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BioSCRAPE installation issues with NumPy 2

Status: Open.

#182 In biocircuits/bioscrape;

· murrayrm opened on Mar 22, 2025

Lineage installation does not build with PyPa

Bioscrape CoreIssues pertaining to core bioscrape functionalityIssues pertaining to core bioscrape functionality

bugSomething isn't workingSomething isn't working

LineagesIssues pertaining to bioscrape lineagesIssues pertaining to bioscrape lineages

Status: Open.

#174 In biocircuits/bioscrape;

· ayush9pandey opened on Jul 12, 2024

Propogate Lineages occasionally duplicating returned cells into multiple bins

LineagesIssues pertaining to bioscrape lineagesIssues pertaining to bioscrape lineages

Status: Open.

#171 In biocircuits/bioscrape;

· WilliamIX opened on Jun 8, 2023

SBML File Import error

Status: Open.

#164 In biocircuits/bioscrape;

· SpencerUyematsu opened on Feb 9, 2023

Ext species duplicate when combining BioCRNpyler external compartment in SubSBML

Status: Open.

#132 In biocircuits/bioscrape;

· oliviaywangn opened on Jul 28, 2022

A Pandas dataframe for sensitivity analysis matrix instead of 3D array

Analysis FeaturesHelper functions for analyzing circuits (e.g. Sensitivity analysis)Helper functions for analyzing circuits (e.g. Sensitivity analysis)

enhancementNew feature or requestNew feature or request

Status: Open.

#130 In biocircuits/bioscrape;

· ayush9pandey opened on Jul 6, 2022

Timing the bioscrape simulations

enhancementNew feature or requestNew feature or request

help wantedExtra attention is neededExtra attention is needed

Status: Open.

#127 In biocircuits/bioscrape;

· ayush9pandey opened on Jun 24, 2022

Possible Timepoint issues in Lineage Simulations

LineagesIssues pertaining to bioscrape lineagesIssues pertaining to bioscrape lineages

Status: Open.

#119 In biocircuits/bioscrape;

· WilliamIX opened on Sep 16, 2021

Unexpected near-duplications in stochastic simulation output with different initial conditions.

Status: Open.

#117 In biocircuits/bioscrape;

· sclamons opened on Aug 14, 2021

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

Bioscrape CoreIssues pertaining to core bioscrape functionalityIssues pertaining to core bioscrape functionality

documentationSoftware and example documentationSoftware and example documentation

invalidThis doesn't seem rightThis doesn't seem right

LineagesIssues pertaining to bioscrape lineagesIssues pertaining to bioscrape lineages

Status: Open.

#116 In biocircuits/bioscrape;

· sclamons opened on Aug 13, 2021

Would be useful to have a simple interface for getting a single-time snapshot at a target population size

enhancementNew feature or requestNew feature or request

LineagesIssues pertaining to bioscrape lineagesIssues pertaining to bioscrape lineages

Status: Open.

#94 In biocircuits/bioscrape;

· sclamons opened on Mar 18, 2021

Add Noise Model to Bioscrape Inference

enhancementNew feature or requestNew feature or request

InferenceIssues Pertaining to Bioscrape Inference, Parameter Identificaiton, and System IdentificationIssues Pertaining to Bioscrape Inference, Parameter Identificaiton, and System Identification

Status: Open.

#62 In biocircuits/bioscrape;

· WilliamIX opened on Sep 16, 2020

 ·  

Inference Milestone End of October