NBI Website EMMA2 is a MAGE-compliant software platform for the evaluation of microarry experiment data sets resulting from genome-wide transcriptomics studies.EMMA2 allows to access the raw transcriptome data sets and provides automated and extensible analysis and visualization pipelines, including but not limited to the normalization of single and multiple microarrays and statistical tests for inferring differentially expressed genes.Read Xplorer is implemented in Java as a Netbeans rich client application.Utilizing a modular programming structure, it enables developers to create their own highly specialized software modules and easily plug them into Read Xplorer.
The former can be used to reconstruct pathways based on EC numbers using KGML data.Funding: Service provision and maintenance funded by de. Conveyor is a workflow engine which uses a novel approach for defining and deploying of analytical workflows. Schweinfurt singles It is based on a full generic object-oriented data model, and allows a datadriven, interface based design of workflows.As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach.A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons.
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Mass spectrometry data can be imported either via mz Data, mz XML, or the Mascot generic format in a data model adapted to the the HUPO proteomics standards initiative (PSI).Qu PE provides protein identification by database searches facilitating an integrated Mascot search engine and the consecutive calculation of protein abundance ratios.For the identification of metabolites based on mass spectra either the GMD database or user defined libraries in NIST are queried.Melt DB supports normalization of metabolite quantities by internal standards (e.g.The system has been adapted to facilitate the creation and functional annotation of sequence features that are specific for eukaryotic genomes, e.g. Funding: Development and maintenance partially funded by de.
NBI Website CARMEN supports functional and comparative genome analysis.To support these studies EDGAR - "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" - was developed.NBI Website Read Xplorer is a freely available comprehensive exploration and evaluation tool for NGS data.Statistical evaluation of the quantified stable-isotope labeled samples (15N, 13C, SILAC) includes significance test, multivariate analysis methods such as analysis of variance, principal component analysis, and various cluster analysis and validation methods. Funding: Service provision and maintenance funded by de. Website Melt DB is a open source framework providing analysis methods for raw GC- and LC-MS metabolome data sets and offers methods to combine the respective results.Flexible tool pipelines allows both the import of pre-processed data as well as the integration of existing open source analysis packages such as XCMS, Mass Spec Wavelet or meta B.