kappa-binaries
KappaTools
KaSim is a stochastic simulator for rule-based models written in Kappa. KaSa is
a static analyser for Kappa models.
Kappy is a python library to launch and analyse runs and outputs of
Kappa models.
User manual
See documentation page on kappalanguage.org.
Kappy API
documentation is online.
The latex sources of the "older" reference manual (and KaSa one) are
available in the man/
directory. To compile the manuel, in addition of
a decent LaTeX distribution you need
gnuplot and
graphviz to generate images (make sure
that dot
is in the PATH of your OS). To generate the pdf of the
manual type
make doc
Installation
Core tools
Released versions come with
binaries for MacOS, Windows and Debian derivatives (as Ubuntu). Nightly
builds of the master branch
are built for these platforms by the continuous integration tools.
If you want or need your own build,
Install opam (the OCaml
package manager) and initialize it (by issuingopam init
)In the source directory, install all the dependencies by
opam install --deps-only .
dune build
You can be more fine grained if you only need the command-line tools
(and therefore could install less dependencies) by doing opam install --deps-only kappa-binaries
followed by make all
If nothing worked for you so far. Well, you're pretty much on your
own... Kappa tools depend upon the OCaml native compiler version
4.05.0 or above as well as dune, findlib, Lwt (>= 2.6.0), Re,
Fmt, Logs and Yojson libraries. Find any way to install them and
you'll be only a make all
away from getting Kappa binaries...
Kappy
You should be able to pip install kappy
.
Under MacOS and linux (and if you're not using a python version so
cutting edge that we haven't notice its release yet), wheels that
contain the core binaries should be available.For other platforms/python versions, you need to get kappa agents by
yourself thanks to the opam package manager byopam install kappa-binaries kappa-agents
(or use an externaly hosted REST API)In order to develop in kappy and run all its tests, you need to
follow the "get your own build section" above as well as install
requests (and future).
Usage
KaSim
In order to run a simulation for 100 time units printing observables values
every 0.5 time unit, type
bin/KaSim kappa_file_1 ... kappa_file_n -l 100 -p 0.5 -o data_file
This will produce a data file of 200 point containing the
trajectory that was produced during the simulation.
Type:
bin/KaSim --help
for a complete list of options.
Kappy
Do:
import kappy
client = kappy.KappaRest("http\://url_of/the_server","project_name")
to get a kappa client that uses the REST API hosted by
http://url_of/the_server and deals with project project_name.
or do:
import kappy
client = kappy.KappaStd()
to get a kappa client that uses a kappa agent installed locally. Add a
string argument specifing the path/to/KaSimAgent
to use a specific agent.
A minimal example of usage is:
model = "\
%agent: A(x[x.A]) \
%var: n_0 100 \
%var: k_on 1e-2 \
'rule' A(x[.]), A(x[.]) <-> A(x[1]), A(x[1]) @ k_on, 1 \
%plot: |A(x[.])| \
%init: n_0 A()"
client.add_model_string(model)
client.project_parse()
sim_params = kappy.SimulationParameter(pause_condition="[T] > 100",plot_period=1)
client.simulation_start(sim_params)
client.wait_for_simulation_stop()
results = client.simulation_plot()
client.simulation_delete()
# Rerun with some overwritten values for algebraic variables
client.project_parse(k_on=5e-2,n_0=500)
client.simulation_start(sim_params)
client.wait_for_simulation_stop()
results' = client.simulation_plot()
client.shutdown()
Tests
Launch the core/integration tests by make check
.
Regenerate the reference files if you've changed something in the
outputs by make build-tests
Launch python tests by nosetests
(after having followed the "Get
your own build" section).
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