Literature DB >> 35179549

SteadyCellPhenotype: A web-based tool for the modeling of biological networks with ternary logic.

Adam C Knapp1,2, Luis Sordo Vieira1, Reinhard Laubenbacher1, Julia Chifman2.   

Abstract

SUMMARY: We introduce SteadyCellPhenotype, a browser based interface for the analysis of ternary biological networks. It includes tools for deterministically finding all steady states of a network, as well as the simulation and visualization of trajectories with publication quality graphics. Simulations allow us to approximate the size of the basin for attractors and deterministic simulations of trajectories nearby specified points allow us to explore the behavior of the system in that neighborhood. AVAILABILITY: https://github.com/knappa/steadycellphenotype MIT License. SITE: https://steadycellphenotype.github.io.
© The Author(s) (2022). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Entities:  

Year:  2022        PMID： 35179549      PMCID： PMC9004642          DOI： 10.1093/bioinformatics/btac097

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  10 in total

1.  D³: Data-Driven Documents.

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Authors:  Christoph Müssel; Martin Hopfensitz; Hans A Kestler
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3.  Logical modelling of regulatory networks with GINsim 2.3.

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4.  SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks.

Authors:  Jie Zheng; David Zhang; Pawel F Przytycki; Rafal Zielinski; Jacek Capala; Teresa M Przytycka
Journal:  Bioinformatics       Date:  2009-11-03       Impact factor: 6.937

Review 5.  Use of CellNetAnalyzer in biotechnology and metabolic engineering.

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Journal:  J Biotechnol       Date:  2017-05-10       Impact factor: 3.307

6.  Metabolic stability and epigenesis in randomly constructed genetic nets.

Authors:  S A Kauffman
Journal:  J Theor Biol       Date:  1969-03       Impact factor: 2.691

7.  A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles.

Authors:  Carlos Espinosa-Soto; Pablo Padilla-Longoria; Elena R Alvarez-Buylla
Journal:  Plant Cell       Date:  2004-10-14       Impact factor: 11.277

8.  A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis.

Authors:  Elisabeth Remy; Sandra Rebouissou; Claudine Chaouiya; Andrei Zinovyev; François Radvanyi; Laurence Calzone
Journal:  Cancer Res       Date:  2015-08-03       Impact factor: 12.701

9.  Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective.

Authors:  Julia Chifman; Seda Arat; Zhiyong Deng; Erica Lemler; James C Pino; Leonard A Harris; Michael A Kochen; Carlos F Lopez; Steven A Akman; Frank M Torti; Suzy V Torti; Reinhard Laubenbacher
Journal:  PLoS Comput Biol       Date:  2017-02-06       Impact factor: 4.475

Review 10.  Array programming with NumPy.

Authors:  Charles R Harris; K Jarrod Millman; Stéfan J van der Walt; Ralf Gommers; Pauli Virtanen; David Cournapeau; Eric Wieser; Julian Taylor; Sebastian Berg; Nathaniel J Smith; Robert Kern; Matti Picus; Stephan Hoyer; Marten H van Kerkwijk; Matthew Brett; Allan Haldane; Jaime Fernández Del Río; Mark Wiebe; Pearu Peterson; Pierre Gérard-Marchant; Kevin Sheppard; Tyler Reddy; Warren Weckesser; Hameer Abbasi; Christoph Gohlke; Travis E Oliphant
Journal:  Nature       Date:  2020-09-16       Impact factor: 49.962
  10 in total

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