IBIMA Projects

Introduction

Welcome to the software server of the IBIMA institute and thank you for visiting us! Here we present many of our bioinformatics tools for online use and/or for download. Also we provide links to the documentation of these tools and to to publications about the methods used by the tools. If you have any questions or proposals, please feel free to write to the IBIMA bioinformatics people.


ExprEssWeb / ArrayNormalizer

The ExprEssWeb-Tool enables users to analyze their gene expression data using a network based approach as described in "ExprEssence — Revealing the essence of differential experimental data in the context of an interaction/regulation network" without installing Cytoscape and using readily prepared interaction networks. You can run this tool using the [Run...]-Button, view the latest changes to the software using the [Changelog]-Button, learn how to use the tool in the Wiki, post bugs you have found in the tool to the Bugzilla -page of the project, ask questions in the forum browse or download the source code using Subversion or view the presentation about the ExprEssWeb tool.


Cytoscape plugin: MultiColoredNodes

MultiColoredNodes is a Cytoscape plugin for mapping more than one value to the color of a network node by drawing pie charts on the nodes. Below we provide a link to the Cytoscape plugin at the Cytoscape app store and to the sourceforge.net-homepage of the project.


Cytoscape plugin: ExprEssence

ExprEssence is a Cytoscape plugin to analyze gene expression data in network centered way. Below we provide a link to the Cytoscape plugin at the Cytoscape app store and to the sourceforge.net-homepage of the project.


Cytoscape plugin: ID Switcher

ID Switcher is a Cytoscape plugin for using another column as ID column in Cytoscape. Below we provide a link to the Cytoscape plugin at the Cytoscape app store, the plugin for download and access to the sources of the plugin using Subversion .


ReXSpecies -- regulation across species

ReXSpecies is a tool to analyze the evolution of regulatory DNA regions as described in . Here you can run the tool or access the Project page at sourceforge.net


Related project: VisCoSe - Visualization and Comparison of consensus Sequences

VisCoSe is a tool to visualize alignments and consensus sequences.


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Homepage, Contact and more...

The homepage of the IBIMA institute is located here.


Technical notes

This site is now (Jan, 10th 2017) secured by a Let's encrypt certificate.

This site had been SSL encrypted using the Certificate Authority (CA) of the University of Rostock based on the CA for the DFN (Deutsches Forschungsnetz -- "German Research Network") based on a CA for the Deutsche Telekom which should be a root CA in your browser. If not, all CA certificates of this chain are available here and here (site in German).

For code-signing, we also use certificates based on the CAs above.

For details about the legal consequences of electronic certificates, please read the wiki article (in German).

You can find our CA certificate here and here. Please note, that some of our older tools are available from a URL of our former affiliation, the University of Greifswald, more specifically from bio.math-inf.uni-greifswald.de. Thank to the University of Greifswald for this redirection! Regularly this page should be accessed using the URL https://imib100.med.uni-rostock.de/. Please be aware of the S in the https of the URL, since the non-SSL version (without the S) currently leads to one of our associated projects, the ROSAGE project.


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