{
  "_id": "6a1fdfccb401979e7343912a",
  "Package": "MEIGOR",
  "Type": "Package",
  "Title": "MEIGOR - MEtaheuristics for bIoinformatics Global Optimization",
  "Version": "1.47.0",
  "Date": "2020-06-09",
  "Authors@R": "c(\nperson(\"Jose A.\", \"Egea\", email = \"josea.egea@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"David\", \"Henriques\", role = \"aut\"),\nperson(\"Alexandre\", \"Fdez. Villaverde\", role = \"aut\"),\nperson(\"Thomas\", \"Cokelaer\", role = \"aut\"))",
  "Maintainer": "Jose A. Egea <josea.egea@gmail.com>",
  "Description": "MEIGOR provides a comprehensive environment for performing\nglobal optimization tasks in bioinformatics and systems\nbiology. It leverages advanced metaheuristic algorithms to\nefficiently search the solution space and is specifically\ntailored to handle the complexity and high-dimensionality of\nbiological datasets. This package supports various optimization\nroutines and is integrated with Bioconductor's infrastructure\nfor a seamless analysis workflow.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "biocViews": "SystemsBiology, Optimization, Software",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:31 UTC",
  "RemoteUrl": "https://github.com/bioc/MEIGOR",
  "RemoteRef": "HEAD",
  "RemoteSha": "ed43619a020b004ac0841b73f0febb37d96dca4c",
  "Packaged": {
    "Date": "2026-06-03 07:56:02 UTC",
    "User": "root"
  },
  "Author": "Jose A. Egea [aut, cre],\nDavid Henriques [aut],\nAlexandre Fdez. Villaverde [aut],\nThomas Cokelaer [aut]",
  "MD5sum": "ba55415a609ea41be49f3e0aceb02e98",
  "_user": "bioc",
  "_type": "src",
  "_file": "MEIGOR_1.47.0.tar.gz",
  "_fileid": "ab33fbcf63ea277ec81e5083a3df4bdb882c46d8c3d65618061ebec1a38ae8b7",
  "_filesize": 1576896,
  "_sha256": "ab33fbcf63ea277ec81e5083a3df4bdb882c46d8c3d65618061ebec1a38ae8b7",
  "_created": "2026-06-03T07:56:02.000Z",
  "_published": "2026-06-03T08:03:24.622Z",
  "_jobs": [
    {
      "job": 79247749292,
      "time": 175,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7378865276"
    },
    {
      "job": 79247749174,
      "time": 387,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7378936628"
    },
    {
      "job": 79247749195,
      "time": 248,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7378889273"
    },
    {
      "job": 79247749178,
      "time": 169,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7378863141"
    },
    {
      "job": 79247749172,
      "time": 123,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7378846540"
    },
    {
      "job": 79247125007,
      "time": 232,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378804496"
    },
    {
      "job": 79247749181,
      "time": 137,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378851457"
    },
    {
      "job": 79247749282,
      "time": 161,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7378860150"
    },
    {
      "job": 79247749169,
      "time": 190,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7378870379"
    },
    {
      "job": 79247749304,
      "time": 171,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7378863912"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 6,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/MEIGOR",
  "_commit": {
    "id": "ed43619a020b004ac0841b73f0febb37d96dca4c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381351
  },
  "_maintainer": {
    "name": "Jose A. Egea",
    "email": "josea.egea@gmail.com",
    "login": "jaegea",
    "description": "",
    "uuid": 42738985
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "Rsolnp",
      "role": "Depends"
    },
    {
      "package": "snowfall",
      "role": "Depends"
    },
    {
      "package": "deSolve",
      "role": "Depends"
    },
    {
      "package": "CNORode",
      "role": "Depends"
    },
    {
      "package": "CellNOptR",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.47.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.46.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "systemsbiology",
    "optimization",
    "software"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 394,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MEIGOR"
  },
  "_mentions": 1,
  "_searchresults": 58,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MEIGOR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "CeSSR",
    "CeVNSR",
    "cur_params",
    "essR",
    "essR_multistart",
    "MEIGO",
    "runBayesFit",
    "rvnds_hamming"
  ],
  "_datasets": [
    {
      "name": "cnolist",
      "title": "A CNOlist from CellNOptR paclage",
      "object": "bayesFitExample",
      "file": "bayesFitExample.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cnolist",
      "title": "A CNOlist from CellNOptR paclage",
      "object": "CNORodeExample",
      "file": "CNORodeExample.RData",
      "class": [
        "CNOlist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cnolist",
      "title": "A CNOlist from CellNOptR paclage",
      "object": "simpleExample",
      "file": "simpleExample.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "cnolist_cellnopt",
      "title": "A CNOlist from CellNOptR paclage",
      "object": "CellNOptR_example",
      "file": "CellNOptR_example.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "model",
      "title": "A model from CellNoptR",
      "object": "bayesFitExample",
      "file": "bayesFitExample.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "model",
      "title": "A model from CellNoptR",
      "object": "CNORodeExample",
      "file": "CNORodeExample.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "model",
      "title": "A model from CellNoptR",
      "object": "simpleExample",
      "file": "simpleExample.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "model_cellnopt",
      "title": "A model from CellNoptR",
      "object": "CellNOptR_example",
      "file": "CellNOptR_example.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "paramsOpt",
      "title": "Optimal parameters for simulation with CNORode",
      "object": "CNORodeExample",
      "file": "CNORodeExample.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "essR-MEIGOR",
      "title": "Global optimization algorithm for MINLPs based on Scatter Search",
      "topics": [
        "essR-package"
      ]
    },
    {
      "page": "MEIGOR-package",
      "title": "Global optimization Toolbox",
      "topics": [
        "MEIGOR-package"
      ]
    },
    {
      "page": "BayesFit",
      "title": "BayesFit",
      "topics": [
        "BayesFit-package",
        "BayesFit"
      ]
    },
    {
      "page": "CeSSR",
      "title": "Global optimization algorithm for MINLPs based on Scatter Search using a Cooperative Strategy",
      "topics": [
        "CeSSR"
      ]
    },
    {
      "page": "CeVNSR",
      "title": "Global optimization algorithm for MINLPs based on VNS using a Cooperative Strategy",
      "topics": [
        "CeVNSR"
      ]
    },
    {
      "page": "cnolist",
      "title": "A CNOlist from CellNOptR paclage",
      "topics": [
        "cnolist"
      ]
    },
    {
      "page": "cnolist_cellnopt",
      "title": "A CNOlist from CellNOptR paclage",
      "topics": [
        "cnolist_cellnopt"
      ]
    },
    {
      "page": "cur_params",
      "title": "Current values of all model parameters",
      "topics": [
        "cur_params"
      ]
    },
    {
      "page": "dhc",
      "title": "Local search algorithm within eSS",
      "topics": [
        "dhc"
      ]
    },
    {
      "page": "essR",
      "title": "Global optimization algorithm for MINLPs based on Scatter Search",
      "topics": [
        "essR"
      ]
    },
    {
      "page": "essR_multistart",
      "title": "Multistart function for eSS",
      "topics": [
        "essR_multistart"
      ]
    },
    {
      "page": "eucl_dist",
      "title": "Computes the euclidean distance between the rows of two different matrices",
      "topics": [
        "eucl_dist"
      ]
    },
    {
      "page": "ith_essR",
      "title": "Auxiliary function to perform parallel runs",
      "topics": [
        "ith_essR"
      ]
    },
    {
      "page": "ith_VNSR",
      "title": "Auxiliary function to perform parallel runs",
      "topics": [
        "ith_VNSR"
      ]
    },
    {
      "page": "MEIGO",
      "title": "MEIGO main function",
      "topics": [
        "MEIGO"
      ]
    },
    {
      "page": "model",
      "title": "A model from CellNoptR",
      "topics": [
        "model"
      ]
    },
    {
      "page": "model_cellnopt",
      "title": "A model from CellNoptR",
      "topics": [
        "model_cellnopt"
      ]
    },
    {
      "page": "nls_fobj",
      "title": "Auxiliary function to evaluate constraints",
      "topics": [
        "nls_fobj"
      ]
    },
    {
      "page": "optim_fobj",
      "title": "Gateway function to evaluate the objective function when the local solvers are invoked.",
      "topics": [
        "optim_fobj"
      ]
    },
    {
      "page": "paramsOpt",
      "title": "Optimal parameters for simulation with CNORode",
      "topics": [
        "paramsOpt"
      ]
    },
    {
      "page": "runBayesFit",
      "title": "Running the BayesFit optimisation",
      "topics": [
        "runBayesFit"
      ]
    },
    {
      "page": "rvnds_hamming",
      "title": "Main VNS function",
      "topics": [
        "rvnds_hamming"
      ]
    },
    {
      "page": "rvnds_local",
      "title": "Local search in VNS",
      "topics": [
        "rvnds_local"
      ]
    },
    {
      "page": "solnp_eq",
      "title": "Gateway function to evaluate the equality constraints when solnp is invoked as local solver",
      "topics": [
        "solnp_eq"
      ]
    },
    {
      "page": "solnp_fobj",
      "title": "Gateway function to evaluate the objective function when solnp is invoked as local solver",
      "topics": [
        "solnp_fobj"
      ]
    },
    {
      "page": "solnp_ineq",
      "title": "Gateway function to evaluate the inequality constraints when solnp is invoked as local solver",
      "topics": [
        "solnp_ineq"
      ]
    },
    {
      "page": "ssm_beyond",
      "title": "Function that expands the search direction when a good offspring solution has been found",
      "topics": [
        "ssm_beyond"
      ]
    },
    {
      "page": "ssm_defaults",
      "title": "Sets the default options for eSSR",
      "topics": [
        "ssm_defaults"
      ]
    },
    {
      "page": "ssm_evalfc",
      "title": "Gateway function to evaluate the objective function in essR",
      "topics": [
        "ssm_evalfc"
      ]
    },
    {
      "page": "ssm_isdif2",
      "title": "Calculates relative errors between two vectors",
      "topics": [
        "ssm_isdif2"
      ]
    },
    {
      "page": "ssm_localsolver",
      "title": "Configure local solver",
      "topics": [
        "ssm_localsolver"
      ]
    },
    {
      "page": "ssm_optset",
      "title": "Assigns values to the options defined by the user",
      "topics": [
        "ssm_optset"
      ]
    },
    {
      "page": "ssm_penalty_function",
      "title": "Calculates the penalized objective function in constrained problems",
      "topics": [
        "ssm_penalty_function"
      ]
    },
    {
      "page": "ssm_round_int",
      "title": "Rounds variables declared as integer of binary",
      "topics": [
        "ssm_round_int"
      ]
    },
    {
      "page": "vns_defaults",
      "title": "Default options for VNS",
      "topics": [
        "vns_defaults"
      ]
    },
    {
      "page": "vns_optset",
      "title": "Set VNS options",
      "topics": [
        "vns_optset"
      ]
    }
  ],
  "_rundeps": [
    "base64enc",
    "BH",
    "BiocGenerics",
    "bitops",
    "bslib",
    "cachem",
    "CellNOptR",
    "cli",
    "CNORode",
    "codetools",
    "cpp11",
    "deSolve",
    "digest",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "future",
    "future.apply",
    "genalg",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "graph",
    "gtable",
    "highr",
    "htmltools",
    "igraph",
    "isoband",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "numDeriv",
    "parallelly",
    "pkgconfig",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RCurl",
    "Rgraphviz",
    "rlang",
    "rmarkdown",
    "Rsolnp",
    "S7",
    "sass",
    "scales",
    "snow",
    "snowfall",
    "stringi",
    "stringr",
    "tinytex",
    "truncnorm",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "MEIGOR-vignette.Rmd",
      "filename": "MEIGOR-vignette.html",
      "title": "MEIGOR: a software suite based on metaheuristics for global optimization in systems biology and bioinformatics",
      "author": "Jose A. Egea, David Henriques, Thomas Cokelaer, Alejandro F. Villaverde, Julio R. Banga, Julio Saez-Rodriguez",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installing MEIGOR",
        "Continuous and mixed-integer problems: Enhanced Scatter Search (eSSR)",
        "Quick start: How to carry out an optimization with SSR",
        "eSSR usage",
        "Problem definition",
        "User options",
        "Global options",
        "Local options",
        "Output",
        "Guidelines for using eSSR",
        "Extra tool: essR_multistart",
        "Examples",
        "Unconstrained problem",
        "Constrained problem",
        "Constrained problem with equality constraints",
        "Mixed integer problem",
        "essR_multistart application",
        "Integer optimization: Variable Neighbourhood Search (VNSR)",
        "Quick start: How to carry out an optimization with VNSR",
        "VNSR usage",
        "Problem definition",
        "VNSR options",
        "Output",
        "Guidelines for using VNSR",
        "Application example",
        "Parallel computation in MEIGO",
        "Quick notes about the parallel computing packages",
        "Snowfall",
        "Usage",
        "Options",
        "Output",
        "CeSSR application example",
        "CeVNSR application example",
        "Applications from Systems Biology",
        "Using eSS to fit a dynamic model",
        "Using VNS to optimize logic models",
        "References"
      ],
      "created": "2024-03-12 12:24:19",
      "modified": "2024-03-12 13:15:23",
      "commits": 2
    }
  ],
  "_score": 4.064457989226918,
  "_indexed": true,
  "_nocasepkg": "meigor",
  "_universes": [
    "bioc",
    "jaegea"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-06-03T08:01:41.000Z",
      "distro": "noble",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "2a788b3700d2c07ffcd32490b0f564901c50a2aa987e0c3180643bd171136f0b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-06-03T07:59:28.000Z",
      "distro": "noble",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "be8e225f070e4587d6212efc064e57abb290e459e93e7de7765975aad0ac7745",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-06-03T07:58:07.000Z",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "618d18738cbab3f38165198f9d0289647e9e9529856581687044ba8bc03a2cea",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-06-03T07:57:36.000Z",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "4faf9732373663a990b1bf2304bc7b57d521c3ea7e15d4317efbc57ea49ebd3c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.47.0",
      "date": "2026-06-03T07:58:42.000Z",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "2796b4f5e8564f4614052ef0bb08149269c7d866b1befedfb1ca6463738cd867",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-06-03T07:57:38.000Z",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "0a7ed5a2ac601215525f8f2a4ba6025fcd9ed581a78e1c7c0aec5ecf8adf17c8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-06-03T07:58:15.000Z",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "7f065f39fb94ab999024a8cf5c90d5c674273f436d7178ffd9bb9601e1549f2f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-06-03T07:57:56.000Z",
      "commit": "ed43619a020b004ac0841b73f0febb37d96dca4c",
      "fileid": "a31484e334bba519fdd80cb50c3931b530d56b0ba9009c4a50b973751361b064",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26871315372"
    }
  ]
}