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pyLM
v1.1
A Python Problem Solving Environment for the simulation of stochastic biological systems
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Functions | |
def | buildEColiCell |
Build a standard E coli cell 0.5 microns across and 2 microns long. More... | |
def | buildDividingEColiCell |
Build a standard E coli cell 0.5 microns across and 4 microns long. More... | |
def | buildSphericalEColiCell |
Build a Spherical E coli cell, one that lacks the gene for elongation. More... | |
def | buildFilamentousEColiCell |
Build a long filamentous E coli cell where the user can specify the length. More... | |
def | packFastGrowingEcoli |
Pack a cell with the protein distribution for fast growing E coli. More... | |
def | packSlowGrowingEcoli |
Pack a cell with the protein distribution for fast growing E coli. More... | |
def pySTDLM.StandardCells.buildDividingEColiCell | ( | sim, | |
crowded = False , |
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crowdedMembrane = False |
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) |
Build a standard E coli cell 0.5 microns across and 4 microns long.
sim | An RDMESimulation object |
crowded | Should the cytosol be crowded (default: false) |
crowdedMembrane | Should the membrane be crowded (default: false) |
def pySTDLM.StandardCells.buildEColiCell | ( | sim, | |
crowded = False , |
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crowdedMembrane = False |
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) |
Build a standard E coli cell 0.5 microns across and 2 microns long.
sim | An RDMESimulation object |
crowded | Should the cytosol be crowded (default: false) |
crowdedMembrane | Should the membrane be crowded (default: false) |
def pySTDLM.StandardCells.buildFilamentousEColiCell | ( | sim, | |
length = 8.0 , |
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crowded = False , |
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crowdedMembrane = False |
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) |
Build a long filamentous E coli cell where the user can specify the length.
sim | An RDMESimulation object |
length | The length of the cell in microns (default: 8) |
crowded | Should the cytosol be crowded (default: false) |
crowdedMembrane | Should the membrane be crowded (default: false) |
def pySTDLM.StandardCells.buildSphericalEColiCell | ( | crowded = False , |
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latticeSpacing = 16 , |
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crowdedMembrane = False |
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) |
Build a Spherical E coli cell, one that lacks the gene for elongation.
sim | An RDMESimulation object |
crowded | Should the cytosol be crowded (default: false) |
crowdedMembrane | Should the membrane be crowded (default: false) |
def pySTDLM.StandardCells.packFastGrowingEcoli | ( | sim | ) |
Pack a cell with the protein distribution for fast growing E coli.
sim | A RDMESimulation object |
def pySTDLM.StandardCells.packSlowGrowingEcoli | ( | sim | ) |
Pack a cell with the protein distribution for fast growing E coli.
sim | A RDMESimulation object |