Systems biology driven software design for the research enterprise. Export

@article{citeulike:2927719, abstract = {BACKGROUND: In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. RESULTS: We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. CONCLUSION: By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.}, author = {Boyle, John and Cavnor, Christopher and Killcoyne, Sarah and Shmulevich, Ilya}, citeulike-article-id = {2927719}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-9-295}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18578887}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18578887}, day = {25}, doi = {10.1186/1471-2105-9-295}, issn = {1471-2105}, journal = {BMC bioinformatics}, keywords = {data-curation, software-design, systems-biology}, month = {June}, pages = {295+}, posted-at = {2009-05-21 12:03:52}, priority = {2}, title = {Systems biology driven software design for the research enterprise.}, url = {http://dx.doi.org/10.1186/1471-2105-9-295}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:2927719 L3 - citeulike-article-id:2927719 N2 - BACKGROUND: In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools. RESULTS: We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model. CONCLUSION: By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data. JF - BMC bioinformatics SN - 1471-2105 TI - Systems biology driven software design for the research enterprise. VL - 9 SP - 295 KW - data-curation KW - software-design KW - systems-biology AU - Boyle, John AU - Cavnor, Christopher AU - Killcoyne, Sarah AU - Shmulevich, Ilya PY - 2008/06/25/ UR - http://dx.doi.org/10.1186/1471-2105-9-295 ER -