Skip to content

Latest commit

 

History

History
182 lines (149 loc) · 18 KB

Using-Smoldyn-with-SED-ML-COMBINE-BioSimulators.md

File metadata and controls

182 lines (149 loc) · 18 KB
Raw

Using Smoldyn with SED-ML and COMBINE archives

Smoldyn provides a BioSimulators-compliant interface for executing Smoldyn simulations through SED-ML and COMBINE archives.

COMBINE archive format for Smoldyn configuration files

OMEX manifests of COMBINE archives should use the format http://purl.org/NET/mediatypes/text/smoldyn+plain for Smoldyn configuration files as illustrated below.

<content location="model.txt" format="http://purl.org/NET/mediatypes/text/smoldyn+plain" master="false"/>

SED-ML model language for Smoldyn configuration files

SED-ML files for Smoldyn simulations should use the language urn:sedml:language:smoldyn for Smoldyn configuration files.

<model id="model" source="model.txt" language="urn:sedml:language:smoldyn"/>

SED-ML model changes

Changes to configurations for Smoldyn simulations can be encoded into SED-ML changeAttribute model changes as illustrated below.

Smoldyn syntax target of SED-ML change Format of newValue of SED-ML change Execution time
define {name} {float} define {name} {float} Preprocessing
difc {species} {float} difc {species} {float} Preprocessing
difc {species}({state}) {float} difc {species}({state}) {float} Preprocessing
difc_rule {species}({state}) {float} difc_rule {species}({state}) {float} Preprocessing
difm {species} {float}+ difm {species} {float}+ Preprocessing
difm {species}({state}) {float}+ difm {species}({state}) {float}+ Preprocessing
difm_rule {species}({state}) {float}+ difm_rule {species}({state}) {float}+ Preprocessing
drift {species} {float}+ drift {species} {float}+ Preprocessing
drift {species}({state}) {float}+ drift {species}({state}) {float}+ Preprocessing
drift_rule {species}({state}) {float}+ drift_rule {species}({state}) {float}+ Preprocessing
surface_drift {species}({state}) {surface} {panel-shape} {float}+ surface_drift {species}({state}) {surface} {panel-shape} {float}+ Preprocessing
surface_drift_rule {species}({state}) {surface} {panel-shape} {float}+ surface_drift_rule {species}({state}) {surface} {panel-shape} {float}+ Preprocessing
killmol {species}({state}) killmol {species}({state}) 0 Simulation
killmol {species}({state}) {prob} killmol {species}({state}) {prob} 0 Simulation
killmolinsphere {species}({state}) {surface} killmolinsphere {species}({state}) {surface} 0 Simulation
killmolincmpt {species}({state}) {compartment} killmolincmpt {species}({state}) {compartment} 0 Simulation
killmoloutsidesystem {species}({state}) killmoloutsidesystem {species}({state}) 0 Simulation
fixmolcount {species}({state}) {num} fixmolcount {species}({state}) {integer} Simulation
fixmolcountincmpt {species}({state}) {num} {compartment} fixmolcountincmpt {species}({state}) {compartment} {integer} Simulation
fixmolcountonsurf {species}({state}) {num} {surface} fixmolcountonsurf {species}({state}) {surface} {integer} Simulation 
<changeAttribute target="fixmolcount red" newValue="10"/>
<changeAttribute target="killmolincmpt red cytosol" newValue="10"/>
<changeAttribute target="killmolinsphere red membrane" newValue="10"/>

SED-ML simulation algorithms

SED-ML files for Smoldyn support the following algorithms and algorithm parameters:

<algorithm kisaoID="KISAO:0000057">
    <listOfAlgorithmParameters>
        <algorithmParameter kisaoID="KISAO_0000254" value="5.0"/>
    </listOfAlgorithmParameters>
</algorithm>

Variables of SED-ML data generators

Variables for SED-ML data generators should use symbols and targets as illustrated below.

  • Time - symbol: urn:sedml:symbol:time
  • Species counts and distributions - target
Smoldyn output file SED variable target Shapes
molcount molcount {species} (numberOfSteps + 1,)
molcountspecies {species}({state}) molcountspecies {species}({state}) (numberOfSteps + 1,)
molcountspecieslist {species}({state})+ molcountspecies {species}({state}) (numberOfSteps + 1,)
molcountinbox {low-x} {hi-x} molcountinbox {species} {low-x} {hi-x} (numberOfSteps + 1,)
molcountinbox {low-x} {hi-x} {low-y} {hi-y} molcountinbox {species} {low-x} {hi-x} {low-y} {hi-y} (numberOfSteps + 1,)
molcountinbox {low-x} {hi-x} {low-y} {hi-y} {low-z} {hi-z} molcountinbox {species} {low-x} {hi-x} {low-y} {hi-y} {low-z} {hi-z} (numberOfSteps + 1,)
molcountincmpt {compartment} molcountincmpt {species} {compartment} (numberOfSteps + 1,)
molcountincmpts {compartment}+ molcountincmpt {species} {compartment} (numberOfSteps + 1,)
molcountincmpt2 {compartment} {state} molcountincmpt2 {species} {compartment} {state} (numberOfSteps + 1,)
molcountonsurf {surface} molcountonsurf {species} {surface} (numberOfSteps + 1,)
molcountspace {species}({state}) {axis} {low} {hi} {bins} 0 molcountspace {species}({state}) {axis} {low} {hi} {bins} (numberOfSteps + 1, bins)
molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi} 0 molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi} (numberOfSteps + 1, bins)
molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi} {low} {hi} 0 molcountspace {species}({state}) {axis} {low} {hi} {bins} {low} {hi} {low} {hi} (numberOfSteps + 1, bins)
molcountspace2d {species}({state}) z {low-x} {hi-x} {bins-x} {low-y} {hi-y} {bins-y} 0 molcountspace2d {species}({state}) z {low-x} {hi-x} {bins-x} {low-y} {hi-y} {bins-y} (numberOfSteps + 1, bins-x, bins-y)
molcountspace2d {species}({state}) {axis} {low-1} {hi-1} {bins-1} {low-2} {hi-2} {bins-2} {low-3} {hi-3} 0 molcountspace2d {species}({state}) {axis} {low-1} {hi-1} {bins-1} {low-2} {hi-2} {bins-2} {low-3} {hi-3} (numberOfSteps + 1, bins-1, bins-2)
molcountspaceradial {species}({state}) {center-x} {radius} {bins} 0 molcountspaceradial {species}({state}) {center-x} {radius} {bins} (numberOfSteps + 1, bins)
molcountspaceradial {species}({state}) {center-x} {center-y} {radius} {bins} 0 molcountspaceradial {species}({state}) {center-x} {center-y} {radius} {bins} (numberOfSteps + 1, bins)
molcountspaceradial {species}({state}) {center-x} {center-y} {center-z} {radius} {bins} 0 molcountspaceradial {species}({state}) {center-x} {center-y} {center-z} {radius} {bins} (numberOfSteps + 1, bins)
molcountspacepolarangle {species}({state}) {center-x} {center-y} {pole-x} {pole-y} {radius-min} {radius-max} {bins} 0 molcountspacepolarangle {species}({state}) {center-x} {center-y} {pole-x} {pole-y} {radius-min} {radius-max} {bins} (numberOfSteps + 1, bins)
molcountspacepolarangle {species}({state}) {center-x} {center-y} {center-z} {pole-x} {pole-y} {pole-z} {radius-min} {radius-max} {bins} 0 molcountspacepolarangle {species}({state}) {center-x} {center-y} {center-z} {pole-x} {pole-y} {pole-z} {radius-min} {radius-max} {bins} (numberOfSteps + 1, bins)
radialdistribution {species-1}({state-1}) {species-2}({state-2}) {radius} {bins} 0 radialdistribution {species-1}({state-1}) {species-2}({state-2}) {radius} {bins} (numberOfSteps + 1, bins)
radialdistribution2 {species-1}({state-1}) {species-2}({state-2}) {low-x} {hi-x} {low-y} {hi-y} {low-z} {hi-z} {radius} {bins} 0 radialdistribution2 {species-1}({state-1}) {species-2}({state-2}) {low-x} {hi-x} {low-y} {hi-y} {low-z} {hi-z} {radius} {bins} (numberOfSteps + 1, bins) 
<variable id="time" symbol="urn:sedml:symbol:time">
<variable id="red" target="molcount red">

Simulation results

The results of Smoldyn simulations executed through SED-ML and COMBINE archives are saved in HDF5 format as described in the BioSimulators documentation. These files can be read with a variety of tools such as HDFView, h5py for Python, and h5read for MATLAB.

Executing Smoldyn through SED-ML and COMBINE archives

COMBINE archives and SED-ML files for Smoldyn simulations can be executed in multiple ways.

Web application and REST API

runBioSimulations is a web application that can execute COMBINE archives and SED-ML files for Smoldyn simulations. runBioSimulations also provides a REST API for executing simulations.

Command-line program

Simulations can be run with the biosimulations-smoldyn command-line progam provided with the Smoldyn Python package as illustrated below. Note, this requires Smoldyn to be installed with the biosimulators option.

pip install smoldyn[biosimulators]
python -m biosimulators.biosimulators -i /path/to/simulation.omex -o /path/to/save/outputs

Python API

Simulations can be run with the exec_sedml_docs_in_combine_archive method provided with the Smoldyn Python package as illustrated below. Note, this requires Smoldyn to be installed with the biosimulators option.

pip install smoldyn[biosimulators]
from smoldyn.biosimulators.combine import exec_sedml_docs_in_combine_archive
archive_filename = '/path/to/simulation.omex'
out_dir = '/path/to/save/outputs'
exec_sedml_docs_in_combine_archive(archive_filename, out_dir)

Docker image

Simulations can be run with the Biosimulators-Smoldyn Docker image as illustrated below:

docker pull ghcr.io/biosimulators/smoldyn
docker run \
  --tty \
  --rm \
  --mount type=bind,source=/path/to/simulation.omex,target=/tmp/project,readonly \
  --mount type=bind,source=/path/to/save/outputs,target=/tmp/results \
  ghcr.io/biosimulators/smoldyn \
    --archive /tmp/project/simulation.omex \
    --out-dir /tmp/results