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Introduction
Bioplatforms Australia, through NCRIS 5.1 Evolving Biomolecular Platforms and Informatics has allocated $9.5 million over four years to the Australian Bioinformatics Facility to enhance the existing bioinformatics capacity of the –omics platforms. $6 million is to be allocated to support embedded bioinformatics within Genomics Australia, Metabolomics Australia and Proteomics Australia, with the remaining $3.5 being provided to support non-embedded activities within these platforms.
The purpose of the Strategic Framework is to provide for the systematic deployment and application of both the embedded and non-embedded bioinformatics funding.
The Framework covers:
- The outcomes of a Bioinformatics Infrastructure Audit used to inform the development of overall strategic objectives for embedded and non-embedded activities.
- An overall platform goal with related strategic objectives.
- Key activities planned to achieve specific strategic objectives.
Bioinformatics Infrastructure Audit (BIA)
Overview
To assist in the development of the ABF Strategic Framework, a Bioinformatics Infrastructure Audit (BIA) was conducted. The BIA was designed to:
- Determine the broad bioinformatics requirements of each of the –omics platforms within the current and future operating contexts, and
- Assess the extent to which the current infrastructure meets these requirements.
Within the context of NCRIS 5.1 infrastructure included personnel, software, platform-specific standards for data capture and storage, primary analysis, annotation, workflow, portals and user support.
The following principles underpinned the BIA:
- The audit was to focus on the current and future requirements and needs of consumers of Bioinformatics services within the –omics platforms.
- The scope (depth and breath) of audit was to be commensurate with available time and resources.
- The audit was to delineate generic infrastructure requirements relevant to all platforms, and specific infrastructure relevant to individual -omics platforms.
Who Participated in the BIA?
A total of 59 invitations were sent of which there were 26 respondents or 44% of the total pool.
The respondents were broken down in the following categories:
- Academic Organisations (University or linked with University) (14)
- Government Agencies (4)
- Research Institutes (8)
Responses were collected by a secure online survey with respondents being provided with secure login access which had the capability to save partially completed submissions.
BIA Questions and Targeted Themed Areas
The audit addressed 81 questions arranged around eight themes. The key BIA results are outlined under each of the themes.
Data Analysis
Information was sought on current research areas, the type of bioinformatics work conducted, and whether in the foreseeable future any problems in obtaining the necessary support for data analysis work would arise.
Systems Biology
- The most significant -omics data currently being integrated in Systems Biology are Genomics and Transcriptomics and in the next couple of years a significant increase in proteomics, metabolomics, epigenomics and interactomics data are likely to enhance the field of Systems Biology.
- Currently, systems biology studies primary focus is on modeling “Gene regulatory networks” and “Protein networks”. The trend moving forward is expected to be the modeling of “Metabolic networks” and “Cellular networks” in the near future.
Genomics/Transcriptomics/Epigenomics
- There has been a substantial increase in the number of sequencing projects using new technologies (such as 454/Roche, Solexa/Ilumina, SOLiD/Applied Biosystems) to study topics ranging from small RNAs through to whole genomes.
- The main comparative genomics activities evident were the identification of homologous genes, QTL mapping, regulatory element analysis, RNA gene finding and haplotype analysis.
- A significant increase, in the short term, of projects conducting genome tiling arrays or small RNA sequencing is anticipated, while other commonly used approaches such as microarrays and EST sequencing are likely to remain at similar levels.
- In the area of epigenomics a major increase in ChIP-Seq and ChIP-on-Chip studies is expected in the next couple of years.
Proteomics
- Mass Spectrometry (MS/MS) and 2D gels appear to be the most predominant approaches for peptide sequencing. A decrease in N-terminal and C-terminal peptide sequencing is expected within the next 3 years.
- Proteomics studies characterizing protein-protein interactions, determining post-translational modifications as well as sub-cellular localization of proteins are likely to continue at current levels in the near future.
Metabolomics
- There is a wide range of methods employed for separation of metabolites with HPLC and MS being the most commonly used. In future activities, HPLC-MS, GC-MS and NMR are estimated to increase.
- There is a diverse number of methods utilized for detection of metabolites - MS and NMR are typically the most employed. In the next 3 years an increase in metabolite detection activities is likely.
Data Formats and Standards
Information was sought on the types of data formats currently used in the group, who defines those formats, and whether in the foreseeable future there will be problems with the formats changing.
- A need for vendors of proprietary biotechnologies to support open standards was identified by a number of organisations/individuals.
Data Volumes and Lifecycle
Information was sought on the amount of current and projected storage required to support research.
- Most organisations/indviduals believe that their current data storage capacity (typically less than 10TB) is meeting current needs.
- Over half the organisations/individuals responding projected storage requirements to 50TB within the next three years.
Software/Pipelines/Analysis Tools
Information was sought on what software/pipelines/analysis tools the groups are currently using, where they are accessed, and whether in the foreseeable future problems accessing the right software/pipelines/analysis tools to conduct analysis.
- A large number of organisations/individuals who responded indicated that they conduct software development with only one respondent indicating that their current software tools satisfy their needs 'very well'.
- Over half of the organisations/individuals responding indicated 'average' or worse satisfaction with current software tools.
Skills and Expertise
Information was sought on what kind of bioinformatics personnel groups currently have and what type of skills and expertise they possess, where staff are receiving training, and where there might be gaps in bioinformatics skills for future projects.
- Several organisations/individual requested bioinformatics experts be embedded for the purposes of upskilling existing personnel.
- Many organisations/individuals specifically identified a lack of access to statistical expertise in plant functional genomics, metabolomics data analysis, complex gel datasets and experimental planning.
Communication and Sharing
Information was sought on the type of group communication currently in place, the mechanisms for communication and sharing used, and future needs and potential gaps.
- Physical distance between activities across Australia combined with a lack of ICT support for the installation and maintenance of remote video conferencing facilities appears to inhibit research collaboration.
IT Systems and Lab Equipment
Information was sought on what IT systems and lab equipment were currently used, where they are accessed from, and future needs to obtain bioinformatics support for these systems and hardware.
- Many organisations/individuals using Laboratory Information Management Systems (LIMS) have developed them in-house.
- Many organisations/individuals identified activities such as sample tracking and data capture as processes that would be enhanced by the further development of LIMS.
Quality Control/Quality Assurance
Information was sought on what quality control/quality assurance policies and processes are in place that bioinformatics solutions needs to integrate with to enable groups to undertake their research.
- Most organisations/individuals indicated that they would not be seeking formal accreditation.
BIA Summary
The results of the BIA provided the necessary context to develop the ABF Platform Goal, Strategic Objectives and an associated set of projects. These are outlined below.
Platform Goal
The overall goal of the Australian Bioinformatics Facility is to work in close collaboration with the three –omics platforms to enhance bioinformatics capability within Genomics Australia, Proteomics Australia and Metabolomics Australia through provision of dedicated bioinformatics staffing and associated infrastructure.
Strategic Objectives
There are five strategic objectives for the ABF which are linked with the overall goal of the platform.
The objectives are:
Strategic Objective 1
Embed enhanced bioinformatics capability within Genomics Australia through provision of dedicated bioinformatics staffing and associated infrastructure.
Strategic Objective 2
Embed enhanced bioinformatics capability within Proteomics Australia through provision of dedicated bioinformatics staffing and associated infrastructure.
Strategic Objective 3
Embed enhanced bioinformatics capability within Metabolomics Australia through provision of dedicated bioinformatics staffing and associated infrastructure.
Strategic Objective 4
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.
Strategic Objective 5
Facilitate collaboration across Genomics Australia, Proteomics Australia and Metabolomics Australia, and across NCRIS investment strategies in order to enhance –omics’ bioinformatics capacity.
Current Projects and Initiatives
A set of key projects and initiatives have been designed to address each of the five Strategic Objectives. These projects were developed following:
- consideration of the outcomes of Bioinformatics Infrastructure Audit
- in-depth discussions with Convenors of each of the three –omics platforms through a pre NCRIS 5.1 consultative group – the Bioinformatics Consultative Capability Group
Initiatives to Support Genomics Australia
Strategic Objective: Embed enhanced bioinformatics capability within Genomics Australia through provision of dedicated bioinformatics staffing and associated infrastructure.
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Embedded Activities |
Dedicated bioinformaticians are funded within the Australian Genome Research Facility (AGRF) to allow AGRF to provide customers of their genomics services with high quality bioinformatics support.
By funding appropriate staff, AGRF can provide the necessary software tools to effectively track the progress of samples through their workflows and ensure the timely delivery of accurate research to customers.
Funding allows the AGRF bioinformatics team to create the necessary pipelines to quality control, manage and analyse data that may not necessarily be delivered to or charged to customers. 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.
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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. |
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Non-embedded activities
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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.
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.
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.
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.
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.
This project involves deploying a LIMS for SABC.
This project involves the provision of a secure, online genomics analysis workflow environment for SABC academic scientists. |
Initiatives to Support Proteomics Australia
Strategic Objective: Embed enhanced bioinformatics capability within Proteomics Australia through provision of dedicated bioinformatics staffing and associated infrastructure.
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Embedded Activities |
This project is for general provision of bioinformatics support of proteomic services that are provided by Proteomics Australia (PA) to its customers.
This project focuses on providing essential information management systems within PA.
This project involves merging three different Protein/Peptide search engines currently used by PA. These engines are: Mascot, X/Tandem and Sequest.
This project is based on the requirement to place a wrapper around PA proteomic applications suite and tools either existing or those written internally. |
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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. |
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Non-embedded activities |
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.
The project involves deployment of a mirror of the commercial Expasy web based data repository.
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).
This project involves the deployment of a secure online issue tracking to support non-embedded and embedded activities of PA.
This project involves the deployment and customisation of one of the leading CRM packages available for the PA Platform |
Initiatives to Support Metabolomics Australia
Strategic Objective: Embed enhanced bioinformatics capability within Metabolomics Australia through provision of dedicated bioinformatics staffing and associated infrastructure.
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Embedded Activities |
This project is for general provision of informatics technology support of the metabolomics services that are supplied by Metabolomics Australia (MA) to their clients.
This project is for general provision of data storage and bioinformatics analysis support to the laboratory based MA teams who generate data for clients.
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.
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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. |
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Non-embedded activities |
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-Omics Cross Platform Project
Facilitate collaboration across Genomics Australia, Proteomics Australia and Metabolomics Australia, and across NCRIS investment strategies in order to enhance –omics’ bioinformatics capacity.
- Proteomics and Genomics common Internet-based data analysis workflow environment
The aim of this project is to customise and deploy a common Proteomics Australia, Genomics Australia and Metabolomics Australia Internet-based analysis workflow environment for their respective data analysis and client service delivery needs.