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                        "timestamp": "2016-09-23T03:37:05Z",
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                        "*": "= BioLib: libraries for the Bio* languages =\n\n''BioLib'' brings together a set of opensource C/C++ libraries and makes them available to all Bio* languages: BioPerl,\nBioRuby, BioPython, BioJAVA and Bioconductor. \n\n'''Currently supported languages: Perl, Python and Ruby (R and JAVA are planned)'''.\n\n== MODULES ==\n\ncurrent BioLib modules:\n\n* [[BioLib Affymetrix]] reads Affymetrix microarray .CEL and .CDF formats\n* [[BioLib Staden io_lib]] reads/writes sequencer trace files, including SFF, ABI, SCF, ALF and PLN formats\n* [[BioLib R/qtl]] support with OO model for Ruby\n\nand soon to be included BioLib modules:\n\n* [[BioliB SAMtools]] libraries for BAM/SAM format, next generation sequencing\n* [[BioliB Emboss]] the European molecular biology open software suite\n* [[BioLib Bio++]] libraries for sequence analysis, phylogenetics, molecular evolution and population genetics\n* [[BioLib libsequence]] library designed to aid writing applications for genomics and evolutionary genetics\n\nIf you have a requirement not listed here: please use the [[Biolib Poll]]!\n\n== NEWS ==\n\n* Biolib is adding SAMtools [http://thebird.nl/biolib/Adding_BioLib_BAM_SAM_Support.html support] (September 2010)\n* Biolib may get into the Google Summer of Code again with some cool project ideas, see the OBF project idea on accessing JAVA from Perl at [[GSoC2010]] and [https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2010#Mapping_the_BEAST_GPU_library_to_Perl_and_R_using_Biolib mapping BEAST at Nescent] (March 2010)\n* We are heading for SWIG generated documentation, as described at [[Biolib_Documentation_1.0]] (February 2010)\n* First [http://emboss.sourceforge.net/ EMBOSS] mappings for Ruby, Perl and Python - a write up on [[mapping EMBOSS]] (November 2009)\n* Xin Shuai and Adam Smith have finalized mapping libsequence and Bio++ libraries to BioLib. See Xin's project [[User:David]] page and [http://gsoc-biolib-libsequence.blogspot.com/ blog], and Adam's project [https://informatics.nescent.org/wiki/PhyloSoC:Mapping_the_Bio%2B%2B_Phylogenetics_toolkit_to_R/BioConductor_and_BioJAVA_using_BioLib page] and [http://gsoc-biopp.blogspot.com/ blog].\n\n== MILESTONES ==\n\n* BOSC Presentation ([http://thebird.nl/download/biolib-bosc2009.pdf slides] July 2009) \n* Microsoft Windows support added with Cygwin (May 2009)\n* BioLib is getting a boost from the Google Summer of Code initiative, thanks to [https://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 NESCent] (April 2009)\n* GNU Science Library (GSL) support is added to the new [[ASciLib]] (A Science Lib) project (April 2009)\n* ''Python'' mappings provided for Affyio and Staden (March 2009)\n* BioLib supports OSX; Affyio mapped to ''Perl'' (February 2009)\n* ''Perl'' and ''Ruby'' mappings provided for the '''Staden [http://sourceforge.net/projects/staden/ io_lib] library''', for reading of trace files in many formats (January 2009)\n* The source repository has moved to [http://github.com/pjotrp/biolib/ github]. The latest changelog is [http://github.com/pjotrp/biolib/commits/master here] (November 2008)\n* ''BioRuby'' is the first to benefit from BioLib's Affy support. See the [http://github.com/pjotrp/bioruby/tree/master/lib/bio/db/microarray/affymetrix Ruby source code] on Github (September 2008)\n* BioLib builds for ''Ruby'' on Linux - both Ruby gem and a [[NIX]] package (August 2008)\n* '''Affyio library''' runs for ''Ruby'' reading Affymetrix cel and cdf info correctly - see also [[BioLib Affymetrix]] (June 2008)\n* An '''example library''' gets built for ''Python'', ''Ruby'' and ''Perl'' using SWIG and cmake 2.6 (June 2008)\n\nsee also the [[Road map]]. There is potential for other languages like JAVA, R and OCaml.\n\n== INTRODUCTION ==\n\nBioLib pools resources and provides the mechanisms for having one code\nbase for all important programming languages.\n\nThe primary mapping mechanism to the Bio* languages is [[SWIG]]. SWIG has\ncome a long way in the last years and maps to all modern high-level\nlanguages. See also [[supported data types]] and [[BioLib_best_practises]] .\n\nThe primary objective of BioLib is compatibility between languages and\nmulti-platform support. The secondary objective of BioLib is\nefficiency - both of CPU and RAM (why bother to write in C,\notherwise).  Think of BioLib as a repository, or kernel, for low-level processing and\nanalysis of biological data. BioLib was incepted at the \nTokyo Biohackathon 2008.\n\nFor more information see the [[Road map]].\n\n== DOCUMENTATION ==\n\nThe API of included BioLib modules can be found in the [http://thebird.nl/apidoc/biolib/index.html API Documentation]. This documentation is generated straight from the source code. Translating the API to the mapped Perl or Ruby methods is straightforward. One example is [http://thebird.nl/apidoc/biolib/index.html here], others are in the test files (for [http://github.com/pjotrp/biolib/tree/master/src/mappings/swig/perl/test Perl], [http://github.com/pjotrp/biolib/tree/master/src/mappings/swig/ruby/test Ruby] and\n[http://github.com/pjotrp/biolib/tree/master/src/mappings/swig/python/test Python]).\n\n== DOWNLOADING ==\n\nFor the latest version of ''BioLib'' see the latest [http://github.com/pjotrp/biolib/tree/master%2Fdoc%2FRELEASE_NOTES.txt?raw=true RELEASE NOTES].\n\nBioLib releases (tgz, tar.bz2 and zip) can be downloaded from:\n\nhttp://bio3.biobeat.org/download/nix-biology/\n\nFor the direct access to the latest source tree use\n\n* [http://github.com/pjotrp/biolib/tree/master Biolib on github]\n* And clone the (master) repository with:\n\n  git clone git://github.com/pjotrp/biolib.git\n\n== INSTALLATION ==\n\n\nQuick instructions : after downloading the source run\n\n  cd biolib\n  ./configure\n  make\n  make test\n  make install\n\nwhich, by default, creates the ''Perl'' bindings. Configuration parameters are:\n\n  ./configure --with-ruby\n\nor\n\n  ./configure --with-python\n\nto install a subset, for example Staden-io-lib for ''Ruby'' use\n\n  ./configure --with-ruby --with-staden\n\nFor more information read the [http://github.com/pjotrp/biolib/tree/master/INSTALL INSTALL] file.\n\n== REQUESTING MODULES ==\n\nIf you need a C/C++/FORTRAN/R module or library linked against one of the popular scripting languages, please make that known through the [[Biolib Poll]]. See also [[Interesting_libraries]].\n\n== CONTRIBUTING ==\n\nAll developers writing low-level bioinformatics libraries are\nencouraged to contribute. A write-up on what it took to map some of the EMBOSS functionality can\nbe found in [[Mapping EMBOSS]]. For a HOWTO read [[Add C Library]]. If you feel you have something that can be\nshared by other developers sign up to the BioLib mailing list (see below).\n\nUnit testing is a critical part of BioLib. Unit tests are conveniently\nwritten in high-level languages.\n\nThe multiplatform build system is based on [[CMake]]. The source trees are\nmaintained with [http://git.or.cz/ git] distributed version control.\n\n== MAILING LIST ==\n\nSubscribe to the BioLib mailing list [http://lists.open-bio.org/mailman/listinfo/biolib-dev here].\n\n== PACKAGING ==\n\nGeneral support for major platforms is aimed for, including 32-bit and 64-bit Linux, OS X, *BSD, Solaris and Windows."
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