LoLab-MSM pysb issues - Githubissues

LoLab-MSM / pysb

Python framework for Systems Biology modeling [Lopez Lab Mods]

BSD 2-Clause "Simplified" License

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DNM: Travis-CI.com test

#50 alubbock closed 3 years ago
0
Do not merge: Travis.com Test PR

#49 alubbock closed 3 years ago
0
Fix altered matplotlib API call

#48 alubbock closed 3 years ago
0
Test whether BNG and Kappa exports produce identical network-free dynamics

#47 lh64 opened 6 years ago
0
lsoda cpu multiprocessing

#46 ortega2247 closed 5 years ago
3
Cytoscapejs

#45 ortega2247 closed 5 years ago
2
Adding logic to download python2

#44 JamesPino closed 5 years ago
2
Change scipy.weave to cython

#43 JamesPino closed 7 years ago
0
Check coverage for sens_analysis

#42 JamesPino closed 7 years ago
1
Change sens analysis to take integrator

#41 JamesPino closed 7 years ago
1
Sensitivity analysis doc string and example

#40 JamesPino closed 7 years ago
1
[WIP] Sensitivity analysis review

#39 alubbock closed 7 years ago
2
Simclass lah

#38 lh64 closed 7 years ago
4
Visualization cytoscape

#37 ortega2247 closed 7 years ago
5
Updated base.py

#36 JamesPino closed 7 years ago
3
Pysb flat export

#35 JamesPino closed 7 years ago
3
we need a pre equilibration function.

#34 ortega2247 opened 8 years ago
2
New Simulator class with custom protocol support

#33 alubbock opened 8 years ago
0
Add simple plotting macros for matplotlib

#32 alubbock opened 8 years ago
0
cupSODA: throw an error if model contains functional rate laws

#31 lh64 closed 7 years ago
1
cupSODA: Raise exception when simulation fails

#30 alubbock opened 8 years ago
0
cupSODA: PySB/cupSODA example

#29 alubbock closed 7 years ago
1
cupSODA: Create cupSODA unit tests

#28 alubbock opened 8 years ago
2
cupSODA: Run cupSODA multiple times if necessary

#27 alubbock opened 8 years ago
0
cupSODA: Make 'param_values' and 'y0' optional to conform to general simulator convention

#26 alubbock closed 7 years ago
1
cupSODA: Improve verbosity handling

#25 alubbock closed 7 years ago
3
Cupsoda simulator

#24 JamesPino closed 8 years ago
3
Convert scipy_weave to cython in integrate.py

#23 JamesPino closed 6 years ago
1
Python 3 - replacement for <> operator?

#22 alubbock closed 6 years ago
1
Modify PySB to detect dangling bonds

#21 lh64 opened 9 years ago
3
Move pyURMDE to separate repo

#20 alubbock closed 9 years ago
1
Create BNG interface using pexpect

#19 alubbock closed 7 years ago
1
Support for identical components in Monomers

#18 lh64 opened 9 years ago
0
Modify Solver.run() in 'dev' branch to allow 'param_values' to be passed as a dictionary

#17 lh64 closed 9 years ago
0
ComplexPattern.is_equivalent_to() requires identical bond numbering

#16 lh64 closed 6 years ago
1
Modify Solver.run() in 'dev' branch to check if 'y0' is an instance 'dict'

#15 lh64 closed 7 years ago
7
Merge pysb.tools.bngSSA simulator back into pysb.bng

#14 JamesPino closed 6 years ago
1
Update pysb.integrate.Solver to select odeint if intergrator='lsoda'

#13 JamesPino closed 9 years ago
2
Speed up Travis-CI builds by factor of 9 or so

#12 alubbock closed 9 years ago
0
Overhead in using custom propensity functions in PySB/GillesPy interface

#11 lh64 closed 9 years ago
1
Problems with reversible synth/deg rules

#10 lh64 opened 9 years ago
3
Bug in 'bind_table_complex' macro

#9 lh64 opened 9 years ago
1
cupSODA.py unit test

#8 lh64 closed 9 years ago
1
Move stochkit to separate repository

#7 lh64 closed 9 years ago
1
pysb.bng._parse_reaction failing if multiple rules generate the same reaction

#6 lh64 closed 9 years ago
2
Improve PySB/cupSODA interface; move to separate repo

#5 lh64 closed 9 years ago
3
Move tropical code to separate repository

#4 ortega2247 closed 9 years ago
2
Travis-CI runs slowly

#3 alubbock closed 9 years ago
1
test_tropical.py fails with the current version of the tropical code

#2 lh64 closed 9 years ago
1
Continuous integration support

#1 alubbock closed 11 years ago
0