miRvestigator Framework

The miRvestigator framework is designed to take as input a list of co-expressed genes and will return the most likely miRNA regulating these genes.

Host-Pathogen Network Portal

This website serves as a portal for computational modeling program to generate an integrated, predictive gene regulatory network model of host/pathogen interactions. Investigated model systems include mouse macrophages and dendritic cells infected with pathogens Leishmania donovani (LD) and Mycobacterium tuberculosis (TB).

Kaviar (queryable database of known variants)

(~Known VARiants) is a very simple tool for answering a very specific question:
What variants have been reported already for a given specific genomic location?



Unipep is a project to provide access to proteomics data from the Serum Biomarker group at the Swiss Federal Institute of Technology (ETH) in Zurich Switzerland, and the Institute for Systems Biology (ISB) in Seattle, Washington USA.


PhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms. Currently there is data from the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae).

PASSEL (PeptideAtlas SRM Experiment Library)

The PeptideAtlas SRM Experiment Library (PASSEL) is a component of the PeptideAtlas project that is designed to enable submission, dissemination, and reuse of SRM experimental results from analysis of biological samples.


 The SRMAtlas is a compendium of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. It results from high-quality measurements of natural and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource for selected/multiple reaction monitoring (SRM/MRM)-based proteomic workflows.


PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.


The practice of systems biology depends upon many software tools, operating on many kinds of data from many different sources. The Gaggle is a framework for exchanging data between independently developed software tools and databases to enable interactive exploration of systems biology data. Read more about the Gaggle.