4/16/2004MSE Presentation II1 ESTMD System -- A Web-based EST Model Database System Yinghua Dong

4/16/2004MSE Presentation II2 Outline Project Review Architecture Design Formal Requirement Specification Test Plan Formal Technical Inspection Project Status References Acknowledgments

4/16/2004MSE Presentation II3 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

4/16/2004MSE Presentation II4 Architecture Design -- Use Case Diagram

4/16/2004MSE Presentation II5 Architecture Design -- Main Object Model (1)

4/16/2004MSE Presentation II6 Architecture Design -- Main Object Model (2)

4/16/2004MSE Presentation II7 Architecture Design -- Object Model of Search In Detail

4/16/2004MSE Presentation II8 Architecture Design -- Object Model of Search By Keyword

4/16/2004MSE Presentation II9 Architecture Design -- Object Model of Gene Ontology

4/16/2004MSE Presentation II10 Architecture Design -- Object Model of GO Classification

4/16/2004MSE Presentation II11 Architecture Design -- Object Model of Pathway Search

4/16/2004MSE Presentation II12 Architecture Design -- Sequence Diagram of Gene Ontology

4/16/2004MSE Presentation II13 Architecture Design -- Sequence Diagram of GO Tree View

4/16/2004MSE Presentation II14 Formal Requirement Specification -- Overview Language: Alloy 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,

4/16/2004MSE Presentation II15 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

4/16/2004MSE Presentation II16 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

4/16/2004MSE Presentation II17 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

4/16/2004MSE Presentation II18 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

4/16/2004MSE Presentation II19 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

4/16/2004MSE Presentation II20 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 Detail Document

4/16/2004MSE Presentation II21 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

4/16/2004MSE Presentation II22 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

4/16/2004MSE Presentation II23 References Modeling Web Application Architectures with UML, Jim Conallen, apers/2003/webapps.pdf apers/2003/webapps.pdf Software Formal Inspections, Software Assurance Technology Center (SATC), 1997, Software Requirements, 2nd Edition, Karl Wiegers, Microsoft Press, 2003, ecklist.doc ecklist.doc Software Engineering: A practitioner’s Approach, 5 th Edition, Roger. S. Pressman, Alloy web site, CIS771 lecture, Dr. Hatcliff CIS 540, CIS 841 lecture, Dr. Gustafson

4/16/2004MSE Presentation II24 Acknowledgments Committee: Dr. Mitchell L. Neilsen Dr. Gurdip Singh Dr. Daniel Andresen

4/16/2004MSE Presentation II25 Suggestions and Comments Thank You!