MRes Course on Post-genomics, Transcriptomics and bio-informatics - D2DPG1

MRes in Advanced Genomic and Proteomic Sciences (AGPS)
UoN Module: D2DPG1 Genomics/Transcriptomics/Bioinformatics.

Location: The Plant Sciences Ground Floor Computer Room

Including notes on improvement for 2008

Monday 15th Oct

09:30 - Introduction to module.
Lectures
09:45 Introduction to genomics
10:30 Introduction to genome databases (Guest speaker - Roberts)
Practical
11:30 How to exploit genome database resources using basic sequence analysis tools such as BLAST
Lecture
14:00 Genome bioinformatics tools (Guest speaker - Bennett)
Resource:
How to exploit genome database resources to investigate gene function
Practical:
Practical assignment to investigate gene function.
student deliverable:
Extensive notes for submission of a 2 page document on 26th.
Tuesday 16th Oct
Morning - experimental design module
Lecture:
14:00 Introduction to general transcriptomics
Macroarrays, microarrays versus gene chips
movie
Wednesday 17th Oct
Lectures:
09:30 Introduction to Affymetrix GeneChips at NASCarrays
10:30 Introduction to Genespring Workgroup
Practical
14:00 Training session in Genespring.
Mini-Project - affy case study.
16:30 student deliverable: Consideration of affy project data sets.
Thursday 18th Oct
Mini-Project - affy case study.
09:30 student deliverable: Self-allocation of affy project data set (30 mins).
Mini-Project - affy case study.
10:30 student deliverable: non-contact research.
From this point, mini-project supervision is self-directed and non-contact. Help can be received by well-formed email. Software is only provided in the module study room. This is also an exercise in self discipline. In 2008 emphasise *no software anywhere else*- also swop Mon/Tues of next week with Thurs/Friday of this week.
Friday 19th Oct
Directed reading In 2008 - link this into the first affy day.:
The chipping forecast - 2002 - please read 2 complete articles (your choice)
The Omics gateway - please attempt 2 different species articles from 2007 (your choice)
Mini-Project - affy case study. 14:00 student deliverable: non-contact research.
Monday 22th Oct
09:30 Tour
Introduction to equipment including:

Liquid handling robots
Robotic colony picker
Nanodrop spectrophotometer
PE Voyager MALDI-TOF
Biorobotics arrayer
In-situ slide cycler
Automated slide wash and processing stations
Agilent Bioanalyser
Affymetrix GeneChip hyb station and scanner
Spotting movie (6MB)
Agilent RNA prep movie (13MB)
Lecture
14:00 Authentigene - a genomics spin-out company
Lecture
15:30 Xspecies - a novel research application of transcriptomics
Tuesday 23rd Oct
Morning - experimental design module
14:00 Guest lectures (Beatrice Schildknecht)
Web Services - Data Integration
Guest practical (Beatrice Schildknecht)
Introduction to Taverna
Wednesday 24th Oct
Mini-Project - affy case study.
All day student deliverable - non-contact research.

Thursday 25th Oct
Mini-Project - affy case study.
All day student deliverable - non-contact research.
11:00 - Basic guidance on powerpoint presentations (voluntary attendance).
Nanodrop film

Friday 26th Oct
10:15 - 15 minute talks by students
student deliverable - please provide a single file powerpoint talk on CD or USB by 10:00:
In 2008 this should be assessed and moved back to Weds.

Leohardt Hesse
Kate Lynch (en route to Ireland - did not attend)
Wycliffe Masanta (did not attend)
Thomas Meriaux
Bhuvandeep Narang
Student Withdrawn
Tom Giles (no talk prepared but attended)
Practical
student deliverable Finishing the summaries:
Gene description from Mon 15th
format: one gene, 2 pages text + up to 2 pages of tables/images per student, intro/methods/results/discussion/refs.
Affy case study from mini-project [Thurs 18th - Thurs 25th]
For 2008, move this information up the page and give the students a: suggested format
format: one case, 2 pages text + up to 2 pages of tables/images per student, intro/methods/results/discussion/refs.
Deadline for BOTH - 17:00 today [26th]
Submit one Word file for each summary by EMAIL to sean@arabidopsis.info
Sean will be available in the room to confirm received emails.
In 2008 report 1 will be due on friday week 1; report 2 on Friday week 2.