Bio 465 Bioinformatics

BYU | Bioinformatics | CS Dept.
Date Topic Reading Due Dates Lecturer
4-Jan Intro to Bioinformatics Chapter 1, EBAPBA
Intro, Cell Movie
Clement, Crandall
6-Jan Using the Supercomputer Supercomputer Documentation putty download Snell
9-Jan Project Selection Projects Crandall, Clement
11-Jan HyPhy HyPhy, Tutorial, HyPhy Methods, Example dataset, DataMonkey server Eduardo
13-Jan Project Work Session Make Assignments for Project Proposal Crandall
16-Jan Holiday       
18-Jan Protein Alignments (Paralogs/Homologs) Chapter 4 EBAPBA Set up your assignment page, Assignment #1 Crandall
20-Jan Sequence Assembly Chapter 5 EBAPBA Assignment #2 Crandall
23-Jan Sequence Assembly illumina, 454 Sequencing , Pacific Biosystems sequencing ,Cap Assembler ,Replication ,Transcription, Translation ,PCR, PCR machines, Cycle Sequencing , Helicos Sequencing, Pyro Sequencing lab HyPhy Clement
25-Jan Assembly Velvet Manual, Velvet Paper , 454 Manual  Clement
27-Jan Project Status Reports Assignment #3 Clement
30-Jan Gene Finding Chapter 6 EBAPBA Project Proposal Due (Abstract, Related Work, Outline (with Milestones), expected Conclusions) instead of Assignment #4 Crandall
1-Feb CpG islands HMM Tutorial Clement
3-Feb Project Status Reports lab Assembly Crandall
6-Feb Training HMMs Genemark, ghmm tutorial, slides from class Clement
8-Feb Artificial Neural Networks Clement
10-Feb Guest Speaker David McAllister from NVidia , CUDA Resources  Assignment #5 Clement 
13-Feb Structure Prediction Chapter 7 EBAPBA Crandall
15-Feb Using Weka Weka Primer , Weka Presentation, Weka download Clement
17-Feb Project Session - Formal Status reports, final report due next week
20-Feb Holiday      
21-Feb GPU Tutorial lab HMM Gene Finding, Assignment #6
22-Feb Guest Speaker - Perry Ridge, ARUP
24-Feb Project Status Reports Final report draft (TA via email) Clement
27 Feb Structure Comparison Protein Bioinformatics Ch 9(blackboard) Clement
29-Feb Superpositioning of 3D structures Clement
2-Mar Project Status Reports 1st round reviews Clement
5-Mar 3D structure visualization Pymol Tutorial Clement
7-Mar Neural Network Lab Work Session labNeural Networks Clement
9-Mar Guest Speaker - Julie Eggington, Myriad Genetics Assignment #7 Crandall
12-Mar Microarrays and Gene Expression Analysis Chapter 9 EBAPBA Crandall
14-Mar Practical Microarray Analysis MAGIC toolkit, Download, Example, Uses, Book Tutorial Clement
16-Mar Project Status Reports Assignment #8 Clement
19-Mar Molecular Geneology Chapter 8 EBAPBA Crandall
21-Mar Paper Presentations Clement
23-Mar Project Status Reports Final report second draft and review responses(TA via email)
26-Mar Regulatory Network Inferrence Pathgen, Airnet, DREAM,Virtual Heart Clement
28-Mar Paper Presentations 2nd round reviews
30-Mar Project Status Reports Clement
2-Apr Pymol Competition   Clement
4-Apr Paper Presentations Crandall
6-Apr Guest Speaker Timothy O'Connor 2nd round responses Clement
9-Apr Eduardo Castro Nallar Research Presentation Assignment #10
11-Apr* Project Work Session labStructure similarity
12-13-Apr Reading Days
Final Exam Project presentations
(Attendance is required)
Final Project Report Due
* All late work due by 11:59 pm on Wednesday, April 13.