Software

The huge amounts of data acquired from PolyOmics technologies can only be handled with intensive bioinformatics support that has to provide an adequate data management, efficient data analysis algorithms, and user-friendly software applications. The Bioinformatics Resource Facility (BRF) as part of the Technology Platform Bioinformatics at the Center for Biotechnology (CeBiTec) can look back on many years of expertise on the development of innovative bioinformatics software applications, in which design and implementation are driven by close collaborations with researchers of the center. Within many projects, experimental data are produced by the CeBiTec Technology Platform Genomics and it is therefore one of our major goals to simplify and automate the subsequent steps for a systematic data processing and analysis as far as possible. For the development of larger software platforms we follow the design principle to build specialized tools for separate scopes that can be interlinked to integrate the various data resources. Technically, we can rely on an extensive hardware infrastructure that provides all necessary storage and compute capacities.

Overview on the Computational Genomics software platform.

Applications developed in the field of genomics comprise the analysis and maintenance of complete genomes. At this, the GenDB system was successfully used for the automatic and manual annotation of more than 150 microbial genomes. Based on the genome annotation data, the CARMEN application can perform a metabolic reconstruction. CARMEN provides two main applications: the generation of de novo models based on KEGG database information and the creation of template based SBML models for comparative genomics. An organism-specific network model of individual or large-scale metabolic pathways can be reconstructed based on genome annotation data that can be obtained from GenDB or alternatively loaded from NCBI GenBank files.
In the field of transcriptomics, the EMMA software is provided as a MAGE-compliant software platform for the evaluation of data resulting from genome-wide transcriptomic studies. Detailed experimental setups and protocols as well as all raw data sets are stored in a separate LIMS component (ArrayLIMS). QuPE is an application for large-scale analyses of proteome data, also including a LIMS component. The software MeltDB was developed for the high-throughput analysis of experimental data from metabolome analyses. The ProMeTra application is one example for the ongoing development of novel software tools to support researchers in the field of systems biology. ProMeTra uses web services technology to enrich metabolic pathway maps with quantitative results from transcriptome, proteome, and metabome experiments.

Fusion - PolyOmics data analysis, visualization and integration

Fusion is a web-based platform for the integrative analysis of omics data providing a collection of new and established tools and visualization methods to support researchers in exploring multi-level omics data.

ReadXplorer - Visualization and Analysis of Mapped Sequences

Next generation sequencing (NGS) technologies offer an ever-growing amount of sequence data. At the same time, sequencing costs are rapidly decreasing, even for complete mammalian genomes. The application scenarios of NGS include sequencing of unknown genomes, closely related strains, re-sequencing of known genomes, and transcriptome sequencing (RNA-seq).

A web-platform for the analysis of metabolomics LC-ESI-MS experiments

ALLocator covers the workflow from raw data processing to metabolite identification and mass isotopomer ratio analysis. The integrated processing pipeline for spectra deconvolution "ALLocatorSD" generates pseudo spectra and automatically identifies peaks emerging from the U-13C-labeled internal standard.

A software platform for the Analysis and Integration of Data from Metabolomics Experiments

MeltDB - A software platform for the Analysis and Integration of Data from Metabolomics Experiments

Metabolomics is a rapidly maturing field and expands the scope of functional genomics beyond microarray analysis and proteomics to the level of the metabolism. Compared to other 'omics', metabolomics is closest to the actual phenotype. The metabolome represents a vast number of compounds, estimations range from 2000 in human to 200.000 in plants.

MGX - Flexible metagenome analysis

Metagenomics, the analysis and interpretation of environmental community sequence data, is one of the most challenging bioinformatics fields due to the computational requirements that are needed to analyse large data volumes as they are produced by current sequencing technologies.

A MAGE-compliant system for the collaborative analysis and integration of microarray data

As a high throughput technique, microarray experiments produce large data sets, consisting of measured data, laboratory protocols, and experimental settings. We have implemented the open source platform EMMA2 to store and analyze these data. 

Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks

New sequencing technologies provide ultra-fast access to novel microbial genome data. For their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction of metabolic networks is highly desirable. The software tool CARMEN performs in silico reconstruction of metabolic networks to interpret genome data in a functional context.

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.

SARUMAN -  short read mapping tool using GPU programming


Since the introduction of next generation sequencing technologies like Solexa, 454, and SOLiD the amount of generated data rises with each new technology upgrade. As the application scenarios especially of the short read techniques include the re-sequencing of known genomes or sequencing of closely related strains, new software tools are needed for the fast mapping of sequencing reads against a reference genome.

Visualizing Functional Genomics Data on High Quality Pathway Maps

ProMeTra is an open source framework that provides visualization methods for multi-omics datasets. The open vector based graphics format SVG is used to facilitate the visualization of the results of complex functional genomics experiments.

A rich internet application for the analysis of mass spectrometry-based quantitative proteomics experiments

QuPE - a rich internet application for quantiative proteomics

In proteomics, tandem mass spectrometry (LC-MS/MS) in combination with isotopic labeling techniques provides a common way to obtain a direct insight into regulation at the protein level. The 'Rich Internet Application' QuPE provides comprehensive data management and analysis functions for these experiments.