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Useful Tools and Web Links

SQUAD

https://www.vital-­it.ch/software/SQUAD

Jimena

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

jimena_c/

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

Cytoscape

https://www.cytoscape.org/

CellDesigner

https://www.celldesigner.org/

PottersWheel

https://www.potterswheel.de/Pages/

Literature

Audretsch C, Lopez D, Srivastava M et al (2013) A semi-quantitative model of quorum-sensing

in staphylococcus aureus, approved by microarray meta-analyses and tested by mutation stud­

ies. Mol BioSyst 9(11):2665–2680. https://doi.org/10.1039/c3mb70117d (PubMed PMID:

23959234)

Brietz A, Schuch KV, Wangorsch G et al (2016) Analyzing ERK 1/2 signalling and targets. Mol

BioSyst 12(8):2436–2446. https://doi.org/10.1039/c6mb00255b

Czakai K, Dittrich M, Kaltdorf M et al (2016) Influence of platelet-rich plasma on the immune

response of human monocyte-derived dendritic cells and macrophages stimulated with asper­

gillus fumigatus. Int J Med Microbiol pii:1438–4221(16)30199-0. https://doi.org/10.1016/j.

ijmm.2016.11.010 ([Epub ahead of print] PubMed PMID: 27965080)

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

SQUAD. BMC Bioinformatics 8:462. https://doi.org/10.1186/1471-­2105-­8-­462 (*Nice original

paper about SQUAD with good examples to practice)

Göttlich C, Müller LC, Kunz M et al (2016) A combined 3D tissue engineered in vitro/in silico lung

tumor model for predicting drug effectiveness in specific mutational backgrounds. J Vis Exp

110:e53885. https://doi.org/10.3791/53885 (*Cancer is modeled here both in vitro and in silico,

the two complementing each other)

Karl S, Dandekar T (2013) Jimena: efficient computing and system state identification for genetic

regulatory networks. BMC Bioinformatics 14:306. https://doi.org/10.1186/1471-­2105-­14-­306

(*Explains analysis using Jimena software, useful for all systems biology modeling)

Karl S, Dandekar T (2015) Convergence behaviour and control in non-linear biological networks.

Sci Rep 5:9746. https://doi.org/10.1038/srep09746 (PubMed PMID: 26068060; PubMed Central

PMCID: PMC4464179 *This work explores the interesting aspect of which proteins direct and

determine the network. The Jimena determines both direct control and dynamic [via network

effects] for each switch in the network [“network nodes”, mostly proteins]. This can then be

used to determine exactly which receptors, kinases, etc. are the main clocks in the network and

whether they do it directly or via network effects)

Li C, Nagasaki M, Koh CH et al (2011) Online model checking approach based parameter estimation

to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional

Petri net with extension. Mol BioSyst 7(5):1576–1592. https://doi.org/10.1039/c0mb00253d

5  Systems Biology Helps to Discover Causes of Disease