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

Bioplatforms_CMYK

BPA Funded participants (data generation facilities):

 

ramaciotti_logo

 

 

agrf_logo

 

 

monash_logo APAF-logo

 

 

ma-logouniversity-of-melbourne

 

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

MassHunter

 

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