355

Graphics Programs, Modeling and Network Analysis

CellDesigner

https://www.celldesigner.org/

CellNetAnalyzer

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

Cytoscape

https://www.cytoscape.org/

COBRA

https://opencobra.github.io/

COPASI

https://copasi.org/

Flux balance analysis https://systemsbiology.ucsd.edu/Downloads/FluxBalanceAnalysis

Jimena

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

MATLAB

https://de.mathworks.com/products/matlab.html

Metatool

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

Odefy

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

PLAS

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

PottersWheel

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

SQUAD

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

YANA/YANAsquare

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

Interaction Database, Drug Interaction Database

catRAPID

https://s.tartaglialab.com/page/catrapid_group

HPRD

https://hprd.org/

iHOP

https://www.ihop-­net.org/UniPub/iHOP/

KEGG

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

NPInter

https://www.bioinfo.org/NPInter/

PlateletWeb

https://plateletweb.bioapps.biozentrum.uni-­wuerzburg.de/

plateletweb.php

Roche Pathways

https://biochemical-­pathways.com/#/map/1

STRING

https://string-­db.org

DrumPID

https://drumpid.bioapps.biozentrum.uni-­wuerzburg.de/

compounds/index.php

STITCH

https://stitch.embl.de/

EcoCyc

https://ecocyc.org/

Localization/Motive Prediction

LocP

https://ekhidna2.biocenter.helsinki.fi/LOCP/

LocSigDB

https://genome.unmc.edu/LocSigDB/

nucloc

https://www.nucloc.org/

NucPred

https://www.sbc.su.se/~maccallr/nucpred/

SignalP

https://www.cbs.dtu.dk/services/SignalP/

TMHMM

https://www.cbs.dtu.dk/services/TMHMM/

Functional Glycomics

https://www.functionalglycomics.org/

ELM

https://elm.eu.org/

Overview of Important Databases and Programs and Their General Use