{"id":16649728,"url":"https://github.com/luispedro/coelho2013_bioinformatics","last_synced_at":"2026-04-24T06:32:45.080Z","repository":{"id":9608168,"uuid":"11531656","full_name":"luispedro/Coelho2013_Bioinformatics","owner":"luispedro","description":"Reproducible code archive for http://dx.doi.org/10.1093/bioinformatics/btt392","archived":false,"fork":false,"pushed_at":"2015-10-07T08:29:11.000Z","size":123,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-19T06:43:44.370Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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/luispedro.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.rst","codeowners":null,"security":null,"support":null}},"created_at":"2013-07-19T16:04:07.000Z","updated_at":"2015-10-07T08:29:12.000Z","dependencies_parsed_at":"2022-09-07T07:51:41.189Z","dependency_job_id":null,"html_url":"https://github.com/luispedro/Coelho2013_Bioinformatics","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luispedro%2FCoelho2013_Bioinformatics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luispedro%2FCoelho2013_Bioinformatics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luispedro%2FCoelho2013_Bioinformatics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/luispedro%2FCoelho2013_Bioinformatics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/luispedro","download_url":"https://codeload.github.com/luispedro/Coelho2013_Bioinformatics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243223715,"owners_count":20256566,"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":"2024-10-12T09:11:41.272Z","updated_at":"2025-12-26T06:38:22.614Z","avatar_url":"https://github.com/luispedro.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Source code  for paper *Determining the subcellular location of new proteins\nfrom microscope images using local features* by Coelho et al. in\n`Bioinformatics \u003chttp://dx.doi.org/10.1093/bioinformatics/btt392\u003e`__\n\nThis repository is **for reproduction of the results in the paper**. If you\nwant to apply the methods to your data, check out the `tutorial on doing so\n\u003chttp://murphylab.web.cmu.edu/software/2013_Bioinformatics_LocalFeatures/tutorial.html\u003e`__.\nIt is a step by step manual on applying the methods to your data.\n\nDependencies\n------------\n\n::\n\n    sudo apt-get install python python-pip python-virtualenv\n    sudo apt-get install dvipng\n\nInstructions\n------------\n\n1. For the Human Protein Atas data, please download from\n   http://murphylab.web.cmu.edu/software/2012_PLoS_ONE_Reannotation/\n\n    Edit the file ``sources/hpa.py`` to point to where you downloaded all the data.\n\n2. Get the randtag data from\n   http://murphylab.web.cmu.edu/software/2013_Bioinformatics_LocalFeatures/ or\n   from `Data Dryad \u003chttp://datadryad.org/resource/doi:10.5061/dryad.2vm70\u003e`__\n\n3. The remaining data should be automatically downloaded when you run::\n\n    doitall.sh\n\nThis will also run the computation.\n\nIf you want to take advantage of multiple processors, edit the file\n``doitall.sh`` and set the ``NR_CPUS`` variable. Note that the whole\ncomputation (i) takes a very long time (days) on a single core and (ii) is\ndesigned to take full advantage of multiples cores.\n\nCitation\n--------\n\nFor referring to this work, please cite:\n\n   *Determining the subcellular location of new proteins from microscope images\n   using local features* by Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik,\n   Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja\n   Simha, Peter B. Berget, Jonathan W. Jarvik, and Robert F.  Murphy (2013).\n   Bioinformatics, [`DOI \u003chttp://dx.doi.org/10.1093/bioinformatics/btt392\u003e`__]\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fluispedro%2Fcoelho2013_bioinformatics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fluispedro%2Fcoelho2013_bioinformatics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fluispedro%2Fcoelho2013_bioinformatics/lists"}