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From Open Bioinformatics Foundation

Contents 1 How do I cite an O|B|F project in my publication? 2 How do I cite an O|B|F affiliated project in my publication? 3 How do I cite an O|B|F related project in my publication? 4 References

How do I cite an O|B|F project in my publication?

• Overall view of the Bio* projects [1]
• BioJava - cite the project website
• BioPerl core and Population genetics modules [2, 3] also see BioPerl Publications
• BioPipe which uses bioperl-run [4]
• BioPython - cite the project website
• BioRuby - no publication details available
• BioSQL - see OBDA below

How do I cite an O|B|F affiliated project in my publication?

• DAS [5]
• MOBY [6]
• EMBOSS [7]
• OBDA - (Lapp et al, in prep)
• Generic Genome Browser [8]
• Chado - no publication details available
• Pise [9]
• openBQS - no publication details available
• BlipKit - no publication details available
• BioMake & Skam

How do I cite an O|B|F related project in my publication?

• BioPHP - no publication details available
• Comparative Genomics Library and CGL Wiki page- (Yandell et al, in prep)

References

1. Mangalam H. The Bio* toolkits--a brief overview. Brief Bioinform 2002 Sep; 3(3) 296-302. pmid:12230038. PubMed HubMed [mangalam]
2. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, and Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002 Oct; 12(10) 1611-8. doi:10.1101/gr.361602 pmid:12368254. PubMed HubMed [bioperl]
3. Stajich JE and Hahn MW. Disentangling the effects of demography and selection in human history. Mol Biol Evol 2005 Jan; 22(1) 63-73. doi:10.1093/molbev/msh252 pmid:15356276. PubMed HubMed [perlymorphism]
4. Hoon S, Ratnapu KK, Chia JM, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, and Stupka E. Biopipe: a flexible framework for protocol-based bioinformatics analysis. Genome Res 2003 Aug; 13(8) 1904-15. doi:10.1101/gr.1363103 pmid:12869579. PubMed HubMed [biopipe]
5. Dowell RD, Jokerst RM, Day A, Eddy SR, and Stein L. The distributed annotation system. BMC Bioinformatics 2001; 2 7. pmid:11667947. PubMed HubMed [das]
6. Wilkinson MD and Links M. BioMOBY: an open source biological web services proposal. Brief Bioinform 2002 Dec; 3(4) 331-41. pmid:12511062. PubMed HubMed [moby]
7. Olson SA. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Brief Bioinform 2002 Mar; 3(1) 87-91. pmid:12002227. PubMed HubMed [emboss]
8. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, and Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res 2002 Oct; 12(10) 1599-610. doi:10.1101/gr.403602 pmid:12368253. PubMed HubMed [gbrowse]
9. Gilbert D. Pise: software for building bioinformatics webs. Brief Bioinform 2002 Dec; 3(4) 405-9. pmid:12511068. PubMed HubMed [pise]

All Medline abstracts: PubMed HubMed