EXAMPLE DATA USAGE

This table contains examples of the broad types of data being stored on med.data.edu.au by others, example software packages we provide to manage the data, and examples of various computers and software packages that have been used by the data custodians and their collaborators to analyse the data.

Data Type Stored Example File Types Data Management System(s) Analysed using Analysis Software
Next-generation sequencing
  • .bam
  • .bam.bai
  • .sam
  • .vcf
  • .vcf.idx
  • .xls
  • .txt
  • .fasta
  • .fastq
  • .ped
  • Aspera
  • MyTardis
  • CKAN
  • Mediaflux
  • Personal computers
  • Institutional servers
  • Nectar virtual machines
  • AWS virtual machines
  • various HPC facilities
  • samtools
  • novosort
  • bowtie2
  • bwa
  • strelka
  • mutect
  • IGV
  • Galaxy
  • GVL (Nectar)
  • endoVL (Nectar)
  • RTG-core
  • SMRT portal
Microarray
  • .idat
  • .gtc
  • Aspera
  • Personal computers
  • Institutional servers
  • GenomeStudio
Mass spectrometry
  • various proprietary formats
  • Filesystem
  • Personal computers
  • Institutional servers
  • various proprietary¬†packages
Histology images
  • .tiff
  • .jpeg
  • .ndpi
  • Mediaflux
  • Aspera
  • Personal computers
  • Institutional servers
  • ImageJ
  • Photoshop
  • proprietary packages
CT, micro-CT
PET
  • .tiff
  • DICOM
  • DaRIS
  • Aspera
  • Mediaflux
  • Personal computers
  • Institutional servers
  • various HPC facilities
  • various specialist
    imaging packages
 MRI, fMRI
  • NIfTI
  • Siemens raw data
  • DaRIS
  • Mediaflux
  • various HPC facilities
  • various specialist
    imaging packages
Participant survey
  • .xls
  • .spv
  • .doc
  • .mat
  • .csv
  • .sav
  • .dta
  • .do
  • Filesystem
  • Personal computers
  • Institutional servers
  • Nectar virtual machines
  • Matlab
  • SPSS
  • Excel
  • STATA
Motion tracking
  • .ssa
  • .mov
  • Posix file organisation
  • Personal computers
  • Institutional servers
  • none (med.data used for data archiving purposes only)
Molecular Modelling
  • .pdb
  • .mol2
  • .sdf
  • .xtc
  • .trr
  • .dcd
  • Posix file organisation
  • Personal computers
  • Institutional servers
  • none (med.data used for data archiving purposes only)