{"id":13744865,"url":"https://github.com/bioscala/bioscala","last_synced_at":"2025-12-18T00:57:19.596Z","repository":{"id":201664489,"uuid":"626044","full_name":"bioscala/bioscala","owner":"bioscala","description":"Bioinformatics for the Scala programming language","archived":false,"fork":false,"pushed_at":"2024-02-11T10:23:51.000Z","size":315,"stargazers_count":109,"open_issues_count":1,"forks_count":20,"subscribers_count":15,"default_branch":"master","last_synced_at":"2024-11-15T16:41:47.862Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Scala","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bioscala.png","metadata":{"files":{"readme":"README","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":"2010-04-23T21:38:31.000Z","updated_at":"2024-08-26T01:29:59.000Z","dependencies_parsed_at":"2024-11-15T16:42:56.642Z","dependency_job_id":null,"html_url":"https://github.com/bioscala/bioscala","commit_stats":null,"previous_names":["bioscala/bioscala"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioscala%2Fbioscala","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioscala%2Fbioscala/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioscala%2Fbioscala/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioscala%2Fbioscala/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bioscala","download_url":"https://codeload.github.com/bioscala/bioscala/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253191766,"owners_count":21868804,"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":"2024-08-03T05:01:17.533Z","updated_at":"2025-12-18T00:57:19.570Z","avatar_url":"https://github.com/bioscala.png","language":"Scala","readme":"The goal of the BioScala project is to create a scalable and functional\nbioinformatics library; which can be used from Scala, Java, JRuby,\nJython and Clojure; building on existing libraries available on the JAVA\nVirtual Machine (JVM), including BioJAVA and BioRuby.\n\nThis is the place for the BioScala project under the liberal BSD license.\n\nSee also the Tutorial\n\n  http://monomorphic.org/bioscala/bioscala-tutorial.html \n\ndesign docs\n\n  http://monomorphic.org/bioscala/bioscala-design.html \n\nand API docs\n\n  http://monomorphic.org/bioscala/api/\n\nThis edition of BioScala has:\n\n  - Strongly typed DNA, RNA Sequence, gapped and IUPAC ambiguous Sequence\n  - Sequences contain lists of Nucleotide, AminoAcid, IUPAC, Gapped, Codon\n  - Flexible Sequence user defined attributes\n  - Transcription of DNA to RNA\n  - Translation of (ambiguous) RNA to AA (using BioJava3)\n  - Formats:\n\t  . Iterator based FASTA reader and writer\n    . Iterator based PAML (PHY) file format reader\n    . Phylip reader/writer (using BioJava)\n  - Alignments and attributes (work in progress)\n  - A translation example of calling into BioRuby\n  - A tutorial in ./doc/tutorial.txt\n\nBioScala uses the simple build tool (sbt) and behaviour driven development/unit\ntesting. See the INSTALL file for more information.\n\nPlease fork from https://github.com/bioscala/bioscala \n\nPjotr Prins\n\nMailing list: http://lists.thebird.nl/listinfo.cgi/bioscala-thebird.nl\n\n\n= INSTALL BioScala =\n\nIt is rather easy to install a working repository of BioScala. The JVM is\nneeded and sbt (simple build tool).\n\nFirst download BioScala from github with:\n\n  git clone http://github.com/bioscala/bioscala.git\n\nInstall Java. On Debian, for example:\n\n  apt-get install openjdk-17-jdk\n\nInstall sbt (Simple build tool) from\n\n  https://www.scala-sbt.org/\n\nInstall sbt and run it on the command line, for example\n\n  # go to base bioscala directory\n  cd bioscala\n  # compile\n  sbt compile\n  # test\n  sbt test\n\nsbt will automatically download Scala and related jars. Then it will compile\nand run the supplied tests.","funding_links":[],"categories":["Scala","[](https://github.com/josephmisiti/awesome-machine-learning/blob/master/README.md#scala)Scala"],"sub_categories":["General-Purpose Machine Learning"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioscala%2Fbioscala","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioscala%2Fbioscala","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioscala%2Fbioscala/lists"}