Intro, Cell Movie
HyPhy Assembly HMM Gene Finding,
Assignment #6Neural Networks Structure similarity2:30pm–5:30pm
(Monday)
(Attendance is required)
| 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 | 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 | 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 | 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 | Neural 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) |
Clement | |
| 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 |
Structure similarity |
||
| 12-13-Apr | Reading Days | |||
| 16-Apr 2:30pm–5:30pm (Monday) |
Final Exam | Project presentations (Attendance is required) |
Final Project Report Due | |