The role of the consortium is to assist you in your Bioinformatics needs. If you have a biological problem where Bioinformatics is a significant bottleneck to your discovery process, get in touch with us!

Automation

→ Are you finding yourself continually having to submit information over and over to the same web form?
→ Do you have a list of items in a spreadsheet and want to calculate something special for every row but don't know how?
→ Do you wish all your data and results could be stored together and searched via the web?
→ Need summaries or diagrams of huge data sets for a paper but don't know where to start?

The VBC has extensive experience in creating custom scripts, databases and software to solve these sorts of issues, allowing you to proceed with the scientific discovery process.

Genomics

The VBC was directly involved in the first genome to be fully sequenced and annotated in Australia, Leptospira borgpetersenii servovar hardjo-bovis. Since then it has been an important part of the analysis and comparison of various genomes in the genii Leptospira, Mycobacterium, Clostridium, Plasmodium, Brachyspira, Neisseria, Pasteurella, and Staphylococcus .

ESTs

In order to deliver a simple EST management tool, the VBC developed EST-PAC, an EST annotation pipeline. EST-PAC can be installed locally and performs basic annotation processes using sequence and domain similarities. The VBC will provide assistance to use this pipeline either locally or install it on our server and add special features on request. Previously, we have used this database to successfully annotate Sarcoptes scabiei ESTs.

Microarrays

The VBC microarray server runs an open-source software platform called BASE, for the storage and analysis of microarray data. The use of BASE allows microarray gene expression data to be stored in a MIAMI compliant manner, and exported using the MAGE-ML standard. A large number of experiments can be stored in a well structured manner making navigation and searching easy. BASE is accessed via a Web interface which allows for collaborations across the world. A detailed security model makes it possible to share only the information and data that one chooses. BASE uses plugins for data analysis which allows many different types of data normalization, transformation, and analysis. The VBC has expertise in maintaining, customizing and extending BASE to meet the requirements of users. For example, the VBC has also developed new analysis plugins for BASE to meet specific needs.

The VBC also has skills in statistical analysis of microarray expression data. This includes appropriate normalizations to remove noise from the data. Analysis is performed using either the BASE platform, commercial analysis software, or the open-source Bioconductor package. The outcome of the analyses may be a list of differentially expressed genes (using appropriate significance tests), various clusterings, or visualizations such as Principal Component Analysis, or Multi-Dimensional Scaling.

Computer Systems

Advice on: