Data Types Used

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)