Muetzelfeldt, Robert

SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).

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.

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 lost To represent these models in a declarative XML-based format, which is closer to the systems biology standard SBML To evaluate the behaviour ...

"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 ...

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 ...

"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, ...

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 ...

"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 ...

"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 ...

"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 ...

"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 ...

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 ...

"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, ...

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 ...

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 ...

"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 ...

Data file for PLaSMo accesssion ID PLM_5, version 1

Data file for PLaSMo accesssion ID PLM_11, version 2

Data file for PLaSMo accesssion ID PLM_11, version 1

Data file for PLaSMo accesssion ID PLM_11, version 2

Data file for PLaSMo accesssion ID PLM_11, version 1

Data file for PLaSMo accesssion ID PLM_4, version 1

Data file for PLaSMo accesssion ID PLM_23, version 1

Data file for PLaSMo accesssion ID PLM_23, version 1

Data file for PLaSMo accesssion ID PLM_23, version 1

Data file for PLaSMo accesssion ID PLM_23, version 1

Data file for PLaSMo accesssion ID PLM_22, version 1

Data file for PLaSMo accesssion ID PLM_22, version 1

Data file for PLaSMo accesssion ID PLM_22, version 1

Data file for PLaSMo accesssion ID PLM_12, version 1

Data file for PLaSMo accesssion ID PLM_12, version 1

Data file for PLaSMo accesssion ID PLM_12, version 1

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

Originally submitted model file for PLaSMo accession ID PLM_11, version 1

Originally submitted model file for PLaSMo accession ID PLM_11, version 2

Originally submitted model file for PLaSMo accession ID PLM_4, version 1

Originally submitted model file for PLaSMo accession ID PLM_23, version 1

Originally submitted model file for PLaSMo accession ID PLM_22, version 1

Originally submitted model file for PLaSMo accession ID PLM_12, version 1