{"id":32402,"name":"lobster","description":"Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation","url":"https://github.com/prescient-design/lobster","last_synced_at":"2025-09-05T05:27:11.133Z","repository":{"id":242571398,"uuid":"760104830","full_name":"prescient-design/lobster","owner":"prescient-design","description":"Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation","archived":false,"fork":false,"pushed_at":"2025-09-02T19:57:30.000Z","size":14454,"stargazers_count":128,"open_issues_count":24,"forks_count":30,"subscribers_count":11,"default_branch":"main","last_synced_at":"2025-09-02T21:24:42.149Z","etag":null,"topics":["biology","bioml","plm","protein-sequences"],"latest_commit_sha":null,"homepage":"https://prescient-design.github.io/lobster-docs/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/prescient-design.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","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":"2024-02-19T19:45:40.000Z","updated_at":"2025-08-27T00:13:03.000Z","dependencies_parsed_at":"2024-06-03T21:08:02.471Z","dependency_job_id":"0566f25c-bf19-46c3-8abe-c69bc301d0a3","html_url":"https://github.com/prescient-design/lobster","commit_stats":null,"previous_names":["prescient-design/lobster"],"tags_count":15,"template":false,"template_full_name":null,"purl":"pkg:github/prescient-design/lobster","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/prescient-design%2Flobster","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/prescient-design%2Flobster/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/prescient-design%2Flobster/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/prescient-design%2Flobster/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/prescient-design","download_url":"https://codeload.github.com/prescient-design/lobster/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/prescient-design%2Flobster/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273714189,"owners_count":25154763,"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","status":"online","status_checked_at":"2025-09-05T02:00:09.113Z","response_time":402,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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"}},"owner":{"login":"prescient-design","name":"Prescient Design","uuid":"115567742","kind":"organization","description":"A Genentech Accelerator","email":"prescient@gene.com","website":"www.gene.com/prescient","location":null,"twitter":"PrescientDesign","company":null,"icon_url":"https://avatars.githubusercontent.com/u/115567742?v=4","repositories_count":1,"last_synced_at":"2023-08-14T20:39:27.044Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/prescient-design","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2023-08-14T20:39:27.069Z","updated_at":"2023-08-14T20:39:27.069Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/prescient-design","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/prescient-design/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"prescient-design/lobster","html_url":"https://github.com/prescient-design/lobster","last_synced_at":"2025-09-04T13:16:33.673Z","status":null,"issues_count":20,"pull_requests_count":126,"avg_time_to_close_issue":2429392.0,"avg_time_to_close_pull_request":237359.13333333333,"issues_closed_count":4,"pull_requests_closed_count":90,"pull_request_authors_count":16,"issue_authors_count":8,"avg_comments_per_issue":0.1,"avg_comments_per_pull_request":0.11904761904761904,"merged_pull_requests_count":81,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":19,"past_year_pull_requests_count":126,"past_year_avg_time_to_close_issue":2429392.0,"past_year_avg_time_to_close_pull_request":237359.13333333333,"past_year_issues_closed_count":4,"past_year_pull_requests_closed_count":90,"past_year_pull_request_authors_count":16,"past_year_issue_authors_count":7,"past_year_avg_comments_per_issue":0.10526315789473684,"past_year_avg_comments_per_pull_request":0.11904761904761904,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":81,"created_at":"2025-07-16T12:08:18.067Z","updated_at":"2025-09-04T13:16:33.675Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/prescient-design%2Flobster","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/prescient-design%2Flobster/issues","issue_labels_count":{"good first issue":6,"help wanted":1},"pull_request_labels_count":{},"issue_author_associations_count":{"COLLABORATOR":12,"NONE":6,"CONTRIBUTOR":2},"pull_request_author_associations_count":{"COLLABORATOR":117,"NONE":6,"CONTRIBUTOR":3},"issue_authors":{"ncfrey":7,"karinazad":5,"etherealsunshine":2,"young-su-ko":2,"abidikhairi":1,"RyanAIResearch":1,"redsphinx":1,"alexj-lee":1},"pull_request_authors":{"karinazad":58,"ncfrey":27,"taylormjs":10,"kleinhenz":8,"cgrambow":5,"fdreyer":3,"edwag":3,"etherealsunshine":2,"Sidney-Lisanza":2,"tomyyyD":2,"young-su-ko":1,"chaitjo":1,"hofmannjl":1,"sjmielke":1,"rcalef":1,"davidegraff":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-05T00:00:10.444Z","repositories_count":10086255,"issues_count":31275313,"pull_requests_count":96382867,"authors_count":10695584,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{"good first issue":6,"help wanted":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"COLLABORATOR":12,"NONE":5,"CONTRIBUTOR":2},"past_year_pull_request_author_associations_count":{"COLLABORATOR":117,"NONE":6,"CONTRIBUTOR":3},"past_year_issue_authors":{"ncfrey":7,"karinazad":5,"etherealsunshine":2,"young-su-ko":2,"abidikhairi":1,"redsphinx":1,"RyanAIResearch":1},"past_year_pull_request_authors":{"karinazad":58,"ncfrey":27,"taylormjs":10,"kleinhenz":8,"cgrambow":5,"edwag":3,"fdreyer":3,"etherealsunshine":2,"tomyyyD":2,"Sidney-Lisanza":2,"sjmielke":1,"young-su-ko":1,"chaitjo":1,"hofmannjl":1,"rcalef":1,"davidegraff":1},"maintainers":[{"login":"karinazad","count":63,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/karinazad"},{"login":"ncfrey","count":34,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ncfrey"},{"login":"taylormjs","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/taylormjs"},{"login":"kleinhenz","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kleinhenz"},{"login":"cgrambow","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/cgrambow"},{"login":"edwag","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/edwag"},{"login":"Sidney-Lisanza","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Sidney-Lisanza"},{"login":"fdreyer","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/fdreyer"},{"login":"sjmielke","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/sjmielke"},{"login":"rcalef","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/rcalef"}],"active_maintainers":[{"login":"karinazad","count":63,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/karinazad"},{"login":"ncfrey","count":34,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/ncfrey"},{"login":"taylormjs","count":10,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/taylormjs"},{"login":"kleinhenz","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/kleinhenz"},{"login":"cgrambow","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/cgrambow"},{"login":"edwag","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/edwag"},{"login":"Sidney-Lisanza","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Sidney-Lisanza"},{"login":"fdreyer","count":2,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/fdreyer"},{"login":"sjmielke","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/sjmielke"},{"login":"rcalef","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/rcalef"}]},"events":null,"keywords":["biology","bioml","plm","protein-sequences"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/push.yml","sha":null,"kind":"manifest","created_at":"2024-06-03T21:07:59.631Z","updated_at":"2024-06-03T21:07:59.631Z","repository_link":"https://github.com/prescient-design/lobster/blob/main/.github/workflows/push.yml","dependencies":[{"id":18391073567,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":18391073568,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v5","direct":true,"kind":"composite","optional":false},{"id":18391073569,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2024-06-03T21:08:00.111Z","updated_at":"2024-06-03T21:08:00.111Z","repository_link":"https://github.com/prescient-design/lobster/blob/main/pyproject.toml","dependencies":[]},{"ecosystem":"pypi","filepath":"requirements-dev.in","sha":null,"kind":"manifest","created_at":"2024-06-03T21:08:00.224Z","updated_at":"2024-06-03T21:08:00.224Z","repository_link":"https://github.com/prescient-design/lobster/blob/main/requirements-dev.in","dependencies":[{"id":18391073603,"package_name":"mypy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false},{"id":18391073604,"package_name":"pytest","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false},{"id":18391073605,"package_name":"pytest-cov","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false},{"id":18391073606,"package_name":"pre-commit","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false},{"id":18391073607,"package_name":"icecream","ecosystem":"pypi","requirements":"*","direct":true,"kind":"development","optional":false}]},{"ecosystem":"pypi","filepath":"requirements.in","sha":null,"kind":"manifest","created_at":"2024-06-03T21:08:00.944Z","updated_at":"2024-06-03T21:08:00.944Z","repository_link":"https://github.com/prescient-design/lobster/blob/main/requirements.in","dependencies":[{"id":18391073644,"package_name":"lightning","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073645,"package_name":"torch","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073646,"package_name":"torchmetrics","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073647,"package_name":"biopython","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073648,"package_name":"torchvision","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073649,"package_name":"universal_pathlib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073705,"package_name":"pandas","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073706,"package_name":"scipy","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073707,"package_name":"pyarrow","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073708,"package_name":"s3fs","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073709,"package_name":"biopandas","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073772,"package_name":"wandb","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073773,"package_name":"jupyter","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073774,"package_name":"ipykernel","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073775,"package_name":"hydra-core","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073776,"package_name":"deepspeed","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073806,"package_name":"torchdata","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073807,"package_name":"datasets","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073808,"package_name":"tokenizers","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073809,"package_name":"transformers","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073810,"package_name":"scikit-learn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073811,"package_name":"matplotlib","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073812,"package_name":"seaborn","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073813,"package_name":"python-dotenv","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073814,"package_name":"torcheval","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073815,"package_name":"fastparquet","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073930,"package_name":"datasketch","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073964,"package_name":"peft","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false},{"id":18391073965,"package_name":"icecream","ecosystem":"pypi","requirements":"*","direct":true,"kind":"runtime","optional":false}]}],"score":null,"created_at":"2025-09-04T15:51:05.487Z","updated_at":"2025-10-07T08:13:45.039Z","avatar_url":"https://github.com/prescient-design.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/32402","html_url":"https://science.ecosyste.ms/projects/32402","bibtex_url":"https://science.ecosyste.ms/projects/32402/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/32402/export.apalike"}