Changing internal and external conditions can influence the long-term behavior of the Boolean network model. The perturbation of a Boolean network by stripping a component of the system or simulating a surplus of another component can lead to different attractors. Obviously, the number of possible perturbations and combinations of perturbations increases with the size of the network. Manual screening a set of possible components for combinations, that have a desired effect on the long-term behavior, can be time consuming. We developed a method to automatically screen for perturbations that lead to a user-specified change in the networks behavior.
Simulation of the network under perturbation conditions allows to get a deeper understanding of the dynamics in the Boolean network model.
Downloads :
Getting Started :
The downloaded jar file is runnable and can be started by double-clicking. To run the application a java version (JRE) 8.71 or later is required (https://java.com/download/).
For automatic screening for perturbations switch to the exhaustive simulation panel via the simulation menubar. On the right side the attractors of the network are displayed. The button "Perturbation Screening" starts the automatic screening routine. This routine is sperated into three major steps :
Finally, the perturbation sets which show the previously selected effects on the long-term behavior of the network are shown.
By double-clicking a perturbation set of interest the resulting attractors are displayed.
The "Save"-Button stores a log-file with the settings of the perturbation screening and its results.
Wissenschaftlicher Mitarbeiter (m/w/d)
Our paper "GatekeepR: an R shiny application for the identification of nodes with high dynamic impact in boolean networks" has been published online first in Bioinformatics.
Our paper "The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices" has been published in JMIR Medical Informatics.
"Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients" has been published in npj Precision Oncology.
Our paper "AMBAR-interactive alteration annotations for molecular tumor boards" has been published in Computer Methods and Programs in Biomedicine.
"A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems" has been published in STAR Protocols.
Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.
"Supporting SURgery with GEriatric Co-Management and AI (SURGE-Ahead): A study protocol for the development of a digital geriatrician" has been published in PLoS One.
"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.
Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.