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UC-Davis-molecular-computing
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ppsim
Python package for simulating population protocols
MIT License
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ppsim no longer works on Google Colab
#41
EricESeverson
opened
1 year ago
1
Fixes #35; Declare build dependency on Cython using pyproject.toml
#40
UnHumbleBen
closed
2 years ago
7
add configurable timeout when enumerating states
#39
dave-doty
opened
2 years ago
0
allow timescale to be configurable to match between different methods of specifying transition rules
#38
dave-doty
closed
2 years ago
1
detect if user specifies parameters in Simulation constructor and do not override if so
#37
dave-doty
opened
2 years ago
0
give more useful error message when initial configuration contains invalid states
#36
dave-doty
opened
2 years ago
0
Declare build dependency on Cython using pyproject.toml
#35
mkoeppe
opened
2 years ago
7
add pandas and numpy lower bound to requirements.txt
#34
dave-doty
opened
2 years ago
1
add example to README with transition probabilities
#33
dave-doty
opened
2 years ago
2
Import a CRN encoded in SBML format
#32
EricESeverson
opened
2 years ago
0
add link to API in README
#31
dave-doty
opened
3 years ago
0
add link to paper at top of README
#30
dave-doty
opened
3 years ago
0
Use Strings internally instead of Specie objects
#29
EricESeverson
opened
3 years ago
0
Bugfix in Simulation.run
#28
EricESeverson
closed
3 years ago
0
Dev
#27
EricESeverson
closed
3 years ago
0
update README
#26
EricESeverson
closed
3 years ago
0
Add CRN section to README
#25
EricESeverson
closed
3 years ago
0
clean up type references in docstrings
#24
dave-doty
opened
3 years ago
1
Version 0.1.3
#23
EricESeverson
closed
3 years ago
0
Version 0.1.2, bugfix in Simulator reactions
#22
EricESeverson
closed
3 years ago
0
Dev
#21
EricESeverson
closed
3 years ago
0
update readme
#20
EricESeverson
closed
3 years ago
0
Update version and README images
#19
EricESeverson
closed
3 years ago
0
Dev
#18
EricESeverson
closed
3 years ago
0
Instantiation of Simulation with a function is needlessly slow
#17
EricESeverson
opened
3 years ago
0
add controllable random number seed for reproducible results
#16
dave-doty
opened
3 years ago
1
Update README.md
#15
EricESeverson
closed
3 years ago
0
support importing common CRN specification formats
#14
dave-doty
opened
3 years ago
0
SimulatorMultiBatch.get_enabled_reactions should check count of reactants with stoichiometric coefficient > 1
#13
dave-doty
closed
3 years ago
0
Dev
#12
dave-doty
closed
3 years ago
0
work on crn example, fix crn unit tests
#11
EricESeverson
closed
3 years ago
0
added Sphinx documentation folder
#10
dave-doty
closed
3 years ago
0
Stochkit xml output
#9
dave-doty
closed
3 years ago
0
updated example CRN notebook
#8
dave-doty
closed
3 years ago
0
GitHub action continuous integration unit tests
#7
dave-doty
closed
3 years ago
0
added ability to specify rate constants in stochastic or mass-action units with conversion between them
#6
dave-doty
closed
3 years ago
0
added ability to specify protocol using CRN notation, along with a simple example notebook, script, and unit tests
#5
dave-doty
closed
3 years ago
0
feature request: simulate large-state-count protocols
#4
dave-doty
opened
3 years ago
1
Update ppsim.py
#3
EricESeverson
closed
3 years ago
0
make GitHub action for testing compiling API documentation
#2
dave-doty
opened
3 years ago
0
make GitHub action for publishing Python package automatically to PyPI
#1
dave-doty
opened
3 years ago
1