfix, priority, parameter estimation

#73 - Storage and combination of parameter fitting results

Issue - State: closed - Opened by matthiaskoenig about 4 years ago
Labels: parameter estimation

#72 - Better cost improvement plot (parameter fitting)

Issue - State: closed - Opened by matthiaskoenig about 4 years ago
Labels: parameter estimation

#70 - How to adjust number of cores used for simulations.

Issue - State: closed - Opened by adriankl about 4 years ago - 1 comment
Labels: wontfix

#63 - Automatically convert units for base keys in unit_conversion

Issue - State: closed - Opened by matthiaskoenig about 4 years ago - 1 comment

#62 - Too much RAM used when running multiple simulation experiments

Issue - State: open - Opened by matthiaskoenig about 4 years ago
Labels: bug

#61 - SED-ML L1V4 support

Issue - State: open - Opened by matthiaskoenig about 4 years ago
Labels: feature, visualization

#60 - PETab support for parameter estimation

Issue - State: open - Opened by matthiaskoenig about 4 years ago
Labels: feature, parameter estimation

#49 - Use model parameters as start values in local parameter fits

Issue - State: open - Opened by matthiaskoenig over 4 years ago
Labels: bug, parameter estimation

#44 - Units not displayed in parameter fitting results

Issue - State: open - Opened by matthiaskoenig over 4 years ago
Labels: bug, parameter estimation

#43 - Latex report of parameter fitting results

Issue - State: closed - Opened by matthiaskoenig over 4 years ago - 1 comment
Labels: wontfix, parameter estimation

#40 - Latex report of SimulationExperiments

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: report

#37 - Interactive reports of ParameterFitting

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: parameter estimation

#36 - Interactive reports of SimulationExperiments

Issue - State: open - Opened by matthiaskoenig over 4 years ago
Labels: visualization, report

#34 - Document SimulationExperiments processing

Issue - State: open - Opened by matthiaskoenig over 4 years ago
Labels: documentation

#32 - Improve parameter fitting plots & results

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: feature, report, parameter estimation

#30 - Ray/docker parallelization and containerization for cluster

Issue - State: open - Opened by matthiaskoenig over 4 years ago
Labels: feature, parameter estimation

#29 - Set initial values based on experimental data

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: feature, parameter estimation

#27 - Serialization of plots to vega using altair (interactive graphics)

Issue - State: open - Opened by matthiaskoenig over 4 years ago
Labels: visualization, report