120

GEO

https://www.ncbi.nlm.nih.gov/geo/

GENEVESTIGATOR https://genevestigator.com/gv/

Rfam

https://rfam.xfam.org/

miRBase

https://www.mirbase.org/

LNCipedia

https://www.lncipedia.org/

SMART

https://smart.embl-­heidelberg.de/

ProDom

https://prodom.prabi.fr/prodom/current/html/home.php

Pfam

https://pfam.xfam.org/

BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi

Conserved domains

https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

ELM

https://elm.eu.org/

KEGG

https://www.genome.jp/kegg/

YANA

https://www.bioinfo.biozentrum.uni-­wuerzburg.de/computing/

yanasquare/

YANAsquare

https://www.bioinfo.biozentrum.uni-­wuerzburg.de/computing/

yanasquare/

COPASI

https://copasi.org/

COBRA

https://opencobra.github.io/

SQUAD

https://www.vital-­it.ch/software/SQUAD (Di Cara et al. 2007).

Jimena

https://www.bioinfo.biozentrum.uni-­wuerzburg.de/computing/

jimena_c/ (Karl and Dandekar 2013, 2015)

CellNetAnalyzer

https://www2.mpi-­magdeburg.mpg.de/projects/cna/cna.html

PLAS

https://enzymology.fc.ul.pt/software/plas/

Odefy

https://www.helmholtz-­muenchen.de/icb/software/odefy/index.html

Roche pathways

https://www.roche.com/sustainability/what_we_do/for_communities_

and_environment/philanthropy/science_education/pathways.htm

Metatool

https://pinguin.biologie.uni-­jena.de/bioinformatik/networks/metatool/

metatool5.0/metatool5.0.html

Useful Links  (continued)

Literature

Di Cara A, Garg A, De Micheli G et al (2007) Dynamic simulation of regulatory networks using

SQUAD.  BMC Bioinform 8:462. (PubMed PMID: 18039375; PubMed Central PMCID:

PMC2238325 * An excellent introduction to the SQUAD software, by the authors of the soft­

ware themselves)

Gleick J (2008) Chaos: making a new science (Paper back). Penguin Putnam Inc., United States

(Original from Viking 1987 * Highly recommended, nice introduction to the science of chaos.

ISBN 10: 0143113453/ISBN 13: 9780143113454)

Heinrich R, Neel BG, Rapoport TA (2002) Mathematical models of protein kinase signal transduc­

tion. Mol Cell 9(5):957–970

Hodges A (2014) “Alan Turing: The Enigma” vintage. Random House, London

9  Complex Systems Behave Fundamentally in a Similar Way