Thus, we have created RNASeqBrowser which is a stand-alone tool that accepts the UCSC genome browser BED and overlaid wiggle files [ 5], and was created using the platform independent Java computer language.
We screened for CfERVs using the platform-independent Java program RetroTector©, designed to identify proviral retrovirus sequences in eukaryotic genomes [14].
To verify the validity of these candidate biomarkers, we replicated microarray experiments using an independent platform, quantitative PCR (Methods).
Also, molecular graphics functionality is carried out using the platform-independent graphics language OpenGL, making it more portable (GRASP2 currently runs on PCs running Microsoft Windows).
De novo assembled transcripts were assigned hierarchical gene ontologies (GOs) terms on the basis of biological processes, molecular functions, and cellular components using the platform-independent Java 6 implementation of the BLAST2GO software (Gotz et al. 2008).
We scanned microarrays with a dual-laser micro-array scanner (GenePix 4000 B; Axon Instruments, Foster City, CA, USA) recorded with GenePix Pro 4.1 software (Axon Instruments) and carried out further analysis using the platform-independent java application ArrayNorm, version 1.7.2 (Pieler et al. 2004).
Quality control was assessed using fifty control SNPs located on each array which were typed using a second independent platform (ABI Taqman).
In subsequent experiments we used an independent platform (Affymetrix mouse gene 1.0 ST expression arrays) for three of the four paradigms, because the gene expression arrays also contained different probes for both mouse-specific snoRNAs and some miRNAs.
Our dataset covers a relatively broad spectrum of NSCLC, and we have validated the signatures using independent samples profiled using the identical platform [10].
RM Osborne has risked infuriating pro-Brexit colleagues by using the platform of the budget and independent OBR advice to make the case for the UK staying in the EU.
