{"id":20469021,"url":"https://github.com/pfnet-research/bmi219-2017-proteinfolding","last_synced_at":"2025-07-06T11:33:18.350Z","repository":{"id":86583011,"uuid":"89817223","full_name":"pfnet-research/BMI219-2017-ProteinFolding","owner":"pfnet-research","description":"UCSF BMI219 Deep Learning (2017), Coding example (Prediction of protein folding with RNN and CNN) ","archived":false,"fork":false,"pushed_at":"2017-05-10T18:45:36.000Z","size":46,"stargazers_count":16,"open_issues_count":0,"forks_count":9,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-13T10:40:40.414Z","etag":null,"topics":["bioinformatics","chainer","deep-learning"],"latest_commit_sha":null,"homepage":"https://minicourses.ucsf.edu/bmi-219-deep-learning-2017","language":"Python","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/pfnet-research.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}},"created_at":"2017-04-29T22:48:45.000Z","updated_at":"2025-01-03T02:17:11.000Z","dependencies_parsed_at":null,"dependency_job_id":"d527e17d-4b4e-4ff3-aef3-4b2a5e4373af","html_url":"https://github.com/pfnet-research/BMI219-2017-ProteinFolding","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/pfnet-research/BMI219-2017-ProteinFolding","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2FBMI219-2017-ProteinFolding","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2FBMI219-2017-ProteinFolding/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2FBMI219-2017-ProteinFolding/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2FBMI219-2017-ProteinFolding/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pfnet-research","download_url":"https://codeload.github.com/pfnet-research/BMI219-2017-ProteinFolding/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2FBMI219-2017-ProteinFolding/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263893624,"owners_count":23526326,"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":["bioinformatics","chainer","deep-learning"],"created_at":"2024-11-15T14:07:39.094Z","updated_at":"2025-07-06T11:33:18.344Z","avatar_url":"https://github.com/pfnet-research.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Protein secondary structure prediction with cascaded CNN and RNN\n\nThis is an example of the application of deep learning to protein secondary structure prediction.\nThis example is based on [1], but some minor modifications are applied.\n\nSee commentary.md for a detailed explanation\n\n\n# Dependency\n\n* [Chainer](http://chainer.org)\n* [NumPy](http://www.numpy.org)\n* [six](https://pypi.python.org/pypi/six)\n\n# Usage\n\nRetrieve dataset\n\n```\nbash get_data.sh\n```\n\nTrain\n```\nPYTHONPATH=\".\" python tools/train.py\n```\n\n# Reference\n\n[1] Li, Z., \u0026 Yu, Y. (2016). Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks. arXiv preprint arXiv:1604.07176.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpfnet-research%2Fbmi219-2017-proteinfolding","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpfnet-research%2Fbmi219-2017-proteinfolding","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpfnet-research%2Fbmi219-2017-proteinfolding/lists"}