Data
omics.data.edu.au is being built to accommodate a range of data types (genomic, transcriptomic, proteomic and metabolomic).
In its first phase of development (during 2016), omics.data.edu.au will accommodate data types and formats generated by the Bioplatforms Australia Antibiotic Resistant Pathogens Initiative. These data are being produced by a number of facilities in the Bioplatforms Australia network, which utilise a number a different specialist technology platforms (see table below).
It is our aim to build omics.data.edu.au to include as many data processing packages used by the data production facilities and others in the Antibiotic Resistant Pathogens project, such that data may be re-processed and re-analysed using omics.data.edu.au.
The data processing tools used across the Antibiotic Resistant Pathogen datasets are listed below.
| Used in the Antibiotic Resistant Pathogens initiative | Genomic | Transcriptomic | Proteomic | Metabolomic |
|---|---|---|---|---|
|
BPA Funded participants (data generation facilities): |
|
|
|
|
| Data generation technologies: |
PacBio Illumina |
Illumina | LC-MS
SWATH-MS |
LC-MS |
|
Data Processing and Analysis Software: |
Assembly SMRT HGAP Annotation Snippy Prokka |
Trimming Trimmomatic Alignment Tophat STAR GSNAP De novo Assembly Trinity |
LC-MS Mascot X! Tandem SWATH-MS ProteinPilot™ PeakView® |
XCMS
MAR ‘in house’ R stats analysis package
|
With respect to numbers of samples, the BPA-funded Antibiotic Resistant Pathogens Initiative is complex and will generate data from:
• 5 bacterial species
• 5 strains of each of those species
• cultures grown under 2 different growth conditions
• 1 DNA sample for genomics sequencing
• and on average, 6 replicate RNA, protein and metabolome samples