Class Schedule
Reading assignments pertain to Introduction to Bioinformatics, 4th Ed.| Date | Lecture topic | Instructor | Reading Assignment |
| 29-Aug | Intro/Molecular Biology Review | Eric Polinko | Ch1: 1-10 & 21-22 |
| 31-Aug | Genomes, Genomics, and the Human Genome Project | EP | Ch2: 59-62 & 88-90 |
| 02-Sep | **LAB** The Internet, Networking, & Unix | EP | |
| 05-Sep | ***NO CLASS - LABOR DAY*** | ||
| 07-Sep | Genomics | EP | Ch2: 64-88 |
| 09-Sep | (hw#1 due @ noon) **LAB** NCBI & UniProt |
EP |
|
| 12-Sep | (Project Version 1 due @ 9am) Genomics Cont'd |
EP | Ch2: 88-100 |
14-Sep | Past, Present, and Future of DNA Sequencing | Dan Russell |
| 16-Sep | (hw#2 due @ noon) Visualization & Organization of Genomic Data |
Miler Lee |
|
| 19-Sep | **Lab** Genome Browsers | ML | |
| 21-Sep | Proteomics | EP | Ch2: 62-64 |
| 23-Sep | **Lab** - BLAST & ClustalΩ |
EP |
|
| 26-Sep | Proteomics Cont'd & Systems Biology | EP | Ch1: 50 Ch7: 282-283 Ch9: 335-340 |
| 28-Sep | Biological Databases | EP | Ch3: 104-109 Ch4: 144-152 |
| 30-Sep | Sequence Database Searching - Scoring Matrices (hw#3 due @ noon) |
EP |
Ch5: 176-186 |
| 03-Oct | Sequence Database Searching - Pairwise Sequence Alignment
(Project Version 2 due @ 9am) |
EP | Ch5: 187-193 |
| 05-Oct | Sequence Database Searching - BLAST & Evaluation | EP | Ch5: 194-196 |
| 07-Oct | (hw#4 due @ noon) **LAB** - High Performance Computing at SaM |
Kim Wong | |
| 10-Oct | RNAseq Analysis | Ansuman Chattopadhyay | Ch2: 62-64 |
| 12-Oct | **LAB** - CLCBio Genomics Workbench |
AC | |
| 14-Oct | (hw#5 due @ noon) **LAB** - CLCBio Genomics Workbench |
AC |
|
| 17-Oct | ***FALL BREAK - CLASS ON TUESDAY*** | ||
| 18-Oct | Integrative Large-scale Genomics Projects |
Miler Lee | |
| 19-Oct | Multiple Sequence Alignment |
ESP | Ch5: 196-197 |
| 21-Oct | **LAB** - Jalview (& pssm lab?) |
EP | |
| 24-Oct | (Project Version 3 due @ 9am) Position-Specific Scoring Matrices |
EP | Ch1: 30-38 Ch5: 198-202 |
| 26-Oct | Exam Review (&/or lecture catch-up/ketchup) | EP | |
| 28-Oct | (hw#6 due @ noon?) Development of a Learning Electronic Medical Record (EMR) System |
Andrew King | Ch3: 133-141 |
| 31-Oct | EXAM I | EP | |
| 2-Nov |
Intro to Protein Structure |
Joel Rosenbaum | Ch10: 298-304, 322-328 |
| 4-Nov | **LAB** - VMD | EP | |
| 7-Nov | Solving Protein Structure via X-ray Crystallography | JR | |
| 9-Nov | **LAB** - Coot |
JR | |
| 11-Nov | Introduction to Biomolecular Simulation ** In 103 Clapp Hall ** |
Jacob Durrant | Ch6: 255-257 |
| 14-Nov | Biomolecular Simulation ** In 103 Clapp Hall ** |
JD | Ch6: 255-257 |
| 16-Nov | **LAB**- Preparing a Simulation Model using VMD | JD | VMD |
| 18-Nov | **LAB** - Running a Simulation using NAMD |
JD | NAMD |
| 21-Nov | **LAB**- Simulation Analyses |
JD | |
| 23/25-Nov | ***NO CLASS - THANKSGIVING*** | ||
| 28-Nov | Scientific Consultant(s) @ BioTeam, Inc. |
Adam Kraut & Adam Marko | BioTeam |
| 30-Nov | Connectomics & Brain Imaging Project Part IV due |
Art Wetzel & Greg Hood |
fMRI Overview |
| 2-Dec | Exam review | EP | Ch5: 181-186 |
| 5-Dec | Lead Bioinf Scientist @ UPMC Presby | Keith Callenberg | |
| 7-Dec | EXAM II | ||
| 9-Dec | **Field Trip to MMBioS!** Creating Stereoscopic 3D Movies |
Art Wetzel, Greg Hood, & Jacob Czech | MMBioS |
| 12-17 Dec |
FINAL ==> Project Presentations Three alternative days/times (TBA) |
||
Last Updated: 25 August 2016
Question or Comments: epolinko@pitt.edu
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