{"id":42107837,"url":"https://github.com/pmlmodelling/fabm-mizer","last_synced_at":"2026-01-26T13:22:01.797Z","repository":{"id":45677036,"uuid":"341277850","full_name":"pmlmodelling/fabm-mizer","owner":"pmlmodelling","description":"FABM implementation of mizer, a dynamic size-structured model for aquatic predators","archived":false,"fork":false,"pushed_at":"2025-11-25T17:45:21.000Z","size":1077,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-11-28T05:32:08.514Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Fortran","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pmlmodelling.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-02-22T17:17:05.000Z","updated_at":"2025-11-27T05:54:58.000Z","dependencies_parsed_at":"2024-01-05T13:45:05.499Z","dependency_job_id":"e2f35336-2863-46ca-9d1c-463900ddbcf2","html_url":"https://github.com/pmlmodelling/fabm-mizer","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/pmlmodelling/fabm-mizer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmlmodelling%2Ffabm-mizer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmlmodelling%2Ffabm-mizer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmlmodelling%2Ffabm-mizer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmlmodelling%2Ffabm-mizer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pmlmodelling","download_url":"https://codeload.github.com/pmlmodelling/fabm-mizer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pmlmodelling%2Ffabm-mizer/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28779338,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-26T11:46:04.308Z","status":"ssl_error","status_checked_at":"2026-01-26T11:46:02.664Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-26T13:22:01.106Z","updated_at":"2026-01-26T13:22:01.792Z","avatar_url":"https://github.com/pmlmodelling.png","language":"Fortran","funding_links":[],"categories":[],"sub_categories":[],"readme":"This is an implementation of [mizer](http://dx.doi.org/10.1111/2041-210X.12256), a dynamic size-structured model for aquatic predators, in [FABM](https://fabm.net).\nIt can be used to model the size spectrum of the higher trophic level community (e.g., all biomass between 1 mg and 1000 kg) or the size structure of individual populations.\nIt is typically used to describe fish, and accordingly supports several different parameterisatons of fisheries.\n\n## Included modules\n\nThis codebase contains separate modules for a single size-structured population (\"size_structured_population\") and a resource spectrum (\"resource_spectrum\").\nMultiple size-structured populations may be added to fabm.yaml to create a multi-species community. It also includes a multi-element version of\nthe size structured population (\"multi_element_mizer\"), which explicitly treats carbon, nitrogen and phosphorus (and, in prey, silicon). This can be coupled to\nelement-resolving prey models such as [ERSEM](https://ersem.com/) and ensures mass of all different elements is conserved.\n\n## Offline simulation\n\nThe `python` subdirectory includes tools for offline simulations with mizer, driven with outputs (environmental conditions and prey)\nof lower trophic level or biogeochemical models. Such outputs usually come from simulations with 1D or 3D models, for instance, GOTM or NEMO.\n\nTo use the tools for offline simulation, you need pyfabm (the Python interface to FABM).\nTo build and install pyfabm, please follow the [instructions on the FABM web site](https://github.com/fabm-model/fabm/wiki/python).\n **Note:** You will need to explicitly activate mizer support within pyfabm by providing `-DFABM_INSTITUTES=\"\u003cOTHER_MODELS\u003e;mizer\" -DFABM_MIZER_BASE=\u003cMIZERDIR\u003e` to cmake. \n\n## Two-way coupled simulation\n\nThrough FABM, these modules can be embedded in variety of hydrodynamic models and combined with models for lower trophic levels to build a two-way coupled end-to-end ecosystem model.\nFor more information on using FABM with various hydrodynamic models, please visit the [FABM wiki](https://fabm.net/wiki).\n\nTo include mizer modules during a FABM build, add the following to your call to CMake: `-DFABM_INSTITUTES=\"\u003cOTHER_MODELS\u003e;mizer\" -DFABM_MIZER_BASE=\u003cMIZERDIR\u003e`.\nHere, `\u003cOTHER_MODELS\u003e` is a semi-colon-separated list of additional FABM packages you want to build, e.g., ersem.\nNB the double quotes are _required_ to prevent your shell (e.g., bash) from interpreting the semi-colon as \"end of command\".\n`\u003cMIZERDIR\u003e` is the root of the mizer repository.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpmlmodelling%2Ffabm-mizer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpmlmodelling%2Ffabm-mizer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpmlmodelling%2Ffabm-mizer/lists"}