Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / biocircuits/bioscrape issues and pull requests
#176 - Default bioscrape installation to core-only without lineage
Pull Request -
State: open - Opened by ayush9pandey 3 months ago
- 2 comments
Labels: Bioscrape Core, Lineages
#175 - Master to dev.
Pull Request -
State: closed - Opened by ayush9pandey 3 months ago
#174 - Lineage installation does not build with PyPa
Issue -
State: open - Opened by ayush9pandey 3 months ago
- 3 comments
Labels: bug, Bioscrape Core, Lineages
#173 - update for NumPy 2.0
Pull Request -
State: closed - Opened by murrayrm 3 months ago
- 5 comments
#172 - Python version compatibility
Issue -
State: closed - Opened by ayush9pandey 3 months ago
- 1 comment
Labels: bug
#171 - Propogate Lineages occasionally duplicating returned cells into multiple bins
Issue -
State: open - Opened by WilliamIX over 1 year ago
Labels: Lineages
#170 - Update documentation of Model construction
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
#169 - Update dev
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
#168 - Update license
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
#167 - Fixes to bibliography
Pull Request -
State: closed - Opened by csoneson over 1 year ago
#166 - Enhanced documentation with Bioscrape v1.2.2
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
- 1 comment
#165 - Enhanced documentation (JOSS REVIEW)
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
- 1 comment
Labels: documentation
#164 - SBML File Import error
Issue -
State: open - Opened by SpencerUyematsu over 1 year ago
#163 - JOSS Review -- A list of minor comments
Issue -
State: closed - Opened by Farnazmdi over 1 year ago
- 8 comments
Labels: documentation
#162 - JOSS Review -- minor comment on figures in the notebook examples
Issue -
State: closed - Opened by Farnazmdi over 1 year ago
- 1 comment
Labels: documentation
#161 - setuptools deprecation and move to pyproject.toml (PEP 517 )
Issue -
State: closed - Opened by ayush9pandey over 1 year ago
- 1 comment
Labels: bug, Bioscrape Core
#160 - Changes to package after JOSS review 1
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
- 3 comments
#159 - Benchmarking bioscrape performance
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
#158 - Add contributing.md
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
Labels: documentation
#157 - JOSS REVIEW - Statement of Need -> Target Audience
Issue -
State: closed - Opened by Robaina over 1 year ago
- 2 comments
Labels: documentation
#156 - JOSS REVIEW - Performance claims in the manuscript not backed
Issue -
State: closed - Opened by Robaina over 1 year ago
- 2 comments
Labels: documentation
#155 - Add contributing.md
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
#154 - Fix advanced examples notebook
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
- 4 comments
#153 - Get latest master changes to dev
Pull Request -
State: closed - Opened by ayush9pandey over 1 year ago
#152 - JOSS Review - Advance example Notebook broken
Issue -
State: closed - Opened by Robaina over 1 year ago
- 3 comments
Labels: bug, documentation
#151 - JOSS REVIEW - Contributing Guidelines
Issue -
State: closed - Opened by Robaina over 1 year ago
- 2 comments
Labels: documentation
#150 - Add setup.cfg for pypi
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
#149 - update readme
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
#148 - Dev to Master for v1.2
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
#147 - test PR on dev
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
#146 - Repo cleanup + Upgrade testing CI env to Python v3.10
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
- 6 comments
#145 - Inference pickling
Pull Request -
State: closed - Opened by WilliamIX almost 2 years ago
- 2 comments
#144 - Add colab links + add more information to README
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
- 1 comment
Labels: enhancement
#143 - Simulator hotfix + Corner dependency
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
- 2 comments
Labels: bug
#142 - Rename workflow to bioscrape.yml
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
#141 - Bioscrape v1.1.0
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
Labels: enhancement, Analysis Features
#140 - Fix #135 by adding dtype double to inference timepoints and data
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
#139 - Directly load SBML model in the Model constructor
Issue -
State: closed - Opened by ayush9pandey almost 2 years ago
- 1 comment
Labels: enhancement, Bioscrape Core
#138 - A cluster of changes to inference
Pull Request -
State: closed - Opened by ayush9pandey almost 2 years ago
- 3 comments
Labels: Inference
#137 - Inference bug fixes
Pull Request -
State: closed - Opened by ayush9pandey about 2 years ago
Labels: bug, Bioscrape Core, Analysis Features
#136 - Fix sensitivity analysis bug #126 and #125
Pull Request -
State: closed - Opened by ayush9pandey about 2 years ago
- 1 comment
Labels: bug, Analysis Features
#135 - Dtype mismatch error when integers are passed in inference routines.
Issue -
State: closed - Opened by ayush9pandey about 2 years ago
Labels: bug, Inference
#134 - Fixes issue #123 : sbml_warnings keyword error
Pull Request -
State: closed - Opened by ayush9pandey about 2 years ago
- 1 comment
Labels: bug, Bioscrape Core
#133 - odeint default simulation values in simulator.pyx cause long simulations
Issue -
State: closed - Opened by ayush9pandey about 2 years ago
- 4 comments
Labels: bug, Bioscrape Core
#132 - Ext species duplicate when combining BioCRNpyler external compartment in SubSBML
Issue -
State: open - Opened by oliviaywangn about 2 years ago
#131 - Merging changes from dev to master
Pull Request -
State: closed - Opened by ayush9pandey about 2 years ago
- 2 comments
Labels: enhancement, Bioscrape Core, Lineages, Inference, Analysis Features
#130 - A Pandas dataframe for sensitivity analysis matrix instead of 3D array
Issue -
State: open - Opened by ayush9pandey about 2 years ago
Labels: enhancement, Analysis Features
#129 - Fix `mcmc_results.csv` file writing
Issue -
State: closed - Opened by ayush9pandey about 2 years ago
Labels: bug, Inference
#128 - Add option to `py_inference` to pass in conditions on changing model parameter conditions for each trajectory in the data.
Issue -
State: closed - Opened by ayush9pandey about 2 years ago
Labels: enhancement, Inference
#127 - Timing the bioscrape simulations
Issue -
State: open - Opened by ayush9pandey over 2 years ago
Labels: enhancement, help wanted
#126 - Sensitivity analysis bug: Original model parameter dictionary is changed after running SSA
Issue -
State: closed - Opened by ayush9pandey over 2 years ago
- 1 comment
Labels: bug, Analysis Features
#125 - Add docstring to `py_sensitivity_analysis`
Issue -
State: closed - Opened by ayush9pandey over 2 years ago
- 1 comment
Labels: enhancement, Analysis Features
#124 - random number as a parameter
Issue -
State: closed - Opened by TiamHeydari over 2 years ago
- 1 comment
#123 - Error while importing SBML in `import_sbml`
Issue -
State: closed - Opened by ayush9pandey over 2 years ago
- 1 comment
#122 - Stochastic Simulating of Styrene polymerization in free radicals
Issue -
State: closed - Opened by teddiclax almost 3 years ago
- 1 comment
#121 - update to version 1.0.4
Pull Request -
State: closed - Opened by WilliamIX about 3 years ago
#120 - Dev to Master Inference Upgrades
Pull Request -
State: closed - Opened by WilliamIX about 3 years ago
#119 - Possible Timepoint issues in Lineage Simulations
Issue -
State: open - Opened by WilliamIX about 3 years ago
Labels: Lineages
#118 - Wp inference
Pull Request -
State: closed - Opened by WilliamIX about 3 years ago
- 2 comments
#117 - Unexpected near-duplications in stochastic simulation output with different initial conditions.
Issue -
State: open - Opened by sclamons about 3 years ago
#116 - Species counts are stored as doubles, not ints, allowing some nasty bugs.
Issue -
State: open - Opened by sclamons about 3 years ago
Labels: documentation, invalid, Bioscrape Core, Lineages
#115 - Infinite loop fix
Pull Request -
State: closed - Opened by sclamons about 3 years ago
#114 - Infinite loop possible in SimulateTurbidostat.
Issue -
State: closed - Opened by sclamons about 3 years ago
Labels: bug, Lineages
#113 - Deterministic safe mode
Pull Request -
State: closed - Opened by WilliamIX about 3 years ago
- 1 comment
#112 - Bioscrape release v1.0.3
Pull Request -
State: closed - Opened by ayush9pandey over 3 years ago
- 1 comment
#111 - New features: Sensitivity analysis
Pull Request -
State: closed - Opened by ayush9pandey over 3 years ago
- 3 comments
Labels: enhancement, Analysis Features
#110 - How to write GeneralODERule to SBML?
Issue -
State: closed - Opened by ayush9pandey over 3 years ago
- 5 comments
#109 - emcee update `sampler.flatchain` to `sampler.get_chain`
Pull Request -
State: closed - Opened by ayush9pandey over 3 years ago
#108 - Removing Bioscrape XML and adding SBML Functionality
Pull Request -
State: closed - Opened by WilliamIX over 3 years ago
- 5 comments
#107 - Add SBML support for the new rule types
Issue -
State: closed - Opened by WilliamIX over 3 years ago
- 1 comment
#106 - Rules and simulator upgrade
Pull Request -
State: closed - Opened by WilliamIX over 3 years ago
#105 - minor bug fixes
Pull Request -
State: closed - Opened by WilliamIX over 3 years ago
#104 - Delay support for inference
Issue -
State: closed - Opened by ayush9pandey over 3 years ago
- 1 comment
#103 - Fix a minor bug in delay simulator
Pull Request -
State: closed - Opened by ayush9pandey over 3 years ago
#102 - Inference updates, new features, and bug fixes
Pull Request -
State: closed - Opened by ayush9pandey over 3 years ago
- 4 comments
#101 - Cython Statistics for SSA Trajectories
Pull Request -
State: closed - Opened by WilliamIX over 3 years ago
- 3 comments
#100 - Fast Emprical Distribution Calculation
Issue -
State: closed - Opened by WilliamIX over 3 years ago
- 1 comment
#99 - Deprecate Bioscrape XML and Replace with SBML
Issue -
State: closed - Opened by WilliamIX over 3 years ago
- 2 comments
Labels: Bioscrape Core
#98 - Turbidostat
Pull Request -
State: closed - Opened by sclamons over 3 years ago
#97 - Serialization
Pull Request -
State: closed - Opened by sclamons over 3 years ago
- 2 comments
#96 - Rules do not fire if no reactions can occur.
Issue -
State: closed - Opened by sclamons over 3 years ago
- 3 comments
Labels: bug, Bioscrape Core
#95 - Lineage.py_get_schnitz() crashes the kernel if called with an out-of-bounds index.
Issue -
State: closed - Opened by sclamons over 3 years ago
- 3 comments
Labels: bug, documentation, Lineages
#94 - Would be useful to have a simple interface for getting a single-time snapshot at a target population size
Issue -
State: open - Opened by sclamons over 3 years ago
- 3 comments
Labels: enhancement, Lineages
#92 - p0 = the initial seed for parameters to start the inference should be able to be a user input
Issue -
State: closed - Opened by ayush9pandey over 3 years ago
- 1 comment
#91 - Summary statistics on convergence should be printed after every inference run
Issue -
State: closed - Opened by ayush9pandey over 3 years ago
- 1 comment
#90 - CSV writing for parameter inference should be controlled by user
Issue -
State: closed - Opened by ayush9pandey over 3 years ago
- 1 comment
#89 - Check rate laws when importing and writing SBML for successful libSBML operation
Issue -
State: closed - Opened by ayush9pandey over 3 years ago
- 2 comments
#85 - Integrating Github Actions
Pull Request -
State: closed - Opened by WilliamIX over 3 years ago
#81 - installation process only works if bioscrape installed in the current folder
Issue -
State: closed - Opened by zoltuz almost 4 years ago
- 4 comments
#79 - Gaussian prior minor bug in probability computation
Issue -
State: closed - Opened by ayush9pandey almost 4 years ago
- 3 comments
#60 - Do rules work for setting parameter values at a certain time during the simulation?
Issue -
State: closed - Opened by ayush9pandey about 4 years ago
- 1 comment
#57 - Model objects (and presumably others) can't be copied with Python's copy.copy because they can't be pickled..
Issue -
State: closed - Opened by sclamons about 4 years ago
- 3 comments
Labels: Bioscrape Core
#52 - Linages Pointer error
Issue -
State: open - Opened by sophiejwalton over 4 years ago
- 2 comments
Labels: bug, Lineages
#51 - distributing bioscrape binaries through conda-forge
Issue -
State: closed - Opened by zoltuz over 4 years ago
- 7 comments
#42 - Perfect volume splitter creating species de novo
Issue -
State: closed - Opened by mkratz over 4 years ago
- 1 comment
Labels: bug, Lineages
#38 - Speeding up Bioscrape Inference
Issue -
State: open - Opened by WilliamIX over 4 years ago
- 3 comments
Labels: enhancement, help wanted, Inference
#34 - Ability to Simulate Lineages with a Chemostat
Issue -
State: closed - Opened by WilliamIX over 4 years ago
- 1 comment
Labels: enhancement, documentation, Lineages
#29 - Saving and loading sbml (finally) fixed
Pull Request -
State: closed - Opened by ayush9pandey over 4 years ago
#21 - ModuleNotFoundError when importing bioscrape from inside bioscrape directory.
Issue -
State: open - Opened by ayush9pandey over 4 years ago
- 5 comments
Labels: bug, Bioscrape Core
#14 - Ability to print easy-to-read representation of a model
Issue -
State: open - Opened by WilliamIX over 4 years ago
Labels: enhancement, documentation, Bioscrape Core