PlaSMo model repository

Collection of models submitted to PLaSMo by Alexandra Graf and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Carl Troein and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Richard Adams and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Rob Smith and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Yin Hoon and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Martin Beaton and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Maria-Luisa Guerriero and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Alexandra Pokhilko and automatically transferred to FAIRDOM Hub.

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.<br><br><strong>Related Publications</strong></strong><br>Wilczek
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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).<br><br><strong>Originally submitted to PLaSMo on 2010-05-04
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"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
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Cytoscape silqueue specific protein detection<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:44:13</strong></strong>

Cytoscape shoot specific diurnal transcript oscillation.<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:42:30</strong></strong>

The seed network, uploaded as a test from Cytoscape<br><br><strong>Originally submitted to PLaSMo on 2012-02-24 11:41:50</strong></strong>

Test for root network<br><br><strong>Originally submitted to PLaSMo on 2012-02-27 14:24:59</strong></strong>

PP interaction network exported from Cytoscape in XGMML<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:32:33</strong></strong>

Trial upload of the pollen netwrok from TiMet<br><br><strong>Originally submitted to PLaSMo on 2012-02-27 12:17:46</strong></strong>

TiMet flower specific protein detection network<br><br><strong>Originally submitted to PLaSMo on 2012-03-02 12:39:54</strong></strong>

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 Publications
Wilczek et al.
...

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 Publications
Wilczek et al.
...

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
...

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
...

"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
...

Cytoscape silqueue specific protein detection

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

Cytoscape shoot specific diurnal transcript oscillation.

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

The seed network, uploaded as a test from Cytoscape

Version Comments

Uploading new version for testing

The seed network, uploaded as a test from Cytoscape

Version Comments

Saving second/third version as a live test

Test for root network

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

Data file for PLaSMo accesssion ID PLM_7, version 2

Data file for PLaSMo accesssion ID PLM_89, version 2

Data file for PLaSMo accesssion ID PLM_5, version 1

Data file for PLaSMo accesssion ID PLM_89, version 1

Data file for PLaSMo accesssion ID PLM_91, version 1

Data file for PLaSMo accesssion ID PLM_90, version 1

Data file for PLaSMo accesssion ID PLM_87, version 1

Data file for PLaSMo accesssion ID PLM_92, version 1

Data file for PLaSMo accesssion ID PLM_85, version 1

Data file for PLaSMo accesssion ID PLM_88, version 1

Simplified model file for PLaSMo accession ID PLM_7, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Simplified model file for PLaSMo accession ID PLM_7, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_7, version 2

Originally submitted model file for PLaSMo accession ID PLM_5, version 1

Originally submitted model file for PLaSMo accession ID PLM_7, version 1

Originally submitted model file for PLaSMo accession ID PLM_89, version 2

Simplified model file for PLaSMo accession ID PLM_89, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Simplified model file for PLaSMo accession ID PLM_89, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Simplified model file for PLaSMo accession ID PLM_90, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Originally submitted model file for PLaSMo accession ID PLM_89, version 1

What is PlaSMo?

PlaSMo stands for Plant Systems-biology Modelling; Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

The original PlaSMo project description is included within the attached document.

Our aims

• To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being
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