Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape - v1.2.2

What's Changed (thanks to JOSS Review: https://github.com/openjournals/joss-reviews/issues/5057)

• Fix advanced examples notebook by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/154
• Add contributing.md by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/158
• Benchmarking bioscrape performance by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/159
• Changes to package after JOSS review 1 by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/160
• Enhanced documentation (JOSS review 2) by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/165
• Enhanced documentation with Bioscrape v1.2.2 by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/166

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by ayush9pandey over 3 years ago

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape - v1.2.0

Bioscrape v1.2 with:

1. Inference bug fixes, parallelization, and new features (check out the Wiki)
2. Sensitivity analysis
3. New readme, updated documentation, and testing.

Detailed release notes:

What's Changed

• Anandh's latest updates by @murrayrm in https://github.com/biocircuits/bioscrape/pull/1
• Merge changes from Anandh's fork by @murrayrm in https://github.com/biocircuits/bioscrape/pull/2
• Working version of bioscrape for BE 240 by @murrayrm in https://github.com/biocircuits/bioscrape/pull/3
• Merge changes from main repository. by @murrayrm in https://github.com/biocircuits/bioscrape/pull/4
• Fixing saving and loading SBML by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/24
• Saving and loading sbml (finally) fixed by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/29
• Bioscrape Inference working version by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/33
• Inference bug fixes by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/50
• Fixed Saved Result Randomized Unit Testing by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/66
• Ode safe mode by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/67
• Bioscrape annotations fix by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/65
• Remove underscore from parameter definition by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/68
• C vector bug fix by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/69
• Dev by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/70
• Lineage beta by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/71
• Dev to master by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/74
• Inference speed ups by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/73
• Update README to fix "build:passing" tag on main page by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/75
• Update current dev from master by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/77
• Add 6 new priors by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/76
• warnings.warn removed by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/80
• Inference bug fixes by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/82
• Pip install 2 by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/87
• Bioscrape release v1.0.3 by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/112
• Dev to Master Inference Upgrades by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/120
• update to version 1.0.4 by @WilliamIX in https://github.com/biocircuits/bioscrape/pull/121
• Merging changes from dev to master by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/131
• Bioscrape v1.1.0 by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/141
• Rename workflow to bioscrape.yml by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/142
• Add colab links + add more information to README by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/144
• Dev to Master for v1.2 by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/148
• update readme by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/149
• Add setup.cfg for pypi by @ayush9pandey in https://github.com/biocircuits/bioscrape/pull/150

New Contributors

• @murrayrm made their first contribution in https://github.com/biocircuits/bioscrape/pull/1

Full Changelog: https://github.com/biocircuits/bioscrape/compare/v0.0.1...v1.2.0

Scientific Software - Peer-reviewed - Jupyter Notebook
Published by ayush9pandey over 3 years ago