Assays
What is an Assay?Filters
Submitter: Dorothee Houry
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
This is the simulation part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Assay type: Molecular Dynamics
Technology type: All-Atom
Investigation: 1 hidden item
This is the analysis part of the Simulation Foundry, Version 1.5.
Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.
Make sure you followed the instructions in "Preparation" before running this.
Submitter: Gudrun Gygli
Biological problem addressed: various analyses of molecular dynamics simulations
Investigation: 1 hidden item
Preparation needed to use Simulation Foundry, Version 1.5.
Please read the manual before working with this Simulation Foundry.
Pay careful attention to the installation instructions.
Note the known issues.
Submitter: Gudrun Gygli
Assay type: Instructions
Technology type: Technical Computer Installation
Investigation: 1 hidden item
This is a collection of data that have been used to analyse data on deep eutectic solvent mixtures of choline chloride:glycerol:water.
Submitter: Gudrun Gygli
Biological problem addressed: Model Analysis Type
Investigation: Deep Eutectic Solvents
Data digitized from publication.
Spigset1999a Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Jeppesen1996 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Oh2012 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Healy1991 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Akinyinka2000 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Kakuda2014 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Haller2002 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Amchin1999 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Kaplan1997 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Blanchard1983a Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Tanaka2014 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Perera2011 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Magnusson2008 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
Data digitized from publication.
Hetzler1990 Description
Submitter: Matthias König
Investigation: MM-PLF: Multiscale modeling for personalized li...
Study: PKDB Caffeine Study
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
This is the SimileXML for the Salazar2009_FloweringPhotoperiod model in PlaSMo. It corresponds to Model 3 in the publication of Salazar et al 2009. The Simile version of this model is also attached here. Instructions to run the Photoperiodism Model in Simile 1. Save all the files into the same folder. 2. Copy and paste the attached ‘lightfunction.pl’ file in the following folder: Program File > Simile6.0 (or other software version)> Functions 3. Download the ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
This is the SimileXML for the Salazar model linked to the T6P/TPS pathway (Wahl et al. Science 2013). The Simile version of this model and the parameter file are also attached here. Time series data of T6P and FT mRNA for Col wild type and tps1 mutant from Fig. 1 in Wahl et al were used to re-optimise Bco, KCO, kT6P and vT6P (which replaces VCO). Note: This set of parameter values has only been optimised and tested for a 16:8 light:dark cycle, and the initial values in the Simile model are for ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
This is part of the GreenLab Functional-Structural Plant Model for Arabidopsis published in Christophe et al 2008. This model was re-factored, to facilitate the integration in the Chew et al Framework Model, and it cannot be run as a standalone model. Related PublicationsAngélique Christophe A E, Véronique Letort B, Irène Hummel A, Paul-Henry Cournède B, Philippe de Reffye C, Jérémie Lecœur (2008). A model-based analysis of the dynamics of carbon balance at the whole-plant level in Arabidopsis ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
This is the Framework Model (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111) that links the following: 1. Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - Carbon Dynamic Model 2. Part of the Christophe et al 2008 Functional-Structural Plant Model 3. Chew et al 2012 Photothermal Model 4. Salazar et al 2009 Photoperiodism Model To run the model in Simile, please download the Evaluation Edition of the software from http://www.simulistics.com/products/simile.php ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
This is a photothermal model for Arabidopsis that predicts flowering time, published in Chew et al (2012). It is an improved version of the model in Wilczek et al (Science 2009). A Simile version of the model is attached. Instructions to run the Photothermal Model in Simile 1. Download the Simile file attached or import the XML into Simile: a. File > Import > XML Model Description 2. To run the model: a. Model > Run or click on the ‘Play’ ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
Data derived from RNAseq
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Reverse Engineering Directed Gene Regulatory Ne...
Study: Supplementary files
Data derived from protein samples
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Reverse Engineering Directed Gene Regulatory Ne...
Study: Supplementary files
Scripts for running network simulations
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Reverse Engineering Directed Gene Regulatory Ne...
Study: Supplementary files
tbd
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Confocal Laser Scanning Microscopy (CLSM)
Investigation: Deep Neural Networks Outperform Human Expert’s ...