Cpt S 471/571: Computational Genomics

Transcription

1 Cpt S 471/571: Computatioal Geomics Sprig 2018, 3 cr. Where: EME B46 (i Pullma), TFLO 256 (Tricities campus) Whe: TuTh 12:00-13:15 Istructor weekly office hour for Sprig 2018: Wedesdays EME 237

2 Course Objectives To itroduce the set of algorithms ad data structures that have applicatios to computatioal geomics To be able to formulate ad/or model a biological problem/system as a computer sciece problem To be able to desig algorithms usig appropriate data structures to solve the uderlyig biological problem To be able to appreciate the role of computer sciece i moder day biological scieces (iterdiscipliary traiig) To see applicability of algorithms & techiques i other domais such as text miig, patter matchig, etc.

3 Course Orgaizatio Topics: Approximate strig matchig Exact strig matchig Probabilistic modelig for biological sequece aalysis Applicatios Geome sequecig, ad aotatio, Read mappig, Gee idetificatio, Clusterig/trascriptomics, Phylogeetics.

4 Course Focus Problem Trasformatio Algorithms & Techiques Specialized Data Structures for Geomic Data

5 Course Material Lecture Notes o the course website Textbook Refereces: Edited by S. Aluru. Hadbook of Computatioal Molecular Biology, ISBN: (available through WSU digital library) Durbi, et al. Biological Sequece Aalysis: Probabilistic Models of Protei ad Nucleic Acids, ISBN: D. Gusfield. Algorithms o Strigs, Trees, ad Sequeces: Computer Sciece ad Computatioal Biology, ISBN: Other Useful Refereces: C. Setubal ad J. Meidais. Itroductio to Computatioal Molecular Biology, ISBN: M.S. Waterma. Itroductio to Computatioal Biology, ISBN:

6 Prerequisites Cpt S 223/233 or equivalet (advaced data structures) CptS 350 or equivalet (algorithm desig & aalysis) Familiarity with basic Probability fudametals Biological backgroud NOT required but a iterest ad icliatio to lear is! C/C++/Java programmig experiece Perl, Pytho ot O.K.

7 Gradig (for Cpt S 571) Homework problems (12.5%) 3 to 4 Programmig projects (45%) 1 Fial Exam (17.5%) Survey project (15%) - 6 weeks Propose papers ad source material Oral presetatio (durig the last 2 weeks of class) 5-page survey paper/report Classroom participatio (10%) Gradig policy: curved

8 Gradig (for Cpt S 471) Homework problems (12.5%) 3 Programmig projects (60%) 1 Fial Exam (17.5%) Classroom participatio (10%) (No Survey project) Gradig policy: curved

9 Course Webpage, Resources ad Aoucemets Cotets to watch out for: Homeworks, projects Survey project details Lecture otes Tetative course schedule Liks to several referece papers, hadouts, ad other useful web resources For s ad project submissios, use WSU Blackboard: Aoucemets & Discussios will happe o Piazza:

10 Classroom practices Take otes! Durig each class there will be a scribe who will be assiged to take active otes. Each studet will get a tur beig a scribe ad assigmet will be roud robi. If you do t pla o attedig a sessio please write ahead of time to iform istructor. Use of laptops ad smart phoes ot allowed i classroom.

11 Homeworks Due i-class o the due date Hardcopies (preferred), if ot a PDF/Doc submissio by mail Alog with the cover sheet

12 Programmig projects Submit o WSU Blackboard dropbox Due 11:59 pm o the respective due dates

13 Late Submissio Policy No late submissio allowed Extesios may be allowed uder extraordiary circumstaces Cotact istructor at least 1 week prior to permissio

14 Collaboratio Policy All assigmets should be doe idividually uless a specific problem states that "collaboratio is permitted". "Collaboratio" is defied as a discussio with other studets i the same class (o outsiders allowed) aimed at obtaiig a better uderstadig of the problem questio ad/or explorig potetial approaches at a very high level that ca lead to a solutio. What is collaboratio? A discussio leadig to a better uderstadig of the problem statemet What is NOT allowed: Presetig or showig or sharig i ay capacity, your solutio or the mai part of it to aother studet A high level discussio aimed at arrivig at a plausible approach to solvig the problem All writig at the ed should be 100% yours. (PS: this is allowed i team projects) Referrig to a olie/web documet showig a solutio to the same or highly related problem posed i the questio Referrig to other sources icludig previous batch studet solutios

15 Collaboratio Policy All collaborative efforts should be explicitly ackowledged/cited i the aswer sheet by all the participats usig the cover sheet. Regardless of whether you collaborate or ot, the fial writig i the aswer sheet should be solely yours. No poits will be deducted for collaboratio as defied above. Ay deviatio from the above guidelies will be cosidered "cheatig" ad will be subject to academic dishoesty code. This icludes sharig (or eve showig of) your solutios, lookig up solutios o the web ad usig them, etc. Depedig o the level of offese, the istructor may decide to fail the studet. You ca lear more about Academic Itegrity o your campus at