Software Developed In house
Bioinformatics tools we have developed in house to address specific data analysis or reporting needs. The packages themselves are open source and freely available; internally they can be accessed via a graphical user interface provided by a local GenePattern server. The tools available can be found at http://bio.proteome.org.au or Plotting Gene Ontology (ZIP 694.1KB) (The PloGO link points to a zip file) and Bioconductor Package
Technique | Software or Workflow | Tool / availability | Publication |
SWATH |
| Wu et al, MCP 2016; SwathXtend library merging module takes a seed library and one or more add-on libraries and generating an extended assay library ready to be used for SWATH extraction | |
BioPlex |
| R Recipes | Breen et al, Scientific Reports 2016 and Cytokine 2015 |
TMT |
| Internal tool | Mirzaei et al, Methods Mol Biol, to appear |
iTRAQ |
| Internal tool | Pascovici et al, JPR 2015 |
Label Free |
| Internal tool | Nielson et al, Methods Mol Biol 2013 |
GO |
| Internal tool Package available | Pascovici et al, Proteomics 2012 |
Areas of expertise/strength
- Statistical and machine-learning based data analysis of a wide variety of novel proteomic techniques (SWATH, immunoassays, protein arrays, labelled isobaric, label free)
- Data analysis capability in areas such as GLM, hierarchical designs, linear and mixed models, classification, machine learning and statistical significance analysis
- Experiment design for proteomics, block design
- Screening for cytokine, chemokines, interleukins and hormones for high through put diagnostics and clinical analysis with in-depth Bio-Plex® analysis
- Agricultural plant proteomics with an emphasis on stress responses to drought, disease or pathogens
- Deriving insights from close collaborations with biologists, analytical chemists, clinicians and various other researchers