In silico knockouts for signaling pathways
Signaling pathways are complex and intertwined processes. The perturbation of biological systems can reveal the complicated interplay and dependencies of pathway components. The computational analysis of knockout behavior is a valuable method to detect inconsistencies in the current knowledge of a pathway. Furthermore, in silico knockouts can confirm the structural topology of the computational model of a signaling pathway and predict unknown systems behavior to support experimental design.
isiKnock is a software to automatically conduct in silico knockouts for signaling pathways. Single as well as multiple knockouts can be performed. The results are visualized using a matrix representation. isiKnock predicts the knockout behavior based on the calculation of signal flows at steady state. For an explanation of the concept of in silico knockouts, we refer to Scheidel et al. 2016 and Amstein et al. 2017.
Download the build jar from the store folder and execute it (from command line: "java -jar isiKnock.jar")
A (not yet up to date, but mostly correct) tutorial and additional information is available at:
http://www.bioinformatik.uni-frankfurt.de/tools/isiKnock/index.php?go=overview
Hannig, J., Giese, H., Schweizer, B., Amstein, L., Ackermann, J., & Koch, I. (2019). isiKnock: In silico knockouts in signaling pathways. Bioinformatics, 35(5), 892–894.
Amstein et al. (2017) Manatee invariants reveal functional pathways in signaling networks. BMC systems biology, 11(1), 72.
Scheidel et al. (2016) In silico knockout studies of xenophagic capturing of Salmonella. PLoS computational biology, 12(12), e1005200.