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It is pertinent to mention here that the biological sciences and bioinformatics community follow a standard representation of molecular coordinates in the PDB file format which is a database compliant format instead of a PDF format thus securing an easy access and exchange of information.
Both Shiny applications are included in the Rmiracle package and can be used independent of MIRACLE via uploading files in a MIRACLE compliant format (see Suppl. File 1 for an example).
WEDELMUSIC [45] is a XML compliant format which can include the image of the score and an associated WAV or MIDI file and it is mainly aimed to support the development of new emerging applications.
The raw data has been deposited in a MIAME compliant format in the GEO database, accession number GSE22592.
Microarray data was generated in a MIAME compliant format and raw data has been deposited in the GEO microarray database (Accession number GSE20388).
Expression and genotype data for each mouse is available in a MIAME compliant format in the Gene Expression Omnibus (NCBI) website, accession # GSE8512.
Gene expression values of 66 tags from 39 hypomethylated genes in CD3-positive cells from five T-PLL cases (including two T-PLLs studied herein) were compared with eight normal CD3-positive samples from peripheral blood using data generated with the Affymetrix U133A array [26] (raw expression data has been deposited in a MIAME compliant format in the GEO database, accession number GSE5788).
All the data from this publication have been deposited in a MIAME compliant format [ 66] at NCBIs Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession numbers GSE30977 and GSE31861.
To allow the wider toxicogenomic community the opportunity to apply different approach to the analysis of the results described here, all data has been made accessible in a MIAME compliant format using the advanced path of data dissemination, namely via MIAME/Env (for details see: nebc.nox.ac.uk/miame/miame_env.html).ac.uk/miame/miame_env.html
The microarray data was submitted in MIAME (Minimum Information About a Microarray Experiment) compliant format to the ArrayExpress database ([ 30], accession number [ArrayExpress:E-MEXP-2291]). E-MEXP-2291] E-MEXP-2291] E-MEXP-2291]
All expression data was deposited in Minimum Information About a Microarray Experiment (MIAME) compliant format at Gene Expression Omnibus, National Center for Biotechnology Information [GEO: SuperSeries GSE7504].
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