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logo\" title=\"Stochastic Kappa Simulator\" align=\"right\" height=\"90\"/\u003e\n# KappaTools\n\n[![Build Status](https://github.com/Kappa-Dev/KappaTools/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/Kappa-Dev/KappaTools/actions/workflows/ci.yml?query=branch%3Amaster)\n[![Join the chat at https://gitter.im/Kappa-Dev/KaSim](https://badges.gitter.im/Kappa-Dev/KaSim.svg)](https://gitter.im/Kappa-Dev/KaSim?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge)\n\nKaSim is a stochastic simulator for rule-based models written in Kappa. KaSa is\na static analyser for Kappa models.\n\nKappy is a python library to launch and analyse runs and outputs of\nKappa models.\n\n\n## Quick startup\n\nIf you are new to Kappa, the easiest way to start experimenting with it is using the webapp.\n\n\u003cp align=\"center\"\u003e\n\u003cimg alt=\"Editor screenshot with contact map\" src=\"./dev/screenshots/editor1.png\" width=\"45%\"\u003e\n\u003cimg alt= \"Plot screenshot\" src=\"./dev/screenshots/plot.png\" width=\"45%\"\u003e\n\u003c/p\u003e\n\u003cp align=\"center\"\u003e\n\u003cimg alt=\"Editor screenshot with contact map 2\" src=\"./dev/screenshots/editor2.png\" width=\"45%\"\u003e\n\u003cimg alt=\"Stories screenshot\" src=\"./dev/screenshots/story.png\" width=\"45%\"\u003e\n\u003c/p\u003e\n\n\nIt's available [directly in your browser](https://tools.kappalanguage.org/try/?model=https%3A//raw.githubusercontent.com/Kappa-Dev/KappaTools/master/examples/abc.ka),\nor for more performance as a downloadable [electron app](https://tools.kappalanguage.org/nightly-builds/), available for MacOS, Windows and Linux.\n\nKappa tools are also available as Command-Line Interface programs, which you can either build following the [instructions below](#core-tools),\nor find the binaries included with the [electron app](https://tools.kappalanguage.org/nightly-builds/) in subdir `resources/bin`.\n\nIf you would like to use python to interact with the Kappa tools, the `kappy` lib is where to look. Here's an example of its usage with `ipython`\n\n```python\nIn [2]: import kappy\n\nIn [3]: model_text = \"%agent: A(x)\\nA(x[.]), A(x[.]) \u003c-\u003e A(x[1]), A(x[1]) @ 1e-2,1\\n%plot: |A(x[.])|\\n%init: 100 A()\"\n\nIn [4]: kappa_client = kappy.KappaStd()\n\nIn [5]: kappa_client.add_model_string(model_text)\nOut[5]: [...]\n\nIn [6]: kappa_client.project_parse()\nOut[6]: [...]\n\nIn [7]: kappa_client.simulation_start(kappy.SimulationParameter(.1,\"[T] \u003e 10\"))\nOut[7]: {'simulation_artifact_simulation_seed': 297327779}\n\nIn [8]: kappa_client.wait_for_simulation_stop()\nOut[8]: [...]\n\nIn [9]: kappa_client.simulation_plot()\nOut[9]:\n  [6.7, 48.0],\n[...]\n  [0.4, 60.0],\n  [0.3, 50.0],\n  [0.2, 64.0],\n  [0.1, 62.0],\n  [0.0, 100.0]]}\n```\n\nSee the [install instructions](#kappy) to start using kappy.\n\n\n## User manual\nSee [documentation page on kappalanguage.org](https://kappalanguage.org/documentation).\n\nKappy [API\ndocumentation is online](https://kasim.readthedocs.io/en/latest/kappy.html).\n\nThe latex sources of the \"older\" reference manual (and KaSa one) are\navailable in the `man/` directory. To compile the manuel, in addition of\na decent LaTeX distribution you need\n[gnuplot](http://www.gnuplot.info/) and\n[graphviz](http://www.graphviz.org/) to generate images (make sure\nthat `dot` is in the PATH of your OS). To generate the pdf of the\nmanual type\n\n`make doc`\n\n## Installation\n\n### Core tools\n\n[Released versions](https://github.com/Kappa-Dev/KaSim/releases) come with\nbinaries for MacOS, Windows and Debian derivatives (as Ubuntu). [Nightly\nbuilds](https://tools.kappalanguage.org/nightly-builds/) of the master branch\nare built for these platforms by the continuous integration tools.\n\nIf you want or need your own build,\n - Install [opam](https://opam.ocaml.org/doc/Install.html) (the OCaml\n   package manager) and initialize it (by issuing `opam init`)\n - In the source directory, install all the dependencies by `opam install \n   --deps-only .`\n - `dune build`\n\nYou can be more fine grained if you only need the command-line tools\n(and therefore could install less dependencies) by doing `opam install\n--deps-only kappa-binaries` followed by `make all`\n\nIf nothing worked for you so far. Well, you're pretty much on your\nown... Kappa tools depend upon the OCaml native compiler version\n4.05.0 or above as well as _dune_, _findlib_, _Lwt_ (\u003e= 2.6.0), _Re_,\n_Fmt_, _Logs_ and _Yojson_ libraries. Find any way to install them and\nyou'll be only a `make all` away from getting Kappa binaries...\n\n### Kappy\n\nYou should be able to `pip install kappy`.\n\n- Under MacOS and linux (and if you're not using a python version so\n  cutting edge that we haven't notice its release yet), _wheels_ that\n  contain the core binaries should be available.\n- For other platforms/python versions, you need to get kappa agents by\n  yourself thanks to the *opam* package manager by `opam install\n  kappa-binaries kappa-agents` (or use an externaly hosted REST API)\n- In order to develop in kappy and run all its tests, you need to\n  follow the \"get your own build section\" above as well as install\n  _requests_ (and _future_).\n\n## Usage\n\n### KaSim\n\nIn order to run a simulation for 100 time units printing observables values\nevery 0.5 time unit, type\n\n`bin/KaSim kappa_file_1 ... kappa_file_n -l 100 -p 0.5 -o data_file`\n\nThis will produce a data file of 200 point containing the\ntrajectory that was produced during the simulation.\n\nType:\n\n`bin/KaSim --help`\n\nfor a complete list of options.\n\n### Kappy\n\nDo:\n\n```python\nimport kappy\nclient = kappy.KappaStd()\n```\n\nto get a kappa client that uses a kappa agent installed locally. Add a\nstring argument specifing the `path/to/KaSimAgent` to use a specific agent.\n\nA minimal example of usage is:\n\n```python\nmodel = \"\\\n%agent: A(x[x.A]) \\\n%var: n_0 100 \\\n%var: k_on 1e-2 \\\n'rule' A(x[.]), A(x[.]) \u003c-\u003e A(x[1]), A(x[1]) @ k_on, 1 \\\n%plot: |A(x[.])| \\\n%init: n_0 A()\"\nclient.add_model_string(model)\nclient.project_parse()\nsim_params = kappy.SimulationParameter(pause_condition=\"[T] \u003e 100\",plot_period=1)\nclient.simulation_start(sim_params)\nclient.wait_for_simulation_stop()\nresults = client.simulation_plot()\nclient.simulation_delete()\n# Rerun with some overwritten values for algebraic variables\nclient.project_parse(k_on=5e-2,n_0=500)\nclient.simulation_start(sim_params)\nclient.wait_for_simulation_stop()\nresults' = client.simulation_plot()\nclient.shutdown()\n```\n\n## Tests\n\nLaunch the core/integration tests by `make check`.\n\nRegenerate the reference files if you've changed something in the\noutputs by `make build-tests`\n\nLaunch python tests by `nosetests` (after having followed the \"Get\nyour own build\" section).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkappa-dev%2Fkappatools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkappa-dev%2Fkappatools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkappa-dev%2Fkappatools/lists"}