UoN Graduate School Course on Post-genomics and bio-informatics
Resource documents.
Suggested reading
Genespring tutorial guide
excel analysis
Resource files
ms1.xls (excel BIG:12MB)
rhd_mutant_data.xls (excel BIG:17.6MB)
1) Seminars are held in Room LR11 (by the Plant Science building foyer)
2) Practicals are held in Room A14 (by the Plant Science building foyer)
Monday 11th Feb
8.20 Bus leaves from UP
9.00am - 9:15 Register in Plant Science building foyer, coffee
9:15 - 10:00 Seminar 1
Introduction to genomics (Sean May)
10:00 - 10:45 Seminar 2
QTLs as a measure of molecular phenotype (Kamal Swarup).
10:45 - 11:00 Coffee - Plant Science building foyer
11:00 - 11:30 Seminar 3
Genome databases (Rebecca Roberts)
11:30 - 1:00 Practical 1
How to exploit genome database resources (Sean May) Using basic sequence analysis tools such as BLAST
1:00 - 1:30 Lunch - Sutton Bonington facilities or bring your own
1:30 - 2:15 Seminar 4
Genome bioinformatics tools (Neil Graham)
2:15 - 3:15 Practical 2
How to exploit genome database resources to investigate gene function, including using analysis tools such as spot history with your gene IDs.
3:15 - 3:30 Coffee - Plant Science building foyer
3:30 - 5:30 Practical 3
Practical assignment to investigate gene function (Sean May / Neil Graham) Groups of 5 students will be provided with a DNA sequence to investigate its gene function using the bioinformatic tools learnt so far. The information assembled will form part of a student presentation made at the end of day 3.
Tuesday 12th Feb
8.20 Bus leaves from UP
9.00am - 9:15 Register in Plant Science building foyer, coffee
9:15 - 9:30 Introduction to the schedule - day 2
9:30 - 10:15 Seminar 5
Introduction to transcriptomics (Sean May)
10:15 - 11:15 Seminar 6
Analysing transcriptome data - a practical example (John Hammond)
11:15 - 11:30 Coffee - Plant Science building foyer
11:30 - 12:15 Tour
Genomic resources (May/ Graham/ Emmerson)
How to use the spotter (movie 6MB)
Agilent RNA preparation (movie 13MB)
12:15 - 1:00 Lunch - Sutton Bonington facilities or bring your own
1:00 - 2:45 Practical 4
A hands-on introduction to analysing transcriptome data (Neil Graham)
2:45 - 3:30 Seminar 7
Connecting functional genomics data together with web services (Beatrice Schildknecht)
3:30 - 3:45 Coffee - Plant Science building foyer
3:45 - 5:00 Practical 5 / Proteomics Tour Circus
The group will split into sub-groups, each of which will be taken (in turn) on a tour of the Proteomics facility. The non-touring groups will start to prepare their powerpoint presentations for tomorrow:
5:00 - 5:15 Seminar 8
An example genome sequencing program
Wednesday 13th Feb
8.20 Bus leaves from UP
9.00am - 9:15 Register in Plant Science building foyer, coffee
9:15 - 10:00 Seminar 9 -
Tea (Alex Marshall)
Dogs (Dan Zadik)
- practical applications in systems biology.
spare talk - xspecies
10:00 - 10:45 Seminar 10
A practical approach to metabolomics (Rob Linforth)
10:45 - 11:00 Coffee - Plant Science building foyer
11:00 - 12:00 Seminar 11 -
Introduction to proteomics (Susan Liddell) Covering methods of protein purification and separation including 1D/2D gels
12:00 - 12:45 Seminar 12
Introduction to metabolomics (Catharine Ortori) Covering methods of sample preparation, separation, detection and data analysis
12:45 - 1:45 Lunch - Sutton Bonington facilities or bring your own
1:45 - 3:00 Practical 6
MASCOT identification of peptides
(Susan Liddell)
3:00 - 3:15 Coffee - Plant Science building foyer
3:15 - 4:15 Practical 7
Preparation of data for student presentation (guided by Sean May)
4:15 - 5:30 Student Seminars
PowerPoint presentations by groups of students describing the resources employed and in silico results investigating the function of their assigned DNA sequences
