Workshops at BioInfoSummer 2007

A number of workshops are available to provide hands-on experience with some bioinformatics software packages. Numbers are strictly limited, so please enrol early to ensure your place.

Introduction to Bioinformatics with ANGIS

9.30am-4.30pm, Monday 10th December

For the first time, Bioinfosummer is hosting a full-day workshop run by an ANGIS professional trainer.

The course will cover most of the following areas:

• Definitions of the major databases used in bioinformatics
• Database sequence searching by keyword or sequence similarity
• Sequence format exchange
• Two sequence alignment
• Multiple sequence alignment
• PCR primer design
• Restriction mapping

The course is aimed at giving the participants an overview of the different programs available. It is intended for new PhD and Honours students who are not familiar with bioinformatics and for staff just getting into this area. It is not intended for seasoned ANGIS users. The course is a mixture of lectures, demonstration and hands on workshops.

Please note that this course clashes with the "Introduction to Biology" lectures on Monday afternoon. We recommend this course especially to biology-experienced students, who need no reintroduction to such concepts as the DNA, RNA, the Central Dogma, Amino Acids, PCR and the like. Mathematicians, computer scientists, statisticians etc are advised to attend the lectures, and possibly the Tuesday sequence workshop.

R and microarray analysis workshop

1.30-3.30pm, Wednesday 12th December; repeated Friday 14th December

Bioconductor is a state-of-the-art open source and open development software project for the analysis and comprehension of genomic data. It is based on R, which is a general purpose, open source language and environment for statistical computing and graphics.

Following a brief introduction to R, covering basic mathematical operations, statistical analysis of data and plotting of functions, this workshop will intoduce you to the Bioconductor packages Affy and Plier for analysing expression measures such as MAS5, RMA and PLIER applied to Affymetrix Oligonucleotide Arrays.

From Sequence to Structure

1.30-3.30pm, Tuesday 11th December

In this workshop, we will become acquainted with the major websites, tools and file formats used in sequence analysis. Beginning with a DNA sequence, we trace the process of translating to its amino acid sequence, its near relatives, its putative function and the likely structure of the associated protein. The workshop includes visiting NCBI, Expasy and PDB websites, and using BLAST, PredictProtein, and DeepView (spdbv). No knowledge of biology is assumed, and only a general knowledge of computing (such as file saving and web browsing) is required. All tools used are available on-line or for free download. We use as examples a family of proteins called Glutathione S-Transferases or GSTs.

Introduction to Phylogeny

1.30-3.30pm, Thursday 13th December

This workshop will provide a practical introduction to techniques of phylogenic inference based on molecular data (DNA and proteins), using freely available software. The Phylip software will be used to construct distance matrices, and infer trees based on the Neighbor-Joining method. The use of Bootstrap to assess the robustness of the inferred tree will also be introduced. Maximum likelihood inference will also be demonstrated.