Skip to content

Issues: biocircuits/bioscrape

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

31 Open 68 Closed
31 Open 68 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Lineage installation does not build with PyPa Bioscrape Core Issues pertaining to core bioscrape functionality bug Something isn't working Lineages Issues pertaining to bioscrape lineages
#174 opened Jul 12, 2024 by ayush9pandey
@ayush9pandey
3
Propogate Lineages occasionally duplicating returned cells into multiple bins Lineages Issues pertaining to bioscrape lineages
#171 opened Jun 8, 2023 by WilliamIX
SBML File Import error
#164 opened Feb 9, 2023 by SpencerUyematsu
@ayush9pandey
Ext species duplicate when combining BioCRNpyler external compartment in SubSBML
#132 opened Jul 28, 2022 by oliviaywangn
A Pandas dataframe for sensitivity analysis matrix instead of 3D array Analysis Features Helper functions for analyzing circuits (e.g. Sensitivity analysis) enhancement New feature or request
#130 opened Jul 6, 2022 by ayush9pandey
@ayush9pandey
Timing the bioscrape simulations enhancement New feature or request help wanted Extra attention is needed
#127 opened Jun 24, 2022 by ayush9pandey
Possible Timepoint issues in Lineage Simulations Lineages Issues pertaining to bioscrape lineages
#119 opened Sep 16, 2021 by WilliamIX
@WilliamIX
Unexpected near-duplications in stochastic simulation output with different initial conditions.
#117 opened Aug 14, 2021 by sclamons
Species counts are stored as doubles, not ints, allowing some nasty bugs. Bioscrape Core Issues pertaining to core bioscrape functionality documentation Software and example documentation invalid This doesn't seem right Lineages Issues pertaining to bioscrape lineages
#116 opened Aug 13, 2021 by sclamons
Would be useful to have a simple interface for getting a single-time snapshot at a target population size enhancement New feature or request Lineages Issues pertaining to bioscrape lineages
#94 opened Mar 18, 2021 by sclamons
3
Add Noise Model to Bioscrape Inference enhancement New feature or request Inference Issues Pertaining to Bioscrape Inference, Parameter Identificaiton, and System Identification
#62 opened Sep 16, 2020 by WilliamIX Inference Milestone End of October
@WilliamIX @sclamons @ayush9pandey
1
Model parsing can fail on some OSX instances unless lxml package installed
#56 opened Aug 13, 2020 by sclamons
Add SBML Events as Bioscrape Rules Bioscrape Core Issues pertaining to core bioscrape functionality enhancement New feature or request
#53 opened Jul 8, 2020 by WilliamIX
@WilliamIX @ayush9pandey
Linages Pointer error bug Something isn't working Lineages Issues pertaining to bioscrape lineages
#52 opened Jun 29, 2020 by sophiejwalton
2
Add docstrings to classes and functions for automated documentation + Clarity enhancement New feature or request
#49 opened Jun 15, 2020 by ayush9pandey
@WilliamIX @sclamons @ayush9pandey
3
Sometimes SingleCellSSAResults have duplicate timepoints bug Something isn't working Lineages Issues pertaining to bioscrape lineages
#48 opened Jun 11, 2020 by WilliamIX
@WilliamIX
py_SimulateInteractingLineages throws and error when initial_cell_states = [] bug Something isn't working Lineages Issues pertaining to bioscrape lineages
#47 opened Jun 11, 2020 by WilliamIX
@WilliamIX
py_initialize_model should be called automatically from the py_simulate wrappers bug Something isn't working Lineages Issues pertaining to bioscrape lineages
#46 opened Jun 11, 2020 by WilliamIX
@WilliamIX
Use cpdef instead of a wrapper "py_<function>" function where appropriate documentation Software and example documentation enhancement New feature or request
#45 opened Jun 8, 2020 by sclamons
1
Speeding up Bioscrape Inference enhancement New feature or request help wanted Extra attention is needed Inference Issues Pertaining to Bioscrape Inference, Parameter Identificaiton, and System Identification
#38 opened May 28, 2020 by WilliamIX
3
Please Document Seg Faults with interacting Lineage Simulations bug Something isn't working help wanted Extra attention is needed question Further information is requested
#36 opened May 28, 2020 by WilliamIX
Cell Counts as Lineage Parameters documentation Software and example documentation enhancement New feature or request Lineages Issues pertaining to bioscrape lineages
#35 opened May 28, 2020 by WilliamIX
Using multiprocessing->map on Lineage simulations produces duplicate simulations bug Something isn't working Lineages Issues pertaining to bioscrape lineages
#32 opened May 22, 2020 by sclamons
3
Add support for diffusion reactions and multiple volumes Bioscrape Core Issues pertaining to core bioscrape functionality enhancement New feature or request help wanted Extra attention is needed
#30 opened Apr 30, 2020 by WilliamIX
Add Multiprocessing example Bioscrape Core Issues pertaining to core bioscrape functionality
#28 opened Apr 28, 2020 by WilliamIX
@WilliamIX
3
ProTip! Type g i on any issue or pull request to go back to the issue listing page.