Crop Bioinformatics Adelaide (CroBiAd)

Crop Bioinformatics Adelaide (CroBiAd) provide bioinformatics expertise to the agriculture industry through the development of novel bioinformatics and biometrics methods for wheat genetics and breeding.

Our bioinformatics activities include:

  • Research - in silico experimentation, such as development of novel methods, tools and pipelines.
  • Consultancy – recommendations in experimental design for projects such as RNA-Seq and various DNA sequencing.
  • Bioinformatics service provision - Data analysis solutions and hands-on bioinformatics workshops in a fee for service model.

Based within the University's School of Agriculture, Food and Wine, we are the South Australian node of the EMBL-Australia Bioinformatics Resource (EMBL-ABR).

image of wheat

Biology as a data science

Biology is becoming ever more data driven. This is in part due to technological advances in DNA sequencing which means that many labs can now generate DNA sequence data at low cost. This has brought new opportunities to the field of crop biology but also carries its own challenges due to the size and complexity of this big data.

Bioinformatics is inherently a multidisciplinary field which intersects biology, computer science and statistics. As such, our group is naturally multidisciplinary too, with different career paths and different areas of expertise.

Genomics for wheat breeding

Our goals are to develop novel bioinformatics and biometrics methods for wheat genetics and breeding.

The size and complexity of the wheat genome exposes some unique problems for bioinformatics. These require the development of novel approaches for data handling and analyses, including:

  • Wheat genomics and transcriptomics
  • Marker development
  • Software development
  • Pipeline and algorithm development

Our research is aligned to Program 5 of the Wheat Hub - the ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate.

Wheat Hub program

Our group has strong collaborations with both local biology-focused groups as well as national and international industry partners. This has been recognised by an Emerging Industry Research Partnership Award.

Key industry and international collaborations

  • Training

    Our group has expertise in the development and delivery of hands-on bioinformatics workshops.

    Contact Ute Baumann

  • Software - public

    CroBiAd develops a wide range of software, predominantly aimed at biology end-users in order to democratise crop genomic resources.

    Because of the nature of our funding and research, much of our code is developed internally and maintained using git repositories on a local GitLab install. As projects approach publication, these resources are published to our public GitHub account.

      POTAGE

      POPSEQ Ordered Triticum aestivum Gene Expression (POTAGE) is a visualisation tool for speeding up gene discovery in wheat.

      Access POTAGE

      DAWN: Diversity Among Wheat geNomes

      DAWN provides access to a variety of public wheat data sets in the context of the International Wheat Genome Sequencing Consortium’s (IWGSC) RefSeq v1.0 genome assembly[1]. This is achieved by pre-processing the data and making it available through a JBrowse genome browser.

      Resources
      Help
      DAWN source data sets

      The following data sets are available through DAWN:

      • Reference sequence
        • IWGSC RefSeq v1.0 genome assembly[1].
      • Gene annotations
        • IWGSC v1.0
        • IWGSC v1.1
      • Markers (as part of IWGSC v1.0 annotation)
        • DArT
        • EST
        • MAS
        • SNP platforms
        • SSR
      • Whole genome shotgun data
        • 16 wheat accessions (BPA[2])
        • Chinese spring (ENA: PRJNA392179[3])
      • Transcriptomic data
      • Exome data
      Citing DAWN
      External resources

      You may also find the following wheat related resources useful:

    • Software - internal
      Access type Resource Description
      School of Agriculture, Food & Wine only

      agwine-blast

      		 A BLAST server containing the IWGSC RefSeq v1.0 assembly.
      Internal network only coching  
      bwpf Bread Wheat Promoter Finder
      blast A BLAST server containing a mix of published and unpublished data sets
      POTAGE A POTAGE server containing published and unpublished data sets
      fetch Simple sequence retrieval for selected genome assemblies
      dev-DAWN Diversity Among Wheat geNomes
      blast-dev  
      GitLab Project/code/software development resources
      bareos Backup server
      Genome Ribbon Web server for visualising structural variants generated from PacBio alignments. Modified to load decompressed CSI BAM index files.

    • Scientific computing infrastructure

      Scientific computing infrastructure

      Research involving large, complex, polyploid genomes such as that of wheat often requires computers with large amounts of RAM.

      However, such infrastructure is not normally available from typical high-performance computing (HPC) providers. As such, we operate our own scientific computing infrastructure, which includes several large memory nodes.

      Current infrastructure
      • A Slurm based cluster consisting of 2 compute nodes with the following specs:
        • 72 CPUs (Intel Xeon E5-2699v3 @ 2.30GHz)
        • 755 GB RAM
        • 880 GB fast local storage (2 x SSD’s in RAID0)
        • Access to 120 TB of clustered storage
      • A stand-alone compute node with the following specs:
        • 64 CPUs (Intel Xeon E7-4830 @ 2.13GHz)
        • 512 GB RAM
        • 1.7 TB fast local storage
        • Access to 120 TB of clustered storage

      Access to resources made available through: