Databases

AutoSNPdb

autoSNPdb is developed and maintained by the Australian Centre for Plant Functional Genomics (ACPFG). The implementation of autoSNPdb allows researchers to query the results of SNP analysis to characterise SNPs between specific groups of individuals or within genes with predicted function.


Locate

A Human & Mouse Protein Subcellular Localisation Database – LOCATE is integrated into SRS and is available to QFAB partners.

    • Public access: http://locate.imb.uq.edu.au
    • Partners: Institute for Molecular Bioscience, The University of Queensland and the ARC Centre in Bioinformatics


Koala

QFAB is underpinning the data collection of genotypes and phenotypes related to childhood obesity with the aim of supporting discovery of biomarkers.

    • Public access: http://koala.imb.uq.edu.au
    • Partners: Mater Children's Hospital, Princess Alexandra Hospital, Mater Adult Hospital, Royal Children's Hospital, Institute for Molecular Bioscience, University of Queensland, South East Aliance of General Practice


Spider Toxins

This database will be the primary worldwide repository for spider toxin sequences and structures.

    • Public access: scheduled for the second quarter of 2008
    • Partners: Institute for Molecular Bioscience - Professor Glenn King


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Semantic Web

BioManta

QFAB provides data access and dedicated resources to the BioManta project


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Data Integration

SRS

SRS is a middleware layer that enables queries across diverse databanks. The results of these queries can then be combined with local data. QFAB maintains up-to-date databanks based on Partners' requirements and provides secure integration of private data.

    • Partners: Institute for Molecular Bioscience, University of Queensland, Queensland University of Technology, Department of Primary Industries and Fisheries, Griffith University, ACPFG, CSIRO.

 

HDI

Health Data Integration, HDIT, is a tool developed by the e-Health Research Centre. It provides private and secure access to an integrated virtual data repository, enabling research and analysis on a larger scale than would be possible on the individual data repositories alone. HDI is available to QFAB Partners and Customers.

 

SRB

The Storage Resource Broker (SRB) is a data grid middleware software produced by San-Diego Supercomputing Centre (SDSC). It provides users with a single file hierarchy for data distributed across multiple storage systems. SRB allows the sharing of large data collections in collaborative environments. 

QFAB SRB server enables access and download of the data from the UCSC& ENSEMBL genome browsers, as well as the SRS databanks.

ENSEMBL & UCSC both have datasets stored in MySQL databases. SRB enables users to query directly
against the ENSEMBL and UCSC MySQL tables and to download the results.

    • Access information
    • Partners: Griffith University, Australian Research Collaboration Service (ARCS)

 


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Pipeline and Workflow

GPFlow

The Gardens Point Flow (GPFlow) is an intuitive workflow environment to support biologists with their research. The workflow wraps legacy tools, presenting a high level interactive web based frontend to biologists. The workflow backend is realized by a commercial grade workflow engine (Windows Workflow Foundation). The goal of GPFlow is flexibility and simplicity. QFAB provides up-to-date data and bioinformatics web services to GPFlow.

 

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Data visualisation

Visible Cell

The Visible Cell project aims to inform advanced in silico studies of cell and molecular organisation in 3D using the mammalian cell as a unitary example of an ordered complex system. QFAB provide pathway data linkage.

 

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Mirrors

UCSC Genome Browser

QFAB provides a mirror of the UCSC Genome Browser which contains the reference sequence and working draft assemblies for a large collection of genomes. Public and private access for partners is available.

 

Ensembl

A mirror of the Ensembl Genome Browser is maintained by Griffith University. Data can be accessed through QFAB SRB server.

 

GenBank, RefSeq, UniProt, OMIM, LOCATE, Reactome, UniGene, Enzyme, KEGG, PDB, InterPro, GO, UniGene, NCBI Taxonomy and others.

QFAB provides automatically updated mirrors of many major bioinformatic public databanks as part of the SRS installation.

    • Partners: Institute for Molecular Bioscience, University of Queensland, Queensland University of Technology, Department of Primary Industries and Fisheries, Griffith University, ACPFG, CSIRO.
    • IMB Web access: srs.imb.qfab.org (login required)
    • Data access through SRB
    • More SRS info


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Prediction Tools

PRIP

PRIP is a predictor for interface residues in protein-RNA interfaces. It takes one or multiple protein sequences in FASTA format and annotates the position of the interface residues within the sequence.

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