BIOL / PBIO / BINF  4550 / 6550

Bioinformatics Applications

Fall Semester 2017, 3 credits

Schedule:
  • Lecture: Normally, two 75 minute lectures per week, 9:30 AM, Tuesdays and Thursdays, room 1501, Plant Sciences.
  • Labs: Computer lab sessions will be interspersed with lectures as appropriate.
1 Tue 15 Aug Introduction Malmberg, Leebens-Mack
2 Thr 17 Aug Unix, Linux, Command-Line Malmberg
3 Tue 22 Aug Lab - Command-Line, Local Resources Malmberg
4 Thr 24 Aug NCBI Searches & Databases Malmberg
5 Tue 29 Aug NCBI, Databases Malmberg
6 Thr 31 Aug Databases, File Formats Malmberg
7 Tue 5 Sep Lab - Genome Browsers Malmberg
8 Thr 7 Sep Align - Scoring Matrices Malmberg
9 Tue 12 Sep Align - Two Sequences Malmberg
10 Thr 14 Sep Align - Multiple Sequences Malmberg
11 Tue 19 Sep Lab - Multiple Sequence Alignments Malmberg
12 Thr 21 Sep Align - Motifs Malmberg
13 Tue 26 Sep Prediction - Genes & Features Malmberg
14 Thr 28 Sep Prediction - Structure Malmberg
15 Tue 3 Oct Prediction - Translational Bioinformatics,
Exam 1 given
Malmberg
16 Thr 5 Oct Sequence Assembly Leebens-Mack
17 Tue 10 Oct Lab - Microbial genome assembly 
Exam 1 due
Leebens-Mack
18 Thr 12 Oct Transcriptome Analyses I Leebens-Mack
19 Tue 17 Oct Transcriptome Analyses II Leebens-Mack
20 Thr 19 Oct Lab - Transcriptome assembly and quantification Leebens-Mack
21 Tue 24 Oct Phylogeny I Leebens-Mack
22 Thr 26 Oct Phylogeny II Leebens-Mack
23 Tue 31 Oct Lab - Phylogenetic Tree Building Leebens-Mack
24 Thr 2 Nov Molecular Evolution Leebens-Mack
25 Tue 7 Nov Lab - Molecular Evolution Leebens-Mack
26 Thr 9 Nov SNP Genotyping Leebens-Mack
27 Tue 14 Nov Lab - Variant Calling Leebens-Mack
28 Thr 16 Nov Function Annotation, Ontologies
Graduate student project reports due
Leebens-Mack
  Tue 21 Nov  ~~ Thanksgiving Holiday ~~ 
  Thr 23 Nov  ~~ Thanksgiving Holiday ~~ 
29 Tue 28 Nov Project Report Presentations Graduate Students
30 Thr 30 Nov Project Report Presentations
Exam 2 given
Graduate Students
  Tue 5 Dec  ~~ No Class - Friday Classes taught on a Tuesday. ~~ 
    11:00 am - Exam 2 Due
This is the day and time an in class final would have been held and due, if we had an in-class final.

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