Beyond standardization: Dynamic software infrastructures for systems biology

Nature Reviews Genetics

Volumn 8, Issue 3, 2007, Pages 235-243

  Swertz, Morris A ^a   Jansen, Ritsert C ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; CAENORHABDITIS ELEGANS; COMPUTER AIDED DESIGN; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER LANGUAGE; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC TRAIT; HUMAN GENOME; INBRED STRAIN; MOLECULAR BIOLOGY; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; REVIEW;

ANIMALS; DATABASES, GENETIC; HUMANS; SOFTWARE; SYSTEMS BIOLOGY;

EID: 33847033243     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2048     Document Type: Review

References (69)

1. Brazma, A., Krestyaninova, M. & Sarkans, U. Standards for systems biology. Nature Rev. Genet. 7, 593-605 (2006).
2. Stein, L. Creating a bioinformatics nation. Nature 417, 119-120 (2002).
3. Abiola, O. et al. The nature and identification of quantitative trait loci: a community's view. Nature Rev. Genet. 4, 911-916 (2003).
4. Jansen, R. C. & Nap, J. P. Genetical genomics: the added value from segregation. Trends Genet. 17, 388-391 (2001).
5. Bystrykh, L. et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nature Genet. 37, 225-232 (2005).
6. Chesler, E. J. et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genet. 37, 233-242 (2005).
7. Alberts, R. et al. Combining microarrays and genetic analysis. Brief. Bioinformatics 6, 135-145 (2005).
8. Keurentjes, J. J. et al. The genetics of plant metabolism. Nature Genet. 38, 842-849 (2006).
9. Li, Y. et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. (2006).
10. Ravichandran, V. & Sriram, R. D. Toward data standards for proteomics. Nature Biotech. 23, 373-376 (2005).
11. Brazma, A. et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genet. 29, 365-371 (2001).
12. Spellman, P. T. et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, RESEARCH0046 (2002).
13. Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004).
14. Etzold, T., Ulyanov, A. & Argos, P. SRS: Information retrieval system for molecular biology data banks. Meth. Enzymol. 266, 114-128 (1996).
15. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European molecular biology open software suite. Trends Genet. 16, 276-277 (2000).
16. Ihaka, R. & Gentleman, R. C. R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5, 399-414 (1996).
17. Wang, X. S., Gorlitsky, R. & Almeida, J. S. From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nature Biotech. 23, 1099-1103 (2005).
18. Foster, I. Service-oriented science. Science 308, 814-817 (2005).
19. Saal, L. H. et al. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol. 3, SOFTWARE0003 (2002).
20. Stein, L. D. et al. The Generic Genome Browser: a building block for a model organism system database. Genome Res. 12, 1599-1610 (2002).
21. Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996-1006 (2002).
22. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
23. Ameur, A., Yankovski, V., Enroth, S., Spjuth, O. & Komorowski, J. The LCB Data Warehouse. Bioinformatics 22, 1024-1026 (2006).
24. Matthews, K. A., Kaufman, T. C. & Gelbart, W. M. Research resources for Drosophila: the expanding universe. Nature Rev. Genet. 6, 179-193 (2005).
25. Alberts, R., Terpstra, P., Bystrykh, L. V., de Haan, G. & Jansen, R. C. A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays. Genetics 171, 1437-1439 (2005).
26. Washietl, S., Hofacker, I. L. & Stadler, P. F. Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA 102, 2454-2459 (2005).
27. Cassman, M. Barriers to progress in systems biology. Nature 438, 1079 (2005).
28. Mattes, W. B., Pettit, S. D., Sansone, S. A., Bushel, P. R. & Waters, M. D. Database development in toxicogenomics: Issues and efforts. Environ. Health Perspect. 112, 495-505 (2004).
29. Zimmermann, P. et al. MIAME/Plant - adding value to plant microarrray experiments. Plant Methods 2, 1 (2006).
30. Xirasagar, S. et al. CEBS object model for systems biology data, SysBio-OM. Bioinformatics 20, 2004-2015 (2004).
31. Jones, A., Hunt, E., Wastling, J. M., Pizarro, A. & Stoeckert, C. J. An object model and database for functional genomics. Bioinformatics 20, 1583-1590 (2004).
32. Fogh, R. H. et al. A framework for scientific data modeling and automated software development. Bioinformatics 21, 1678-1684 (2005).
33. Quackenbush, J. Top-down standards will not serve systems biology. Nature 440, 24 (2006).
34. Baxter, S. M., Day, S. W., Fetrow, J. S. & Reisinger, S. J. Scientific software development is not an oxymoron. PLoS Comput. Biol. 2, e87 (2006).
35. Hunt, A. & Thomas, D. The Pragmatic Programmer: From Journeyman To Master (Addison-Wesley, Boston, 1999).
36. Tseng, M. M. & Jiao, J. in Handbook of Industrial Engineering, Technology and Operation Management (John Wiley & Sons, New York, 2001).
37. Czarnecki, K. & Eisenecker, U. W. Generative Programming: Methods, Techniques, and Applications (Addison-Wesley, Boston, 2000).
38. Clements, P. & Northrop, L. Salion, Inc.: A Software Product Line Case Study. Technical Report Carnegie Mellon CMU/SEI-2002-TR-038 [online], 〈http://www.sei.cmu.edu/publications/documents/02.reports/02tr038. html〉(2002).
39. Clements, P. & Northrop, L. Software Product Lines: Practices and Patterns (Adisson-Wesley, Boston, 2001).
40. Weiss, D. M. & Lai, C. T. R. Software Product-Line Engineering: A Family Based Software Development Process (Addison-Wesley, Boston, 1999).
41. Brownsword, L. & Clements, P. A Case Study In Successful Product Line Development. Technical Report Carnegie Mellon CMU/SEI-96-TR-016 [online], 〈http://www.sei.cmu.edu/publications/documents/96. reports/96.tr.016.html〉 (1996).
42. Nadkarni, P. M. et al. Managing attribute-value clinical trials data using the ACT/DB client-server database system. J. Am. Med. Inform. Assoc. 5, 139-151 (1998).
43. Eker, J. et al. Taming heterogeneity - The ptolemy approach. Proc. IEEE Comput. Syst. Bioinform. Conf. 91, 127-143 (2003).
44. Fall, A. & Fall, J. A domain-specific language for models of landscape dynamics. Ecol. Modell. 141, 1-18 (2001).
45. Jaring, M., Krikhaar, R. L. & Bosch, J. Representing variability in a family of MRI scanners. Softw. Pract. Exper. 34, 69-100 (2004).
46. Covitz, P. A. et al. caCORE: A common infrastructure for cancer informatics. Bioinformatics 19, 2404-2412 (2003).
47. Swertz, M. A. et al. Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics 20, 2075-2083 (2004).
48. Wilkinson, M. D. & Links, M. BioMOBY: an open source biological web services proposal. Brief. Bioinform. 3, 331-341 (2002).
49. Oinn, T. et al. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20, 3045-3054 (2004).
50. Letondal, C. A web interface generator for molecular biology programs in Unix. Bioinformatics 17, 73-82 (2001).
51. Shah, S. P. et al. Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 5, 40 (2004).
52. Garcia, C. A., Thoraval, S., Garcia, L. J. & Ragan, M. A. Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. BMC Bioinformatics 6, 87 (2005).
53. Tang, F. et al. Wildfire: distributed, Grid-enabled workflow construction and execution. BMC Bioinformatics 6, 69 (2005).
54. Garwood, K. L. et al. Pedro: a configurable data entry tool for XML. Bioinformatics 20, 2463-2465 (2004).
55. Sarkans, U. et al. The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics 21, 1495-1501 (2005).
56. Goesmann, A. et al. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. J. Biotechnol. 106, 157-167 (2003).
57. Tobias, J. et al. The CAP cancer protocols - a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid. BMC Med. Inform. Decis. Mak. 6, 25 (2006).
58. Kuipers, O. P. et al. Transcriptome analysis and related databases of Lactococcus lactis. Antonie Van Leeuwenhoek 82, 113-122 (2002).
59. Wilkinson, M., Schoof, H., Ernst, R. & Haase, D. BioMOBY successfully integrates distributed heterogeneous bioinformatics web services. The PlaNet exemplar case. Plant Physiol. 138, 5-17 (2005).
60. Stevens, R. D. et al. Exploring Williams-Beuren syndrome using myGrid. Bioinformatics 2, I303-I310 (2004).
61. Lampel, J. & Mintzberg, H. Customizing customization. Sloan Manage. Rev. 38, 21 (1996).
62. Ulrich, K. The role of product architecture in the manufacturing firm. Res. Policy 24, 419-440 (1995).
63. Bass, L., Clements, P. & Kazman, R. Software Architecture in Practice (Addison-Wesley, Boston, (2003).
64. Buschmann, F., Meunier, R., Rohnert, H., Sommerlad, P. & Stal, M. Pattern-Oriented Software Architecture: A System of Patterns (John Wiley & Sons, New York, 1996).
65. Fowler, M. Patterns of Enterprise Application Architecture (Addison-Wesley, Boston, 2002).
66. Batory, D., Cardone, R. & Smaragdakis, Y. Proceedings of the 1st Software Product-line Conference (Kluwer Academic, 2006).
67. van Deursen, A. & Klint, P. Little languages: little maintenance? J. Softw. Maint. Evol. 10, 75-92 (1998).
68. Van Ommering, R. Building product populations with software components. Proc. 24th Conf. on Software Engineering 255-265 (ACM, New York, 2002).
69. Krueger, C. Eliminating the adoption barrier. IEEE Softw. 19, 29-31 (2002).