Bioinformatics Workshop, Saturday 9 & Sunday 10 July 2011, James Cook University, Cairns Campus

April 29, 2011

Join our Workshop “Bioinformatics

This workshop is aimed at biologist with basic bioinformatics expertise and will be comprised of four half-day sessions covering the following topics:

1. Analysis and interpretation of mass spectrometry data.

In this session several different algorithms for searching tandem mass spectrometry data will be examined (including Mascot, X! Tandem and OMSSA), this will include the theory behind the algorithms and practical exercises in performing searches. Other topics will include search valida- tion using PeptideProphet and ProteinProphet, statistical methods used to validate protein identifications and protein quantitation techniques using mass spectrometry, including label free and isobaric tagging methods. The workshop is designed to provide a theoretical background to the concepts behind protein identification using mass spectrometry as well as practical experience in the techniques discussed.

2. A practical, bioinformatic workflow for the semi-automated analysis of large sequence datasets generated by next-generation sequencing.

In this session, individual components of a practical bioinformatic workflow system for the semi- automated analysis of large transcriptomic datasets generated by next-generation sequencing will be presented through remote connection to a server located at the Department of Veterinary Science, University of Melbourne (GasserLab). These components include assembly of large-scale nucleotide sequence data, sequence annotation and characterisation using information available in public databases, prediction and annotation of putative peptides, probabilistic functional networking of protein-encoding genes and prediction of essential molecules and putative drug targets. This workflow is intended to guide biologically meaningful analyses of large-scale sequence datasets in a time-efficient manner and is designed for researchers with basic bioinformatic expertise.

3. A practical bioinformatics-flavoured introduction to data retrieval, storage, manipulation and presentation using Python.

In this session the scripting language Python will be introduced and used in practical exercises illustrating techniques for the retrieval, storage and manipulation of massively large datasets.

4. Parasite epidemiology.

This session will be an introduction to epidemiology (including basic biostatistics) and data management. It will enable the parasitologist to interpret epidemiological publications and understand the principles of epidemiology for translation of work from the bench to field (specifically how to design, conduct and analyse epide- miological field trials). The session will be informal and consist of both theoretical and practical sessions. The practical session will focus on basic analyses using SPSS.

The instructors will be Jason Mulvenna (QTHA) for mass spectrometry, Cinzia Cantacessi (Uni. of Melbourne, Gasser Lab) for next generation sequencing, Tim McComb (UQ and Ansaldo STS) for python scripting and large datasets and Darren Gray (QIMR, McManus Lab) for epidemiology. All of the presenters have a wealth of experience and have published extensively in their respective fields.

At this stage there will be no or a small nominal fee for the workshop. As it is intended to be a practical workshop attendance will be restricted to 18 people due to computer and room availability. Spots will be assigned on a first in first served basis so be quick to contact Jason Mulvenna ( if you want to attend. Lunch, morning and afternoon tea will be provided.

This workshop is supported by James Cook University, the Australian Society for Parasitology Inc., and the Queensland Tropical Health Alliance.

Download a PDF flyer: Bioinformatics Workshop




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