{"id":28712452,"url":"https://github.com/polusai/mm-workflows","last_synced_at":"2025-07-13T02:05:49.866Z","repository":{"id":101925493,"uuid":"561067786","full_name":"PolusAI/mm-workflows","owner":"PolusAI","description":"Molecular modeling workflows and extensions for workflow inference compiler","archived":false,"fork":false,"pushed_at":"2024-10-30T16:34:20.000Z","size":5545,"stargazers_count":5,"open_issues_count":5,"forks_count":12,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-06-14T23:05:53.187Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Common Workflow Language","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PolusAI.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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}},"created_at":"2022-11-02T21:52:05.000Z","updated_at":"2025-01-02T20:21:15.000Z","dependencies_parsed_at":null,"dependency_job_id":"368c14c1-50ca-45e6-b2a5-c95af93f1cfc","html_url":"https://github.com/PolusAI/mm-workflows","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/PolusAI/mm-workflows","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fmm-workflows","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fmm-workflows/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fmm-workflows/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fmm-workflows/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PolusAI","download_url":"https://codeload.github.com/PolusAI/mm-workflows/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PolusAI%2Fmm-workflows/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265080235,"owners_count":23708118,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":"2025-06-14T23:05:53.034Z","updated_at":"2025-07-13T02:05:49.811Z","avatar_url":"https://github.com/PolusAI.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Molecular Modeling Workflows\n\nThis repository contains workflows for various molecular modeling tasks. The workflows can be compiled \u0026 executed using the [Workflow Inference Compiler](https://github.com/PolusAI/workflow-inference-compiler).\n\n![BPS Poster](BPS_poster.svg)\n\n## Quick Start\nFirst, follow the [installation instructions](https://github.com/PolusAI/workflow-inference-compiler#quick-start) for WIC.\n\nThen, clone this repository and run the following commands:\n```\ncd install\n./install_biobb_adapters.sh\ncd ..\nmm-workflows --generate_schemas\nwic --generate_schemas\n```\n\nSome of the workflows require an Nvidia CUDA GPU. Please see the Nvidia [installation guides](https://docs.nvidia.com/cuda/#installation-guides) for more information.\n(Moreover, you'll also need to configure it to work with docker. Good luck!)\n\nIf all goes well, then you can try running the tutorial, which is based on the following [gromacs tutorial](https://mmb.irbbarcelona.org/biobb/availability/tutorials/cwl).\n```\nwic --yaml ../mm-workflows/examples/gromacs/tutorial.wic --graphviz --run_local --quiet\n```\n\nThat last command will infer edges, compile to CWL, generate a GraphViz diagram of the root workflow, and run it locally.\n\n```yaml\nlabel: Conjugate Gradient\nsteps:\n  - grompp:\n      in:\n        config: !ii\n          mdp:\n            integrator: cg\n            nsteps: 1000\n  - mdrun:\n      in:\n        # Use GPU by default\n        bonded_terms: !ii cpu\n        pme_terms: !ii cpu\n  - gmx_energy:\n      in:\n        config: !ii\n          terms: [Potential]\n        output_xvg_path: !ii energy_min_cg.xvg\n```\nThe subworkflow [`examples/gromacs/cg.wic`](https://github.com/PolusAI/mm-workflows/blob/main/examples/gromacs/cg.wic) in `mm-workflows` is shown above, and the GraphViz diagram of the root workflow [`examples/gromacs/tutorial.wic`](https://github.com/PolusAI/mm-workflows/blob/main/examples/gromacs/tutorial.wic) in `mm-workflows` is shown below.\n\n![Workflow](examples/gromacs/tutorial.wic.gv.png)\n\nIf you add the --parallel flag to the above command then, in another terminal, you can view the plots in real-time:\n```\nconda activate wic\ncd install \u0026\u0026 ./install_timeseriesplots.sh \u0026\u0026 cd ..\ntimeseriesplots\n```\n\n![Plots](examples/gromacs/plots.png)\n\n## Jupyter notebook visualization\n\nYou can view 3D molecular structures in the Jupyter notebook `src/vis/viewer.ipynb`. The visualization currently needs to be in its own conda environment.\n\n```\ninstall/install_conda.sh\nconda create --name vis\nconda activate vis\ninstall/install_nglview.sh\npip install -e \".[all]\"\n```\n\n![Plots](docs/tree_viewer.png)\n\n\n## Visualizing the results\n\nThis particular workflow creates files which represent 3D coordinates, so we can view them in the Jupyter notebook `src/vis/viewer.ipynb`. Make sure you are using the `vis` conda environment as mentioned in the installation guide.\n\n![Multistep](protein.png)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpolusai%2Fmm-workflows","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpolusai%2Fmm-workflows","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpolusai%2Fmm-workflows/lists"}