451TopicsProblem SetsSeminar
08-25
Course Introduction
Course SyllabusOffice HoursIntroductory Slides
08-27
Unix, not Eunuchs
Unix SlidesRitchie DM and Thompson K (1974) The UNIX Time-Sharing System Comm ACM 17 365-75
09-01
Shell Games
Shell Games SlidesHistory @ 451
09-03
Shell Games (cont'd)
Bill of RightsStreams DemonstrationHistory @ 451
09-08
Computational Experimentation
Peng RD (2011) Reproducible Research in Computational Science Science 334 1226-7Sandve GK, Nekrutenko A, Taylor J and Hovig E (2013) Ten Simple Rules for Reproducible Computational Research PLOS Computational Biology 9 e1003285Baggerly KA and Coombes KR (2009) Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology The Annals of Applied Statistics 3 1309-34Bioinformatics, September, 2026
09-10
Protein Data Bank
Worldwide Protein Data BankBernstein FC, Koetzle TF, Williams GJB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T and Tasum M (1977) The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures Eur J Biochem 80 319-24Berman HM (2007) The Protein Data Bank: a historical perspective Acta Crystallographica Section A 64 88-95RCSB PDBPDBselectHobohm U, Scharf M, Schneider R and Sander C (1992) Selection of representative protein data sets Prot Sci 1 409-17Dunbrack Lab—PISCES
09-15
Protein Folds
09-17
Presentation Graphics
09-22
Presentation Graphics (cont'd)
09-24
Solvent Accessibility
09-29
Hydrogen Bonding
10-01
Secondary Structure
10-06
Midterm Exam
10-08
Sequence Alignment (Global)
10-13
Secondary Structure Prediction
10-15
No Class—Fall Recess
10-20
Tertiary Structure Prediction
10-22
Tertiary Structure Prediction (cont'd)
10-27
Molecular Dynamics
10-29
Docking
11-03
Sequence Alignment (Local)
11-05
Sequence Alignment (Local) (cont'd)
11-10
Phylogeny
11-12
High–Throughput Sequencing
11-17
Alignment to a Reference Sequence
11-19
Variant Calling
11-24
No Class—Thanksgiving Recess
11-26
No Class—Thanksgiving Recess
12-01
Various and Sundry Tools
12-03
Various and Sundry Tools (cont'd)
12-08
Using the Literature
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