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Volumn 13, Issue 2, 2012, Pages 244-257

A toolbox for developing bioinformatics software

Author keywords

Programming; Project management; Software development; Software quality

Indexed keywords

RNA;

EID: 84858236105     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr035     Document Type: Article
Times cited : (19)

References (52)
  • 2
    • 77957944901 scopus 로고    scopus 로고
    • Computational science:... Error
    • Merali Z. Computational science:... Error. Nature 2010; 467:775-777.
    • (2010) Nature , vol.467 , pp. 775-777
    • Merali, Z.1
  • 4
    • 0036391032 scopus 로고    scopus 로고
    • The state of ISO 9000 certification: a study of Swedish organizations
    • Poksinska B, Dahlgaard JJ, Antoni M. The state of ISO 9000 certification: a study of Swedish organizations. TQM Magazine 2002;14:10.
    • (2002) TQM Magazine , vol.14 , pp. 10
    • Poksinska, B.1    Dahlgaard, J.J.2    Antoni, M.3
  • 6
    • 0000801578 scopus 로고
    • The new new product development game
    • Jan 01. Online journal
    • Takeuchi H, Nonaka I. The new new product development game. Harv Bus Rev 1986. Jan 01. Online journal.
    • (1986) Harv Bus Rev
    • Takeuchi, H.1    Nonaka, I.2
  • 10
    • 58149203231 scopus 로고    scopus 로고
    • InterPro: the integrative protein signature database
    • Hunter S, Apweiler R, Attwood TK, et al. InterPro: the integrative protein signature database. Nucleic Acids Res 2009;37:D211-5.
    • (2009) Nucleic Acids Res , vol.37
    • Hunter, S.1    Apweiler, R.2    Attwood, T.K.3
  • 11
    • 33847105467 scopus 로고    scopus 로고
    • Agile methods in biomedical software development: a multi-site experience report
    • Kane DW, Hohman MM, Cerami EG, et al. Agile methods in biomedical software development: a multi-site experience report. BMC Bioinformatics 2006;7:273.
    • (2006) BMC Bioinformatics , vol.7 , pp. 273
    • Kane, D.W.1    Hohman, M.M.2    Cerami, E.G.3
  • 12
    • 33749320683 scopus 로고    scopus 로고
    • Scientific software development is not an oxymoron
    • Baxter SM, Day SW, Fetrow JS, et al. Scientific software development is not an oxymoron. PLoSComput Biol 2006;2: e87.
    • (2006) PLoSComput Biol , vol.2
    • Baxter, S.M.1    Day, S.W.2    Fetrow, J.S.3
  • 14
    • 34247868161 scopus 로고    scopus 로고
    • eMovie: a storyboard-based tool for making molecular movies
    • Hodis E, Schreiber G, Rother K, et al. eMovie: a storyboard-based tool for making molecular movies. Trends Biochem Sci 2007;32:199-204.
    • (2007) Trends Biochem Sci , vol.32 , pp. 199-204
    • Hodis, E.1    Schreiber, G.2    Rother, K.3
  • 15
    • 34447338596 scopus 로고    scopus 로고
    • PROTMAP2D: visualization, comparison, and analysis of 2D maps of protein structure
    • Pietal MJ, Tuszynska I, Bujnicki JM. PROTMAP2D: visualization, comparison, and analysis of 2D maps of protein structure. Bioinformatics 2007;23:1429-30.
    • (2007) Bioinformatics , vol.23 , pp. 1429-1430
    • Pietal, M.J.1    Tuszynska, I.2    Bujnicki, J.M.3
  • 16
    • 40449086374 scopus 로고    scopus 로고
    • From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal
    • Smit S, Rother K, Heringa J, et al. From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. RNA 2008;14:410-416.
    • (2008) RNA , vol.14 , pp. 410-416
    • Smit, S.1    Rother, K.2    Heringa, J.3
  • 17
    • 84858245295 scopus 로고    scopus 로고
    • Fast structural alignment of biomolecules using a hash table, N-grams and string descriptors
    • Bauer RA, Rother K, Moor P, et al. Fast structural alignment of biomolecules using a hash table, N-grams and string descriptors. Algorithms 2009;2:17.
    • (2009) Algorithms , vol.2 , pp. 17
    • Bauer, R.A.1    Rother, K.2    Moor, P.3
  • 18
    • 79959292152 scopus 로고    scopus 로고
    • ModeRNA: a tool for comparative modeling of RNA 3D structure
    • Rother M, Rother K, Puton T, et al. ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res 2011;39:4007-22.
    • (2011) Nucleic Acids Res , vol.39 , pp. 4007-4022
    • Rother, M.1    Rother, K.2    Puton, T.3
  • 19
    • 58149191269 scopus 로고    scopus 로고
    • MODOMICS: a database of RNA modification pathways, 2008 update
    • Czerwoniec A, Dunin-Horkawicz S, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res 2009;37:D118-21.
    • (2009) Nucleic Acids Res , vol.37
    • Czerwoniec, A.1    Dunin-Horkawicz, S.2    Purta, E.3
  • 21
    • 77953006555 scopus 로고    scopus 로고
    • IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities
    • Rother K, Hoffmann S, Bulik S, et al. IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities. Biophys J 2010;98:2478-86.
    • (2010) Biophys J , vol.98 , pp. 2478-2486
    • Rother, K.1    Hoffmann, S.2    Bulik, S.3
  • 22
    • 0242559057 scopus 로고    scopus 로고
    • Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins
    • Rother K, Preissner R, Goede A, et al. Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics 2003;19: 2112-21.
    • (2003) Bioinformatics , vol.19 , pp. 2112-2121
    • Rother, K.1    Preissner, R.2    Goede, A.3
  • 23
    • 21244502261 scopus 로고    scopus 로고
    • Molecular packing and packing defects in helical membrane proteins
    • Hildebrand PW, Rother K, Goede A, et al. Molecular packing and packing defects in helical membrane proteins. Biophys J 2005;88:1970-77.
    • (2005) Biophys J , vol.88 , pp. 1970-1977
    • Hildebrand, P.W.1    Rother, K.2    Goede, A.3
  • 24
    • 44049094995 scopus 로고    scopus 로고
    • Hydrogenbonding and packing features of membrane proteins: functional implications
    • Hildebrand PW, Gunther S, Goede A, et al. Hydrogenbonding and packing features of membrane proteins: functional implications. Biophys J 2008;94:1945-53.
    • (2008) Biophys J , vol.94 , pp. 1945-1953
    • Hildebrand, P.W.1    Gunther, S.2    Goede, A.3
  • 25
    • 78649907609 scopus 로고    scopus 로고
    • Correlation to protein conformation of wide-angle X-ray scatter parameters
    • Elshemey WM, Elfiky AA, Gawad WA. Correlation to protein conformation of wide-angle X-ray scatter parameters. Protein J 2010;29:545-50.
    • (2010) Protein J , vol.29 , pp. 545-550
    • Elshemey, W.M.1    Elfiky, A.A.2    Gawad, W.A.3
  • 26
    • 34748893838 scopus 로고    scopus 로고
    • PyCogent: a toolkit for making sense from sequence
    • Knight R, Maxwell P, Birmingham A, et al. PyCogent: a toolkit for making sense from sequence. Genome Biol 2007; 8:R171.
    • (2007) Genome Biol , vol.8
    • Knight, R.1    Maxwell, P.2    Birmingham, A.3
  • 27
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: freely available Python tools for computational molecular biology and bioinformatics
    • Cock PJ, Antao T, Chang JT, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009;25:1422-3.
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.1    Antao, T.2    Chang, J.T.3
  • 28
    • 80255140476 scopus 로고    scopus 로고
    • RNA and protein 3D structure modeling: similarities and differences
    • Jan 22 [Epub ahead of print]
    • Rother K, Rother M, Boniecki M, et al. RNA and protein 3D structure modeling: similarities and differences. J Mol Model 2011. Jan 22 [Epub ahead of print].
    • (2011) J Mol Model
    • Rother, K.1    Rother, M.2    Boniecki, M.3
  • 29
    • 0024061028 scopus 로고
    • Statistical geometry in sequence space: a method of quantitative comparative sequence analysis
    • Eigen M, Winkler-Oswatitsch R, Dress A. Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. Proc Natl Acad Sci USA 1988;85:5913-7.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 5913-5917
    • Eigen, M.1    Winkler-Oswatitsch, R.2    Dress, A.3
  • 30
    • 0024474755 scopus 로고
    • How old is the genetic code? Statistical geometry of tRNA provides an answer
    • Eigen M, Lindemann BF, Tietze M, et al. How old is the genetic code? Statistical geometry of tRNA provides an answer. Science 1989;244:673-9.
    • (1989) Science , vol.244 , pp. 673-679
    • Eigen, M.1    Lindemann, B.F.2    Tietze, M.3
  • 31
    • 0030770590 scopus 로고    scopus 로고
    • Graphs in sequence spaces: a review of statistical geometry
    • Nieselt-Struwe K. Graphs in sequence spaces: a review of statistical geometry. Biophys Chem 1997;66:111-31.
    • (1997) Biophys Chem , vol.66 , pp. 111-131
    • Nieselt-Struwe, K.1
  • 32
    • 0029988290 scopus 로고    scopus 로고
    • GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space
    • Kuznetsov I, Morozov P. GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space. Comput Appl Biosci 1996;12:297-301.
    • (1996) Comput Appl Biosci , vol.12 , pp. 297-301
    • Kuznetsov, I.1    Morozov, P.2
  • 33
    • 36448954303 scopus 로고    scopus 로고
    • FR3D: finding local and composite recurrent structural motifs in RNA 3D structures
    • Sarver M, Zirbel CL, Stombaugh J, et al. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol 2008;56:215-52.
    • (2008) J Math Biol , vol.56 , pp. 215-252
    • Sarver, M.1    Zirbel, C.L.2    Stombaugh, J.3
  • 36
    • 26444508905 scopus 로고    scopus 로고
    • Death by UML fever
    • Bell AE. Death by UML fever. ACM Queue 2004;2:9.
    • (2004) ACM Queue , vol.2 , pp. 9
    • Bell, A.E.1
  • 37
    • 70149115417 scopus 로고    scopus 로고
    • Making sense of revision-control systems
    • O'Sullivan B. Making sense of revision-control systems. Commun ACM 2009;52:7.
    • (2009) Commun ACM , vol.52 , pp. 7
    • O'Sullivan, B.1
  • 39
    • 84858166160 scopus 로고    scopus 로고
    • (10 May, date last accessed)
    • Foundation DS. Django Framework. www.djangoproject. com (10 May 2011, date last accessed).
    • (2011) Django Framework
    • Foundation, D.S.1
  • 40
    • 84858166165 scopus 로고    scopus 로고
    • (10 May, date last accessed)
    • Testing Framework. http://c2.com/cgi/wiki?TestingFramework (10 May 2011, date last accessed).
    • (2011) Testing Framework
  • 46
    • 18644368714 scopus 로고    scopus 로고
    • The Bioperl toolkit: Perl modules for the life sciences
    • Stajich JE, Block D, Boulez K, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002;12: 1611-8.
    • (2002) Genome Res , vol.12 , pp. 1611-1618
    • Stajich, J.E.1    Block, D.2    Boulez, K.3
  • 47
    • 51749088608 scopus 로고    scopus 로고
    • BioJava: an open-source framework for bioinformatics
    • Holland RC, Down TA, Pocock M, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics 2008;24:2096-7.
    • (2008) Bioinformatics , vol.24 , pp. 2096-2097
    • Holland, R.C.1    Down, T.A.2    Pocock, M.3
  • 50
    • 84858197932 scopus 로고    scopus 로고
    • Agile42. (06 May, date last accessed)
    • Agile42. Scrum Lego City. http://www.agile42.com/cms/pages/lego_city_game/ (06 May 2011, date last accessed).
    • (2011) Scrum Lego City
  • 52
    • 77957931288 scopus 로고    scopus 로고
    • Publish your computer code: it is good enough
    • Barnes N. Publish your computer code: it is good enough. Nature 2010;467:753.
    • (2010) Nature , vol.467 , pp. 753
    • Barnes, N.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.