jimena.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: Jimena
http://jimena.bioapps.biozentrum.uni-wuerzburg.de/computing/jimena
Skip to main content. Is a Java genetic regulatory network simulation framework which focuses on computational efficacy and a modularized architecture to facilitate the development and testing of new algorithms and models surrounding GRNs. It features. Network import from yED graph files. Full support of the exponential interpolation model implemented in SQUAD. Full support of the polynomial interpolation models implemented in Odefy. Several discrete update schemes. Perturbation support in all models.
jimena.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: GUITutorial
http://jimena.bioapps.biozentrum.uni-wuerzburg.de/computing/jimena/guitutorial
Skip to main content. The GUI allows you to comfortably study the behavior of networks for different interaction parameters (decays, weights etc.), simulation methods, perturbations and network states. It also features some basic analyses (e.g. stable state search for discrete and continuous models). All result can be exported as data tables. The GUI can be started by double-clicking on the jimena.jar file. Dt: The step size used by the differential equation solver in all simulations and analyses. Simula...
yana.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: Computing
http://yana.bioapps.biozentrum.uni-wuerzburg.de/computing/ingeno
Skip to main content. Latest YANA software version, please cite: Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. Staphylococcus aureus. Physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35. Comparing proteomics and metabolomics allows insights into Staphylococcus aureus. YANAsquare GUI software package. 2 Tutorial on t...
jimena.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: ExampleNetwork
http://jimena.bioapps.biozentrum.uni-wuerzburg.de/computing/jimena/examplenetwork
Skip to main content. Arabidopsis thaliana flower organ specification network. An Arabidopsis thaliana flower organ specification gene regulatory network. Sánchez-Corralesa Y, Álvarez-Buylla E R, Mendoza L: The Arabidopsis thaliana flower organ specification gene regulatory network determines a robust differentiation process. Journal of Theoretical Biology 264 (2010) 971 983. Right-click and Save Link As to save). A network that controls the differentiation process of T-helper cells.
yana.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: Computing
http://yana.bioapps.biozentrum.uni-wuerzburg.de/computing
Skip to main content. Latest YANA software version, please cite: Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. Staphylococcus aureus. Physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35. Comparing proteomics and metabolomics allows insights into Staphylococcus aureus. YANAsquare GUI software package. 2 Tutorial on t...
yana.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: Scripts
http://yana.bioapps.biozentrum.uni-wuerzburg.de/computing/scripts
Skip to main content. Script 1. TATAbox finder. Perl TATA-cntrl-chrm.pl [sequence file] [result outfile] [random generated sequence file] sequence length. Sequence length: Length of randomly generated sequences, default: 40 when not specified. Script to test CPEs (TATA-Boxes) in a randomly generated sequence library of a given sequence length. Software package tre agrep is required, which is available at laurikari.net/tre/download. Perl TATA-cntrl-chrm.pl will generate a readme manual page.
yana.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: Education software
http://yana.bioapps.biozentrum.uni-wuerzburg.de/computing/education_software
Skip to main content. Dynamic modelling of protein networks. Software required for our education due to version compatibility. Squad 2 requires Java SE runtime environment 6, not newer. Java SE 6 can be downloaded from. Squad tutorial please read: http:/ www.enfin.org/wiki/squad-tutorial. Please cite the original paper and author:. To run squad under win7/8, you have to uninstall JRE 7 firstly if you have it installed before. Then download. Celldesigner 3.5.1. Celldesigner 3.5.1. Step 1. framework 3&...
yana.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: Jimena_C
http://yana.bioapps.biozentrum.uni-wuerzburg.de/computing/jimena_c
Skip to main content. Is a Java genetic regulatory network simulation framework which focuses on computational efficacy and a modularized architecture to facilitate the development and testing of new algorithms and models surrounding GRNs. It features. Network import from yED graph files. Full support of the exponential interpolation model implemented in SQUAD. Full support of the polynomial interpolation models implemented in Odefy. Several discrete update schemes. Perturbation support in all models.
yana.bioapps.biozentrum.uni-wuerzburg.de
Lehrstuhl für Bioinformatik: YANAvergence
http://yana.bioapps.biozentrum.uni-wuerzburg.de/computing/yanavergence
Skip to main content. Https:/ www.ncbi.nlm.nih.gov/pubmed/21472852). Latest YANA software version, please cite: Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. Staphylococcus aureus. Physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35. Comparing proteomics and metabolomics allows insights into Staphylococcus aureus.