Links to Systems biology tools and models developed within the SYSCOL project:


geneXplain platform

The geneXplain platform is an online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications that we have used for the modeling of colorectal cancer in SYSCOL. Publicly available data is continuously integrated into the platform. GeneXplain GmbH provides a number of state-of-the-art modules; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field.


TCF class

TCF class is a classification of human transcription factors (TFs) and their mouse orthologs based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). This provides a comprehensive classification of human transcription factors based on their DNA-binding domains.


Boot Rank

An algorithm which uses bootstrapping to rank single nucleotide polymorphisms (SNPs) for disease association. Used to predict disease in individuals based on their genetic sequence.



A novel method developed to identify composite regulatory elements in promoters using a library of known examples. A practical advantage of this method is first the ability to detect a high number of different types of composite elements, and second direct biological interpretation of the identified results.


VISual Plotting Interface for Genetics

A web application to produce multi-track, multi-scale, multi-region plots of genetic data. Designed to allow users to integrate data from multiple sources for interpretation and to easily create publication-ready figures.



A web-based tool in which users can upload their individual SNP data and obtain predicted expression levels for the set of predictable genes across the 14 different cell types. Our tool thus allows users with biological knowledge to study the possible effects that their set of SNPs might have on these genes and predict their cell-specific expression levels relative to the population.



Enhancer Element Locator, or EEL, is a tool for locating distal gene enhancer elements in mammalian genomes by comparative genomics.



A suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds.



Altrans is a method for the relative quantification of splicing events from RNA-sequencing data.