메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Bioinformatic pipelines in Python with Leaf

Author keywords

Bioinformatic pipelines; Data analysis; Python

Indexed keywords

AUTOMATED FEATURES; CHANGING ENVIRONMENT; CONSISTENCY CHECKS; DEVELOPMENT APPROACH; DEVELOPMENT ENVIRONMENT; DEVELOPMENT PROCESS; PROCESSING OPTIMIZATIONS; PYTHON;

EID: 84879068611     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-201     Document Type: Article
Times cited : (4)

References (31)
  • 2
    • 0033397980 scopus 로고    scopus 로고
    • Python: a programming language for software integration and development
    • [PMID:10660911]
    • Sanner MF. Python: a programming language for software integration and development. J Mol Graph Model 1999, 17:57-61. [PMID:10660911].
    • (1999) J Mol Graph Model , vol.17 , pp. 57-61
    • Sanner, M.F.1
  • 3
    • 40749084477 scopus 로고    scopus 로고
    • A comparison of common programming languages used in bioinformatics
    • 10.1186/1471-2105-9-82, 2267699, 18251993
    • Fourment M, Gillings MR. A comparison of common programming languages used in bioinformatics. BMC Bioinformatics 2008, 9:82. [http://www.biomedcentral.com/1471-2105/9/82/abstract], 10.1186/1471-2105-9-82, 2267699, 18251993.
    • (2008) BMC Bioinformatics , vol.9 , pp. 82
    • Fourment, M.1    Gillings, M.R.2
  • 4
    • 65749098202 scopus 로고    scopus 로고
    • Dynamically typed languages
    • Tratt L
    • Tratt L Dynamically typed languages. Adv Comput 2009, 77:149-184. Tratt L.
    • (2009) Adv Comput , vol.77 , pp. 149-184
  • 6
    • 0035500136 scopus 로고    scopus 로고
    • Agile software development, the people factor
    • Cockburn A, Highsmith J. Agile software development, the people factor. Computer 2001, 34(11):131-133.
    • (2001) Computer , vol.34 , Issue.11 , pp. 131-133
    • Cockburn, A.1    Highsmith, J.2
  • 10
    • 79960570447 scopus 로고    scopus 로고
    • Why and Where: A Characterization of Data Provenance
    • Berlin, Heidelberg: Springer Berlin Heidelberg, Bussche J, Vianu V
    • Buneman P, Khanna S, Wang-Chiew T. Why and Where: A Characterization of Data Provenance. Database Theory - ICDT 2001, Volume 1973 316-330. Berlin, Heidelberg: Springer Berlin Heidelberg, Bussche J, Vianu V, [http://www.springerlink.com/index/10.1007/3-540-44503-X_20].
    • Database Theory - ICDT 2001, Volume 1973 , pp. 316-330
    • Buneman, P.1    Khanna, S.2    Wang-Chiew, T.3
  • 11
    • 84857392540 scopus 로고    scopus 로고
    • The case for open computer programs
    • 10.1038/nature10836, 22358837
    • Ince DC, Hatton L, Graham-Cumming J. The case for open computer programs. Nature 2012, 482(7386):485-488. [http://dx.doi.org/10.1038/nature10836], 10.1038/nature10836, 22358837.
    • (2012) Nature , vol.482 , Issue.7386 , pp. 485-488
    • Ince, D.C.1    Hatton, L.2    Graham-Cumming, J.3
  • 12
    • 84879601576 scopus 로고    scopus 로고
    • Leaf Home Page
    • Leaf Home Page. , http://www.neuronelab.dmi.unisa.it/leaf
  • 13
    • 84879603063 scopus 로고    scopus 로고
    • Leaf source code repository
    • Leaf source code repository. , https://github.com/franapoli/pyleaf
  • 15
    • 38049150833 scopus 로고    scopus 로고
    • Automation of in-silico data analysis processes through workflow management systems
    • Romano P. Automation of in-silico data analysis processes through workflow management systems. Brief Bioinformatics 2008, 9:57-68. [http://bib.oxfordjournals.org/content/9/1/57].
    • (2008) Brief Bioinformatics , vol.9 , pp. 57-68
    • Romano, P.1
  • 16
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • [PMID:20738864 PMCID: PMC2945788], 10.1186/gb-2010-11-8-r86, 2945788, 20738864
    • Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945788/] [PMID:20738864 PMCID: PMC2945788], 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
    • (2010) Genome Biol , vol.11 , Issue.8
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 17
    • 33747833111 scopus 로고    scopus 로고
    • Taverna: a tool for building and running workflows of services
    • 10.1093/nar/gkl320, 1538887, 16845108
    • Hull D, Wolstencroft K, Stevens R, Goble C, Pocock MR, Li P, Oinn T. Taverna: a tool for building and running workflows of services. Nucleic Acids Res 2006, 34(Web Server):W729-W732. [http://nar.oxfordjournals.org/content/34/suppl_2/W729.full], 10.1093/nar/gkl320, 1538887, 16845108.
    • (2006) Nucleic Acids Res , vol.34 , Issue.WEB SERVER
    • Hull, D.1    Wolstencroft, K.2    Stevens, R.3    Goble, C.4    Pocock, M.R.5    Li, P.6    Oinn, T.7
  • 18
    • 2942544409 scopus 로고    scopus 로고
    • Pegasys: software for executing and integrating analyses of biological sequences
    • [PMID:15096276 PMCID:PMC406494], 10.1186/1471-2105-5-40, 406494, 15096276
    • Shah SP, He DY, Sawkins JN, Druce JC, Quon G, Lett D, Zheng GX, Xu T, Ouellette BF. Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 2004, 5:40. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC406494/] [PMID:15096276 PMCID:PMC406494], 10.1186/1471-2105-5-40, 406494, 15096276.
    • (2004) BMC Bioinformatics , vol.5 , pp. 40
    • Shah, S.P.1    He, D.Y.2    Sawkins, J.N.3    Druce, J.C.4    Quon, G.5    Lett, D.6    Zheng, G.X.7    Xu, T.8    Ouellette, B.F.9
  • 19
    • 79953305104 scopus 로고    scopus 로고
    • Conveyor: a workflow engine for bioinformatic analyses
    • 10.1093/bioinformatics/btr040, 21278189
    • Linke B, Giegerich R, Goesmann A. Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics 2011, 27(7):903-911. [http://bioinformatics.oxfordjournals.org/content/27/7/903], 10.1093/bioinformatics/btr040, 21278189.
    • (2011) Bioinformatics , vol.27 , Issue.7 , pp. 903-911
    • Linke, B.1    Giegerich, R.2    Goesmann, A.3
  • 22
    • 0043026713 scopus 로고    scopus 로고
    • Biopipe: a flexible framework for protocol-based Bioinformatics analysis
    • 403782, 12869579, Chia Jm
    • Hoon S, Ratnapu KK, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E, Chia Jm Biopipe: a flexible framework for protocol-based Bioinformatics analysis. Genome Res 2003, 13(8):1904-1915. [http://genome.cshlp.org/content/13/8/1904], 403782, 12869579, Chia Jm.
    • (2003) Genome Res , vol.13 , Issue.8 , pp. 1904-1915
    • Hoon, S.1    Ratnapu, K.K.2    Kumarasamy, B.3    Juguang, X.4    Clamp, M.5    Stabenau, A.6    Potter, S.7    Clarke, L.8    Stupka, E.9
  • 23
    • 77958489718 scopus 로고    scopus 로고
    • Ruffus: a lightweight Python library for computational pipelines
    • 10.1093/bioinformatics/btq524, 20847218
    • Goodstadt L. Ruffus: a lightweight Python library for computational pipelines. Bioinformatics 2010, 26(21):2778-2779. [http://bioinformatics.oxfordjournals.org/content/26/21/2778], 10.1093/bioinformatics/btq524, 20847218.
    • (2010) Bioinformatics , vol.26 , Issue.21 , pp. 2778-2779
    • Goodstadt, L.1
  • 24
    • 84861746974 scopus 로고    scopus 로고
    • Bpipe : a tool for running and managing Bioinformatics pipelines
    • Sadedin SP, Pope B, Oshlack A. Bpipe : a tool for running and managing Bioinformatics pipelines. Bioinformatics 2012, [http://bioinformatics.oxfordjournals.org/content/early/2012/04/11/bioinformatics.bts167.abstract].
    • (2012) Bioinformatics
    • Sadedin, S.P.1    Pope, B.2    Oshlack, A.3
  • 26
    • 84871567829 scopus 로고    scopus 로고
    • Flex: The Fast Lexical Analyzer
    • flex: The Fast Lexical Analyzer. , http://www.gnu.org/software/flex
  • 27
    • 84870683469 scopus 로고    scopus 로고
    • Bison - GNU parser generator
    • Bison - GNU parser generator. , http://www.gnu.org/software/bison/
  • 28
    • 84871592168 scopus 로고    scopus 로고
    • Graphviz - Graph Visualization Software
    • Graphviz - Graph Visualization Software. , http://www.graphviz.org
  • 29
    • 67651098662 scopus 로고    scopus 로고
    • Mechanisms of change in gene copy number
    • [PMID:19597530], 10.1038/nrg2593, 2864001, 19597530
    • Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nature Rev. Genet 2009, 10(8):551-564. [http://www.ncbi.nlm.nih.gov/pubmed/19597530] [PMID:19597530], 10.1038/nrg2593, 2864001, 19597530.
    • (2009) Nature Rev. Genet , vol.10 , Issue.8 , pp. 551-564
    • Hastings, P.J.1    Lupski, J.R.2    Rosenberg, S.M.3    Ira, G.4
  • 30
    • 35948984173 scopus 로고    scopus 로고
    • PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    • 10.1101/gr.6861907, 2045149, 17921354
    • Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007, 17(11):1665-1674. [http://genome.cshlp.org/content/17/11/1665.abstract], 10.1101/gr.6861907, 2045149, 17921354.
    • (2007) Genome Res , vol.17 , Issue.11 , pp. 1665-1674
    • Wang, K.1    Li, M.2    Hadley, D.3    Liu, R.4    Glessner, J.5    Grant, S.F.6    Hakonarson, H.7    Bucan, M.8
  • 31
    • 84879602192 scopus 로고    scopus 로고
    • A simple and efficient access to R from Python
    • A simple and efficient access to R from Python. , http://rpy.sourceforge.net


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.