Groups: Knowledge spreadsheets for symbolic biocomputing

Database

Volumn 2013, Issue , 2013, Pages

  Travers, Michael ^a   Paley, Suzanne M ^a   Shrager, Jeff ^a   Holland, Timothy A ^a   Karp, Peter D ^a  

^a SRI INTERNATIONAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

BACTERIAL GENE; BIOLOGY; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA BASE; ESCHERICHIA COLI; GENETIC DATABASE; GENETICS; HUMAN; KNOWLEDGE; KNOWLEDGE BASE; METABOLISM; METABOLOME; PROCEDURES;

COMPUTATIONAL BIOLOGY; DATABASES AS TOPIC; DATABASES, GENETIC; ESCHERICHIA COLI; GENES, BACTERIAL; HUMANS; KNOWLEDGE; KNOWLEDGE BASES; METABOLIC NETWORKS AND PATHWAYS; METABOLOME; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 84895855956     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat061     Document Type: Article

References (23)

1. Caspi,R., Altman,T., Dreher,K. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 40, D742-D753.
2. Karp,P.D., Paley,S.M., Krummenacker,M. et al. (2010) Pathway tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform., 11, 40-79.
3. Pathway/Genome Database Websites. In: http://BioCyc.org/otherpgdbs.shtml (April 2013, date last accessed).
4. How to Use a Pathway Tools Website: Groups Section. In: http://biocyc.org/PToolsWebsiteHowto.shtml#groups (April 2013, date last accessed).
5. Herndon,T., Ash,M. and Pollin,R. Does high public debt consistently stifle economic growth? In: http://www.peri.umass.edu/236/hash/ 31e2ff374b6377b2ddec04deaa6388b1/publication/566/ (April 2013, date last accessed).
6. European Spreadsheet Risk Interest Group Conference (2013), http://www.eusprig.org/index.htm (April 2013, date last accessed).
7. Hull,D., Wolstencroft,K., Stevens,R. et al. (2006) Taverna: a tool for building and running workflows of services. Nucleic Acids Res., 34, W729-W732.
8. Berthold,M.R., Cebron,N., Dill,F. et al. (2008) KNIME: the Konstanz Information Miner. In: Studies in Classification, Data Analysis, and Knowledge Organization. Springer, Berlin, Heidelberg.
9. Lieberman,L. (1992) Dominoes and Storyboards: Beyond 'Icons on Strings', http://web.media.mit.edu/~lieber/Lieberary/Mondrian/Dominoes.ps (April 2013, date last accessed).
10. Goecks,J., Nekrutenko,A., Taylor,J. et al. (2010) A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
11. Travers,M. (2002) Biobike, https://bitbucket.org/mt/biobike/ (April 2013, date last accessed).
12. Crow,D. (2010) Google squared: web scale, open domain information extraction and presentation. In: European Conference on Information Retrieval, Industry Day. Springer-Verlag, Berlin Heidelberg.
13. Wolstencroft,K., Owen,S., Horridge,M. et al. (2012) RightField: scientific knowledge acquisition by stealth through ontology-enabled spreadsheets, In: EKAW, pp.438-441.
14. Latendresse,M. and Karp,P.D. (2010) An advanced web query interface for biological databases. Database, 2010, baq006.
15. Grossmann,S., Bauer,S., Robinson,P. et al . (2007) Improved detection of overrepresentation of gene-ontology annotations with parent child analysis. Bioinformatics, 23, 3024-3031.
16. Khatri,P., Draghici,S., Ostermeier,G.C. et al. (2002) Profiling gene expression using onto-express. Genomics, 79, 266-270.
17. Rivals,I., Personnaz,L., Taing,L. et al. (2007) Enrichment or depletion of a go category within a class of genes: which test? Bioinformatics, 23, 401-407.
18. Travers,M. (1994) mtlisp, https://github.com/mtravers/mtlisp/ (April 2013, date last accessed).
19. Paley,S.M. and Karp,P.D. (1996) Adapting EcoCyc for use on the world wide web. Gene, 172, GC43-GC50.
20. Travers,M. WuWei - an AJAXy web toolkit for common Lisp. In: http://www.wuwei.name (April 2013, date last accessed).
21. Queinnec,C. (2004) Continuations and web servers. Higher Order Symbolic Comput., 17, 277-295.
22. Naeem,M.K., Rauf,S., Iqbal,H. et al. (2013) In silico studies of C3 metabolic pathway proteins of wheat (Triticumaestivum). Biomed Res. Int., 2013, 294759.
23. BioCyc and Pathway Tools Download Information. In: http://biocyc.org/ download.shtml (April 2013, date last accessed).