BiGi Services


GenDB

GenDB is a genome annotation system for prokaryotic genomes. The system has been developed as an extensible and user friendly framework for both bioinformatics researchers and biologists to use in their genome projects. The GenDB annotation engine will automatically identify, classify and annotate genes using a large collection of software tools. Many groups view this automatic annotation as the first step that needs to be followed by expert annotation of the genome.
Funding: Development and maintenance partially funded by de.NBI

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GenDBE

GenDBE was developed based on the GenDB genome annotation system that was originally designed for prokaryotic genomes only. The system has been adapted to facilitate the creation and functional annotation of sequence features that are specific for eukaryotic genomes, e.g. intron and exon gene structures.

Funding: Development and maintenance partially funded by de.NBI

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CARMEN

CARMEN supports functional and comparative genome analysis. It provides the visualization of automatically obtained metabolic networks based on KEGG database information and stores the generated data in standardized SBML format which can be visualized using e.g. the CellDesigner software. CARMEN provides two main methods for the generation of SBML: KGML-based reconstruction and SBML-based reconstruction. The former can be used to reconstruct pathways based on EC numbers using KGML data. The latter performs a comparative metabolic reconstruction of two organisms based on bidirectional best BLAST hits and requires an SBML template.
Funding: Service provision and maintenance funded by de.NBI.

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EDGAR

The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. 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. To support these studies EDGAR - "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" - was developed.
Funding: Development and maintenance partially funded by de.NBI

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ReadXplorer

ReadXplorer is a freely available comprehensive exploration and evaluation tool for NGS data. It extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions. ReadXplorer 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 ReadXplorer.
Funding: Development and maintenance partially funded by de.NBI

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EMMA2

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. Also, co-regulated genes can be detected using integrated cluster analysis methods and gene expression can be mapped onto proteome data or pathways and vice versa. In addition to routine data analysis algorithms, the system can be integrated with other components containing additional data sources (e.g., genome annotation systems like GenDB). Detailed experimental setups and protocols as well as all raw data sets are provided to EMMA2 via ArrayLIMS, a separate microarray Laboratory Information Management System. ArrayLIMS allows to store the standardized data, i.e. the hybridization steps (e.g. RNA production), production of the hybridization targets, and the hybridization itself, as well as the raw images of the hybridized and the scanned slides with the corresponding data files. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

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QuPE

QuPE is a repository and algorithmic framework to store and analyze isotopic labeled tandem mass spectrometry-based (LC-MS/MS) quantitative proteomics experiements. Mass spectrometry data can be imported either via mzData, mzXML, or the Mascot generic format in a data model adapted to the the HUPO proteomics standards initiative (PSI). QuPE provides protein identification by database searches facilitating an integrated Mascot search engine and the consecutive calculation of protein abundance ratios. 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. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

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MeltDB

MeltDB 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, MassSpecWavelet or metaB. For the identification of metabolites based on mass spectra either the GMD database or user defined libraries in NIST are queried. MeltDB supports normalization of metabolite quantities by internal standards (e.g. Ribitol) and also dry weight or cell volumina and allows to apply standard statistics methods (T-Tests, AOV, Hierachical Clustering) and explorative visualizations (PCA, ICA, Heatmaps Clustering results) on them using the R software collection. The integration of genomic and transcriptomic data sets originating from GenDB or EMMA2 is achieved via SOAP based web services enabling interactive visualizations of metabolite concentrations together with transcript measurements mapped on e.g. KEGG pathways. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

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ProMeTra

ProMeTra enables the generation of visualizations of metabolite concentrations together with transcript or protein abundances mapped on metabolic pathways. The open, vector based graphics format SVG is used to facilitate this visualization of multi-omics experiments. ProMeTra supports CSV and EXCEL documents as input and can also directly integrate datasets originating from MeltDB, QuPE or EMMA2.
Funding: Service provision and maintenance funded by de.NBI.

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MGX

MGX aims at the analysis and interpretation of environmental community sequence data. This field of research, termed metagenomics, is particularly challenging due to the computational requirements that are needed to analyse large data volumes, as they are produced by current sequencing technologies. The server/client application MGX provides, first, the necessary infrastructure to cope with these large amounts of sequence data, and second, offers easy mechanisms for the inclusion of novel algorithms into this platform. Find this service in BioTools here.
Funding: Service provision and maintenance funded by de.NBI.

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Conveyor workflows

Conveyor is a workflow engine which uses a novel approach for defining and deploying of analytical workflows. It is based on a full generic object-oriented data model, and allows a datadriven, interface based design of workflows. The engine is extensible by plugins, allowing almost any functionality to be included in a workflow. In addition, various workflows are available as ready-to-use analysis tools optimized for high-throughput data. Currently, access to these tools requires a command-line login to the systems of the Bioinformatics Core Facility at Giessen University but we are planning to provide them within a virtual machine or via web-based frontends.
Funding: Development and maintenance partially funded by de.NBI.

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BiBiServ Tools

The Bielefeld Bioinformatics Server (BiBiServ) is part of the Institute for Bioinformatics (IFB) within the Center for Biotechnology (CeBiTec). It is dedicated to provide software as a service (SaaS) persistently by hosting the software emerged from bioinformatic research groups at the Bielefeld University as well as from close collaborators. Currently, more than 50 software tools and various educational media are available online. These include tools from different research areas such as RNA structure prediction and comparison, comparative genomics, sequence alignment, primer design, evolutionary relationships and many more. Find these services in BioTools here:

Funding: Service provision and maintenance partially funded by de.NBI.

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MetaProtServ

Metaproteomics data from tandem mass spectrometry experiments can be analyzed using the MetaProteomeAnalyzer tool. Mass spectra in Mascot Generic Format are loaded and stored to a database, can be searched against Protein databases (fasta format). To allow identification of taxonomic and functional relationships between identified proteins, the software groups proteins into metaproteins and gathers metadata on proteins from UniProt, Kegg Pathways and NCBI taxonomies to allow the user a meaningful interpretation of the data. Additionally BLAST searches can be submitted, different samples can be compared and a variety of data exporters are available.

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