Biological problem addressed 'Model Analysis Type'

Related assays

228 Assays visible to you, out of a total of 343

The main input is the ENA review paper (Function and Regulation of the Saccharomyces cerevisiae ENA Sodium ATPase System, Ruiz&Ariño 2007) and the papers referenced.
Another source are the papers linked from the ENA page of SGD http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=ENA1

Contributor: Falko Krause

Biological problem addressed: Gene Expression

Snapshots: No snapshots

A boolean network was created using booleannet (after experimenting with Squad and CellNetAnalyzer). This network can be simulated and visualized using additional software components that will be part of the pyMantis CMS that is developed by the Translucent project.

Contributor: Falko Krause

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

A interaction network analysis tool (currently based on the BioGrid - PSICQUIC web services) was created that helps to discover interactions of Yeast proteins. The tool will at some point be freely available on the www as part of the pyMantis CMS created within the Translucent project.

Contributor: Falko Krause

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

No description specified

Contributor: Falko Krause

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Elucidation of protein networks involved in the regulation of cation homeostasis using protein interaction datasets.

Contributor: Falko Krause

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Development of bioinformatic tools to investigate the role of transcription factors and 14-3-3 proteins in the regulation of genes involved in cation homeostasis.

Contributor: Falko Krause

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Based on a kinetic model a description of the potassium current is achieved. Its properties with respect to changes in membrane potential and potassium concentrations are derived.

Contributor: Falko Krause

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Proton fluxes ensue a change in the membrane potential to which the potassium uptake responds. The membrane potential changes depend on the extrusion of protons, buffering capacities of the media and experimental parametes.

Contributor: Falko Krause

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Analytical methods and computational analyses (regression, fitting) will be employed to find properties of the Trk system under different external conditions.

Contributor: Falko Krause

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

No description specified

Contributor: Jay Moore

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.

Contributor: Sara Jabbari

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

Steady state study of the effect of altering gene regulation on yields of end-products, focusing on butanol.

Contributor: Sara Jabbari

Biological problem addressed: Gene Expression

Snapshots: No snapshots

Theoretical analysis of hypothetical sigma factor competition.
Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.

Contributor: Ulf Liebal

Biological problem addressed: Gene Expression

Snapshots: No snapshots

We use BSA115 strain which lacks RsbU and RsbW proteins. Therefore, there is limited post-transcriptional regulation of sigmaB activity.

There occurs an unexpected drop in the beta-Gal activity after sigB induction. This modelling effort aims to clarify the reasons.

The dynamic model describes response of yeast metabolic network on metabolic perturbation (i.e. glucose-pulse). One compartmental ODE-based model of yeast anaerobic metabolism includes: glycolysis, pentose phosphate reactions, purine de novo synthesis pathway, purine salvage reactions, redox reactions and biomass growth. The model describes metabolic perturbation of steady state growing cells in chemostat.

No description specified
No description specified

Contributor: Sebastian Henkel

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

- Comparison of metabolic flux distribution in carbon core metabolism (EMP, PPP, TCA) of Bacillus subtilis under 3 different conditions: "salt-free" reference, "stress" chemostat, "osmoprotected" chemostat.
- Model created using OpenFLUX and Microsoft Excel
- Model computed using MatLAB

Using PCA, three components, beam size 8.
Clustering via MCL from Biolayout Express 3D

Data is taken from "Genome-Wide Gene Expression Analysis of the Switch between Acidogenesis and Solventogenesis in Continuous Cultures of Clostridium acetobutylicum." Grimmler et al. 2011
DOI: 10.1159/000320973

Contributor: Sebastian Curth

Biological problem addressed: Gene Expression

Snapshots: No snapshots

Pyruvate formate-lyase (PFL) is an important enzyme in the metabolic pathway of lactic acid bacteria (LAB) and is held responsible for the regulation of the shift between homolactic acid to mixed acid fermentation. PFL catalysis the reversible reaction of acetyl-CoA and formate into pyruvate and CoA. A glycyl radical, who is regenerated within the reaction, is involved; therefore, PFL works only under strictly anaerobic conditions. For its activation, the C-terminal domain has to bind to the
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Contributor: Stefan Henrich

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Metabolic network of S. pyogenes including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors

Contributor: Jennifer Levering

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

Metabolic network of Enterococcus faecalis including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors

Contributor: Nadine Veith

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

No description specified

Using Taverna for mining and MATLAB for conversion into specific formats (cytoscape, SBTOOLBOX2)

Cytoscape based analysis and yED based representation of clostridial Reactomes

Contributor: Sebastian Curth

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

No description specified

Contributor: Sebastian Curth

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

The model describes the behaviour of E. coli in a stationary chemostat with different oxygen availability.

Using TFinfer2 to analyse data from "Characterization of MG1655 and mutant strains under conditions of glucose excess and limitation"

Contributor: Botond Cseke

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.

Contributor: Jacky Snoep

Biological problem addressed: Enzymology

Snapshots: No snapshots

In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus

Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates.
https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate

Mathematical model for GAPDH kinetics, saturation with BPG, NADPH, NADP, GAP and Pi

Contributor: Jacky Snoep

Biological problem addressed: Enzymology

Snapshots: No snapshots

Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP

Contributor: Jacky Snoep

Biological problem addressed: Enzymology

Snapshots: No snapshots

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

Contributor: Jacky Snoep

Biological problem addressed: Enzymology

Snapshots: No snapshots

Modelling the degradation of BPG, GAP and DHAP at high temperature

The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place.
To answer these questions a computational modelling approach was developed. This
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Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact)
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We here create a kinetic model for a single enzyme within the T. brucei trypanothione synthesis pathway, the enzyme trypanothione synthetase based on the insights from the laboratory experiments

The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length

Contributor: Jurgen Haanstra

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of HK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

Kinetic characterisation en mathematical modelling of PGI.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of PFK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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Kinetic characterisation en mathematical modelling of ALD.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of TPI.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of G3PDH.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of GAPDH.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of PGK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of PGM.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of ENO.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation en mathematical modelling of PK.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Kinetic characterisation and mathematical modelling of LDH.

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).

OptKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.

Contributor: Natalie Stanford

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

RobustKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.

Contributor: Natalie Stanford

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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Inhibition of lactate flux due to glucose transport inhibitor

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Genome scale metabolic model of Sulfolobus solfataricus
specific scenario: modelling of L-fucose degradation pathways

Contributor: Jacqueline Wolf

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both
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Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Ron Henkel

Biological problem addressed: Cell Cycle

Snapshots: No snapshots

No description specified

Contributor: Matthias König

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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Construction and manual curated Genome Scale Metabolitic model of M. hyopneumoniae. Dynamic flux balance analysis was performed for glucose uptake

Contributor: Niels Zondervan

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

BPG stability analysis

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

PGK 70C model

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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PGK - GAPDH models

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

We have developed a method for comparative analysis of pairs of complex networks based on gene co-expression analysis. We apply this modeling analysis to data set for gene expressions in multiple tissues of mus musculus and homo sapiens.

These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.

Data and Python scripts to run the analysis of literature data that estimates rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.

General sandbox

Contributor: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Dawie Van Niekerk

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

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No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

In future we should split these versions into separate Assays, and link to the four, original component models, when they are imported with the PlaSMo resource into FairdomHub (expected late 2018)

Contributor: Andrew Millar

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Contains the analysis of the internal metabolite concentrations of the 40 independend samples
Pearson correlation was used to generate heatmaps
Pearson correlation with p-value cutof of 0.001 was used and as input for a correlation network (grouping using H-clust)
Principal component analysis was performed on samples, F-ion and H-ion data combined and seperately
Zip files contains the data (FC.txt), PCA and heatmap plots and the script to re-generate these plots

Contributor: Niels Zondervan

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

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
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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Originally submitted to PLaSMo on 2015-09-02 18:27:55

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

To check if all works fine after struts update. Checking editorial options

Additional Attributes
tested:


Yes, against schema




Originally submitted to PLaSMo on 2013-11-22 15:15:40

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

"3PG is an acronym for Physiological Principles Predicting Growth. It is a generalized forest carbon allocation model, published by Landsberg and Waring (1997), that works with any forest biome and can be run as an Excel spreadsheet by practicing foresters given a few days of training. The model uses relatively simple and readily available inputs such as species growth tables, latitude, aspect, weather records, edaphic variables, stand age, and stand density to derive monthly estimates of gross
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Penman Evaporation over water ( mm/day ). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).

Related Publications
Porter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82..

Originally submitted to PLaSMo on 2011-02-04 15:17:42

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Number of days between 2 Julian days allowing for change of year and leap years. Assumptions : The gap between the two dates is less than 1 year also JDAY1 is before JDAY2. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).  Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82.. Originally submitted to PLaSMo on 2011-02-04 15:24:25
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Transform Calendar day to Julian Day. Converts day, month, year into the equivalent Julian Day allowing for leap years. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82.. Originally submitted to PLaSMo on 2011-02-04 15:30:45

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

To calculate leaf and sheath dimensions for main stems and tillers given the emergence length of their leaves and empirical relationships linking leaf number to maximum laminar length. All sizes are in mm. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box.Related
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

To calculate today's daylength and photoperiod. Daylength is calculated following the treatment of Sellers, Physical Climatology,pp 15-16 and Appendix 2. Daylength is calculated with a correction for atmospheric refraction equivalent to 50 minutes of a degree. Photoperiod is calculated assuming that light is perceived until the centre of the sun is 6 degrees below the horizon. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

To return daily thermal time with base TBASE. Thermal time for a day is calculated by splitting the 24 hour period into 8 * 3 hour periods whose relative contribution to thermal time for the day is based on a cosinusoidal variation in temperature between observed maximum and minimum values. See Weir,A.H. et al.,(1984).J.Agric.Sci.,Camb.,102,371-382. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).     All variables and parameters that are inputs
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

To return Vapour pressure calculated from Wet and Dry Bulb Temperatures. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).

Related Publications
Porter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen.. Eur. J. Agron. 2(2): 69-82..

Originally submitted to PLaSMo on 2011-02-04 15:55:57

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

To return today's vernalising effect (see Weir,A.H. et al.,(1984).J.Agric.Sci.,Camb.,102,371-382). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box.Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). Reads and processes todays weather data. Calculates Penman evaporation and converts day/month/year to Julian day (allowing for year change and leap years). We acknowledge Mikhail Semenov for kindly allowing us to supply this Rothamsted weather data set with this model. Euler integration with 1 day time steps.Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

To calculate the phenological stage of the crop. Note the following definition: phase = the period between two phenological stages, ie. the phase sowing to emergence. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box. Euler integration with 1 day time steps.Related
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Originally submitted to PLaSMo on 2010-12-20 14:54:15

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover",  J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 1".Related PublicationsSeaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental approaches to the circadian control of starch turnover. Journal of the Royal Society Interface. Originally submitted
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A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover",  J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2".Related PublicationsSeaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental approaches to the circadian control of starch turnover. Journal of the Royal Society Interface. Originally submitted
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A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover",  J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 3".Related PublicationsSeaton, Ebenhoeh, Millar, Pokhilko (2013). Regulatory principles and experimental approaches to the circadian control of starch turnover. Journal of the Royal Society Interface. Originally submitted
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Creator - Dr. Daniel D. Seaton. Graphical overview of Arabidopsis clock model P2011 in SBGN, from SBGN-ED in VANTED v2. N.B. to pass PlaSMo validation before update, the <sbgn> tag was back-edited from the correct string <sbgn xmlns="http://sbgn.org/libsbgn/0.2"> to <sbgn xmlns="http://sbgn.org/libsbgn/pd/0.1"> in this file. The file is still correctly opened in VANTED after this modification. The unmodified version is also attached. Related PublicationsFlis et al. (2015). Open
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This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.3.1 is public model ID PLM_1041, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.4.1 is public model ID PLM_1042, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.5.1 is public model ID PLM_1043, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.6.1 is public model ID PLM_1044, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6 Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412 Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64
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Biological problem addressed: Gene Regulatory Network

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The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.

Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6

Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412
Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64
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Validation. Validated against original implementation running under GNU FORTRAN 95. To allow the maximum flexiblity during validation the original FORTRAN code was modified slightly (note that no code lines were deleted). The code was run with high precision so that values were directly comparable with those in Simile even after hundreds of thousands of iterations. The values of all the variables in the original code were printed to the screen so that they could be checked against their Simile
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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukOriginally submitted to PLaSMo on 2011-07-16 12:31:04

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Biological problem addressed: Gene Regulatory Network

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
Final model as submitted but with time changed to t for compatibilty with SBSI
Originally submitted to PLaSMo on 2011-07-16
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Biological problem addressed: Gene Regulatory Network

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
Pokhilko Arabidopsis clock model as submitted, SBSI compatible and tanh light function of Kevin Stratford
Originally submitted
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Biological problem addressed: Gene Regulatory Network

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
Corrected version for SBSI with Kevin Stratford's tanh light function, as in the Locke tanh models. Confirmed will now run and
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Biological problem addressed: Gene Regulatory Network

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
this version has a graphical representation in Cell Designer. It runs in Cell Designer, Copasi and SBSI, but not run optimization
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Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
this version is similar to version 5 (but csymbol time is replaced to t), it has a graphical representation in Cell Designer,
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
This version was modified from version 6 in Copasi by replacement of "light function" to L in all equations.
Originally submitted
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Biological problem addressed: Gene Regulatory Network

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
Alexandra's P2011 clock model with:

- skeleton photoperiod for Graf et al. PNAS 2010.

- parameter changes to simulated prr9
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Biological problem addressed: Gene Regulatory Network

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Alexandra Pokhilko's model of the Arabidopsis clock, private drafts created in preparation for publication (Mol. Syst. Biol.), or as working versions with various modifications after publication. The published model version is also in PlaSMo as PLM_64 here.Comments
Matlab files are attached to version 1
2012-01-31 11:08:51 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
Alexandra's P2011 model with skeleton photoperiod for Graf et al.PNAS 2010.

A Copasi file is attached. Note that another version
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Biological problem addressed: Gene Regulatory Network

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Millar lab working model, extends the Arabidopsis clock model by incorporating multiple sites of inhibition of clock gene expression by TOC1. Model is included into submitted publication "Global Mapping at the Core of the Arabidopsis Circadian Clock Defines a Novel Network Structure of the Oscillator" with Paloma Mas Version 1 has two errors corrected in version 2. This private record is now superseded by the published version, which is public as PLM_70.Version Comments
The last version, which
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Biological problem addressed: Gene Regulatory Network

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Millar lab working model, extends the Arabidopsis clock model by incorporating multiple sites of inhibition of clock gene expression by TOC1. Model is included into submitted publication "Global Mapping at the Core of the Arabidopsis Circadian Clock Defines a Novel Network Structure of the Oscillator" with Paloma Mas Version 1 has two errors corrected in version 2. This private record is now superseded by the published version, which is public as PLM_70.Version Comments
This is a tidied-up and
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Biological problem addressed: Gene Regulatory Network

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Model of the arabidopsis circadian clock obtained from the Bio-PEPA model. The model is based on Alexandra Pokhilko's 2010 deterministic model and includes a scaling factor omega to translate from continuous "concentrations" to discrete amounts. Light function is a smooth function switching between 0 and 1, and is parameterised in order to allow to automate experimentation with different light conditions and photoperiods.Related PublicationsMaria Luisa Guerriero, Alexandra Pokhilko, Aurora Piñas
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The first version of the model corresponds to the one published in Pokhilko et al Mol Syst Biol 2010, which is also presented on the Mol. Syst. Biol. website and was submitted to the Biomodels database. Note: minor errors in published supplementary information are documented in a file attached to version 1; the published SBML files are correct. The second version has some names slightly modified for compatibility with the SBSI platform. Both first and second versions have values of  "dawn" fixed
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The first version of the model corresponds to the one published in Pokhilko et al Mol Syst Biol 2010, which is also presented on the Mol. Syst. Biol. website and was submitted to the Biomodels database. Note: minor errors in published supplementary information are documented in a file attached to version 1; the published SBML files are correct. The second version has some names slightly modified for compatibility with the SBSI platform. Both first and second versions have values of  "dawn" fixed
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The first version of the model corresponds to the one published in Pokhilko et al Mol Syst Biol 2010, which is also presented on the Mol. Syst. Biol. website and was submitted to the Biomodels database. Note: minor errors in published supplementary information are documented in a file attached to version 1; the published SBML files are correct. The second version has some names slightly modified for compatibility with the SBSI platform. Both first and second versions have values of  "dawn" fixed
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Biological problem addressed: Gene Regulatory Network

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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
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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
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Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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
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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
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This model is termed P2012 and derives from the article: Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. Alexandra Pokhilko, Paloma Mas & Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It updates the P2011 model from Pokhilko et al. Mol. Syst. Biol. 2012, Plasmo ID PLM_64, by including: TOC1 as a
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This model is termed P2012 and derives from the article: Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. Alexandra Pokhilko, Paloma Mas & Andrew J Millar BMC Syst. Biol. 2013; 7: 23, submitted 10 Oct 2012 and published 19 March 2013. Link The model describes the circuit depicted in Fig. 1 of the paper (GIF will be attached soon). It updates the P2011 model from Pokhilko et al. Mol. Syst. Biol. 2012, Plasmo ID PLM_64, by including: TOC1 as a
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P2011 model from PLM_43 version 6, optimised by Andrew Millar with SBSI PGA optimisation. A limited parameter set were free to optimise over < 10-fold range (less for RNA degradation rates), against ROBuST RNA data for clock genes in WT and mutants at 17C in LD, and period data in the same mutants in LL. The full SBSI costing is included, using costs from mid-June 2012 (note that costs returned with original optimisation in May were incorrectly reported).Originally submitted to PLaSMo on
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Biological problem addressed: Gene Regulatory Network

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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Originally submitted to PLaSMo on 2012-05-31 22:18:27

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Biological problem addressed: Gene Regulatory Network

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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.Version Comments
Version 2 is the 'public' version with the StepFunction, PLM_64v4. For some reason this was crashing SBSI, but was then cleaned up by passing through Copasi. Thus the file name of this version was Arabidopsis_clock_P2011_exCopasi.xml

This version should be suitable for SBSI optimisation to LD-LL data sets, because it
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Biological problem addressed: Gene Regulatory Network

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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Version Comments


PLM_67v2 set up for LDLL transition at 314h, with wider parameter ranges for most parameters. This is the model file used in LDLL_run2.




Originally submitted to PLaSMo on 2012-05-31 22:18:27

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Biological problem addressed: Gene Regulatory Network

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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.Version Comments
PLM_67v3 model, with TWO stepfunctions. Simulates fine but as of 21 March 2013 did not optimise.

Step2 is usually off because amplitude=0, but can produce LD-DD transition at 262h. To do so, initiate with amplitudeStep1=0 and amplitudeStep2=1.

NB the step1 will still go to LL at 314h, so need to stop DD costing before
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Biological problem addressed: Gene Regulatory Network

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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.Version Comments
Derived from PLM_67v3 - LDLL transition at 314h, with wider parameter ranges, as used in LDLL_run2 - but with one modification in Copasi, to cL_m degradation to ensure light rate > dark rate. Value of m1 previously 0.54, now 0.3. Simulation in Copasi was identical.

Copasi file also attached.
Originally submitted to
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Biological problem addressed: Gene Regulatory Network

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Andrew's "ongoing work" record for the P2011 clock model. Many different versions, with annotations made during SBSI development in 2011-2013 - see version records.

Version Comments


Corrected m1 parameter and range, tested in SBSI




Originally submitted to PLaSMo on 2012-05-31 22:18:27

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Biological problem addressed: Gene Regulatory Network

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A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
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Biological problem addressed: Gene Regulatory Network

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A cell-level model of the Arabidopsis root elongation zone. This spatial model is divided up into biological cells which are further divided into simulation boxes. The original model was designed to investigate how canal cells can accumulate auxin over time rather than to investigate the transport of auxin through the canal cells per se. The main outputs of the simulations in the original paper were the steady state ratios of auxin in the canal cell protoplasts to that in the parenchyma cell
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Validation Validated against original code running under GNU FORTRAN 95. Comments on numerical integration No integration needed. Comments on running the (Simile) model The variable "num errors" accumulates the number of times the ribulose bis-phosphate limited photosynthesis rate cannot be calculated. See the documentation dialogue for the Simile variable "jl_electron transport" for details.Additional AttributesOriginal Model: Language: FORTRAN 95 Author:Daniel P. Rasse File name of original
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Biological problem addressed: Gene Regulatory Network

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This is the representation of major parts of the central metabolism in monocotyledon plants. The information has been derived from the MetaCrop [2] database, a manually curated repository of high quality information concerning the metabolism of crop plants. This includes pathways, reactions, locations, transport processes, and moreOriginally submitted to PLaSMo on 2012-03-05 11:52:18

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Biological problem addressed: Gene Regulatory Network

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"The CENTURY model is a general model of plant-soil nutrient cycling which is being used to simulate carbon and nutrient dynamics for different types of ecosystems including grasslands, agricultural lands, forests and savannas.  CENTURY is composed of a soil organic matter/ decomposition submodel, a water budget model, a grassland/crop submodel, a forest production submodel, and management and events scheduling functions. It computes the flow of carbon, nitrogen, phosphorus, and sulfur through
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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’
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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
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DALEC (Data Assimilation Linked Ecosystem Carbon) represents the C cycle with a simple box model of pools connected via fluxes. There are five pools: C content of foliage (Cf); woody stems and coarse roots (Cw) and fine roots (Cr); and of fresh leaf and fine root litter (Clitter) and soil organic matter (SOM) plus WD (CSOM/WD).  The fluxes among pools are based on the following assumptions: All C fixed during a day is either expended in autotrophic respiration or else allocated to one of three
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Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Originally
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Biological problem addressed: Gene Regulatory Network

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Temperature-sensitive version of Pokhilko 2010 Arabidopsis clock model, from Biomodels BIOMD00273, prepared by Mirela Domijan for the Gould et al. paper on cryptochrome influences on circadian rhythms.    Molecular Systems Biology 9 Article number: 650  doi:10.1038/msb.2013.7 Published online: 19 March 2013 Citation: Molecular Systems Biology 9:650 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures Gould, Ugarte, Domijan et al. doi:10.1038/msb.2013.7Version
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Biological problem addressed: Gene Regulatory Network

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Model outputs mRNA expression of PIF4/5 that is under control of the Pokhilko extended circadian clock. The first version (Model 2a in the supplementary file) has inhibition of PIFs from TOC1. The second version (Model 2c) has PIF activity promoted by LHY/CCA1 - this is currently the most accurate model when compared to data. Models shall be updated later to include PIF4/5 protein levels. Parameter values for this and other External Coincidence models found in supplementary file.Originally submitted
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Biological problem addressed: Gene Regulatory Network

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Model outputs mRNA expression of PIF4/5 that is under control of the Pokhilko extended circadian clock. The first version (Model 2a in the supplementary file) has inhibition of PIFs from TOC1. The second version (Model 2c) has PIF activity promoted by LHY/CCA1 - this is currently the most accurate model when compared to data. Models shall be updated later to include PIF4/5 protein levels. Parameter values for this and other External Coincidence models found in supplementary file.Version Comments
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Biological problem addressed: Gene Regulatory Network

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Model that eliminates several light inputs. RVE8, NOX are incorporated. Individual representation of CCA1 and LHY. Several changes in conections and light inputs. Fogelmark reports eight parameter sets. This SBML file contains the first parameter set Related PublicationsFogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003705Originally
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Biological problem addressed: Gene Regulatory Network

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SBGN model of glycolysis

Originally submitted to PLaSMo on 2012-03-05 11:43:15

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Biological problem addressed: Gene Regulatory Network

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sbgn model of signalling

Originally submitted to PLaSMo on 2012-03-05 11:53:41

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Biological problem addressed: Gene Regulatory Network

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"LINTUL simulates potential growth of a crop, i.e. its dry matter accumulation under ample supply of water and nutrients in a pest-, disease- and weed-free environment, under the prevailing weather conditions. The rate of dry matter accumulation is a function of irradiation and crop characteristics. The model makes use of the common observation that the crop growth rate under favourable conditions is proportional to the amount of light intercepted (Monteith, 1977). Dry matter production is,
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Biological problem addressed: Gene Regulatory Network

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This is a verified version of the model named  LINTUL in this repository. The model is verified against the benchmark FST implmmentation. LINTUL assumes non-limiting conditions. See the "LINTUL" model entry in this repository for a description

Originally submitted to PLaSMo on 2011-02-23 00:08:23

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Biological problem addressed: Gene Regulatory Network

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This version is derived from a model from the article: Extension of a genetic network model by iterative experimentation and mathematical analysis. Locke JC, Southern MM, Kozma-Bognár L, Hibberd V, Brown PE, Turner MS, Millar AJ Mol. Syst. Biol. 2005; 1: 2005.0013 16729048,  SBML model of the interlocked feedback loop network The model describes the circuit depicted in Fig. 4 and reproduces the simulations in Figure 5A and 5B. It provides initial conditions, parameter values and rules for the
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This is a version derived from a model from the article: Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ Mol. Syst. Biol.2006;Volume:2;Page:59 17102804,   The model describes a three loop circuit of the Arabidopsis circadian clock. It provides initial conditions, parameter values and reactions for the production rates of the following species: LHY
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Test by Martin for simileXML

Originally submitted to PLaSMo on 2012-03-08 11:39:23

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Biological problem addressed: Gene Regulatory Network

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Test by Martin for simileXML

Version Comments


Version 2, the product of many seconds of research..




Originally submitted to PLaSMo on 2012-03-08 11:39:23

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Biological problem addressed: Gene Regulatory Network

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This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration.   In the original paper, the model is used twice, once for the trees and once for the grass under the trees, with the grass receiving light not intercepted by the trees.   The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and
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This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration.   In the original paper, the model is used twice, once for the trees and once for the grass under the trees, with the grass receiving light not intercepted by the trees.   The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and
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Biological problem addressed: Gene Regulatory Network

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Validation: Validated against the original running in Excel. Each calculation in the model was individually validated as well. Comments on numerical integration: Euler integration with time steps of 1. In Simile the "time units" were set to "day" and execution was for 364 days as the simulation starts at time 0 (not time 1 as in the Excel model). Comments on running Simile model: Users must specify the temperature controlled growing season themselves. To do this use the following steps which take
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Model files accompanying Seaton et al., Molecular Systems Biology, 2015 Abstract: Clock?regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best?understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN?BINDING, KELCH REPEAT, F?BOX 1 (FKF1) transcription.
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Biological problem addressed: Gene Regulatory Network

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This is a modified version of Biomodels89, containing a light-forcing function. This variant is configured to run cycles of LD8:16Related Publicationsocke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ. (2006). Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. . Mol Syst Biol . Originally submitted to PLaSMo on 2012-03-29 10:24:44

Neuronal musch signalling sbml diagram

Originally submitted to PLaSMo on 2012-03-05 12:33:43

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Biological problem addressed: Gene Regulatory Network

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 This model is derived from Biomodels 299 - the Leloup et al Neurospora clock model. This variant contains an embedded light-forcing function (SBO:000475) that provides a periodic light input. In this model, after 72h of LD12:12, the amplitude of Vs ( the light dependent parameter ) increases to 4.1, leading to chaotic oscillations. For this to happen, the periodic light function needs to produce a square-wave pattern.    Execution of this model will result in the behaviour depicted in Figure 2D
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This model, derived from Biomodels299, is a variant of the Neurospora Circadian clock model of Leloup et al., 1999. It is supplemented with a periodic light function (SBO:0000475) that is parameterized to produce sinusoidal oscillations in the light sensitive parameter Vs with an amplitude of 5. These sinusoidal wave-form maintains entrained oscillations even with high light input, and is described in Figures 6 and 7 of Gonze and Goldbeter, 2000.Related PublicationsDidier Gonze and Albert Goldbeter
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Draft of MEP pathway for isoprenoid synthesis, created 2012-2013 by Oender Kartal in the Gruissem lab. He notes "It contains some annotations and references for the parameter values and rate equations and produces a stable steady state, so you can do some control analysis. It simulates day-metabolism, since the MEP Pathway is supposedly active during the day." Unpublished, for use by TiMet consortium only.

Originally submitted to PLaSMo on 2013-09-13 09:10:53

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Biological problem addressed: Gene Regulatory Network

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Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.Comments
No parameters constrained in version 1 file.
2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk
Compiled successfully in SBSI for optimisation.
2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
Version 1 is file P2012_NoSinkNoABAParamsNom38_freshCopasi.xml
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

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Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.Comments
No parameters constrained in version 1 file.
2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk
Compiled successfully in SBSI for optimisation.
2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.ukVersion Comments
Version 2 is file P2012_fin_NoABAv4.xml of 6th March.

It
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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
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The model is an extensio of PLM_67v3 with an additional an additional variable Temp in ODE 25. This change allows to simulated warm pulses that affect EC stability using COPASI. 

Originally submitted to PLaSMo on 2014-03-10 13:16:25

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

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The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al.,
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The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al.,
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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
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Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.

Related Publications
Sorokina et al (2011). BMicroarray data can predict diurnal changes of starch content in the picoalga Ostreococcus.. BMC Systems Biology. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21352558

Originally submitted to PLaSMo on 2011-08-12 15:34:00

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

The model is applied to spring wheat, with ample supply of nutrients and water, also without pests, diseases and weeds. Radiation and temperature, being the most important environmental factors, and crop characteristics determine growth and development. Crop growth and development are simulated based on underlying chemical, physiological and physical processes. Dry matter accumulation is calculated from daily crop CO2 assimilation based on leaf CO2 assimilation and taking into account the respiration
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This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by replacing it with immediate light input. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where the light accumulator (acc) has been eliminated by setting its value to 1. This model was used to generate Figure 2F in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to environmental signals. New Phytologist. Originally submitted to
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2B in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the transcription rate of CCA1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2C in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the activation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2E in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the dark in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related PublicationsLaura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses to
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a version of the T2011.1.2 Ostreococcus tauri 1-loop clock model where light input to the degradation rate of TOC1 has been eliminated by setting the rate to the value it had in the light in the original model. This model was used to generate Figure 2D in Dixon et al. New Phytologist (2014)Related Publications Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar (2014). Light and circadian regulation of clock components aids flexible responses
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

TiMet flower specific protein detection network

Originally submitted to PLaSMo on 2012-03-02 12:39:54

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Trial upload of the pollen netwrok from TiMet

Originally submitted to PLaSMo on 2012-02-27 12:17:46

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Trial upload of the pollen netwrok from TiMet

Version Comments


Live pollen upload test




Originally submitted to PLaSMo on 2012-02-27 12:17:46

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

PP interaction network exported from Cytoscape in XGMML

Originally submitted to PLaSMo on 2012-03-02 12:32:33

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Test for root network

Originally submitted to PLaSMo on 2012-02-27 14:24:59

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

The seed network, uploaded as a test from Cytoscape

Version Comments


Saving second/third version as a live test




Originally submitted to PLaSMo on 2012-02-24 11:41:50

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

The seed network, uploaded as a test from Cytoscape

Version Comments


Uploading new version for testing




Originally submitted to PLaSMo on 2012-02-24 11:41:50

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Cytoscape shoot specific diurnal transcript oscillation.

Originally submitted to PLaSMo on 2012-03-02 12:42:30

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Cytoscape silqueue specific protein detection

Originally submitted to PLaSMo on 2012-03-02 12:44:13

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

"TRIFFID (Top-down Representation of Interactive Foliage and Flora Including Dynamics)" is a dynamic global vegetation model, which updates the plant distribution and soil carbon based on climate-sensitive CO2 fluxes at the land-atmosphere interface. The surface CO2 fluxes associated with photosynthesis and plant respiration are calculated in the MOSES 2 tiled land-surface scheme (Essery et al (In preparation)), on each atmospheric model timestep (normally 30 minutes), for each of 5 plant functional
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).Comments
Not formulated to easily allow addition of the ISSF to replace the present light
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).Comments
Not formulated to easily allow addition of the ISSF to replace the present light
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Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.Related PublicationsWilczek et al. (2009). Effects of Genetic Perturbation
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Photothermal model for Arabidopsis development, as published, converted to Simile format by Yin-Hoon Chew. Note that the XML file is just a dummy SBML file, the .SML is the working model file. Simile can read csv files (as attached) for meteorological data (hourly temperature, sunrise, sunset). Users only need to change the directory of the input variables. I have also attached the set of parameter values for each genotype.Related PublicationsWilczek et al. (2009). Effects of Genetic Perturbation
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

tbd

Contributor: Malte Herold

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Related PublicationsMe and Helena (2014). some book. Moore A, Zielinski T, Millar AJ (2014). Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure.. Methods in molecular biology (Clifton, N.J.). Retrieved from: doi.org/10.1007/978-1-4939-0700-7_2Stein JM (1975). The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.. Biochemical pharmacology.
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots