Software and databases used

Software

Babelomics 5.0 has been mainly written in Java, but for some of the functionalities we have used R 3.1.2 and Bioconductor 3.0, and also some external Java libraries.

• For Affymetrix Microarray normalization APT 1.12 and Affy 1.44.0 packages are used.
• For the rest of microarrays data normalization we have used some homemade scripts build using Limma 3.22.4 and Biobase 2.26.0
• Limma 3.22.4 and Apache Commons Math 2.1 are used for differential expression and correlation analysis.
• Weka 3.7 library has been used for some predictors and clustering analysis.
• In Genomics Data, we have used for Association Analysis:
  • microarrays data: Plink v1.07
  • sequence data: AssotesteR 0.1-10
• For cancer data analysis, we integrated OncodriveFM v0.6.0 and OncodriveClust v0.5.0

Databases

For many of the analysis a cross reference database and a regulatory and pathway information is needed, here you can find which genomics and functional databases we have integrated to build Babelomics 5.0:

• Ensembl 78 (December 2014) and Biomart were used as main biological databases.
• TAIR10 2010-09 for Arabidopsis Thaliana.
• RECON1 (December 2014) for Genome-Scale Metabolic Network.

Protein-Protein Interaction databases in SNOW tool:

• IntAct (IntAct Molecular Interaction Database, http://www.ebi.ac.uk/intact/, doi: 10.1093/nar/gkp878)
• MINT (Molecular INTeraction database, PMCID: PMC1751541)
• BIND (Biomolecular Interaction Network Database, PMID: 12519993)
• DIP (Database of Interacting Proteins, PMCID: PMC102387)
• HPRD (Human Protein Reference Database, doi: 10.1093/nar/gkn892.)

Protein-Protein Interaction databases in NetworkMiner tool:

• IntAct (2011-01-19 version)
• MINT (2011-01-19 version)
• BioGRID (version 3.1.72)