Current Projects

Embedded Activities

• Bioinformatics support of genomic services to clients.

This project is for general provision of bioinformatics support of the genomic services that are supplied by the Australian Genome Research Facility (AGRF) to their clients through provision of dedicated bioinformatics staffing and associated infrastructure.

• LIMS

This project focuses on providing the necessary software tools to allow the lab-based teams at the AGRF to effectively track the progress of samples through their workflows and ensure the timely delivery of accurate research to clients.

• Bioinformatics pipelines and tools to support data generating services

This project is for the general provision of bioinformatics support to the AGRF bioinformatics based teams who generate data for clients and encompassing the necessary infrastructure to provide quality controlled data to the lab teams generating data for customers as well as creating the necessary pipelines to manage data and analyse data that may not necessarily be delivered to or charged to customers.

Strategic Objective: Provide non-embedded support for the –omics platforms through direct engagement with specific identified embedded activities and through identification and dissemination of national and international best practice in bioinformatics.

Non-embedded activities

• Pipeline to conduct quality control, mapping and/or clustering

The project involves implementing a generic computational pipeline to conduct quality control, mapping and/or clustering of sequence reads generated by the new sequencing technologies (i.e. SOLEXA, SOLiD). The pipeline will support directly both chromatin-modification and small RNA studies.

• Customisation of the generic pipeline for methylated genomic DNA

This project involves modifications to the generic pipeline which will be customized to handle the distinct sequence characteristics and/or bisulphite-treated genomic DNA modifications.

• Comparative analysis of DNA methylation data

This projects aims to develop the infrastructure to allow verification of reproducibility of wet lab experiments for both technical and biological replicates of chromatin-modification studies. A comparative analysis will be conducted across samples to identify statistically significant biological findings.

• Comparative analysis of chromatin-modification data

This projects aims to develop the infrastructure to allow verification of reproducibility of wet lab experiments for both technical replicates and biological replicates of chromatin-modification studies. A comparative analysis will be conducted across samples to identify statistically significant biological findings.

• Comparative analysis of small RNA data

This projects aims to develop the infrastructure to allow verification of reproducibility of wet lab experiments for both technical replicates and biological replicates of small RNA studies. A comparative analysis will be conducted across samples to identify statistically significant biological findings.

• Deploy a Laboratory Information Management System (LIMS)

This project involves deploying a LIMS for SABC.

• Internet based genomics workflow / pipeline environment

This project involves the provision of a secure, online genomics analysis workflow environment for SABC academic scientists.

Embedded Activities

• Bioinformatics support of proteomic services to clients.

This project is for general provision of bioinformatics support of proteomic services that are provided by Proteomics Australia (PA) to its customers.

• Data Repository

This project focuses on providing essential information management systems within PA.

• Search Engine Merging

This project involves merging three different Protein/Peptide search engines currently used by PA. These engines are: Mascot, X/Tandem and Sequest.

• Bioinformatics pipelines and tools to support data generating services

This project is based on the requirement to place a wrapper around PA proteomic applications suite and tools either existing or those written internally.

Strategic Objective: Provide non-embedded support for the –omics platforms through direct engagement with specific identified embedded activities and through identification and dissemination of national and international best practice in bioinformatics.

Non-embedded activities

• Toolbox for file conversions

This project involves developing standardised file conversion toolbox to convert vendor specific file formats into open formats. It requires that the toolbox is encapsulated in a web service for use by other applications.

• Expasy mirror

The project involves deployment of a mirror of the commercial Expasy web based data repository.

• Internet based proteomics workflow / pipeline environment

This project involves the provision of secure, online proteomics workflow environment for use by PA staff. It includes expansion of existing proteomics pipelines to include Search Engine Merging Projects and spectra pre-filtering tools such as Multiple Reaction Monitoring (MRM).

• PA Project Issue Tracking

This project involves the deployment of a secure online issue tracking to support non-embedded and embedded activities of PA.

• Customer relationship management (CRM)

This project involves the deployment and customisation of one of the leading CRM packages available for the PA Platform

Embedded Activities

• General informatics support for metabolomics analytical services to clients

This project is for general provision of informatics technology support of the metabolomics services that are supplied by Metabolomics Australia (MA) to their clients.

• Bioinformatics pipeline and tools to support data generating and analysis services

This project is for general provision of data storage and bioinformatics analysis support to the laboratory based MA teams who generate data for clients.

• Service workflow and accounts management

This project focuses on providing the essential software tools to allow the MA lab-based teams to effectively track the progress of samples through their workflows with their multiple analytical platforms and ensure the timely delivery of accurate results to clients, the efficient processing of accounts and the efficient keeping of records for subsequent reporting purposes.

Strategic Objective: Provide non-embedded support for the –omics platforms through direct engagement with specific identified embedded activities and through identification and dissemination of national and international best practice in bioinformatics.

Non-embedded activities

• Develop/deploy a Metabolomics Australia Data and Sample Management System

  • User Management Module Provision of a secure, online user management module for the Metabolomics Australia Data and Sample Management System

  • Sample Management Module Provision of a secure, online sample management module allowing users to submit samples, track samples through experimental workflows and receive results

  • Data Management Module Provision of secure, online metabolomics repository to capture all relevant MA experimental workflows. It includes storage of raw data files as well as all relevant meta data associated with an experiment.

• MA Project Issue Tracking – This project involves the development of a secure online issue tracking, milestone tracking, roadmap and source code access to support the non embedded bioinformatics activities of MA.