{ "_id": "6a3b95425cdecea1d6825019", "Package": "BoolNet", "Type": "Package", "Title": "Construction, Simulation and Analysis of Boolean Networks", "Version": "2.1.9", "Date": "2023-10-02", "Authors@R": "c(person(\"Christoph\", \"Müssel\", role = \"aut\"),\nperson(\"Martin\", \"Hopfensitz\", role = \"aut\"),\nperson(\"Dao\", \"Zhou\", role = \"aut\"),\nperson(c(\"Hans\", \"A.\"), \"Kestler\", email = \"hans.kestler@uni-ulm.de\", role = c(\"aut\", \"cre\")),\nperson(\"Armin\", \"Biere\", role = \"ctb\", comment=\"contributed PicoSAT code\"),\nperson(c(\"Troy\", \"D.\"), \"Hanson\", role = \"ctb\", comment=\"contributed uthash macros\"))", "Description": "Functions to reconstruct, generate, and simulate\nsynchronous, asynchronous, probabilistic, and temporal Boolean\nnetworks. Provides also functions to analyze and visualize\nattractors in Boolean networks\n.", "License": "Artistic-2.0", "LazyLoad": "yes", "ByteCompile": "TRUE", "Encoding": "UTF-8", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-24 08:23:47 UTC", "User": "root" }, "Author": "Christoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou\n[aut], Hans A. Kestler [aut, cre], Armin Biere [ctb]\n(contributed PicoSAT code), Troy D. Hanson [ctb] (contributed\nuthash macros)", "Maintainer": "Hans A. Kestler ", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://hkestler.r-universe.dev", "Date/Publication": "2023-10-02 15:30:35 UTC", "RemoteUrl": "https://github.com/cran/BoolNet", "RemoteRef": "HEAD", "RemoteSha": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "MD5sum": "d3bf5cd13dc70f85e65cf78656839ff6", "_user": "hkestler", "_type": "src", "_file": "BoolNet_2.1.9.tar.gz", "_fileid": "1e69294b1bb59dc874e03add2281bcd30fe95a122d2d700d532140b7fb1ae986", "_filesize": 1936548, "_sha256": "1e69294b1bb59dc874e03add2281bcd30fe95a122d2d700d532140b7fb1ae986", "_created": "2026-06-24T08:23:47.000Z", "_published": "2026-06-24T08:28:50.781Z", "_distro": "resolute", "_jobs": [ { "job": 83149963116, "time": 138, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7844080702" }, { "job": 83149963230, "time": 157, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7844086250" }, { "job": 83149963138, "time": 143, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7844082605" }, { "job": 83149963139, "time": 129, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7844076335" }, { "job": 83149963030, "time": 96, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7844063659" }, { "job": 83149963062, "time": 256, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7844122126" }, { "job": 83149963055, "time": 117, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7844071906" }, { "job": 83149963009, "time": 191, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7844098743" }, { "job": 83149458082, "time": 177, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7844028143" }, { "job": 83149962903, "time": 108, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7844067981" }, { "job": 83149962933, "time": 105, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7844066813" }, { "job": 83149962913, "time": 107, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7844067962" }, { "job": 83149962899, "time": 122, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7844073462" } ], "_buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/BoolNet", "_commit": { "id": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "author": "Hans A. Kestler ", "committer": "cran-robot ", "message": "version 2.1.9\n", "time": 1696260635 }, "_maintainer": { "name": "Hans A. Kestler", "email": "hans.kestler@uni-ulm.de", "login": "hkestler", "description": "", "uuid": 7150663 }, "_registered": true, "_dependencies": [ { "package": "igraph", "version": ">= 0.6", "role": "Imports" }, { "package": "XML", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 4, "_updates": [], "_tags": [], "_stars": 3, "_contributors": [ { "user": "hkestler", "count": 25, "uuid": 7150663 } ], "_userbio": { "uuid": 7150663, "type": "user", "name": "hkestler", "followers": 0 }, "_downloads": { "count": 575, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BoolNet" }, "_mentions": 73, "_searchresults": 197, "_rbuild": "4.6.0", "_assets": [ "extra/BoolNet.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "hkestler", "_cranurl": false, "_releases": [ { "version": "1.3", "date": "2009-11-16" }, { "version": "1.4", "date": "2010-02-28" }, { "version": "1.41", "date": "2010-05-22" }, { "version": "1.42", "date": "2010-06-16" }, { "version": "1.43", "date": "2011-01-24" }, { "version": "1.44", "date": "2011-04-11" }, { "version": "1.45", "date": "2011-11-22" }, { "version": "1.46", "date": "2012-01-17" }, { "version": "1.50", "date": "2012-04-10" }, { "version": "1.51", "date": "2012-06-11" }, { "version": "1.60", "date": "2012-12-12" }, { "version": "1.61", "date": "2013-03-20" }, { "version": "1.62", "date": "2013-12-03" }, { "version": "1.63", "date": "2014-03-31" }, { "version": "2.0", "date": "2014-07-17" }, { "version": "2.0.1", "date": "2014-08-26" }, { "version": "2.0.2", "date": "2014-12-11" }, { "version": "2.1.0", "date": "2015-02-23" }, { "version": "2.1.1", "date": "2015-02-25" }, { "version": "2.1.3", "date": "2016-11-21" }, { "version": "2.1.4", "date": "2018-06-07" }, { "version": "2.1.5", "date": "2019-04-16" }, { "version": "2.1.7", "date": "2022-09-04" }, { "version": "2.1.8", "date": "2023-02-27" }, { "version": "2.1.9", "date": "2023-10-02" } ], "_exports": [ "attractorsToLaTeX", "binarizeTimeSeries", "chooseNetwork", "fixGenes", "generateCanalyzing", "generateNestedCanalyzing", "generateRandomNKNetwork", "generateState", "generateTimeSeries", "getAttractors", "getAttractorSequence", "getBasinOfAttraction", "getPathToAttractor", "getStateSummary", "getTransitionProbabilities", "getTransitionTable", "loadBioTapestry", "loadNetwork", "loadSBML", "markovSimulation", "perturbNetwork", "perturbTrajectories", "plotAttractors", "plotNetworkWiring", "plotPBNTransitions", "plotSequence", "plotStateGraph", "reconstructNetwork", "saveNetwork", "sequenceToLaTeX", "simplifyNetwork", "simulateSymbolicModel", "stateTransition", "symbolicToTruthTable", "testAttractorRobustness", "testIndegree", "testNetworkProperties", "testTransitionRobustness", "toPajek", "toSBML", "truthTableToSymbolic" ], "_datasets": [ { "name": "cellcycle", "title": "Mammalian cell cycle network", "object": "cellcycle", "file": "cellcycle.rda", "class": [ "BooleanNetwork" ], "fields": [], "table": false, "tojson": false }, { "name": "examplePBN", "title": "An artificial probabilistic Boolean network", "object": "examplePBN", "file": "examplePBN.rda", "class": [ "ProbabilisticBooleanNetwork", "BooleanNetworkCollection" ], "fields": [], "table": false, "tojson": false }, { "name": "igf", "title": "Boolean model of the IGF pathway", "object": "igf", "file": "igf.rda", "class": [ "SymbolicBooleanNetwork" ], "fields": [], "table": false, "tojson": false }, { "name": "yeastTimeSeries", "title": "Yeast cell cycle time series data", "object": "yeastTimeSeries", "file": "yeastTimeSeries.rda", "class": [ "matrix", "array" ], "fields": {}, "rows": 4, "table": true, "tojson": true } ], "_help": [ { "page": "attractorsToLaTeX", "title": "Create LaTeX state table of attractors", "topics": [ "attractorsToLaTeX" ] }, { "page": "binarizeTimeSeries", "title": "Binarize a set of real-valued time series", "topics": [ "binarizeTimeSeries" ] }, { "page": "cellcycle", "title": "Mammalian cell cycle network", "topics": [ "cellcycle" ] }, { "page": "chooseNetwork", "title": "Extract a single Boolean network from a probabilistic Boolean network", "topics": [ "chooseNetwork" ] }, { "page": "examplePBN", "title": "An artificial probabilistic Boolean network", "topics": [ "examplePBN" ] }, { "page": "fixGenes", "title": "Simulate knocked-out or over-expressed genes", "topics": [ "fixGenes" ] }, { "page": "generateRandomNKNetwork", "title": "Generate a random N-K Boolean network", "topics": [ "generateRandomNKNetwork" ] }, { "page": "generateState", "title": "Generate a state vector from single gene values", "topics": [ "generateState" ] }, { "page": "generateTimeSeries", "title": "Generate time series from a network", "topics": [ "generateTimeSeries" ] }, { "page": "generationFunctions", "title": "Generation functions for biologically relevant function classes", "topics": [ "generateCanalyzing", "generateNestedCanalyzing" ] }, { "page": "getAttractors", "title": "Identify attractors in a Boolean network", "topics": [ "getAttractors" ] }, { "page": "getAttractorSequence", "title": "Decode the state sequence of a synchronous attractor", "topics": [ "getAttractorSequence" ] }, { "page": "getBasinOfAttraction", "title": "Get states in basin of attraction", "topics": [ "getBasinOfAttraction" ] }, { "page": "getPathToAttractor", "title": "Get state transitions between a state and its attractor", "topics": [ "getPathToAttractor" ] }, { "page": "getStateSummary", "title": "Retrieve summary information on a state", "topics": [ "getStateSummary" ] }, { "page": "getTransitionProbabilities", "title": "Get a matrix of transitions and their probabilities in probabilistic Boolean networks", "topics": [ "getTransitionProbabilities" ] }, { "page": "getTransitionTable", "title": "Retrieve the transition table of a network", "topics": [ "getTransitionTable" ] }, { "page": "igf", "title": "Boolean model of the IGF pathway", "topics": [ "igf" ] }, { "page": "loadBioTapestry", "title": "Import a network from BioTapestry", "topics": [ "loadBioTapestry" ] }, { "page": "loadNetwork", "title": "Load a Boolean network from a file", "topics": [ "loadNetwork" ] }, { "page": "loadSBML", "title": "Load an SBML document", "topics": [ "loadSBML" ] }, { "page": "markovSimulation", "title": "Identify important states in probabilistic Boolean networks", "topics": [ "markovSimulation" ] }, { "page": "perturbNetwork", "title": "Perturb a Boolean network randomly", "topics": [ "perturbNetwork" ] }, { "page": "perturbTrajectories", "title": "Perturb the state trajectories and calculate robustness measures", "topics": [ "perturbTrajectories" ] }, { "page": "plotAttractors", "title": "Plot state tables or transition graphs of attractors", "topics": [ "plotAttractors" ] }, { "page": "plotNetworkWiring", "title": "Plot the wiring of a Boolean network", "topics": [ "plotNetworkWiring" ] }, { "page": "plotPBNTransitions", "title": "Visualize the transitions in a probabilistic Boolean network", "topics": [ "plotPBNTransitions" ] }, { "page": "plotSequence", "title": "Plot a sequence of states", "topics": [ "plotSequence" ] }, { "page": "plotStateGraph", "title": "Visualize state transitions and attractor basins", "topics": [ "plotStateGraph" ] }, { "page": "print.AttractorInfo", "title": "Print attractor cycles", "topics": [ "print.AttractorInfo" ] }, { "page": "print.BooleanNetwork", "title": "Print a Boolean network", "topics": [ "print.BooleanNetwork" ] }, { "page": "print.MarkovSimulation", "title": "Print the results of a Markov chain simulation", "topics": [ "print.MarkovSimulation" ] }, { "page": "print.ProbabilisticBooleanNetwork", "title": "Print a probabilistic Boolean network", "topics": [ "print.BooleanNetworkCollection", "print.ProbabilisticBooleanNetwork" ] }, { "page": "print.SymbolicSimulation", "title": "Print simulation results", "topics": [ "print.SymbolicSimulation" ] }, { "page": "print.TransitionTable", "title": "Print a transition table", "topics": [ "print.BooleanStateInfo", "print.TransitionTable" ] }, { "page": "reconstructNetwork", "title": "Reconstruct a Boolean network from time series of measurements", "topics": [ "reconstructNetwork" ] }, { "page": "saveNetwork", "title": "Save a network", "topics": [ "saveNetwork" ] }, { "page": "sequenceToLaTeX", "title": "Create LaTeX table of state sequences", "topics": [ "sequenceToLaTeX", "sequenceToLaTeX.BooleanNetwork", "sequenceToLaTeX.data.frame" ] }, { "page": "simplifyNetwork", "title": "Simplify the functions of a synchronous, asynchronous, or probabilistic Boolean network", "topics": [ "simplifyNetwork" ] }, { "page": "simulateSymbolicModel", "title": "Simulate a symbolic Boolean network", "topics": [ "simulateSymbolicModel" ] }, { "page": "stateTransition", "title": "Perform a transition to the next state", "topics": [ "stateTransition" ] }, { "page": "symbolicToTruthTable", "title": "Convert a symbolic network into a truth table representation", "topics": [ "symbolicToTruthTable" ] }, { "page": "testNetworkProperties", "title": "Test properties of networks by comparing them to random networks", "topics": [ "testAttractorRobustness", "testIndegree", "testNetworkProperties", "testTransitionRobustness" ] }, { "page": "toPajek", "title": "Export a network to the Pajek file format", "topics": [ "toPajek" ] }, { "page": "toSBML", "title": "Export a network to SBML", "topics": [ "toSBML" ] }, { "page": "truthTableToSymbolic", "title": "Convert a network in truth table representation into a symbolic representation", "topics": [ "truthTableToSymbolic" ] }, { "page": "yeastTimeSeries", "title": "Yeast cell cycle time series data", "topics": [ "yeastTimeSeries" ] } ], "_rundeps": [ "cli", "cpp11", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "rlang", "vctrs", "XML" ], "_vignettes": [ { "source": "BoolNet_package_vignette.Snw", "filename": "BoolNet_package_vignette.pdf", "title": "Detailed introduction to all major features of BoolNet", "engine": "utils::Sweave", "headings": [ "Introduction", "Assembling networks", "Network analysis", "Import and export", "Appendix" ], "created": "2013-11-20", "modified": "2022-09-04 13:40:09", "commits": 7 } ], "_score": 5.85076872692888, "_indexed": true, "_nocasepkg": "boolnet", "_universes": [ "hkestler" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.9", "date": "2026-06-24T08:26:13.000Z", "distro": "resolute", "arch": "aarch64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "0091ac7560c0edc6517aa6c2e708a2626d6f1cef473a57eb763616c53124abd6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.7.0", "os": "linux", "version": "2.1.9", "date": "2026-06-24T08:26:23.000Z", "distro": "resolute", "arch": "x86_64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "07a92ae59edebfb8a0d4a661b9159fd4871b4a299ac53d9beb11fef1da46bdb7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.6.0", "os": "linux", "version": "2.1.9", "date": "2026-06-24T08:26:18.000Z", "distro": "resolute", "arch": "aarch64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "67072c2f76e5d15127c64a1a7ed45aded4e01df46b546930ac08e73e0358435d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.6.0", "os": "linux", "version": "2.1.9", "date": "2026-06-24T08:25:56.000Z", "distro": "resolute", "arch": "x86_64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "f8d8d83688d642265cdce4229d80f256d832fc8130f8e8fa150ab3e504d657e4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.5.3", "os": "mac", "version": "2.1.9", "date": "2026-06-24T08:25:31.000Z", "arch": "aarch64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "d43a7b0bcd2c13e66058d3c3ff84e24d2ba9402498ef7f9dd11d1b147ce8f73a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.5.3", "os": "mac", "version": "2.1.9", "date": "2026-06-24T08:27:33.000Z", "arch": "x86_64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "ef8eb9af3f6383c61eebfb69054eb7161c052a1d795b0e20a545caba15790f1e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.6.0", "os": "mac", "version": "2.1.9", "date": "2026-06-24T08:25:43.000Z", "arch": "aarch64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "921a07ad53c676d2a9f34966ea16a7872dadadcf6ae0ec91118d333bcddcc2ae", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.6.0", "os": "mac", "version": "2.1.9", "date": "2026-06-24T08:26:35.000Z", "arch": "x86_64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "9b6fb4adf43b7cf087edd20f773e6c1e5bc3d95b86d295702ae802e55cc53c0e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.9", "date": "2026-06-24T08:25:54.000Z", "arch": "emscripten", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "7968b32b0ef6bfa7f7a1d81f7f41698659df2aadab17e37a4cb5ad97dc3fd976", "status": "success", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.7.0", "os": "win", "version": "2.1.9", "date": "2026-06-24T08:25:09.000Z", "arch": "x86_64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "931b042abbcd6769c2ad172ea5c9b23548208e5716cdf6849e8218ca7086702c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.5.3", "os": "win", "version": "2.1.9", "date": "2026-06-24T08:25:13.000Z", "arch": "x86_64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "833c114fcadf37a456bc7fe11cbb73d9105e82592950b85acdcb778c06667036", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" }, { "r": "4.6.0", "os": "win", "version": "2.1.9", "date": "2026-06-24T08:25:12.000Z", "arch": "x86_64", "commit": "af3a714c5bfa72ee7507db9c4eaf90ba2cd91809", "fileid": "a2ff6c6659eaabf2cdc3fd95382b21e882857a47d0a6a3b215399007bb7b31bf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hkestler/actions/runs/28085203438" } ] }