The Victorian Bioinformatics Consortium, based at Monash University, brings
together researchers with expertise in medicine, biotechnological,
agricultural, and veterinary research, bioinformatics, statistics and
computer science.
The VBC's role in
ARC/NHMRC Research Network for Parasitology
is to provide bioinformatics support to network members.
Below is a summary of the areas in which we can assist you.
If you
have a biological problem where Bioinformatics is a significant bottleneck to
your discovery process,
please contact 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
- Assembly and scaffolding of contigs and reads
- Automatic identification and annotation of sequence features: genes, RNAs,
IS elements
- Pre-computed protein analyses: BLAST, HMMER, PSORT, TMHMM
- Ability to search, edit and data-mine your genomic data using our
custom Wasabi software
- Preparation of submission to NCBI
- Orthologous gene clustering
- Comparitive genomic analyses
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
- Base calling for chromatograms using Phred
- Cleaning of the produced sequences from bacterial and vector contamination
- Assembly of the different reads into sequence consensus
- Annotation and data mining of the sequences
- Storage of sequences and results from annotation and data mining processes
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
- Design oligoes/probes for your microarray experiment
- Store microarray data securely and share the data with
collaborators anywhere in the world
- Analyse microrray data using a variety of open source and
commercial software programs
- Consult with experts in microarray analysis for assistance
with normalization of data, statistical analysis and
identification of significantly under- or over-expressed
genes
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:
- Unix systems administration
- Installation and setup of bioinformatics software
- Database schema design
- Web site construction
- Design and construction of server hardware
- Deployment of storage arrays
