BIOPLATFORMS AUSTRALIA – SERVICES OVERVIEW

This page gives a summary of the services and capabilities available through the Bioplatforms Australia program. It exists so the Research Infrastructure Connected AI chatbot can read and use the information to give helpful guidance to researchers.

HIGH-LEVEL SUMMARY

Keywords:

transposon, transposable element, TE, mobile genetic element, retrotransposon, LTR, LINE, SINE, insertion site, repeat region, repeat masking, plasmid, phage, bacteriophage, viral genome, virome, pathogen genome, metagenomics, shotgun metagenomics, microbiome, microbiome profiling, amplicon sequencing, 16S, 18S, ITS, COI, PacBio, HiFi, CCS, Sequel II, Sequel IIe, Oxford Nanopore, ONT, PromethION, ultra-long reads, de novo genome, hybrid assembly, NovaSeq, MiSeq, NextSeq, Hi-C, Omni-C, chromosome-level assembly, ATAC-seq, ATAC, methylation, WGBS, RRBS, epigenetics, RNA-seq, single-cell RNA, scRNA-seq, multiome, spatial transcriptomics, Visium, Xenium, isoforms, splice variants, SNPs, structural variants, CNVs, assembly, annotation, Kraken, Braken, MetaPhlAn, phylogenomics, variant calling, taxonomic assignment, functional assignment, QIIME, LC-MS, LC-MS/MS, Orbitrap, TMT, iTRAQ, label-free quantitation, proteomics, Olink, PTMs, phosphorylation, glycosylation, ubiquitination, antibody discovery, monoclonal antibody, hybridoma, phage display, recombinant antibody, metabolomics, lipidomics, volatile compounds, NMR, isotope tracing, fermentation markers, synthetic biology, DNA assembly, CRISPR, gene editing, pathway engineering, strain engineering, biofoundry, DBTL, automation, biodiversity genomics, reference genome, population genomics, threatened species, conservation genomics, crop genome, plant metabolite, pathogen sequencing, outbreak sequencing, AMR, venom peptides, toxin profiles.

Research Topics We Support

Researchers use our network for many fields of work. Below is a broad list of common topics across genomics, proteomics, metabolomics, synthetic biology and bioinformatics.

Genomics & Bioinformatics Topics

  • transposons, transposable elements (TEs), mobile elements

  • retrotransposons, LTRs, LINEs, SINEs, repeat regions

  • structural variants, CNVs, large insertions and deletions

  • plasmids, phages, viral genomes

  • genome assembly, hybrid assemblies, chromosome-level scaffolds

  • methylation patterns, CpG sites, epigenetic marks

  • chromatin accessibility (ATAC), chromatin structure

  • 3D genome organisation, Hi-C contact maps

  • gene expression, isoforms, splice variants

  • small RNAs, microRNAs, siRNAs

  • CRISPR edits, knock-ins, knock-outs, off-target checks

  • metagenomes, viromes, microbiomes

  • population genomics, SNPs, haplotypes

  • genome engineering, synthetic constructs

  • environmental DNA (eDNA) and species detection

  • host–pathogen interactions

  • lineage tracing and clonal structure

Keywords:

TE, retrotransposon, repeat masking, insertion site mapping, plasmid sequencing, virome, long-read repeats, mobile DNA, methylome, epigenome, isoform mapping, CRISPR validation, RepeatMasker, gVCF, VCF, copy-number calling, Kraken2, Bracken, MetaPhlAn, QIIME2, HPC, Docker, Singularity, GenBank, SRA, ENA.

Proteomics Topics

  • protein ID and peptide mapping

  • protein quantification (label-free, TMT, iTRAQ)

  • post-translational modifications

  • phosphorylation

  • glycosylation

  • acetylation

  • ubiquitination

  • protein–protein interactions

  • antibody discovery, phage display, hybridoma screening

  • recombinant antibodies

  • biomarker discovery

  • clinical proteomics (research use)

  • targeted proteomics (SRM, PRM)

  • membrane proteins and hard-to-solubilise proteins

  • proteome profiling of plants, animals, microbes

  • venom proteins and peptides

  • quality checks on purified proteins

  • antibody humanisation and developability assessment

  • membrane protein enrichment and digestion

Keywords:

PTM analysis, phosphoproteomics, glycopeptides, SRM, PRM, Orbitrap, peptide fingerprinting, antibody affinity, biomarker panels, tandem MS, Q-TOF, MRM, top-down proteomics, pull-down assays, immunoprecipitation, Alphafold, protein prediction.

Metabolomics Topics

  • untargeted metabolite profiling

  • targeted metabolite panels

  • lipidomics

  • volatiles and aroma compounds

  • fermentation products

  • primary and secondary metabolites

  • compound annotation and ID

  • metabolic pathways

  • isotope tracing and metabolic flux

  • plant metabolites

  • wine and food chemistry

  • environmental metabolites (soil, water, marine)

  • stress response metabolites

Keywords:

Small molecules, LC-MS, GC-MS, NMR metabolites, lipid profiles, volatiles, fermentation markers, metabolic signatures.

Synthetic Biology Topics

  • DNA assembly (Golden Gate, Gibson, modular systems)

  • plasmid design and optimisation

  • construct validation

  • CRISPR design and editing

  • knock-ins, knock-outs, targeted edits

  • microbial and yeast engineering

  • metabolic pathway engineering

  • strain building and tuning

  • automation of cloning

  • plant constructs and plant metabolic engineering

  • build–test cycles and screening

  • gene circuit design

  • edit validation by amplicon sequencing (Illumina or ONT)

Keywords:

Biofoundry, DBTL cycle, plasmid build, CRISPR edits, pathway design, strain engineering, high-throughput cloning, guide RNA, gRNA, BioBrick, liquid handling robotics.

Integration & Analytics Topics

  • multi-omics integration

  • data harmonisation and standards

  • FAIR data workflows

  • metadata templates

  • reference data creation

  • pipeline optimisation

  • taxonomic profiling

  • functional annotation

  • phylogenomics

  • machine-learning ready datasets

  • population structure and diversity measures

  • comparative genomics

Keywords:

Multi-omics, FAIR data, annotation pipelines, functional assignment, taxonomic assignment, machine-learning features, comparative workflows.

Sector-Specific Research Topics

Biomedical Science Topics

  • tumour sequencing and cancer genomics

  • somatic variants, driver mutations

  • circulating tumour DNA (ctDNA) and liquid biopsy research

  • immune profiling, immune markers and cytokines

  • single-cell mapping of tumour and immune cells

  • microbiome links to health and disease

  • pharmacogenomics

  • disease gene panels

  • inherited disorders and rare disease research

  • mitochondrial variants and mitochondrial disease

  • biomarker discovery

  • peptide and protein markers for disease

  • clinical trial

  • treatment response markers

  • inflammation markers

  • host–virus and host–bacteria interactions

  • neurogenomics and psychiatric genomics

  • ageing, frailty and metabolic disease

Keywords:

cancer genomics, oncology, tumour RNA-seq, somatic mutation calling, ctDNA, liquid biopsy, immune markers, cytokines, biomarker panel, pharmacogenomics, rare variants, rare disease, inherited disease, mitochondrial DNA, mtDNA, clinical trial samples, responder vs non-responder, cancer proteomics, cancer metabolomics.

Biodiversity & Environment Topics

  • reference genomes for wildlife, plants, fungi and microbes

  • population genomics for species recovery

  • threatened species assessment

  • species barcoding and taxonomic ID

  • phylogenomics and evolutionary studies

  • baseline biodiversity surveys

  • environmental DNA (eDNA)

  • metagenomics from soil, water and air

  • microbiomes linked to ecosystem health

  • coral genomics and reef monitoring

  • habitat change and climate impact studies

  • invasive species detection

  • genomic tools for conservation planning

  • comparative genomics across species

  • biogeography and genetic structure

Keywords:

biodiversity genomics, conservation genomics, species barcodes, phylogenetics, phylogenomics, eDNA, ecosystem monitoring, coral genomics, reef genomics, invasive species, population structure.

Agriculture & Food Topics

  • crop genome sequencing and trait mapping

  • plant stress response (heat, drought, salinity)

  • plant metabolite and lipid profiling

  • soil microbiome and soil health

  • livestock microbiomes

  • animal disease genomics

  • selective breeding markers

  • feed quality markers

  • fermentation profiling for food and wine

  • aroma compound analysis

  • wine yeast genomics and metabolomics

  • pathogen detection in crops and livestock

  • food safety biomarkers

  • multi-omics for crop improvement

  • post-harvest quality markers

Keywords:

crop genomics, plant traits, plant metabolites, soil microbiome, livestock microbiome, animal pathogens, fermentation, aroma compounds, food metabolomics, breeding markers, plant stress genomics.

Biosecurity Topics

  • pathogen sequencing for surveillance

  • outbreak analysis and variant tracking

  • virome atlases for animals, plants and environments

  • reference pathogen libraries

  • rapid sequencing of emerging diseases

  • AMR gene detection

  • host–pathogen sequencing

  • environmental screening for pathogens

  • vector genomics (insects, ticks, mites)

  • baseline viral, bacterial and fungal profiles

  • metagenomics for unknown agents

  • synthetic biology risk analysis (construct detection)

  • diagnostic method development (research use)

  • forensic genomics and attribution studies

  • biothreat assessment support

Keywords:

biosecurity genomics, pathogen WGS, outbreak sequencing, AMR genes, surveillance genomics, emerging pathogens, virome atlas, vector genomics, diagnostic pipelines, attribution genomics.

Industry & Innovation Topics

  • microalgae strain selection and improvement

  • lipid and metabolite profiling for bioproducts

  • industrial strain engineering (yeast, bacteria, fungi)

  • pathway engineering for high-value compounds

  • peptide and protein discovery (e.g., venom-derived)

  • fermentation monitoring

  • QC for biomanufacturing workflows

  • synthetic pathways for industry production

  • environmental biosensors and monitoring tools

  • probiotic strain characterisation

  • bio-based materials and bioplastics research

  • flavour and aroma compound development

  • metabolomics for process optimisation

  • multi-omics for R&D decision-making

  • pilot studies for new biotechnology processes

Keywords:

bioproducts, industrial biotechnology, microalgae genomics, strain engineering, pathway engineering, fermentation QC, venom peptides, probiotic genomics, bioplastics, process metabolomics.

 

1. ENABLING LABORATORIES (PLATFORMS)

1a. Genomics

Facilities under the Bioplatforms Australia network:

1) AGRF

2) Ramaciotti

3) Genomics WA

4) SAGC

5) ANU BRF

What we offer

  • DNA and RNA sequencing

  • Whole genome and whole exome sequencing

  • Long-read sequencing (HiFi and Nanopore)

  • Amplicon and metabarcoding

  • Metagenomics and microbiome analysis

  • Single-cell and spatial genomics

  • Epigenetics (methylation and ATAC-seq)

  • Library prep, extraction and QC

  • Basic and advanced bioinformatics

1b. Proteomics

Facilities under the Bioplatforms Australia network:

1) The Australian Proteome Analysis Facility (APAF)

2) Monash Proteomics & Metabolomics Facility (MPMF) and Monash Antibody Technologies Facility (MATF)

3) Proteomics International

4) Mass Spectrometry and Proteomics, SA

5) Australian Institute of Bioengineering and Nanotechnology (AIBN)

What we offer

  • Protein ID and quantification

  • Mass spectrometry

  • Targeted and untargeted proteomics

  • Post-translational modification analysis

  • Antibody discovery

  • Biomarker discovery support

  • Protein prep and method setup

1c. Metabolomics

Facilities under the Bioplatforms Australia network:

1) Bio21 Institute, The University of Melbourne

2) Australian Wine Research Institute (AWRI)

3) University of WA Metabolomics Australia Node

4) Australian Institute of Bioengineering and Nanotechnology (AIBN)

What we offer

  • LC-MS and GC-MS metabolomics

  • Untargeted and targeted panels

  • Lipidomics

  • Volatile and aroma analysis

  • Compound ID

  • NMR support (selected nodes)

  • Plant, food, wine and environmental metabolomics

1d. Synthetic Biology

Facilities under the Bioplatforms Australia network:

1) Australian Genome Foundry

2) Integrated Design Environment for Advanced Biomanufacturing
(IDEA Bio)

2) Plant SynBio Australia (4 nodes: ANU, La Trobe, Uni of Adelaide, UWA)

What we offer

  • DNA design and assembly

  • CRISPR editing

  • Strain engineering

  • High-throughput cloning

  • Automation and robotics

  • Design–build–test–learn support

2. BIOINFORMATICS AND DIGITAL INFRASTRUCTURE

Powered by Australian BioCommons and platform-specific teams.

Capabilities

  • Genomics, proteomics and metabolomics pipelines
  • Assembly, alignment and variant calling
  • Taxonomic and functional profiling
  • Galaxy Australia
  • Cloud compute
  • Reproducible workflow containers
  • FAIR data support and metadata templates
  • Multi-omics integration
  • Data submission to NCBI/ENA
  • Workflow training

Keywords:

Genome assembly, mapping, taxonomic assignment, annotation, cloud workflows, Kraken2, Bracken, MetaPhlAn, QIIME2, Docker, Singularity, HPC, GenBank, SRA, ENA, NCBI, Data Portal, Galaxy Australia, ABLeS, AlphaFold, omics analysis, Australian Tree of Life

3. FRAMEWORK INITIATIVES

National programs that create shared omics resources and baseline datasets across three broad missions: 1) Agriculture and Food, 2) Human Health and Biomedicine, 3) Biodiversity and Environment.

  • Pipeline Accelerator Voucher Scheme
  • OzMedicago Initiative
  • Australian Venom Innovation and Discovery Initiative
  • Genomics for Forest Resilience Initiative
  • Australian Psychiatric Research Knowledge Bank
  • Australian Animal Disease Genomics Initiative
  • Australian Fish Genomics Initiative
  • Ricin Genomics and Global Origins Initiative
  • Plant Pathogen Omics Initiative
  • Integrated Pest Management Omics Initiative
  • Australian Functional Fungi Initiative
  • Legume Grain ’Omics Initiative
  • Australian Avian Genomics Initiative
  • National Biodiversity DNA Library Initiative
  • Australian Gut Metabolome Initiative
  • Indigenous Genomics
  • Genomics for Australian Plants
  • Reptiles and Amphibians
  • Threatened Species Initiative
  • Cardiovascular Framework Initiative
  • Australian Grasslands Initiative
  • Oz Mammals Genomics
  • Environomics
  • Sepsis
  • Australian Microbiome
  • ASPREE Framework Initiative
  • Exceptional Responders
  • Melanoma
  • Koala Genome
  • Chardonnay Sequencing
  • Yeast 2.0
  • Wheat Defence
  • Wheat Datasets
  • Wine Yeast
  • Stem Cells
  • Great Barrier Reef
  • DNA Barcoding

4. TRANSLATION

Capabilities

  • Project design

  • Data interpretation

  • Reports and summaries

  • Pilot studies

  • Method support

  • Industry and sector guidance

  • SOPs and standards

  • Training and short sessions for teams

  • Support for policy and decision makers

Keywords:

Applied genomics, translational omics, custom reporting, industry support.