Bioinformatics Services

Sydney Bioinformatics offers a range of professional bioinformatics services including collaborative research, expert assistance, advice, consultancy, customized data analysis, and software development.

A consultation involves staff of Sydney Bioinformatics meeting with life science researchers seeking advice or assistance in regard to bioinformatics. The purpose is to develop and understanding of the overall research program and the specific research questions requiring a bioinformatics approach, in order to suggest ways of approaching the problem.

Consultations are provided at no charge to staff and students of the University of Sydney and its affiliated teaching hospitals and research institutes. A fee may apply for consultations provided to researchers from outside of the University of Sydney.

Please contact Sebastien Gerega (9036 3276) to arrange a consultation.

Sydney Bioinformatics staff and affiliated academics are also available to work on collaborative projects with life science researchers. These projects will usually be formed as a result of a consultation where a body of work has been identified that requires specific bioinformatics expertise.

A small team comprising a Project Officer and an affiliated academic with expertise in the particular area of bioinformatics will work collaboratively with the researchers to complete the piece of bioinformatics research in the context of the larger research program.

Examples of typical collaborative research projects include:

• conducting statistical analyses of transcriptomic or proteomic expression data. (For example, see Lin et al., PNAS, 101:12718-12723, 2004.)
• predicting the 3D structure of a particular protein and using the structure to help interpret or understand the biological function or mechanism of action of the protein. (For example, see: Arthur JW et al., Bioinformatics, 22:2192-2195, 2006.)
• constructing, analysing, and interpreting evolutionary relationships between genes and protein using phylogenetics. (For example, see: Ball et al., Gene, 396:203-213, 2007.)

Collaborative research projects will usually result in one or more publications with authorship shared between the life science researchers and the Project Officer and academic contributing to the project.

A fee is charged to recover the costs of completing the project. Fees for researchers affiliated with the University of Sydney or its affiliated research institutes and teaching hospitals can be found here.

For further information about collaborative projects, including fees for researchers not affiliated with the University of Sydney, please contact Dr Jonathan Arthur (9036 3132).

Sydney Bioinformatics is open to alternative ways of providing bioinformatics services and support to researchers. For example:

• some large or complex projects may be better suited as the subject of a PhD project through a co-supervised student, or alternatively demand the attention of a dedicated postdoctoral researcher or research assistant funded by a joint grant
• some larger institutes may have (or seek) their own bioinformatics staff they want to "link in" to Sydney Bioinformatics' wider network of academics and staff in order to draw on their expertise and receive professional support
• some smaller research groups may legitimately be unable to afford even the heavily discounted fees associated with collaborative research project

To discuss alternative options, please contact Dr Jonathan Arthur (9036 3132).

What types of microarrays does Sydney Bioinformatics work with?
Sydney Bioinformatics does not perform the microarray experiments but analyses the data obtained from the experiments. We will perform the analysis of any type of array including Illumina BeadArrays, Affymetrix arrays, cDNA arrays etc.

When should I contact Sydney Bioinformatics?
We recommend contacting us as early as possible so that we can advise on the experimental design. This ensures that your experiment is designed to have the greatest chance of providing statistically significant answers to your specific questions.

What is the typical duration and cost of a project?
The length and cost of an analysis varies greatly between projects. A differential expression analysis of Affymetrix microarray data will usually take between 5 and 15 hours to perform. Additional components such as gene ontology analysis or clustering will increase the time required and cost. More information about the fees associated with project work can be found here. Alternatively, contact Sebastien Gerega (9036 3276) to obtain more information.

At the completion of the project, can I be trained to perform the analysis? Can I be present during the analysis and observe the process?
Many researchers ask whether, at the completion of the project, they can be trained to perform the analysis. Due to multiple projects usually being undertaken in parallel, it is not possible to watch the analysis as it is performed. However, when the project work is complete, there is the option of obtaining one-on-one training (the additional time spent on the training is charged at the same rate as the project work). It is important to note that the majority of software used by Sydney Bioinformatics is command line based. Therefore, one-on-one training is not recommended for those without some previous experience with scripting or programming languages.

What happens at the completion of a project?
When the project work is complete, you will receive a project report summarising the analysis and results. Data files, figures and images will be uploaded to the Sydney Bioinformatics website for you to download. If required, an additional consultation can be organised to explain the findings in person. Typically, the findings of a project will be published and Sydney Bioinformatics staff contributing to the project would share authorships on the manuscript. As work on the manuscript begins, we ask you to contact us so we can contribute during this phase.