The Center for Integrative Bioinformatics (CIBI) offers various software suites containing applications, workflows, and training for integrated omics and image data analysis. It is focused on providing high-performance tools and libraries which are designed for several applications, from proteomics to sequence analysis, to advanced image analysis and processing. Additionally, the CIBI Service Center also emphasizes integrative ability through generic programming, extensions, and workflow integration. By providing many open access tools, CIBI enables reproducible analysis of various types of high-throughput biological data. Alternatively, it allows users to efficiently develop their own tools, utilizing the various large libraries offered.
Proteomics & Metabolomics
The bioinformatics software solution for complete analysis of raw mass-spectrometry data
Our Proteomics and Metabolomics software solution is provided by the partners at the Eberhard-Karls-University Tuebingen and the IPB Halle team. This universal software suite integrates tools for basic conversion tasks, signal processing and filtration algorithms, as well as alignment, quantification and peptide and metabolite identification in the OpenMS Proteomics Pipeline. Data can be visualized with TOPPView and external resources such as BioInfraProt’s PIA and databases such as the ELIXIR proteomics resource PRIDE or MassBank (Software maintained at the IBP Halle) can be integrated.
Learn more about the available resources and their integration into workflow systems.
Genomics
A comprehensive software solution for Next-Generation sequencing data
The CIBI Genomics suite is provided by our partner at the Free University Berlin and offers highly efficient tools for analysing high-throughput sequencing data including quality control and read data curation, alignment, database search, variant detection, RNA structure identification and many more. The tools seamlessly integrate with existing pipelines, while supporting all the standard file formats, e.g. FastQ, GenBank, SAM/BAM, VCF and many more, making it easy to work with your data for any type of project.
Learn more about the available applications and their integration into workflow systems.
Imaging
A powerful software stack for bio-image analysis
The Bio-Image Suite is provided by our partner at the MPI of Molecular Cell Biology and Genetics and offers a powerful image analysis package. Key features of our image suite are the real-time visualization and processing of huge n-dimensional images as well as image restoration, segmentation and tracking, feature extraction and many more.
Learn more about the available software package and its integration into KNIME.
Workflows
Intelligent and scalable integration of -omics and image data
Topical high-throughput data analysis requires a flexible yet easy-to-understand integration platform in order to deliver precise and reusable solutions for scientific and industrial use cases. As the Center for Integrative Bioinformatics, we know that experiments in the life sciences often involve tools from a variety of domains such as mass spectrometry, next
generation sequencing, or image processing. We tightly integrate our tools into the KNIME Analytics Platform in close cooperation with our team at the University of Konstanz using a node extension framework called Generic Knime Nodes and thus linking large-scale analysis of -omics and image data with the enormous data mining capabilities of KNIME.
Learn more about the available Bioinformatics extensions and the KNIME Image processing extensions.
Libraries
The resourceful library collection for programmers
You could not find the right application you were looking for in our available software suites? You have an ingenious idea for a new application but do not want to reinvent the wheel for existing algorithms and data structures? Then strive through our software libraries for proteomics, genomics and bio-image analysis. Our libraries are the backend of our software suites and contain state-of-the-art algorithms and data structures developed in our labs. The libraries are open-source and well maintained undergoing sophisticated quality control mechanisms including continues integration, unit and integration tests, code reviews etc.. The libraries are supported for all major platforms: Windows, macOS and various Linux distributions.
Proteomics Library: OpenMS
OpenMS offers an open-source software C++ library for LC/MS data management and analyses. It provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it.
Resources:
• GitHub: https://github.com/OpenMS
• Documentation: http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html
• Tutorials: http://www.openms.de/tutorials/
Genomics Library: SeqAn
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools while providing competitive performance.
Resources:
• GitHub: https://github.com/SeqAn
• Documentation: http://docs.seqan.de/seqan/master/
• Tutorials: https://seqan.readthedocs.io/en/master/
Bio-Image Analysis Library: ImageJ
ImageJ is an open source Java image processing program inspired by NIH Image. It runs on any computer with a Java 1.8 or later virtual machine. ImageJ has a strong, established user base, with thousands of plugins and macros for performing a wide variety of tasks.
Resources:
• GitHub: https://github.com/imagej
• Documentation: https://imagej.net/Introduction
• Tutorials: https://imagej.net/Category:Tutorials