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

#171 - Propogate Lineages occasionally duplicating returned cells into multiple bins

Issue - State: open - Opened by WilliamIX about 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 over 1 year ago

#149 - update readme

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago

#148 - Dev to Master for v1.2

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago

#147 - test PR on dev

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago

#146 - Repo cleanup + Upgrade testing CI env to Python v3.10

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago - 6 comments

#145 - Inference pickling

Pull Request - State: closed - Opened by WilliamIX over 1 year ago - 2 comments

#144 - Add colab links + add more information to README

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago - 1 comment
Labels: enhancement

#143 - Simulator hotfix + Corner dependency

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago - 2 comments
Labels: bug

#142 - Rename workflow to bioscrape.yml

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago

#141 - Bioscrape v1.1.0

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago
Labels: enhancement, Analysis Features

#140 - Fix #135 by adding dtype double to inference timepoints and data

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago

#139 - Directly load SBML model in the Model constructor

Issue - State: closed - Opened by ayush9pandey over 1 year ago - 1 comment
Labels: enhancement, Bioscrape Core

#138 - A cluster of changes to inference

Pull Request - State: closed - Opened by ayush9pandey over 1 year ago - 3 comments
Labels: Inference

#137 - Inference bug fixes

Pull Request - State: closed - Opened by ayush9pandey almost 2 years ago
Labels: bug, Bioscrape Core, Analysis Features

#136 - Fix sensitivity analysis bug #126 and #125

Pull Request - State: closed - Opened by ayush9pandey almost 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 almost 2 years ago
Labels: bug, Inference

#134 - Fixes issue #123 : sbml_warnings keyword error

Pull Request - State: closed - Opened by ayush9pandey almost 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 almost 2 years ago - 4 comments
Labels: bug, Bioscrape Core

#131 - Merging changes from dev to master

Pull Request - State: closed - Opened by ayush9pandey almost 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 almost 2 years ago
Labels: enhancement, Analysis Features

#129 - Fix `mcmc_results.csv` file writing

Issue - State: closed - Opened by ayush9pandey almost 2 years ago
Labels: bug, Inference

#127 - Timing the bioscrape simulations

Issue - State: open - Opened by ayush9pandey about 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 about 2 years ago - 1 comment
Labels: bug, Analysis Features

#125 - Add docstring to `py_sensitivity_analysis`

Issue - State: closed - Opened by ayush9pandey about 2 years ago - 1 comment
Labels: enhancement, Analysis Features

#124 - random number as a parameter

Issue - State: closed - Opened by TiamHeydari about 2 years ago - 1 comment

#123 - Error while importing SBML in `import_sbml`

Issue - State: closed - Opened by ayush9pandey about 2 years ago - 1 comment

#122 - Stochastic Simulating of Styrene polymerization in free radicals

Issue - State: closed - Opened by teddiclax over 2 years ago - 1 comment

#121 - update to version 1.0.4

Pull Request - State: closed - Opened by WilliamIX almost 3 years ago

#120 - Dev to Master Inference Upgrades

Pull Request - State: closed - Opened by WilliamIX almost 3 years ago

#119 - Possible Timepoint issues in Lineage Simulations

Issue - State: open - Opened by WilliamIX almost 3 years ago
Labels: Lineages

#118 - Wp inference

Pull Request - State: closed - Opened by WilliamIX almost 3 years ago - 2 comments

#116 - Species counts are stored as doubles, not ints, allowing some nasty bugs.

Issue - State: open - Opened by sclamons almost 3 years ago
Labels: documentation, invalid, Bioscrape Core, Lineages

#115 - Infinite loop fix

Pull Request - State: closed - Opened by sclamons almost 3 years ago

#114 - Infinite loop possible in SimulateTurbidostat.

Issue - State: closed - Opened by sclamons almost 3 years ago
Labels: bug, Lineages

#113 - Deterministic safe mode

Pull Request - State: closed - Opened by WilliamIX almost 3 years ago - 1 comment

#112 - Bioscrape release v1.0.3

Pull Request - State: closed - Opened by ayush9pandey about 3 years ago - 1 comment

#111 - New features: Sensitivity analysis

Pull Request - State: closed - Opened by ayush9pandey about 3 years ago - 3 comments
Labels: enhancement, Analysis Features

#110 - How to write GeneralODERule to SBML?

Issue - State: closed - Opened by ayush9pandey about 3 years ago - 5 comments

#109 - emcee update `sampler.flatchain` to `sampler.get_chain`

Pull Request - State: closed - Opened by ayush9pandey about 3 years ago

#108 - Removing Bioscrape XML and adding SBML Functionality

Pull Request - State: closed - Opened by WilliamIX about 3 years ago - 5 comments

#107 - Add SBML support for the new rule types

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

#106 - Rules and simulator upgrade

Pull Request - State: closed - Opened by WilliamIX about 3 years ago

#105 - minor bug fixes

Pull Request - State: closed - Opened by WilliamIX about 3 years ago

#104 - Delay support for inference

Issue - State: closed - Opened by ayush9pandey about 3 years ago - 1 comment

#103 - Fix a minor bug in delay simulator

Pull Request - State: closed - Opened by ayush9pandey about 3 years ago

#102 - Inference updates, new features, and bug fixes

Pull Request - State: closed - Opened by ayush9pandey about 3 years ago - 4 comments

#101 - Cython Statistics for SSA Trajectories

Pull Request - State: closed - Opened by WilliamIX about 3 years ago - 3 comments

#100 - Fast Emprical Distribution Calculation

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

#99 - Deprecate Bioscrape XML and Replace with SBML

Issue - State: closed - Opened by WilliamIX about 3 years ago - 2 comments
Labels: Bioscrape Core

#98 - Turbidostat

Pull Request - State: closed - Opened by sclamons about 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

#90 - CSV writing for parameter inference should be controlled by user

Issue - State: closed - Opened by ayush9pandey over 3 years ago - 1 comment

#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 over 3 years ago - 4 comments

#79 - Gaussian prior minor bug in probability computation

Issue - State: closed - Opened by ayush9pandey over 3 years ago - 3 comments

#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 almost 4 years ago - 3 comments
Labels: Bioscrape Core

#52 - Linages Pointer error

Issue - State: open - Opened by sophiejwalton about 4 years ago - 2 comments
Labels: bug, Lineages

#51 - distributing bioscrape binaries through conda-forge

Issue - State: closed - Opened by zoltuz about 4 years ago - 7 comments

#42 - Perfect volume splitter creating species de novo

Issue - State: closed - Opened by mkratz about 4 years ago - 1 comment
Labels: bug, Lineages

#38 - Speeding up Bioscrape Inference

Issue - State: open - Opened by WilliamIX about 4 years ago - 3 comments
Labels: enhancement, help wanted, Inference

#34 - Ability to Simulate Lineages with a Chemostat

Issue - State: closed - Opened by WilliamIX about 4 years ago - 1 comment
Labels: enhancement, documentation, Lineages

#29 - Saving and loading sbml (finally) fixed

Pull Request - State: closed - Opened by ayush9pandey about 4 years ago

#21 - ModuleNotFoundError when importing bioscrape from inside bioscrape directory.

Issue - State: open - Opened by ayush9pandey about 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 about 4 years ago
Labels: enhancement, documentation, Bioscrape Core

#13 - Add progress bar for stochastic simulations

Issue - State: closed - Opened by WilliamIX about 4 years ago - 1 comment
Labels: enhancement, Bioscrape Core

#12 - Quasi-steady-state Algebraic Rules

Issue - State: closed - Opened by WilliamIX about 4 years ago - 1 comment
Labels: enhancement, question, Bioscrape Core

#11 - Update Documentation

Issue - State: closed - Opened by WilliamIX about 4 years ago - 3 comments
Labels: enhancement, help wanted, documentation, Bioscrape Core, Lineages, Analysis Features

#10 - Ability to return Jacobians and Sensitivity Matrices

Issue - State: closed - Opened by WilliamIX about 4 years ago - 3 comments
Labels: enhancement, Bioscrape Core, Analysis Features

#8 - Add SBML support for delays

Issue - State: closed - Opened by WilliamIX about 4 years ago - 1 comment
Labels: enhancement, Bioscrape Core