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.

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.

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. 

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.

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.

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.