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ESTMD System -- A Web-based EST Model Database System

ESTMD System -- A Web-based EST Model Database System. Yinghua Dong. Outline. Project Review Architecture Design Formal Requirement Specification Test Plan Formal Technical Inspection Project Status References Acknowledgments. Project Review. Objective

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ESTMD System -- A Web-based EST Model Database System

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  1. ESTMD System -- A Web-based EST Model Database System Yinghua Dong MSE Presentation II

  2. Outline • Project Review • Architecture Design • Formal Requirement Specification • Test Plan • Formal Technical Inspection • Project Status • References • Acknowledgments MSE Presentation II

  3. Project Review Objective Build a web-based, user-friendly Expressed Sequence Tags model database (ESTMD) system to help biologists search expression sequences and related information to make further decisions MSE Presentation II

  4. Architecture Design -- Use Case Diagram MSE Presentation II

  5. Architecture Design -- Main Object Model (1) MSE Presentation II

  6. Architecture Design -- Main Object Model (2) MSE Presentation II

  7. Architecture Design -- Object Model of Search In Detail MSE Presentation II

  8. Architecture Design-- Object Model of Search By Keyword MSE Presentation II

  9. Architecture Design -- Object Model of Gene Ontology MSE Presentation II

  10. Architecture Design -- Object Model of GO Classification MSE Presentation II

  11. Architecture Design -- Object Model of Pathway Search MSE Presentation II

  12. Architecture Design-- Sequence Diagram of Gene Ontology MSE Presentation II

  13. Architecture Design-- Sequence Diagram of GO Tree View MSE Presentation II

  14. Formal Requirement Specification-- Overview • Language: Alloy 1.1 -- a structural modeling language based on first-order logic • Tool: ACA (Alloy Constraint Analyzer) • Purpose: explore abstract software designs, simulate execution of operations, and check user-specified properties of a model • Scopes: Gene Ontology Query and Gene Ontology Tree Generation • References: Dr. John Hatcliff, CIS 771 Lectures Alloy web site, http://sdg.lcs.mit.edu/alloy MSE Presentation II

  15. FRS (cont’d) -- For Gene Ontology Query • The user who submits a form is the user who gets the form's query result. all f : Form | f.whoPut = f.query.whoGet • The link belongs to the result which its corresponding output item belongs to. all l : Link | l.linkedBy in l.linkBelongTo.includeOutputItem • The input item is written by the user who put the corresponding query form. all ii: InputItem | ii.belongToUser=ii.belongToForm.whoPut MSE Presentation II

  16. FRS (cont’d) -- For Gene Ontology Query • Each sequence ID links to a sequence link all oi: OutputItem | oi /in SequenceID <-> oi.linkTo /in Sequence_link • Each GOID links to a tree link all oi: OutputItem | oi /in GOID <-> oi.linkTo /in TreeView_link • Detail Document MSE Presentation II

  17. FRS (cont’d) -- For Gene Ontology Tree Generation • No Item is its own ancestor. no i: Item | i in i.+parents • There is exactly one Root in each tree. one i: Item | i /in Root • Each item except Root is Root's descendant. all i: Item - Root | Root in i.+parents • Root has no parents or ancestor all r: Root | no r.+parents • Leaf has no children or descendant all l: Leaf | no l.+children • NonLeafItem must have at least one parent and at least one child. all nl: nonLeafItem | some nl.parents && some nl.children MSE Presentation II

  18. FRS (cont’d) -- For Gene Ontology Tree Generation • Operation – Add a new Item in the tree op AddItem (l: Leaf'!) { // pre-condition l !in Item // post-condition Item' = Item + l all p: l.parents' | p in Item // frame-condition Root' = Root all i: Item | i.parents' = i.parents } • Detail Document MSE Presentation II

  19. Test Plan • Test Phases: • Unit testing, Integration testing, and System testing • Test Items: • Connection between server and database • Each page • Test Features: • Features to be tested: each function • Features not to be tested: quality of the data MSE Presentation II

  20. Test Plan (cont’d) • Methodology: • Functional testing (Black box) method • Pass/Fail Criteria • The system will pass if the authentication works correctly and if the results from the queries are displayed within one minute. • Otherwise the test will fail and the code will be revised. • Deliverables: • Test plan, Test case specification, and Test result • Detail Document MSE Presentation II

  21. Formal Technical Inspection • Purpose To ensure consistency in the software development life cycle and quality of the software requirements • Organization • Developer: Yinghua Dong • Inspectors: Acharaporn Pattaravanichanon (Ann) and Zhigang Xie • Software Inspection Checklist * Completeness * Consistency * Correctness * Feasibility * Modifiablility * Traceability * Understandability * Clarity * Functionality * Reliability • Detail Document MSE Presentation II

  22. Project Status • Finished: • Documentation: 1/2 of the whole project • Implementation: About 1/3 • Future Work: • Implementation: 2/3 workload • Documentation: User Manual, Test Report, and Evaluation • Final Presentation MSE Presentation II

  23. References • Modeling Web Application Architectures with UML, Jim Conallen, http://www3.software.ibm.com/ibmdl/pub/software/rational/web/whitepapers/2003/webapps.pdf • Software Formal Inspections, Software Assurance Technology Center (SATC), 1997, http://satc.gsfc.nasa.gov/fi/fipage.html • Software Requirements, 2nd Edition, Karl Wiegers, Microsoft Press, 2003, http://www.processimpact.com/process_assets/requirements_review_checklist.doc • Software Engineering: A practitioner’s Approach, 5th Edition, Roger. S. Pressman, • Alloy web site, http://sdg.lcs.mit.edu/alloy • CIS771 lecture, Dr. Hatcliff • CIS 540, CIS 841 lecture, Dr. Gustafson MSE Presentation II

  24. Acknowledgments Committee: • Dr. Mitchell L. Neilsen • Dr. Gurdip Singh • Dr. Daniel Andresen MSE Presentation II

  25. Suggestions and Comments Thank You! MSE Presentation II

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