isiKnock: in silico knockouts in signaling pathways

Jennifer Hannig; Heiko Giese; Börje Schweizer; Leonie Amstein; Jörg Ackermann; Ina Koch

doi:10.1093/bioinformatics/bty700

isiKnock: in silico knockouts in signaling pathways

Bioinformatics. 2019 Mar 1;35(5):892-894. doi: 10.1093/bioinformatics/bty700.

Authors

Jennifer Hannig^{1

2}, Heiko Giese¹, Börje Schweizer¹, Leonie Amstein¹, Jörg Ackermann¹, Ina Koch¹

Affiliations

¹ Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
² Department of KITE - Kompetenzzentrum für Informationstechnologie, Technische Hochschule Mittelhessen, Friedberg, Germany.

PMID: 30102342
DOI: 10.1093/bioinformatics/bty700

Abstract

Summary: isiKnock is a new software that automatically conducts in silico knockouts for mathematical models of signaling pathways. The software allows for the prediction of the behavior of biological systems after single or multiple knockout. The implemented algorithm applies transition invariants and the novel concept of Manatee invariants. A knockout matrix visualizes the results. The tool enables the analysis of dependencies, for example, in signal flows from the receptor activation to the cell response at steady state.

Availability and implementation: isiKnock is an open-source tool, freely available at http://www.bioinformatik.uni-frankfurt.de/tools/isiKnock/. It requires at least Java 8 and runs under Microsoft Windows, Linux, and Mac OS.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Computer Simulation
Signal Transduction
Software*