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Incongruity between kappa.run_simulation() and bng.run_ssa() outputs
#343 opened Feb 13, 2018 by glucksfall

3
Large model Solver/Simulator construction errors in Python 3
#298 opened Sep 24, 2017 by bgyori

2
matlab exporter doesn't handle Expressions
#228 opened Sep 7, 2016 by jmuhlich
Diagram generation with rate expressions
#199 opened Apr 4, 2016 by bgyori

1
pysb_flat exporter should wrap to 80 columns where possible
#186 opened Dec 8, 2015 by jmuhlich
Write tests for fixes in #175 and #176 testing
#177 opened Nov 4, 2015 by jmuhlich
change solver.verbose to use logging and expand use of logging where appropriate
#148 opened Sep 4, 2015 by jmuhlich v2.0.0

1
michaelis-menten example model
#145 opened Sep 4, 2015 by jmuhlich v1.1.1

1
move generator/bng.py content into bng.py
#144 opened Sep 4, 2015 by jmuhlich v2.0.0

1
in tyson_oscillator.py, switch parameter expressions to proper Expressions
#143 opened Sep 4, 2015 by jmuhlich v2.0.0

1
remove commented bits from bng.py, core.py, and examples/run_tyson_oscillator.py
#142 opened Sep 4, 2015 by jmuhlich v2.0.0
use rulebender antlr grammar to parse bngl files
#136 opened Sep 4, 2015 by jmuhlich
make ODE integrator have same return value/structure as run_ssa
#133 opened Sep 4, 2015 by jmuhlich v2.0.0

2
document return format for run_ssa
#132 opened Sep 4, 2015 by jmuhlich v1.1.1
render_reactions.py and render_species.py require pygraphviz which isn't a declared dependency
#130 opened Aug 28, 2015 by jmuhlich

1
Review macros.py/_verify_sites_complex in light of new callable ComplexPattern implementation
#126 opened Aug 27, 2015 by johnbachman v1.1.1
Observable.match clashes with sympy.Symbol.match
#115 opened Jan 17, 2015 by jmuhlich v2.0.0
check for Canopy compatibility
#109 opened Dec 23, 2014 by jmuhlich

1
pysb.integrate.Solver._use_inline is not documented
#106 opened Dec 11, 2014 by jmuhlich v1.1.1
scipy.weave.inline can be excessively slow on windows 7
#105 opened Dec 9, 2014 by jmuhlich

1
please make path to BNG2.pl configurable
#100 opened Nov 24, 2014 by keszybz

4
document Docker setup
#98 opened Oct 2, 2014 by jmuhlich
package and/or automatically fetch perl and bionetgen
#96 opened Sep 19, 2014 by jmuhlich

1
MATLAB exporter
#91 opened Jun 24, 2014 by MarcHafner
storing sympy expressions for large models uses too much memory bug
#79 opened Jun 13, 2013 by jmuhlich

1

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