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RuleWorld
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bionetgen
Rule-based modeling framework
https://bionetgen.org/
MIT License
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Time-dependent rate laws?
#275
hodgensc
opened
1 month ago
1
Missing links for BioNetGen
#274
anamariemartinez
closed
3 months ago
0
Add support for use of parameters in simulate settings, such as t_start=>t0, where t0 is defined in the parameters block.
#273
wshlavacek
closed
3 months ago
2
SBML export of symbolic rateLaws
#272
paulflang
closed
4 months ago
2
Automatically generated variable names not being exported to SBML file
#271
jrfaeder
closed
5 months ago
1
TotalRate keyword is ignored in generating .net, SBML, and other outputs
#270
jrfaeder
opened
6 months ago
0
Clean fix to catch species that refer to observables or functions
#269
ASinanSaglam
closed
11 months ago
0
ASinan Saglam/issue264
#268
ASinanSaglam
closed
11 months ago
0
BNG2.pl should catch species block issues
#267
ASinanSaglam
closed
11 months ago
1
Fix dead link in README
#266
himoto
closed
12 months ago
1
SSA performance bug regarding order of reactions
#265
leon9812
opened
1 year ago
4
BioNetGen does not export "initialAssigments" in SBML files
#264
NikosMemmos
closed
11 months ago
8
Small Update
#263
cjarmstrong97
closed
1 year ago
0
Bundled CVODE contains CMake script with C99 compatibility issue
#262
fweimer-rh
opened
1 year ago
1
Fixes and updates
#261
cjarmstrong97
closed
1 year ago
1
Disallow multiple bonds per component
#260
ASinanSaglam
opened
1 year ago
0
visualize regulatory graphs should automatically combine forward and reverse rule nodes
#259
jrfaeder
opened
1 year ago
0
Use parameters as arguments in actions
#258
jrfaeder
closed
1 year ago
1
Documentation update
#257
cjarmstrong97
closed
2 years ago
0
Website update
#256
cjarmstrong97
closed
2 years ago
0
Updated links & information to match new BNG RTD
#255
cjarmstrong97
closed
2 years ago
0
Docs update
#254
cjarmstrong97
closed
2 years ago
0
Website update
#253
cjarmstrong97
closed
2 years ago
0
Added check that parameter is defined.
#252
jrfaeder
closed
2 years ago
0
parameter_scan does not check for valid parameter
#251
jrfaeder
closed
2 years ago
0
Homepage update
#250
cjarmstrong97
closed
2 years ago
0
Small update
#249
cjarmstrong97
closed
2 years ago
0
Beginning of BNG Homepage Revision
#248
cjarmstrong97
closed
2 years ago
0
Write cppfile/cpyfile
#247
ASinanSaglam
closed
2 years ago
0
Missing compartment topology connections in VCell bngl output
#246
jrfaeder
opened
2 years ago
1
BioNetGen 2.8.0 appears to change the case requirements for states
#245
jonrkarr
opened
2 years ago
1
Python could be clearer about lack of perl
#244
luciansmith
closed
2 years ago
2
Allowed toXML support for Arrhenius rate law
#243
cjarmstrong97
closed
2 years ago
0
Added toXML support for population maps
#242
cjarmstrong97
closed
2 years ago
0
Preventing print-outs when simulating a bionetgen model
#241
TorkelE
closed
2 years ago
7
GitHub actions CI setup
#240
ASinanSaglam
closed
2 years ago
0
Added toXML support for energy patterns
#239
cjarmstrong97
closed
2 years ago
0
Bump nokogiri from 1.11.4 to 1.12.5 in /docs
#238
dependabot[bot]
opened
2 years ago
2
Add "toXML" support for "population maps" block
#237
cjarmstrong97
closed
2 years ago
1
Add "toXML" support for "energy patterns" block
#236
cjarmstrong97
closed
2 years ago
1
GraphML export
#235
ASinanSaglam
closed
2 years ago
0
BUG: Using "<" in PatternQuantifier results in invalid XML
#234
cjarmstrong97
opened
2 years ago
0
Time dependent file
#233
ASinanSaglam
closed
2 years ago
0
Handling of reversible reaction across compartments
#232
dweindl
opened
2 years ago
6
Bump addressable from 2.7.0 to 2.8.0 in /docs
#231
dependabot[bot]
closed
2 years ago
0
Automate releasing to BioSimulators
#230
jonrkarr
opened
3 years ago
0
Bump nokogiri from 1.11.2 to 1.11.4 in /docs
#229
dependabot[bot]
closed
2 years ago
0
Bump rexml from 3.2.4 to 3.2.5 in /docs
#228
dependabot[bot]
closed
2 years ago
0
Time dependent file
#227
ASinanSaglam
closed
3 years ago
1
Bump kramdown from 1.16.2 to 2.3.1 in /docs
#226
dependabot[bot]
closed
3 years ago
1
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