The Cancer Genomics Linkage Application will enable the integration and re-use of the cancer genomics data available from public repositories such as the International Cancer Genome Consortium (ICGC). This will be accomplished through the capability being developed by the “Early Activity” of the Genomics Virtual Laboratory (GVL-EA). It will enable researchers, such as Professors Andrew Biankin, John Mattick (Garvan Institute for Medical Research) or Sean Grimmond (Queensland Centre for Medical Genomics), to access genomic datasets of international importance and to integrate them with their own clinical and genomic datasets in order to explore, discover and validate key genomic abnormality that cause cancer. The product will further provide the mechanism for such researchers to publish and to make available their analysis for re-use by the community.

The product aims to provide the ability for biologists and clinicians to easily integrate their own research data with datasets from multiple data sources. The Integration of the datasets into a common location and enabling access and mining using best practice workflow tools will enable the Australian cancer researchers to accelerate their discovery processes and to be internationally competitive. Although this project will have a particular focus on pancreatic cancer research as carried out by the Australian Pancreatic Cancer Genome Initiative (APGI), the application can also support the wider cancer research community.

Download the application from here.

Friday, 31 August 2012

The Project Team


Development Team

Dr Dominique Gorse (QFAB) –Project Manager

Dominique Gorse is leading the development of QFAB’s platform for integrated and accessible bioinformatics which is designed to support large multi-institution research projects and to provide advanced bioinformatics solutions to the biotechnology, pharmaceutical, clinical and research communities.

Dominique has over 19 years' experience in software development, information management, data mining and data modelling applied to life science. Over the years, he has developed expertise in using Agile project management methodologies for the efficient delivery of quality projects and their alignment with business objectives. He has a strong record of growing technology companies such as Synt:em, (France, 1996-2001), and Bio-Layer (Australia, 2001-2007). 

Dr Xin-Yi Chua (QFAB) – Scrum Master and Project Lead

Xin-Yi Chua is a Senior Bioinformatician at the Queensland Facility for Advanced Bioinformatics (QFAB). She received her doctorate at the Queensland University of Technology for her work in applying machine learning approaches to enhance performance in inferring transcriptional regulatory interactions in bacteria using the comparative genomics approach. From this work she has also developed a keen interest in visual analytics and investigating methods to capture information from large scale genomic data to facilitate intuitive and rapid comprehension. This is motivated by the need to reduce the now apparent gap between data generation and data analysis; the ability to automate repeatable discovery processes and quickly highlight regions of interest for further verification will increase how researchers can maximize their efforts. 

Pierre-Alain Chaumeil (QFAB) – Software Developer

Pierre-Alain Chaumeil has a background in Bioinformatics having completed a Bachelor of Science majoring in Biology of Organisms and a Master degree in Bioinformatics. He has programming skills in different languages such as Java, Perl, Eiffel, C/C++ and Python.

Pierre-Alain was involved in the development of QFAB Systems Biology Platform to provide Australian researchers in R&D organisations and industry with direct, scalable access to the most internationally comprehensive, expert-curated and integrated genomic, proteomic and metabolic datasets available, and to industry-standard tools for data integration, analysis, visualization and electronic collaboration.

Anne Kunert (QFAB) – Software Developer

Anne Kunert has a background in Computer Sciences, having completed a Diploma Degree in Computer Science and Arts at the Technical University of Dortmund (Germany). Anne joined the QFAB team as software developer in early 2012. She has experience in a diverse range of interdisciplinary IT projects, particularly in software development for life science research applications. 

Product Owners

Dr Mark Cowley

Representative of Cancer Bioinformatics at Garvan Institute of Medical Research 
Mark Cowley is a Senior Research Officer of the Cancer Bioinformatics group at the Garvan Institute of Medical Research headed by Dr Jianmin Wu. The group aims to apply computational and statistical methods to model biological and clinical questions related to cancer biology and translational research. Currently the group is working on integrative analysis of multidimensional "-omics" datasets, generated by deep sequencing of the cancer genome, transcriptome, epigenome, and proteome, as well as in vitro and in vivo functional screens, with the aim of identifying candidate driver mutations and pathways aberrations in pancreatic cancer.

John Pearson

Representative of the Queensland Centre for Medical Genomics
John Pearson is the Senior Bioinformatics Manager at Queensland Centre for Medical Genomics (QCMG). One of his current research interests is next generation sequencing using Life Technologies SOLiD, Illumina HiSeq and Ion Torrent PGM. 

Dr Cas Simons

Representative of the Institute for Molecular Bioscience
Cas Simons is a Senior Bioinformatician at the Institute for Molecular Bioscience (IMB). He has a demonstrated ability to utilise both genomic and transcriptomic data from a wide variety of sources to investigate the complex transcriptional outputs of eukaryote genomes and deliver high impact research outcomes. His research background includes using the power of next generation sequencing to understand the transcriptional output of the cell. One highlight of his work was the discovery of a novel class of small RNAs that are tightly associated with mammalian splice sites. 

Dr Jeff Christiansen

Representative of the Australian National Data Service
Jeff Christiansen is a Senior Business Analyst at the Australian National Data Service (ANDS), primarily working on biology-themed projects. His background is in both biological research and data management, primarily in the areas of gene expression and imaging.

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