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Workflow Related Issues in MBP Development

Workflow Related Issues in MBP Development. Chengzhi Liang ICIS Workshop, Peth March 3, 2010. Key Issues. Search Simple keyword search without domain knowledge required Refined search, eg , ID/accession search Advanced search, eg , mart functions Browse

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Workflow Related Issues in MBP Development

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  1. Workflow Related Issues in MBP Development Chengzhi Liang ICIS Workshop, Peth March 3, 2010

  2. Key Issues • Search • Simple keyword search without domain knowledge required • Refined search, eg, ID/accession search • Advanced search, eg, mart functions • Browse • All datasets in the database, to give user summary info for each dataset • Integration of software programs for various purpose, eg, • Data input tools, curation tools, QC tools • Germplasm list management • Breeding prediction/simulation tools • Visualization tools, eg, for segregation events, graphical reporting • Configurable • Each program is pluggable, ie, can be replaced by another program of same functionality seamlessly • Well-defined data exchange format, via file or db records • Pipeline set up • Software program repository • Register all programs (allow different versions) • Automatic updateable – to relieve the burden of users

  3. IRIS Web • ‘Ad hoc’ development for rice data • Serve as pioneer work for MBP • Will also be an advertisement site for MBP • Project management • JIRA • All new feature requests will go there • Replace CropWiki for issue tracking • Two projects • IRIS • MBP • Most tasks will be shared

  4. Some Technical-side Issues • Top down approach (vs. Bottom up) • GUI/workflow/pipeline (vs. Domain model) • User demand-driven (vs. Technology-driven) • User expectation (vs. available low-level coding support) • Code refactoring (vs. Coding w/ pre-design) • Ad hoc (data-usage centric) + abstraction (vs. pre-designed objects) • Useful for high level of functionalities • Solid foundation for the latter above; However, • Interface is not a simple assembly of underlying parts • Extra layer of complexity can’t be resolved by reduction • Data storage vs. utilization • Time to use the other direction • Eg, simple search, pipeline (one-click) for dummies • Separate data from interface • User interface is diverse – refactor common ones • Maximizing re-usage of non-interface codes • Reducing time to convert interface from one to another

  5. Current IRIS Website Development

  6. External Workflow Example: GenePattern

  7. ICIS Workbook for Data Input & QA • Most breeders use Excel-based input tools • Do we need to keep a simplest Excel-based workbook for data input and QA? • Not possible to store all genomic data on a laptop • Only subset of MBP features available to non-internet users • The workbook will be integrated into the work flow • Used independently – load data local only • Used in pipeline – combine w/ other features in MBP • Issue: • Not all programs will be java-based

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