bioSyntax: syntax highlighting for computational biology
Abstract Background Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the data structure complexity. Results bioSyntax (https://biosyntax.org/) is a...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-08-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2315-y |
| _version_ | 1818335807766790144 |
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| author | Artem Babaian Anicet Ebou Alyssa Fegen Ho Yin Kam German E. Novakovsky Jasper Wong Dylan Aïssi Li Yao |
| author_facet | Artem Babaian Anicet Ebou Alyssa Fegen Ho Yin Kam German E. Novakovsky Jasper Wong Dylan Aïssi Li Yao |
| author_sort | Artem Babaian |
| collection | DOAJ |
| description | Abstract Background Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the data structure complexity. Results bioSyntax (https://biosyntax.org/) is a freely available suite of biological syntax highlighting packages for vim, gedit, Sublime, VSCode, and less. bioSyntax improves the legibility of low-level biological data in the bioinformatics workspace. Conclusion bioSyntax supports computational scientists in parsing and comprehending their data efficiently and thus can accelerate research output. |
| first_indexed | 2024-12-13T14:29:18Z |
| format | Article |
| id | doaj.art-5e643f3b9df9461bb3aaa5e12877be23 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-13T14:29:18Z |
| publishDate | 2018-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-5e643f3b9df9461bb3aaa5e12877be232022-12-21T23:41:51ZengBMCBMC Bioinformatics1471-21052018-08-011911610.1186/s12859-018-2315-ybioSyntax: syntax highlighting for computational biologyArtem Babaian0Anicet Ebou1Alyssa Fegen2Ho Yin Kam3German E. Novakovsky4Jasper Wong5Dylan Aïssi6Li Yao7Terry Fox Laboratory, BC Cancer Research CentreDepartement de Formation et de Recherches Agriculture et Ressources Animales, Institut National Polytechnique Felix Houphouet-BoignyFaculty of Science, University of British ColumbiaFaculty of Mathematics, University of WaterlooDepartment of Medical Genetics, University of British ColumbiaGenome Science and Technology, University of British ColumbiaDepartment of General and Interventional Cardiology, University Heart Center HamburgTHU-PKU Joint Center for Life Sciences, Tsinghua UniversityAbstract Background Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the data structure complexity. Results bioSyntax (https://biosyntax.org/) is a freely available suite of biological syntax highlighting packages for vim, gedit, Sublime, VSCode, and less. bioSyntax improves the legibility of low-level biological data in the bioinformatics workspace. Conclusion bioSyntax supports computational scientists in parsing and comprehending their data efficiently and thus can accelerate research output.http://link.springer.com/article/10.1186/s12859-018-2315-ySyntax highlightingVimSublimeCommand line interfaceSAMVCF |
| spellingShingle | Artem Babaian Anicet Ebou Alyssa Fegen Ho Yin Kam German E. Novakovsky Jasper Wong Dylan Aïssi Li Yao bioSyntax: syntax highlighting for computational biology BMC Bioinformatics Syntax highlighting Vim Sublime Command line interface SAM VCF |
| title | bioSyntax: syntax highlighting for computational biology |
| title_full | bioSyntax: syntax highlighting for computational biology |
| title_fullStr | bioSyntax: syntax highlighting for computational biology |
| title_full_unstemmed | bioSyntax: syntax highlighting for computational biology |
| title_short | bioSyntax: syntax highlighting for computational biology |
| title_sort | biosyntax syntax highlighting for computational biology |
| topic | Syntax highlighting Vim Sublime Command line interface SAM VCF |
| url | http://link.springer.com/article/10.1186/s12859-018-2315-y |
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