PySCeS User Guide¶

PySCeS: the Python Simulator for Cellular Systems is an extendable toolkit for the analysis and investigation of cellular systems. PySCeS is available for download at http://pysces.github.io and on GitHub where the source code is maintained: https://github.com/PySCeS/pysces

Introduction¶

Welcome! This user guide will get you started with the basics of modelling cellular systems with PySCeS. It is meant to be read in conjunction with the chapter on The PySCeS Model Description Language, which specifies the syntax of the input file read by the program. If you already have PySCeS installed continue straight on; if not, Installing and configuring contains instructions on building and installing PySCeS.

PySCeS is distributed under the PySCeS (BSD style) licence and is made freely available as Open Source software. See LICENCE.txt for details.

The continued development of PySCeS depends, to a large degree, on support and feedback from Systems Biology community. If you use PySCeS in your work please cite it using the following reference:

Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr Modelling cellular systems with PySCeS, Bioinformatics, 21, 560-561, DOI 10.1093/bioinformatics/bti046.

We hope that you will enjoy using our software. If, however, you find any unexpected features (i.e. bugs) or have any suggestions on how we can improve PySCeS please let us know by opening an issue on Github.

The PySCeS development team.

Getting started¶

Loading PySCeS¶

In this section we assume you have PySCeS installed and configured (see Installing and configuring for details) and a correctly formatted PySCeS input file that describes a cellular system in terms of its reactions, species and parameters (refer to The PySCeS Model Description Language). Note that on all platforms PySCeS model files have the extension .psc.

To begin modelling we need to start up an interactive Python shell (we suggest IPython) and load PySCeS with import pysces:

Python 3.9.6 (default, Jun 30 2021, 10:22:16)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.26.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import pysces
Matplotlib backend set to: "TkAgg"
Matplotlib interface loaded (pysces.plt.m)
Pitcon routines available
NLEQ2 routines available
SBML support available
You are using NumPy (1.20.3) with SciPy (1.7.1)
Assimulo CVode available
RateChar is available
Parallel scanner is available

PySCeS environment
******************
pysces.model_dir = /home/jr/Pysces/psc
pysces.output_dir = /home/jr/Pysces


***********************************************************************
* Welcome to PySCeS (1.0.0) - Python Simulator for Cellular Systems   *
*                http://pysces.sourceforge.net                        *
* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2021  *
* Triple-J Group for Molecular Cell Physiology                        *
* Stellenbosch University, ZA and VU University Amsterdam, NL         *
* PySCeS is distributed under the PySCeS (BSD style) licence, see     *
* LICENCE.txt (supplied with this release) for details                *
* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *
***********************************************************************

PySCeS is now ready to use. If you would like to test your installation try running the test suite:

pysces.test()

This also copies the test models supplied with PySCeS into your model directory.

Creating a PySCeS model object¶

This guide uses the test models supplied with PySCeS as examples; if you would like to use them and have not already done so, run the PySCeS tests (described in the previous section).

Before modelling, a PySCeS model object needs to be instantiated. As a convention we use mod as the instantiated model instance. The following code creates such an instance using the test input file, pysces_test_linear1.psc:

>>> mod = pysces.model('pysces_test_linear1')
Assuming extension is .psc
Using model directory: /home/jr/Pysces/psc
/home/jr/Pysces/psc/pysces_test_linear1.psc loading .....
Parsing file: /home/jr/Pysces/psc/pysces_test_linear1.psc

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

When instantiating a new model object, PySCeS input files are assumed to have a .psc extension. If the specified input file does not exist in the input file directory (e.g. misspelled filename), a list of existing input files is shown and the user is given an opportunity to enter the correct filename.

Advanced¶

The model constructor can also be used to specify a model directory other than the default model path:

>>> mod = pysces.model('pysces_test_linear1', dir='/my/own/directory/for/psc')

Alternatively, input files can also be loaded from a string:

>>> F = open('/home/jr/Pysces/psc/pysces_test_linear1.psc', 'r')
>>> pscS = F.read()
>>> F.close()
>>> mod = pysces.model('test_lin1s', loader='string', fString=pscS)
Assuming extension is .psc
Using model directory: /home/jr/Pysces/psc
Using file: test_lin1s.psc
/home/jr/Pysces/psc/orca/test_lin1s.psc loading .....
Parsing file: /home/jr/Pysces/psc/orca/test_lin1s.psc

Calculating L matrix . . . . . . .  done.
Calculating K matrix . . . . . . .  done.

Note that now the input file is saved and loaded as model_dir/orca/test_lin1s.psc.

Loading the model object¶

Once a new model object has been created it needs to be loaded. During the load process the input file is parsed, the model description is translated into Python data structures and a stoichiometric structural analysis is performed.

Note

In PySCeS 0.7.1+ model loading is now automatically performed when the model object is instantiated. This behaviour is controlled by the autoload argument (default = True). To keep backwards compatibility with older modelling scripts, whenever doLoad() is called a warning is generated.

To force re-loading of a model from the input file, use mod.reLoad().

Once loaded, all the model elements contained in the input file are made available as model (mod) attributes so that in the input file where you might find initialisations such as s1 = 1.0 and k1 = 10.0, these are now available as mod.s1 and mod.k1. For variable species and compartments an additional attribute is created, which contains the element’s initial (as opposed to current) value. These are constructed as <name>_init

>>> mod.s1
1.0
>>> mod.s1_init
1.0
>>> mod.k1
10.0

Any errors generated during the loading process (almost always) occur as a result of syntax errors in the input file. These error messages may not be intuitive; for example, 'list out of range' exception usually indicates a missing multiplication operator(3( instead of 3*() or unbalanced parentheses.

Basic model attributes¶

Some basic model properties are accessible once the model is loaded:

mod.ModelFile, the name of the model file that was used.
mod.ModelDir, the input file directory.
mod.ModelOutput, the PySCeS work/output directory.
Parameters are available as attributes directly as specified in the input file, e.g. k1 is mod.k1.
External (fixed) species are made available in the same way.
Internal (variable) species are treated in a similar way except that an additional attribute (parameter) is created to hold the species’ initial value (as specified in the input file), e.g., from s1, mod.s1 and mod.s1_init are instantiated as model object attributes.
Compartments are also are assigned an initial value.
Rate equations are translated into objects that return their current value when called, e.g. mod.R1().

All basic model attributes that are described here can be changed interactively. However, if the model rate equations need to be changed, this should be done in the input file after which the model should be re-instantiated and reloaded.

Groups of model properties (either tuples, lists or dictionaries)¶

mod.species the model’s variable species names (ordered relative to the stoichiometric matrix rows).
mod.reactions reaction names ordered to the stoichiometric matrices columns.
mod.parameters all parameters (including fixed species)
mod.fixed_species only the fixed species names
mod.__rate_rules__ a list of rate rules defined in the model

Advanced¶

The following attributes are used by PySCeS to store additional information about the basic model components; generally they are supplied by the parser and should almost never be changed directly.

mod.__events__ a list of event object references which can be interrogated for event information. For example, if you want a list of event names try [ev.name for ev in mod.__events__]
mod.__rules__ a dictionary containing information about all rules defined for this model
mod.__sDict__ a dictionary of species information
mod.__compartments__ a dictionary containing compartment information

Modelling¶

Structural Analysis¶

As part of the model loading procedure, doLoad() automatically performs a stoichiometric (structural) analysis of the model. The structural properties of the model are captured in the stoichiometric matrix (N), kernel matrix (K) and link matrix (L). These matrices can either be displayed with a mod.showX() method or used in further calculations as NumPy arrays. The formal definition of these matrices, as they are used in PySCeS, is described in 1.

The structural properties of a model are available in two forms, as new-style objects which have all the array properties neatly encapsulated, or as legacy attributes. Although both exist it is highly recommended to use the new objects.

Structural Analysis - new objects¶

For alternate descriptions of these model properties see the next (legacy) section.

mod.Nmatrix view with mod.showN()
mod.Nrmatrix view with mod.showNr()
mod.Lmatrix view with mod.showL()
mod.L0matrix
mod.Kmatrix view with mod.showK()
mod.K0matrix
mod.showConserved() displays any moiety conserved relationships (if present).
mod.showFluxRelationships() shows the relationships between dependent and independent fluxes at steady state.

All new structural objects have an array attribute which holds the actual NumPy array data, as well as ridx and cidx which hold the row and column indices (relative to the stoichiometric matrix) as well as the following methods:

.getLabels() return the matrix labels as tuple([rows], [columns])
.getColsByName() extract column(s) with label
.getRowsByName() extract row(s) with label
.getIndexes() return the matrix indices (relative to the Stoichiometric matrix) as tuple((rows), (columns))
.getColsByIdx() extract column(s) referenced by index
.getRowsByIdx() extract row(s) referenced by index

Structural Analysis - legacy¶

mod.nmatrix, N: displayed with mod.showN()
mod.kmatrix, K: displayed with mod.showK()
mod.lmatrix, L: displayed with mod.showL() (an identity matrix means that no conservation relationships exist, i.e. there is no linear dependence between species).
If there are linear dependencies in the differential equations then the reduced stoichiometric matrix of linearly independent, differential equations Nr is available as mod.nrmatrix and is displayed with mod.showNr(). If there is no dependence Nr = N.
In the case where there is linear dependence the moiety conservation sums can be displayed by using mod.showConserved(). The conservation totals are calculated from the initial values of the variable species as defined in the model file.
When the K and L matrices exist, their dependent parts (K0, L0) are available as mod.kzeromatrix and mod.lzeromatrix.
mod.showFluxRelationships() shows the relationships between dependent and independent fluxes at steady state.

If the mod.showX() methods are used, the row and column titles of the various matrices are displayed with the matrix. Additionally, all of the mod.showX() methods accept an open file object as an argument. If this file argument is present, the method’s results are output to a file and not printed to the screen. Alternatively, the order of each matrix dimension, relative to the stoichiometric matrix, is available as either a row or column array (e.g. mod.krow, mod.lrow, mod.kzerocol).

Time simulation¶

PySCeS has interfaces to two ODE solvers, either LSODA from ODEPACK (part of SciPy) or SUNDIALS CVODE (using Assimulo). If Assimulo is installed, PySCeS will automatically select CVODE if compartments, events or rate rules are detected during model load as LSODA is not able capable of event handling or changing compartment sizes. If, however, you would like to select the solver manually this is also possible:

>>> mod.mode_integrator = 'LSODA'
>>> mod.mode_integrator = 'CVODE'

There are three ways of running a simulation:

Defining the start, end time and number of points and using the mod.Simulate() method directly:

>>> mod.sim_start = 0.0
>>> mod.sim_end = 20
>>> mod.sim_points = 50
>>> mod.Simulate()

Using the mod.doSim() method where only the end time and points need to be specified. For example, running a 20-point simulation from time 0 to 10:
```
>>> mod.doSim(end=10.0, points=20)
```
Or using mod.doSimPlot() which runs the simulation and graphically displays the results. In addition to doSim()’s arguments the following arguments may be used:
```
>>> mod.doSimPlot(end=10.0, points=21, plot='species', fmt='lines', filename=None)
```

where:

plot can be one of 'species', 'rates' or 'all'.

fmt is the plot format, UPI backend dependent (default= '' ) or the CommonStyle 'lines' or 'points'.

filename if not None (default), then the plot is exported as filename.png

Another way of quickly visualising the results of a simulation is to use the mod.SimPlot() method.

>>> mod.SimPlot(plot='species', filename=None, title=None, log=None, format='lines')

where:

plot: output to plot (default= 'species' ) + 'all' rates and species + 'species' species + 'rates' reaction rates + ['S1', 'R1', ] a list of model attributes (species, rates)
filename (optional) if not None file is exported to filename (default=None)
title the plot title (default=None)
log use log axis for 'x', 'y', 'xy' (default=None)
fmt plot format, UPI backend dependent (default= '' ) or the CommonStyle 'lines' or 'points'.

Called without arguments, mod.SimPlot() plots all the species concentrations against time.

Simulation results¶

Starting with PySCeS versions 0.7.x the simulation results have been consolidated into a new mod.data_sim object. By default species concentrations/amounts, reaction rates and rate rules are automatically added to the data_sim object. If extra information (parameters, compartments, assignment rules) is required this can easily be added using mod.CVODE_extra_output, a list containing any model attribute which is not added by default.

The mod.data_sim object has many methods for extracting simulation data including:

data_sim.getTime() returns a vector of time points
data_sim.getSpecies() returns array([[time], [species]])
data_sim.getRates() returns array([[time], [rates]])
data_sim.getRules() returns array([[time], [rate rules]])
data_sim.getXData returns array([[time], [CVODE_extra_output]])
data_sim.getSimData(*args) return an array consisting of time plus any available data series:
```
>>> mod.data_sim.getSimdata('s1', 'R1', 'Rule1', 'xData2')
```
data_sim.getAllSimData() return an array of all simulation data
data_sim.getDataAtTime(time) return the results of the simulation at time.
data_sim.getDataInTimeInterval(time, bound) return the simulation data in the interval [time-bound, time+bound], if bound is not specified it is assumed to be the step size.

All the data_sim.get* methods by default only return a NumPy array containing the requested data, however if the argument lbls is set to True then both the array as well as a list of column labels is returned:

>>> data, Slabels = mod.data_sim.getSpecies(lbls=True)

This is very useful when using the PySCeS plotting interface (see Plotting) to plot simulation results.

For quick reference, simulation results are also available as a Numpy record array (mod.sim). This allows the user to directly reference a particular model attribute, e.g. mod.sim.Time, mod.sim.R1, or mod.sim.s1. Each of these calls returns a vector of values of the particular model attribute over the entire simulation (length of mod.sim_time).

Advanced¶

PySCeS sets integrator options that attempt to configure the integration algorithms to suit a particular model. However, almost every integrator option can be overridden by the user. Simulator settings are stored in the PySCeS mod.__settings__ dictionary. For LSODA some useful keys (default values indicated) are (mod.__settings__[*key*]):

'lsoda_atol': 1.0e-12
'lsoda_rtol': 1.0e-7
'lsoda_mxordn': 12
'lsoda_mxords': 5
'lsoda_mxstep': 0

where atol and rtol are the absolute and relative tolerances, while mxstep=0 means that LSODA chooses the number of steps (up to 500). If this is still not enough, PySCeS automatically increases the number of steps necessary to find a solution.

The following options can be set for CVODE, with their defaults indicated:

'cvode_abstol': 1.0e-15
'cvode_mxstep': 1000
'cvode_reltol': 1.0e-9
'cvode_stats': False
'cvode_return_event_timepoints': True

where atol, rtol and mxstep are as above. If CVODE cannot find a solution in the given number of steps it automatically increases cvode_mxstep and tries again, however, it also keeps track of the number of times that this adjustment is required and if a specific threshold is passed it will begin to increase cvode_reltol by 1.0e3 (to a maximal value of 1.0e-3). If cvode_stats is enabled CVODE will display a report of its internal parameters after the simulation is complete. Finally, CVODE will by default also output the time points when events are triggered, even if these were not originally specified in mod.sim_time. To disable this behaviour and strictly report only the times in mod.sim_time, set cvode_return_event_timepoints to False.

Steady-state analysis¶

PySCeS solves for a steady state using either the non-linear solvers HYBRD, NLEQ2 or forward integration. By default PySCeS has solver fallback enabled which means that if a solver fails or returns an invalid result (e.g., contains negative concentrations) it switches to the next available solver. The solver chain is as follows:

HYBRD (can handle ‘rough’ initial conditions, converges quickly).
NLEQ2 (highly optimised for extremely non-linear systems, more sensitive to bad conditioning and slightly slower convergence).
FINTSLV (finds a result when the change in max([species]) is less than 0.1%; slow convergence).

Solver fallback can be disabled by setting mod.mode_solver_fallback = 0. Each of the three solvers is highly configurable and although the default settings should work for most models, configurable options can be set by way of the mod.__settings__ dictionary.

To calculate a steady state use the mod.doState() method:

>>> mod.doState()
(hybrd) The solution converged.

The results of a steady-state evaluation are stored as arrays as well as individual attributes and can be easily displayed using the mod.showState() method:

mod.showState() displays the current steady-state values of both the species and fluxes.
For each reaction (e.g. R2) a new attribute mod.J_R2, which represents its steady-state value, is created.
Similarly, each species (e.g. mod.s2) has a steady-state attribute mod.s2_ss.
mod.state_species is an array of steady-state species values in mod.species order.
mod.state_flux is an array of steady-state fluxes in mod.reactions order.

There are various ways of initialising the steady-state solvers although, in general, the default values should be sufficient.

mod.mode_state_init initialises the solver using either the initial values specified in the input file (0), or a value close to zero (1). The default behaviour is to use the initial values.

The steady-state data object¶

Since PySCeS version 0.7 the mod.data_sstate object by default stores steady-state data (species, fluxes, rate rules) in a manner similar to mod.data_sim. One notable exception is that the current steady-state values are also made available as attributes to this object (e.g. species S1’s steady-state value is stored as mod.data_sstate.S1). Using the mod.STATE_extra_output list it is possible to store user-defined data in the data_sstate object. Steady-state data can be easily retrieved using the by now familiar .get* methods.

data_sstate.getSpecies() returns a species array
data_sstate.getFluxes() returns a flux array
data_sstate.getRules() returns a rate rule array
data_sstate.getXData() returns an array defined in STATE_extra_output
data_sstate.getStateData(*args) return user defined array of data ('S1','R2')
data_sstate.getAllStateData() return all steady-state data as an array

All these methods also accept the lbls=True argument in which case they return both array data and a label list:

>>> ssdat, sslbl = mod.data_sstate.getSpecies(lbls=True)

Stability analysis¶

PySCeS can analyse the stability of systems that can attain a steady state. It does this by calculating the eigenvalues of the Jacobian matrix for the reduced system of independent ODEs.

mod.doEigen() calculates a steady-state and performs the stability analysis
mod.showEigen prints out a stability report
mod.doEigenShow() combines both of the above

The eigenvalues are also available as attributes mod.lambda1 etc. By default the eigenvalues are stored as mod.eigen_values but if mod.__settings__['mode_eigen_output'] = 1 is set, in addition to the eigenvalues the left and right eigenvectors are stored as mod.eigen_vecleft and mod.eigen_vecright, respectively. Please note that there is currently no guarantee that the order of the eigenvalue array corresponds to the species order.

Metabolic Control Analysis¶

For ease of use the following methods are collected into a set of meta-routines that all first solve for a steady state and then perform the required Metabolic Control Analysis (MCA) 2, 3 evaluation methods.

Elasticities¶

The elasticities towards both the variable species and parameters can be calculated using mod.doElas() which generates as output:

Scaled elasticities referenced as mod.ecRate_Species, e.g. mod.ecR4_s2.
mod.showEvar() displays the non-zero elasticities calculated with respect to the variable species.
mod.showEpar() displays the non-zero parameter elasticities.

As a prototype we also store the elasticities in an object, mod.ec.*; this may become the default way of accessing elasticity data in future releases but has not been fully stabilised yet.

Control coefficients¶

Both control coefficients and elasticities can be calculated using a single method, mod.doMca().

mod.showCC() displays the complete set of flux and concentration control coefficients.
Individual concentration-control coefficients are referenced as mod.ccSpecies_Rate, e.g. mod.ccs1_R4.
Similarly, mod.ccJFlux_Rate is a flux-control coefficient, e.g. mod.ccJR1_R4.

As it is generally common practice to use scaled elasticities and control coefficients, PySCeS calculated these by default. However, it is possible to calculate unscaled elasticities and control coefficients by setting the attribute mod.__settings__['mode_mca_scaled'] = 0, in which case the model attributes are attached as mod.uec and mod.ucc respectively.

As a prototype we also store the control coefficients in an object, mod.cc.*; this may become the default way of accessing control coefficient data in future releases but has not been fully stabilised yet.

Response coefficients¶

PySCeS can calculate the parameter response coefficients for a model with the mod.doMcaRC() method. Unlike the elasticities and control coefficients, the response coefficients are made available as a single attribute mod.rc. This attribute is a data object, containing the response coefficients as attributes and has the following methods:

rc.var_par individual response coefficients can be accessed as attributes made up of variable_parameter e.g. mod.rc.R1_k1
rc.get('var', 'par') return a response coefficient
rc.list() returns all response coefficients as a dictionary of {key: value} pairs
rc.select('attr', search='a') select all response coefficients that refer to 'attr' e.g. select('R1') or select('k2')
rc.matrix: the matrix of response coefficients
rc.row: row labels
rc.col: column labels

Response coefficients with respect to moiety-conserved sums¶

The mod.doMcaRC() method only calculates response coefficients with respect to explicit model parameters. However, in models with moiety-conservation the total concentration of all the species that form part of a particular moiety-conserved cycle is also a parameter of the model. PySCeS infers such moiety-conserved sums from the initial species concentrations specified by the user. In some cases it might be interesting to consider the effects that a change in the total concentration of a moiety will have on the steady-state. This analysis may be done with the method mod.doMcaRCT().

Since moiety-conserved sums are not explicitly named in PySCeS model files, 'T_' is prepended to all the species names listed in mod.Consmatrix.row. For instance, if the dependent species in a moiety-conserved cycle is 'A', then 'T_A' designates the moiety-conserved sum.

The object mod.rc is augmented with the results of mod.doMcaRCT(). Response coefficients may thus be accessed with mod.rc.get('var', 'T_par').

Parameter scanning¶

Single dimension parameter scans¶

PySCeS has the ability to quickly generate and plot single dimension parameter scans. Scanning a parameter typically involves changing a parameter through a range of values and recalculating the steady state at each step. Two methods are provided which simplify this task, mod.Scan1() is provided to generate the scan data while mod.Scan1Plot() is used to visualise the results. The first step is to define the scan parameters:

mod.scan_in is a string defining the parameter to be scanned e.g. 'k0'
mod.scan_out is a list of strings representing the attribute names to be tracked in the output, e.g. ['J_R1','J_R2','s1_ss','s2_ss']
You also need to define the range of points that you would like to scan over. For a linear range NumPy has a useful function numpy.linspace(start, end, points) (NumPy can be accessed by importing it in your Python shell via import numpy). If you need to generate a log range use numpy.logspace(start, end, points).

Both numpy.linspace and numpy.logspace use the number of points (including the start and end points) in the interval as an input. Additionally, the start and end values of numpy.logspace must be entered as indices, e.g. to start the range at 0.1 and end it at 100 you would write numpy.logspace(-1, 2, steps). Setting up a PySCeS scan session might look something like:
```
>>> import numpy
>>> mod.scan_in = 'x0'
>>> mod.scan_out = ['J_R1','J_R6','s2_ss','s7_ss']
>>> scan_range = numpy.linspace(0,100,11)
```

Before starting the parameter scan, it is important to check that all the model attributes involved in the scan do actually exist. For example, mod.J_R1 is created when mod.doState() is executed, likewise all the elasticities (mod.ecR_S) and control coefficients (mod.ccJ_R) are only created when the mod.doMca() method is called. If all the attributes exist you can perform a parameter scan using the mod.Scan1(scan_range) method which takes your predefined scan range as an argument:

>>> mod.Scan1(scan_range)

Scanning ...
11 (hybrd) The solution converged.
(hybrd) The solution converged ...

done.

When the scan has been successfully completed, the results are stored in the array (mod.scan_res) that has mod.scan_in as its first column followed by columns that represent the data defined in mod.scan_out (if invalid steady states are generated during the scan they are replaced by NaN). Scan1 also reports the scan parameter values which generated the invalid states. If one or more of the specified input or output parameters are not valid model attributes, they will be ignored. Once the parameter scan data has been generated, the next step is to visualise it using the mod.Scan1Plot() method:

>>> mod.Scan1Plot(plot=[], title=None, log=None, format='lines', filename=None)

plot if empty, mod.scan_out is used, otherwise any subset of mod.scan_out (default= [])
filename the filename of the PNG file to save (default= None, no export)
title the plot title (default= None)
log if None a linear axis is assumed, otherwise one of ['x', 'y', 'xy'] (default= None)
format the backend dependent line format (default= 'lines') or the CommonStyle 'lines' or 'points'.

Called without any arguments, Scan1Plot() plots all of mod.scan_out against mod.scan_in.

In a similar way that simulation results are captured in the mod.sim array, 1D-scan results are also available as a Numpy record array (mod.scan) for quick reference and easy access by the user. All the model attributes defined in mod.scan_in and mod.scan_out can be accessed in this way, e.g. mod.scan.x0, mod.scan.J_R1, mod.scan.s2_ss, etc.

Two-dimensional parameter scans¶

Two-dimensional parameter scans can also easily be generated using the mod.Scan2D method:

>>> mod.Scan2D(p1, p2, output, log=False)

p1 is a list of [model parameter 1, start value, end value, points]
p2 is a list of [model parameter 2, start value, end value, points]
output the steady-state variable e.g. 'J_R1' or 'A_ss'
log if True scan using log ranges for both axes

To plot the results of two dimensional scan use the mod.Scan2DPlot method. Note: the GnuPlot interface must be active for this to work (see the section on Plotting later on in this guide).

>>> mod.Scan2DPlot(title=None, log=None, format='lines', filename=None)

filename the filename of the PNG file (default= None, no export)
title the plot title (default= None)
log if None a linear axis is assumed, otherwise one of ['x', 'xy', 'xyz'] (default= None)
format the backend dependent line format (default= 'lines') or the CommonStyle 'lines' or 'points'.

Multi-dimensional parameter scans¶

This PySCeS feature allows multi-dimensional parameter scanning. Any combination of parameters is possible and can be added as leader parameters that change independently or follower parameters whose change is coordinated with the previously defined parameter. Unlike mod.Scan1() this function is accessed via the pysces.Scanner class that is separately instantiated with a loaded PySCeS model object:

>>> sc1 = pysces.Scanner(mod)
>>> sc1.addScanParameter('x3', 1, 10, 11)
>>> sc1.addScanParameter('k2', 0.1, 1000, 5, log=True)
>>> sc1.addScanParameter('k4', 0.1, 1000, 5, log=True, follower=True)
>>> sc1.addUserOutput('J_R1', 's1_ss')
>>> sc1.Run()

... scan: 55 states analysed

>>> sc1_res = sc1.getResultMatrix()
>>> print sc1_res[0]
array([1., 0.1, 0.1, 97.94286647, 49.1380999])

>>> print sc1_res[-1]
array([1.0e+01, 1.0e+03, 1.0e+03, -3.32564878e+00, 3.84227702e-03])

In this scan we define two independent (x3, k2) and one dependent (k3) scan parameters and track the changes in the steady-state variables J_R1 and s1_ss. Note that k2 and k4 use a logarithmic scale. Once run the input parameters cannot be altered, however, the output can be changed and the scan rerun.

sc1.addScanParameter(name, start, end, points, log, follower) where name is the input parameter (as a string), start and end define the range with the required number of points, While log and follower are boolean arguments indicating the point distribution and whether the axis is independent or not.
sc1.addUserOutput(*args) an arbitrary number of model attributes to be output can be added (this method automatically tries to determine the level of analysis necessary), e.g. addUserOutput('J_R1', 'ecR1_k2')
sc1.Run() run the scan, if subsequent runs are required after changing output attributes, use sc1.RunAgain(). Note that it is not possible to change the input parameters once a scan has been run, if this is required a new Scanner object should be created.
sc1.getResultMatrix(stst=False) return the scan results as an array containing both input and output. If stst = True append the steady-state fluxes and concentrations to the user output so that output has dimensions [scan_parameters]+[state_species+state_flux]+[Useroutput], otherwise return the default [scan_parameters]+[Useroutput].
sc1.UserOutputList the list of output names
sc1.UserOutputResults an array containing only the output
sc1.ScanSpace the generated list of input parameters.

Parallel parameter scans¶

When performing large multi-dimensional parameter scans, PySCeS has the option to perform the computation in parallel, either on a single machine with a multi-core CPU, or on a multi-node cluster. This requires a working ipyparallel installation (see also Installation). The functionality is accessed via the pysces.ParScanner class, which has the same methods as the pysces.Scanner class (see above) with a few multiprocessing-specific additions.

The parallel scanner class is instantiated with a loaded PySCeS model object:

>>> sc1 = pysces.ParScanner(mod, engine='multiproc')

The additional engine argument specifies the parallel computation engine to use:

'multiproc' - use Python’s internal multiprocessing module (default)
'ipcluster' - use ipcluster (refer to ipyparallel documentation)

There are two ways to run the scan:

sc1.Run() - runs the scan with a load-balancing task client; tasks are queued and sent to nodes as these become available.
sc1.RunScatter() - compute tasks are evenly distributed amongst compute nodes (“scattered”) and the results are returned (“gathered”) once all the computations are complete. No load balancing is performed. May be slightly faster than sc1.Run() if the individual tasks are very similar. Not available with multiproc !

Further input and output processing is as for pysces.Scanner. A few example scripts illustrating the parallel scanning procedure are provided in the pysces/examples folder of the installation.

Plotting¶

The PySCeS plotting interface has written to facilitate the use of multiple plotting back-ends via a Unified Plotting Interface (UPI). Using the UPI we ensure that a specified subset of plotting methods is back-end independent (although the UPI can be extended with back-end specific methods). So far Matplotlib (default) and GnuPlot back-ends have been implemented.

The common UPI functionality is accessible as pysces.plt.* while back-end specific functionality is available as pysces.plt.m (Matplotlib) and pysces.plt.g (GnuPlot).

While the Matplotlib is activated by default, GnuPlot needs to be enabled (see Configuration section) and then activated using pysces.plt.p_activateInterface('gnuplot'). All installed interfaces can be activated or deactivated as required:

>>> pysces.plt.p_activateInterface(interface)
>>> pysces.plt.p_deactivateInterface(interface)

where interface is either 'matplotlib' or 'gnuplot'. The PySCeS UPI defines currently has the following methods:

plot(data, x, y, title='', format='') plot a single line data[y] vs data[x]

data the 2D-data array

x x column index

y y column index

title is the line legend text (key)

format is the backend format string (default=’’)

plotLines(data, x, y=[], titles=[], formats=['']) plot multiple lines, i.e. data[y1, y2, ] vs data[x]

data the data array

x x column index

y is a list of line indexes, if empty all of y not including x is plotted

titles a list of line keys, if empty Line1, Line2, etc. is used

formats a list (per line) of format strings, if formats only contains a single item, this format is used for all lines.

splot(data, x, y, z, title='', format='') plot a surface, i.e. data[z] vs data[y] vs data[x]

data the data array

x x column index

y y column index

z z column index

title the surface key (legend text)

format a format string (default=’’)

splotSurfaces(data, x, y, z=[], titles=[], formats=['']) plot multiple surfaces, i.e. data[z1, z2, ] vs data[y] vs data[x]

data the data array

x x column index

y y column index

z a list of z column indexes, if empty all data not including x, y are plotted

titles a list of surface keys, if empty Surf1, Surf2, etc. is used

formats is a list (per line) of format strings (default=’’). If formats only contains a single item, this format is used for all surfaces.

replot() replot the current figure using all active interfaces (useful with GnuPlot type interfaces)

save(name, directory=None, dfmt='\%.8e') save the plot data and (if possible) the back-end specific format file

filename the filename

directory optional (default = current working directory)

dfmt the data format string (default= '\%.8e')

export(name, directory=None, type='png') export the current plot as a <type> file (currently only PNG is guaranteed to be available on all back-ends).

filename the filename

directory optional (default = current working directory)

type the file format (default= 'png').

setGraphTitle(title='PySCeS Plot') set the graph title, unset if title=None

title (string, default=’PySCeS Plot’) the graph title

setAxisLabel(axis, label='') sets one or more axis labels

axis x, y, z, xy, xz, yz, zyx

label label string (default= None). When alled with only the axis argument, clears the label of that axis.

setKey(value=False) enable or disable the current plot key, no arguments removes key.

value boolean (default= False)

setLogScale(axis) set axis to log scale

axis is one of x, y, z, xy, xz, yz, zyx

setNoLogScale(axis) set axis to a linear scale

axis is one of x, y, z, xy, xz, yz, zyx

setRange(axis, min=None, max=None) set one or more axis ranges

axis is one of x, y, z, xy, xz, yz, zyx

min is the range(s) lower bound (default=None, back-end auto-scales)

max is the range(s) upper bound (default=None, back-end auto-scales)

setGrid(value) enable or disable the graph grid

value (boolean) True (on) or False (off)

plt.closeAll() Close all active Matplolib figures.

Displaying data¶

Displaying/saving model attributes¶

All of the showX() methods, with the exception of mod.showModel() operate in exactly the same way. If called without an argument, they display the relevant information to the screen. Alternatively, if given an open, writable (ASCII mode) file object as an argument, they write the requested information to the open file. This allows the generation of customised reports containing only information relevant to the model.

mod.showSpecies() prints the current values of the model species (mod.M).
mod.showSpeciesI() prints the initial values of the model species (mod.Mi), as parsed from the input file.
mod.showPar() prints the current values of the model parameters.
mod.showState() prints the current steady-state fluxes and species.
mod.showConserved() prints any moiety conserved relationships (if present).
mod.showFluxRelationships() shows the relationships between dependent and independent fluxes at steady state.
mod.showRateEq() prints the reaction stoichiometry and rate equations.
mod.showODE() prints the ordinary differential equations.

Note

The mod.showModel() method is not recommended for saving models as a PySCeS input file, use the Core2 based pysces.interface.writeMod2PSC method instead:

>>> pysces.interface.writeMod2PSC(mod, filename, directory, iValues=True, getstrbuf=False)

filename: writes <filename>.psc or <model_name>.psc if None
directory: (optional) an output directory
iValues: if True (default) then the model initial values are used (or the current values if False)
getstrbuf: if True a StringIO buffer is returned instead of writing to disk

For example, assuming you have loaded a model and run mod.doState() the following code opens a Python file object (rFile), writes the steady-state results to the file associated with the file object (results.txt) and then closes it again:

>>> rFile = open('results.txt','w')
>>> mod.showState()      # print the results to screen
>>> mod.showState(rFile) # write the results to the file results.txt
>>> rFile.close()

Writing formatted arrays¶

The showX() methods described in the previous sections allow the user a convenient way to write the predefined matrices either to screen or file. However, for maximum flexibility, PySCeS includes a suite of array writers that enable one to easily write, in a variety of formats, any array to a file. Unlike the showX() methods, the Write_array methods are specifically designed to write to data to a file.

In most modelling situations it is rare that an array needs to be stored or displayed that does not have specific labels for its rows or columns. Therefore, all the Write_array methods take list arguments that can contain either the row or column labels. Obviously, these lists should be equal in length to the matrix dimension they describe and in the correct order.

There are currently three custom array writing methods that work either with a 1D (vector) or 2D (matrix) array. To allow an easy comparison of the output of these methods, all the following sections use the same example array as input.

`Write_array()`¶

The basic array writer is the Write_array() method. Using the default settings this method writes a ‘tab delimited’ array to a file. It is trivial to change this to a ‘comma delimited’ format by using the separator = ',' argument. Numbers in the array are formatted using the global number format.

If column headings are supplied using the Col = [] argument they are written above the relevant column and if necessary truncated to fit the column width. If a column name is truncated it is marked with a * and the full length name is written as a comment after the array data. Similarly row data can be supplied using the Row = [] argument in which case the row names are displayed as a comment which is written after the array data.

Finally, if the close_file argument is enabled the supplied file object is automatically closed after writing the array. The full call to the method is:

>>> mod.Write_array(input, File=None, Row=None, Col=None, separator=' ')

which generates the array

## Write_array_linear1_11:12:23
#s0           s1           s2
-3.0043e-001  0.0000e+000  0.0000e+000
 1.5022e+000 -5.0217e-001  0.0000e+000
 0.0000e+000  1.5065e+000 -5.0650e-001
 0.0000e+000  0.0000e+000  1.0130e+000
# Row: R1 R2 R3 R4

By default, each time an array is written, PySCeS includes an array header consisting of the model name and the time the array was written. This behaviour can be disabled by setting: mod.write_array_header = 0

`Write_array_latex()`¶

The Write_array_latex() method functions similarly to the generic Write_array() method except that it generates a formatted array that can be included directly in a LaTeX document. Additionally, there is no separator argument, column headings are not truncated and row labels appear to the left of the matrix.

>>> mod.Write_array_latex(input, File=None, Row=None, Col=None)

which generates

%% Write_array_latex_linear1_11:45:03
\[
\begin{array}{r|rrr}
  & $\small{s0}$ & $\small{s1}$ & $\small{s2}$ \\ \hline
 $\small{R1}$ &-0.3004 & 0.0000 & 0.0000 \\
 $\small{R2}$ & 1.5022 &-0.5022 & 0.0000 \\
 $\small{R3}$ & 0.0000 & 1.5065 &-0.5065 \\
 $\small{R4}$ & 0.0000 & 0.0000 & 1.0130 \\
\end{array}
\]

and in a typeset document appears as:

s0

s1

s2

R1

-0.3004

0.0000

0.0000

R2

1.5022

-0.5022

0.0000

R3

0.0000

1.5065

-0.5065

R4

0.0000

0.0000

1.0130

Installing and configuring¶

PySCeS is developed primarily in Python and has been designed to operate on multiple operating systems, i.e. Linux, Microsoft Windows and macOS. PySCeS makes use of NumPy and SciPy for a number of functions and needs a working SciPy stack (https://www.scipy.org) to install and run.

General requirements¶

Python 3.6+
Numpy 1.14+
SciPy 1.0+
Matplotlib (with TkAgg backend)
GnuPlot (optional, alternative plotting back-end)
IPython or the Jupyter notebook (optional, highly recommended for interactive modelling sessions)
libSBML (optional). Python bindings for SBML support can be installed via
```
$ pip install python-libsbml
```

This software stack provides a powerful scientific programming platform which is used by PySCeS to provide a flexible Systems Biology Modelling environment.

PySCeS itself has been modularised into a main package and a (growing) number of support modules which extend its core functionality. It is highly recommended that the following packages/modules are also installed:

Assimulo to enable CVODE support. This can be installed on Anaconda via the conda-forge channel, or compiled from source (https://jmodelica.org/assimulo).
ipyparallel for parallel parameter scans (see https://ipyparallel.readthedocs.io/)
pysces_metatool (available via https://github.com/PySCeS/pysces-metatool) to add elementary mode analysis support to PySCeS.

By default PySCeS installs with a version of ZIB’s NLEQ2 non-linear solver. This software is distributed under its own non-commercial licence. Please see https://github.com/PySCeS/pysces for details.

Installation¶

Binary install packages for all three OSs and Python versions 3.6-3.9 are provided. Anaconda users can conveniently install PySCeS with:

$ conda install -c conda-forge -c pysces pysces

Any dependencies will be installed automatically, including the optional dependencies Assimulo, ipyparallel and libSBML.

Alternatively, you can use pip to install PySCeS from PyPI. Core dependencies will be installed automatically.

$ pip install pysces

To install the optional dependences:

pip install "pysces[parscan]" - for ipyparallel
pip install "pysces[sbml]" - for libSBML
pip install "pysces[cvode]" - for Assimulo
pip install "pysces[all]" - for all of the above

Note

Installation of Assimulo via pip may well require C and Fortran compilers to be properly set up on your system, as binary packages are only provided for a very limited number of Python versions and operating systems on PyPI. This is not guaranteed to work! If you require Assimulo, the conda install is by far the easier option as up-to-date binaries are supplied for all OS and recent Python versions.

Compilation from source¶

As an alternative to a binary installation, you can also build your own PySCeS installation from source. This requires Fortran and C compilers.

Windows build¶

The fastest way to build your own copy of PySCeS is to use Anaconda Python.

Download and install Anaconda for Python 3

Obtain Git for Windows

Create a PySCeS environment using conda and activate it:
> conda create -n pyscesdev -c conda-forge python=3.8 numpy scipy \
        matplotlib sympy packaging pip wheel nose ipython \
        python-libsbml fortran-compiler assimulo
> conda activate pyscesdev
Clone and enter the PySCeS code repository using git
(pyscesdev)> git clone https://github.com/PySCeS/pysces.git pysces-src
(pyscesdev)> cd pysces-src
Now you can build and install PySCeS into the pyscesdev environment
(pyscesdev)> python setup.py build
(pyscesdev)> python setup.py install

Linux build¶

All modern Linux distributions ship with gcc and gfortran. In addition, the Python development headers (python-dev or python-devel, depending on your distro) need to be installed.

Clone the source from Github as described above, change into the source directory and run:

$ python setup.py install

macOS build¶

The Anaconda build method, described above for Windows, should also work on macOS.

Alternatively, Python 3 may be obtained via Homebrew and the compilers may be installed via Xcode.

Clone the source from Github as described above, change into the source directory and run:

$ python setup.py install

Configuration¶

PySCeS has two configuration (*.ini) files that allow one to specify global (per installation) and local (per user) options. Currently the multiuser options are only fully realised on Linux based systems. Global options are stored in the pyscfg.ini file which is created in your PySCeS installation directory upon install. The example below is a Windows version; the exact values of install_dir and gnuplot_dir (if available) will depend on your individual OS and Python setup and are determined on install.

[Pysces]
install_dir = c:\Python38\Lib\site-packages\pysces
gnuplot_dir = c:\model\gnuplot\binaries
model_dir = os.path.join(os.path.expanduser('~'),'Pysces','psc')
output_dir = os.path.join(os.path.expanduser('~'),'Pysces')
silentstart = False
change_dir_on_start = False

The [Pysces] section contains information on the installation directory, the directory where the GnuPlot executable(s) can be found and the default model file and output directories.

This section also contains two further key-value pairs. If silentstart (default False) is set to True, informational messages about the PySCeS installation are not printed to the console on startup. The key change_dir_on_start specifies if the working directory should be changed to the PySCeS output directory (typically $HOME/Pysces or %USERPROFILE%\Pysces) on startup. When set to False (the default), the working directory is not changed.

As we shall see some of these defaults can be overridden by the local configuration options.

[ExternalModules]
nleq2 = True

[PyscesModules]
pitcon = True

These sections define whether third-party algorithms (NLEQ2 and PITCON) are available for use, while the last section allows the alternate plotting backends to be enabled or disabled:

[PyscesConfig]
gnuplot = True
matplotlib = True

The user configuration file (pys_usercfg.ini) is created when PySCeS is imported/run for the first time. On Windows this is in %USERPROFILE%\Pysces while on Linux and macOS this is in $HOME/Pysces. Once created, the user configuration files can be edited and will be used for every subsequent PySCeS session.

[Pysces]
output_dir = C:\mypysces
model_dir = C:\mypysces\pscmodels
gnuplot = False

For example, the above user configuration on a Windows system customises the default model and output directories and disables GnuPlot (enabled globally above). If required, gnuplot_dir can also be set to point to an alternate location on a per-user basis. The configuration keys silentstart and change_dir_on_start can also be overridden here on a per-user basis.

Once you have PySCeS configured to your personal requirements you are ready to begin modelling.

References¶

Footnotes

1: Hofmeyr, J.-H.S. (2001) Metabolic control analysis in a nutshell, in T.-M. Yi, M. Hucka, M. Morohashi, and H. Kitano, eds, Proceedings of the 2nd International Conference on Systems Biology, pp. 291-300.
2: Kacser, H. and Burns, J. A. (1973), The control of flux, Symp. Soc. Exp. Biol. 32, 65-104.
3: Heinrich and Rappoport (1974), A linear steady-state treatment of enzymatic chains: General properties, control and effector strength, Eur. J. Biochem. 42, 89-95.

Input file guide¶

The PySCeS Model Description Language¶

PySCeS: the Python Simulator for Cellular Systems is an extendable toolkit for the analysis and investigation of cellular systems. It is available for download from: http://pysces.github.io. This section deals with the PySCeS Model Description Language (MDL), a human-readable format for defining kinetic models.

PySCeS uses an ASCII text based input file to describe a cellular system in terms of its stoichiometry, kinetics, compartments and parameters. Input files may have any filename with the single restriction that, for cross platform compatibility, they must end with the extension .psc. Since version 0.7, the PySCeS MDL has been updated and extended to be compatible with models defined in the SBML standard.

We hope that you will enjoy using our software. If, however, you find any unexpected features (i.e. bugs) or have any suggestions on how we can improve PySCeS please let us know by opening an issue on Github.

Defining a PySCeS model¶

A kinetic model¶

The basic description of a kinetic model in the PySCeS MDL contains the following information:

whether any fixed (boundary) species are present
the reaction network stoichiometry
rate equations for each reaction step
parameter and boundary species initial values
the initial values of the variable species

Although it is in principle possible to define an ODE based model without reactions or free species, for practical purposes PySCeS requires a minimum of a single reaction. Once this information is obtained it can be organised and written as a PySCeS input file. While this list is the minimum information required for a PySCeS input file, the MDL allows the definition of advanced models that contain compartments, global units, functions, rate and assignment rules.

Model keywords¶

Since PySCeS 0.7 it is now possible to define keywords that specify model information. Keywords have the general form

<keyword>: <value>

The Modelname (optional) keyword, containing only alphanumeric characters (or _), describes the model filename (typically used when the model is exported via the PySCeS interface module) while the Description keyword is a (short) single line model description.

Modelname: rohwer_sucrose1
Description: Sucrose metabolism in sugar cane (Johann M. Rohwer)

Two keywords (optional) are available for use with models that have one or more compartments defined. Both take a boolean (True/False) as their value:

Species_In_Conc specifies whether the species symbols used in the rate equations represent a concentration (True, default) or an amount (False).

Output_In_Conc tells PySCeS to output the results of numerical operations on species in concentrations (True, default) or in amounts (False).

Species_In_Conc: True
Output_In_Conc: False

Global unit definition¶

PySCeS 0.7+ supports the (optional) definition of a set of global units. In doing so we have chosen to follow the general approach used in the Systems Biology Modelling Language (SBML L2V3) specification. The general definition of a PySCeS unit is: `<UnitType>: <kind>, <multiplier>, <scale>, <exponent>` where kind is a string describing the base unit (for SBML compatibility this should be an SI unit) e.g. mole, litre, second or metre. The base unit is modified by the multiplier, scale and index using the following relationship: <multiplier> * (<kind> * 10**<scale>)**<index>. The default unit definitions are:

UnitSubstance: mole, 1, 0, 1
UnitVolume: litre, 1, 0, 1
UnitTime: second, 1, 0, 1
UnitLength: metre, 1, 0, 1
UnitArea: metre, 1, 0, 2

Please note that defining these values does not affect the numerical analysis of the model in any way.

Symbol names and comments¶

Symbol names (i.e. reaction, species, compartment, function, rule and parameter names etc.) must start with either an underscore or letter and be followed by any combination of alpha-numeric characters or an underscore. Like all other elements of the input file names are case sensitive:

R1
_subA
par1b
ext_1

Explicit access to the “current” time in a time simulation is provided by the special symbol _TIME_. This is useful in the definition of events and rules (see section on Advanced model construction for more details).

Comments can be placed anywhere in the input file in one of two ways, as single line comment starting with a # or as a Python-styled multi-line triple quoted “””<comment>”””:

# everything after this is ignored

"""
This is a comment
spread over a
few lines.
"""

Compartment definition¶

By default (as is the case in all PySCeS versions < 0.7) PySCeS assumes that the model exists in a single unit volume compartment. In this case it is not necessary to define a compartment and the ODEs therefore describe changes in concentration per time. However, if a compartment is defined, PySCeS assumes that the ODEs describe changes in substance amount per time. Doing this affects how the model is defined in the input file (especially with respect to the definitions of rate equations and species) and the user is strongly advised to read the Users Guide before building models in this way. The general compartment definition is Compartment: <name>, <size>, <dimensions>, where <name> is the unique compartment id, <size> is the size of the compartment (i.e. length, volume or area) defined by the number of <dimensions> (e.g. 1,2,3):

Compartment: Cell, 2.0, 3
Compartment: Memb, 1.0, 2

Function definitions¶

A relatively recent addition to the PySCeS MDL is the ability to define SBML-styled functions. Simply put these are code substitutions that can be used in rate equation definitions to, for example, simplify the kinetic law. The general syntax for a function is Function: <name>, <arglist> {<formula>} where <name> is the unique function id, <arglist> is one or more comma separated function arguments. The <formula> field, enclosed in curly braces, may only make use of arguments listed in the <arglist> and therefore cannot reference model attributes directly. If this functionality is required a forcing function/assignment rule (see Assignment rules) may be what you are looking for.

Function: rmm_num, Vf, s, p, Keq {
Vf*(s - p/Keq)
}

Function: rmm_den, s, p, Ks, Kp {
s + Ks*(1.0 + p/Kp)
}

The syntax for function definitions has been adapted from Antimony.

Defining fixed species¶

Boundary species, also known as fixed or external species, are a special class of parameter used when modelling biological systems. The PySCeS MDL fixed species are declared on a single line as FIX: <fixedlist>. The <fixedlist> is a space-separated list of symbol names which should be initialised like any other species or parameter:

FIX: Fru_ex Glc_ex ATP ADP UDP phos glycolysis Suc_vac

If no fixed species are present in the model then this declaration should be omitted entirely.

Reaction stoichiometry and rate equations¶

The reaction stoichiometry and rate equation are defined together as a single reaction step. Each step in the system is defined as having a name (identifier), a stoichiometry (substrates are converted to products) and rate equation (the catalytic activity, described as a function of species and parameters). All reaction definitions should be separated by an empty line. The general format of a reaction in a model with no compartments is:

<name>:
    <stoichiometry>
    <rate equation>

The <name> argument follows the syntax as discussed in Symbol names and comments above; however, when more than one compartment has been defined it is important to locate the reaction in its specific compartment. This is done using the @ operator:

<name>@<compartment>:
    <stoichiometry>
    <rate equation>

where <compartment> is a valid compartment name. In either case this then followed (either directly or on the next line) by the reaction stoichiometry.

Each <stoichiometry> argument is defined in terms of reaction substrates, appearing on the left hand side, and products on the right hand side of an identifier which labels the reaction as either reversible (=) or irreversible (>). If required each reagent’s stoichiometric coefficient (PySCeS accepts both integer and floating point) should be included in curly braces {} immediately preceding the reagent name. If these are omitted a coefficient of one is assumed.

{2.0}Hex_P = Suc6P + UDP  # reversible reaction
Fru_ex > Fru              # irreversible reaction
species_5 > $pool         # a reaction to a sink

The PySCeS MDL also allows the use of the $pool token that represents a placeholder reagent for reactions that have no net substrate or product. The reversibility of a reaction is only used when exporting the model to other formats (such as SBML) and in the calculation of elementary modes. It does not affect the numerical evaluation of the rate equations in any way.

Central to any reaction definition is the <rate equation> (SBML kinetic law). This should be written as valid Python expression and may fall across more than one line. Standard Python operators + - * / ** are supported (note the Python power e.g. 2^4 is written as 2**4). There is no shorthand for multiplication with a bracket so -2(a+b)^h would be written as -2*(a+b)**h} and normal operator precedence applies:

+, -

addition, subtraction

*, /

multiplication, division

+x,-x

positive, negative

**

exponentiation

Operator precedence increases from top to bottom and left to right (adapted from the Python Reference Manual).

The PySCeS MDL parser has been developed to parse and translate different styles of infix into Python/Numpy-based expressions. The following functions are supported in any mathematical expression:

log, log10, ln, abs (note, log is defined as natural logarithm, equivalent to ln)

pow, exp, root, sqrt

sin, cos, tan, sinh, cosh, tanh

arccos, arccosh, arcsin, arcsinh, arctan, arctanh

floor, ceil, ceiling, piecewise

notanumber, pi, infinity, exponentiale

Logical operators are supported in rules, events, etc., but not in rate equation definitions. The PySCeS parser understands Python infix as well as libSBML and NumPy prefix notation.

and or xor not

> gt(x,y) greater(x,y)

< lt(x,y) less(x,y)

>= ge(x,y) geq(x,y) greater_equal(x,y)

<= le(x,y) leq(x,y) less_equal(x,y)

== eq(x,y) equal(x,y)

!= neq(x,y) not_equal(x,y)

Note that currently the MathML delay and factorial functions are not supported. Delay is handled by simply removing it from any expression, e.g. delay(f(x), delay) would be parsed as f(x). Support for piecewise has been recently added to PySCeS and will be discussed in the advanced features section (see Piecewise).

A reaction definition when no compartments are defined:

R5: Fru + ATP = Hex_P + ADP
    Vmax5/(1 + Fru/Ki5_Fru)*(Fru/Km5_Fru)*(ATP/Km5_ATP) /
    (1 + Fru/Km5_Fru + ATP/Km5_ATP + Fru*ATP/(Km5_Fru*Km5_ATP) + ADP/Ki5_ADP)

and using the previously defined functions:

R6:
    A = B
    rmm_num(V2,A,B,Keq2)/rmm_den(A,B,K2A,K2B)

When compartments are defined, note how now the reaction is now given a location. This is because the ODEs formed from these reactions must be in changes in substance (amount) per time, thus the rate equation is multiplied by its compartment size. In this particular example the species symbols represent concentrations (Species_In_Conc: True):

R1@Cell:
    s1 = s2
    Cell*(Vf1*(s1 - s2/Keq1)/(s1 + KS1*(1 + s2/KP1)))

If Species_In_Conc: True the location of the species is defined when it is initialised.

The following example shows the species symbols explicitly defined as amounts (Species_In_Conc: False):

R4@Memb: s3 = s4
    Memb*(Vf4*((s3/Memb) - (s4/Cell)/Keq4)/((s3/Memb)
    + KS4*(1 + (s4/Cell)/KP4)))

Please note that at this time we are not certain if this form of rate equation is translatable into valid SBML in a way that is interoperable with other software.

Species and parameter initialisation¶

The general form of any species (fixed, free) and parameter is simply:

property = value

Initialisations can be written in any order anywhere in the input file but for enhanced human readability these are usually placed after the reaction that uses them or grouped at the end of the input file. Both decimal and scientific notation are allowed with the following provisions that neither floating point (1.) nor scientific shorthand (1.e-3) syntax should be used, instead use the full form (1.0e-3, 0.001 or 1.0).

Variable or free species are initialised differently depending on whether compartments are present in the model. Although the variable species concentrations are determined by the parameters of the system, their initial values are used in various places, calculating total moiety concentrations (if present), time simulation initial values (e.g. time=zero) and as initial guesses for the steady-state algorithms. If an empty initial species pool is required it is not recommended to initialise these values to zero (in order to prevent potential divide-by-zero errors) but rather to a small value (e.g. 1.0e-8).

For a model with no compartments these initial values are assumed to be concentrations:

NADH = 0.001
ATP  = 2.3e-3
sucrose = 1

In a model with compartments it is expected that the species are located in a compartment (even if Species_In_Conc: False); this is done using the @ symbol:

s1@Memb = 0.01
s2@Cell = 2.0e-4

A word of warning, the user is responsible for making sure that the units of the initialised species match those of the model. Please keep in mind that all species (and anything that depends on them) are defined in terms of the Species_In_Conc keyword. For example, if the preceding initialisations were for R1 (see Reaction section) then they would be concentrations (as Species_In_Conc: True). However, in the next example, we are initialising species for R4 and they are therefore in amounts (Species_In_Conc: False).

s3@Memb = 1.0
s4@Cell = 2.0

Fixed species are defined in a similar way and although they technically parameters, they should be given a location in compartmental models:

# InitExt
X0 = 10.0
X4@Cell = 1.0

However, fixed species are true parameters in the sense that their associated compartment size does not affect their value when it changes size. If compartment size-dependent behaviour is required, an assignment or rate rule should be considered.

Finally, the parameters should be initialised. PySCeS checks if a parameter is defined that is not present in the rate equations and if such parameter initialisations are detected a harmless warning is generated. If, on the other hand, an uninitialised parameter is detected a warning is generated and a value of 1.0 assigned:

# InitPar
Vf2 = 10.0
Ks4 = 1.0

Advanced model construction¶

Assignment rules¶

Assignment rules or forcing functions are used to set the value of a model attribute before the ODEs are evaluated. This model attribute can either be a parameter used in the rate equations (this is traditionally used to describe an equilibrium block), a compartment, or an arbitrary parameter (commonly used to define some sort of tracking function). Assignment rules can access other model attributes directly and have the generic form !F <par> = <formula>, where <par> is the parameter assigned the result of <formula>. Assignment rules can be defined anywhere in the input file:

!F S_V_Ratio = Mem_Area/Vcyt
!F sigma_test = sigma_P*Pmem + sigma_L*Lmem

These rules would set the value of <par>, whose value can be followed using the simulation and steady state extra_output functionality (see Simulation results and The steady-state data object).

Rate rules¶

PySCeS includes support for rate rules, which are essentially directly encoded ODEs that are evaluated after the ODEs defined by the model stoichiometry and rate equations. Unlike the SBML rate rule, PySCeS allows one to directly access a reaction symbol in the rate rules (this is automatically expanded when the model is exported to SBML). The general form of a rate rule is RateRule: <name> {<formula>}, where <name> is the model attribute (e.g. compartment or parameter) whose rate of change is described by the <formula>. It may also be defined anywhere in the input file:

RateRule: Mem_Area {
(sigma_P)*(Mem_Area*k4*(P)) + (sigma_L)*(Mem_Area*k5*(L))
}

RateRule: Vcyt {(1.0/Co)*(R1()+(1-m1)*R2()+(1-m2)*R3()-R4()-R5())}

Remember to initialise any new parameters defined in the rate rules.

Events¶

Time-dependant events may be defined whose definition follows the event framework described in the SBML L2V1 specification. The general form of an event is Event: <name>, <trigger>, <delay> { <assignments> }. As can be seen, an event consists of essentially three parts, a conditional <trigger>, a set of one or more <assignments> and a <delay> between when the trigger is fired (and the assignments are evaluated) and the eventual assignment to the model. Assignments have the general form <par> = <formula>. Events have access to the “current” simulation time using the _TIME_ symbol:

Event: event1, _TIME_ > 10 and A > 150.0, 0 {
V1 = V1*vfact
V2 = V2*vfact
}

The following event illustrates the use of a delay of ten time units as well as the prefix notation (used by libSBML) for the trigger (PySCeS understands both notations):

Event: event2, geq(_TIME_, 15.0), 10 {
V3 = V3*vfact2
}

Note

In order for PySCeS to handle events it is necessary to have Assimulo installed (refer to General requirements).

Piecewise¶

Although technically an operator, piecewise functions are sufficiently complicated to warrant their own section. A piecewise operator is essentially an if, elif, …, else logical operator that can be used to conditionally “set” the value of some model attribute. Currently piecewise is supported in rule constructs and has not been tested directly in rate equation definitions. The piecewise function’s most basic incarnation is piecewise(<val1>, <cond>, <val2>), which is evaluated as:

if <cond>:
    return <val1>
else:
    return <val2>

Alternatively, piecewise(<val1>, <cond1>, <val2>, <cond2>, <val3>, <cond3>)

if <cond1>:
    return <val1>
elif <cond2>:
    return <val1>
elif <cond3>:
    return <val3>

Or piecewise(<val1>, <cond1>, <val2>, <cond2>, <val3>, <cond3>, <val4>)

if <cond1>:
    return <val1>
elif <cond2>:
    return <val2>
elif <cond3>:
    return <val3>
else:
    return <val4>

can also be used. A “real-life” example of an assignment rule with a piecewise function:

!F Ca2plus=piecewise(0.1, lt(_TIME_,60), 0.1, gt(_TIME_,66.0115), 1)

In principle there is no limit on the number of conditional statements present in a piecewise function; the condition can be a compound statement (a or b and c) and may include the _TIME_ symbol.

Reagent placeholder¶

Some models contain reactions that are defined as only having substrates or products, with the fixed (external) species not specified:

R1: A + B >

R2: > C + D

The implication is that the relevant reagents appear from or disappear into a constant pool. Unfortunately the PySCeS parser does not accept such an unbalanced reaction definition and requires these pools to be represented with a $pool token:

R1: A + B > $pool

R2: $pool > C + D

$pool is neither counted as a reagent nor does it ever appear in the stoichiometry (think of it as dev/null) and no other $<str> tokens are allowed.

Example PySCeS input files¶

Basic model definition¶

PySCeS test model: pysces_test_linear1.psc - this file is distributed with PySCeS and copied to your model directory (typically $HOME/Pysces/psc) after installation, when running pysces.test() for the first time.

FIX: x0 x3

R1: x0 = s0
    k1*x0 - k2*s0

R2: s0 = s1
    k3*s0 - k4*s1

R3: s1 = s2
    k5*s1 - k6*s2

R4: s2 = x3
    k7*s2 - k8*x3

# InitExt
x0 = 10.0
x3 = 1.0
# InitPar
k1 = 10.0
k2 = 1.0
k3 = 5.0
k4 = 1.0
k5 = 3.0
k6 = 1.0
k7 = 2.0
k8 = 1.0
# InitVar
s0 = 1.0
s1 = 1.0
s2 = 1.0

Advanced example¶

This model includes the use of Compartments, KeyWords, Units and Rules:

Modelname: MWC_wholecell2c
Description: Surovtsev whole cell model using J-HS Hofmeyr's framework

Species_In_Conc: True
Output_In_Conc: True

# Global unit definition
UnitVolume: litre, 1.0, -3, 1
UnitSubstance: mole, 1.0, -6, 1
UnitTime: second, 60, 0, 1

# Compartment definition
Compartment: Vcyt, 1.0, 3
Compartment: Vout, 1.0, 3
Compartment: Mem_Area, 5.15898, 2

FIX: N

R1@Mem_Area: N = M
  Mem_Area*k1*(Pmem)*(N/Vout)

R2@Vcyt: {244}M = P # m1
  Vcyt*k2*(M)

R3@Vcyt: {42}M = L # m2
  Vcyt*k3*(M)*(P)**2

R4@Mem_Area: P = Pmem
  Mem_Area*k4*(P)

R5@Mem_Area: L = Lmem
  Mem_Area*k5*(L)

# Rate rule definition
RateRule: Vcyt {(1.0/Co)*(R1()+(1-m1)*R2()+(1-m2)*R3()-R4()-R5())}
RateRule: Mem_Area {(sigma_P)*R4() + (sigma_L)*R5()}

# Rate rule initialisation
Co = 3.07e5 # uM p_env/(R*T)
m1 = 244
m2 = 42
sigma_P = 0.00069714285714285711
sigma_L = 0.00012

# Assignment rule definition
!F S_V_Ratio = Mem_Area/Vcyt
!F Mconc = (M)/M_init
!F Lconc = (L)/L_init
!F Pconc = (P)/P_init

# Assignment rule initialisations
M_init = 199693.0
L_init = 102004
P_init = 5303
Mconc = 1.0
Lconc = 1.0
Pconc = 1.0

# Species initialisations
N@Vout = 3.07e5
Pmem@Mem_Area = 37.38415
Lmem@Mem_Area = 8291.2350678770199
M@Vcyt = 199693.0
L@Vcyt = 102004
P@Vcyt = 5303

# Parameter initialisations
k1 = 0.00089709
k2 = 0.000182027
k3 = 1.7539e-010
k4 = 5.0072346e-005
k5 = 0.000574507164

"""
Simulate this model to 200 for maximum happiness and
watch the surface to volume ratio and scaled concentrations.
"""

This example illustrates almost all of the features included in the PySCeS MDL. Although it may be slightly more complicated than the basic model described above it is still, by our definition, human readable.

Module documentation¶

PySCeS Module documentation¶

PyscesUtils¶

The PyscesUtils module holds a collection of methods of general use such as timers and array export fucntionality that can be accessed as pysces.write.

pysces.PyscesUtils.ConvertFileD2U(Filelist)[source]¶

Converts a [Filename] from rn to n inplace no effect if the line termination is correct

Filelist a file or list of files to convert

pysces.PyscesUtils.ConvertFileU2D(Filelist)[source]¶

Converts a [Filename] from n to rn inplace no effect if the line termination is correct:

Filelist a file or list of files to convert

pysces.PyscesUtils.CopyModels(*args, **kwargs)[source]¶

pysces.PyscesUtils.CopyTestModels(*args, **kwargs)[source]¶

class pysces.PyscesUtils.TimerBox[source]¶

A timer “container” class that can be used to hold user defined timers

normal_timer(name)[source]¶

Creates a normal timer method with <name> in the TimerBox instance. Normal timers print the elapsed time since creation when called.

name the timer name

reset_step(name)[source]¶

Reset the number of steps of timer <name> in the TimerBox to zero

name the step timer whose steps should be reset

step_timer(name, maxsteps)[source]¶

Creates a step timer method with <name> in the TimerBox instance. Step timers print the elapsed time as well as the next step out of maxsteps when called.

name the timer name
maxsteps the maximum number of steps associated with this timer

stop(name)[source]¶

Delete the timer <name> from the TimerBox instance

name the timer name to delete

pysces.PyscesUtils.VersionCheck(ver='0.1.5')[source]¶

class pysces.PyscesUtils.WriteOutput[source]¶

This code is adapted from:

CBMPy: CBTools module

exportArray2CSV(arr, fname)[source]¶

Export an array to fname.csv

arr the an array like object

fname the output filename

sep [default=’,’] the column separator

exportArray2TXT(arr, fname)[source]¶

Export an array to fname.txt

arr the an array like object

fname the output filename

sep [default=’,’] the column separator

exportLabelledArray(arr, names, fname, sep=',', sformat='%f')[source]¶

Write a 2D array type object to file

arr the an array like object

names the list of row names

fname the output filename

sep [default=’,’] the column separator

format [default=’%s’] the output number format

exportLabelledArray2CSV(arr, names, fname)[source]¶

Export an array with row names to fname.csv

arr the an array like object

names the list of row names

fname the output filename

exportLabelledArray2TXT(arr, names, fname)[source]¶

Export an array with row names to fname.txt

arr the an array like object

names the list of row names

fname the output filename

exportLabelledArrayWithHeader(arr, names, header, fname, sep=',', format='%f')[source]¶

Export an array with row names and header

arr the an array like object

names the list of row names

header the list of column names

fname the output filename

sep [default=’,’] the column separator

format [default=’%s’] the output number format

appendlist [default=False] if True append the array to fname otherwise create a new file

exportLabelledArrayWithHeader2CSV(arr, names, header, fname)[source]¶

Export an array with row names and header to fname.csv

arr the an array like object

names the list of row names

header the list of column names

fname the output filename

exportLabelledArrayWithHeader2TXT(arr, names, header, fname)[source]¶

Export an array with row names and header to fname.txt

arr the an array like object

names the list of row names

header the list of column names

fname the output filename

exportLabelledLinkedList(arr, fname, names=None, sep=',', format='%s', appendlist=False)[source]¶

Write a 2D linked list [[…],[…],[…],[…]] and optionally a list of row labels to file:

arr the linked list

fname the output filename

names the list of row names

sep [default=’,’] the column separator

format [default=’%s’] the output number format

appendlist [default=False] if True append the array to fname otherwise create a new file

pysces.PyscesUtils.str2bool(s)[source]¶

Tries to convert a string to a Python boolean

s True if ‘True’, ‘true’ or’1’ else False

PyscesPlot2¶

PyscesPlot2 is a new graphics susbsystem for PySCeS which will include a Unified Plotting Interface which can take advantage of different plotting backends via a common user interface.

class pysces.PyscesPlot2.FIFOBuffer(size)[source]¶

Simple fixed size FIFO buffer.

add(x)[source]¶

get()[source]¶

class pysces.PyscesPlot2.GnuPlotUPI(work_dir=None, gnuplot_dir=None)[source]¶

PySCeS/GnuPlot is reborn, leaner and meaner than ever before. This class enables plotting with GnuPlot via a subprocess link:

work_dir optional argument setting directory for dat file(s)
gnuplot_dir optional argument specifying the location of pgnuplot.exe (win32) or gnuplot

GnuPlot backend to the Unified Plotting Interface.

CommonStyleDefs = {'lines': 'w l', 'points': 'w p'}¶

DATF_FORMAT = '%.8e'¶

PAUSE_TIME = 0.1¶

Terminals = {'png': 'medium size 800,600', 'windows': '', 'x11': ''}¶

export(name, directory=None, outtype='png')[source]¶

Export the current plot as a <format> file.

filename the filename
directory optional (default = current working directory)
outtype the file format (default=’png’).

Currently only PNG is guaranteed to be available in all interfaces.

g_file_write_array(arr, dfmt=None)[source]¶

Write a normal (2D) dataset to temp file. Dumps the array to file using the format:

arr the array (r>0, c>1)
fmt default ‘%.8e’

g_file_write_array3D(arr, yaxis=1, dfmt=None)[source]¶

Write a GnuPlot format 3D dataset. The yaxis argument specifies the column that should be used to split the dataset into GnuPlot slices.

arr the array (r>1, c>2)
fmt default ‘%.8e’
yaxis default 1

g_pause()[source]¶: A small pause defined by self.PAUSE_TIME (multiplied by 2 when in multiplot).

g_write(cmd)[source]¶

Write a command to the GnuPlot interpreter

cmd the GnuPlot command

plot(data, x, y, title='', format='w l')[source]¶

Plot a single line data[y] vs data[x] where:

data the data array
x x column index
y y column index
title is the line key
format is the GnuPlot format string (default=’w l’)

Format can also be the CommonStyle ‘lines’ or ‘points’.

plotLines(data, x, y=[], titles=[], formats=['w l'])[source]¶

Plot a multiple lines data[y1, y2, ] vs data[x] where:

data the data array
x x column index
y is a list of line indexes, if empty all of y not including x is plotted
titles is a list of line keys if empty Line1, Line2, Line3 is used
formats is a list (per line) of GnuPlot format strings (default=’w l’).

If formats only contains a single item, this format is used for all lines and can also be the CommonStyle ‘lines’ or ‘points’.

replot()[source]¶: Replot the current GnuPlot plot

replotAndWait(seconds=0.5)[source]¶: Replot the current GnuPlot plot and wait default (seconds = 0.5) or until enter is pressed (seconds = -1)

save(name, directory=None, dfmt=None)[source]¶

Save the last plot as a GnuPlot file name.plt which references name.dat.

name the name of the GnuPlot plt and and datafile
directory (optional) the directory to use (defaults to working directory)
dfmt is ignored and uses the value of self.DATF_FORMAT

set(key, value='')[source]¶: Send set <key> or optionally set <key> <value> to GnuPlot.

setAxisLabel(axis, label='')[source]¶

Set the axis label:

axis = x, y, z, xy, xz, yz, zyx
label = string (default=’’)

Called with only the axis argument clears the axis label.

setDataFileNumberFormat(format='%.8e')[source]¶

Sets the format string for data written to file

format format string (default=’%.8e’)

setGraphTitle(title='PySCeS Plot')[source]¶

Set the graph title, unset if title argument is None

title (string, default=’PySCeS Plot’) the graph title

setGrid(value)[source]¶

Display or remove graph grid.

value (boolean) True (on) or False (off)

setKey(value=False)[source]¶

Enable or disable the current plot key, no arguments removes key.

value boolean (default = False)

setLogScale(axis)[source]¶

Set axis to logscale where:

axis = x, y, z, xy, xz, yz, zyx

setMultiplot()[source]¶: Begin a multiplot session

setNoLogScale(axis)[source]¶

Set axis to a linear scale where:

axis = x, y, z, xy, xz, yz, zyx

setOrigin(xpos=0, ypos=0)[source]¶

Set the origin (lower left corner) of the next plot. Uses GnuPlot screen coordinates. If no arguments are supplied reset origin to 0,0.

xpos of next plot (default = 0)
ypos of next plot (default = 0)

setRange(axis, min=None, max=None)[source]¶

Set axis range where:

axis = x, y, z, xy, xz, yz, zyx
min = range(s) lower bound (default=None) autoscale
max = range(s) upper bound (default=None) autoscale

If only the axis argument is provided, GnuPlot will autoscale the ranges to the data.

setSize(width=1.0, height=1.0)[source]¶

Set the size of the next plot relative to the GnuPlot canvas (e.g. screen) size which is defined to be 1. For example if width = height = 0.5 the plot is 1/4 the size of the viewable canvas. If no arguments are supplied reset size to 1,1.

width of next plot (default = 1.0)
height of next plot (default = 1.0)

setSizeAndOrigin(width=1, height=1, xpos=0, ypos=0)[source]¶

Set the size and origin of the next plot. If no arguments are supplied, reset the size to 1,1 and origin to 0.0

width of next plot (default = 1.0)
height of next plot (default = 1.0)
xpos of next plot (default = 0)
ypos of next plot (default = 0)

setTerminal(name, options='')[source]¶: Sets the terminal, gnuplot: set terminal name options

splot(data, x, y, z, titles='', format='w l')[source]¶

Plot a surface data[z] vs data[y] vs data[x] where:

data the data array
x x column index
y y column index
z z column index
titles is the surface key
format is the GnuPlot format string (default=’w l’)

Format can also be the CommonStyle ‘lines’ or ‘points’.

splotSurfaces(data, x, y, z=[], titles=[], formats=['w l'])[source]¶

Plot data[z1, z2, ] vs data[y] vs data[x] where:

data the data array
x x column index
y y column index
z list of z column indexes, if empty all of z not including x, y are plotted
titles is a list of surface keys, if empty Surf1, Surf2, Surf3 is used
formats is a list (per line) of GnuPlot format strings (default=’w l’).

If formats only contains a single item, this format is used for all surface and can also be the CommonStyle ‘lines’ or ‘points’.

unset(key, value='')[source]¶: Send unset <key> or optionally unset <key> <value> to GnuPlot.

unsetMultiplot()[source]¶: End a multiplot session.

class pysces.PyscesPlot2.MatplotlibUPI(work_dir=None, backend=None)[source]¶

Refactored Matplotlib backend to the Unified Plotting Interface

work_dir (optional) working directory

CommonStyleDefs = {'lines': '-', 'points': 'o'}¶

MAX_OPEN_WINDOWS = 10¶

closeAll()[source]¶: Close all open matplotlib figures.

export(name, directory=None, outtype='png')[source]¶

Export the current plot as a <format> file.

filename the filename
directory optional (default = current working directory)
outtype the file format (default=’png’).

Currently only PNG is guaranteed to be available in all interfaces.

hold(hold=False)[source]¶

Enable plot holding where each new graph is plotted on top of the previous one.

hold boolean (default = False)

isnotebook()[source]¶

plot(data, x, y, title='', format='-')[source]¶

Plot a single line data[y] vs data[x] where:

data the data array
x x column index
y y column index
title is the line key
format is the Matplotlib format string (default=’-‘)

Format can also be the CommonStyle ‘lines’ or ‘points’.

plotLines(data, x, y=[], titles=[], formats=['-'])[source]¶

Plot a multiple lines data[y1, y2, ] vs data[x] where:

data the data array
x x column index
y is a list of line indexes
titles is a list of line keys
formats is a list (per line) of Matplotlib format strings.

If formats only contains a single item, this format is used for all lines and can also be the CommonStyle ‘lines’ or ‘points’.

pyplot = None¶

save(name, directory=None, dfmt='%.8e')[source]¶

Save the plot data to

filename the filename
directory optional (default = current working directory)
dfmt the data format string (default=’%.8e’)

setAxisLabel(axis, label='')[source]¶

Set the axis label:

axis = x, y, z, xy, xz, yz, zyx
label = string (default=’’)

Called with only the axis argument clears the axis label.

setGraphTitle(title='PySCeS Plot')[source]¶

Set the graph title, unset if title=None

title (string, default=’PySCeS Plot’) the graph title

setGrid(value)[source]¶

Display or remove graph grid.

value (boolean) True (on) or False (off)

setKey(value=False)[source]¶

Enable or disable the current plot key, no arguments removes key.

value boolean (default = False)

setLineWidth(width=1)[source]¶

Sets the line width for current axis

width the line width

setLogScale(axis)[source]¶

Set axis to logscale where:

axis = x, y, z, xy, xz, yz, zyx

setNoLogScale(axis)[source]¶

Set axis to a linear scale where:

axis = x, y, z, xy, xz, yz, zyx

setRange(axis, min=None, max=None)[source]¶

Set axis range where

axis = x, y, z, xy, xz, yz, zyx
min = range(s) lower bound (default=None) autoscale
max = range(s) upper bound (default=None) autoscale

class pysces.PyscesPlot2.PlotBase[source]¶

Abstract class defining the Unified Plotting Interface methods. These methods should be overridden and the class extended by interface specific subclasses.

CommonStyleDefs = {'lines': '', 'points': ''}¶

axisInputStringToList(input)[source]¶

Extracts axis information from a string input, returns a boolean triple representing (x=True/False, y=True/False, z=True/False).

input the input string

export(name, directory=None, outtype='png')[source]¶

Export the current plot as a <format> file.

filename the filename
directory optional (default = current working directory)
outtype the file format (default=’png’).

Currently only PNG is guaranteed to be available in all interfaces.

plot(data, x, y, title='', format='')[source]¶

Plot a single line data[y] vs data[x] where:

data the data array
x x column index
y y column index
title is the line key
format is the XXX format string (default=’’)

Format can also be the CommonStyle ‘lines’ or ‘points’

plotLines(data, x, y=[], titles=[], formats=[''])[source]¶

Plot a multiple lines data[y1, y2, ] vs data[x] where:

data the data array
x x column index
y is a list of line indexes, if empty all of y not including x is plotted
titles is a list of line keys, if empty Line1,Line2,Line3 is used
formats is a list (per line) of XXX format strings.

If formats only contains a single item, this format is used for all lines and can also be the CommonStyle ‘lines’ or ‘points’.

save(name, directory=None, dfmt='%.8e')[source]¶

Save the plot data and (optionally) XXX format file

filename the filename
directory optional (default = current working directory)
dfmt the data format string (default=’%.8e’)

setAxisLabel(axis, label='')[source]¶

Set the axis label:

axis = x, y, z, xy, xz, yz, zyx
label = string (default=’’)

Called with only the axis argument clears the axis label.

setGraphTitle(title='PySCeS Plot')[source]¶

Set the graph title, unset if title=None

title (string, default=’PySCeS Plot’) the graph title

setGrid(value)[source]¶

Display or remove graph grid.

value (boolean) True (on) or False (off)

setKey(value=False)[source]¶

Enable or disable the current plot key, no arguments removes key.

value boolean (default = False)

setLogScale(axis)[source]¶

Set axis to logscale where:

axis = x, y, z, xy, xz, yz, zyx

setNoLogScale(axis)[source]¶

Set axis to a linear scale where:

axis = x, y, z, xy, xz, yz, zyx

setRange(axis, min=None, max=None)[source]¶

Set axis range where

axis = x, y, z, xy, xz, yz, zyx
min = range(s) lower bound (default=None) autoscale
max = range(s) upper bound (default=None) autoscale

splot(data, x, y, z, titles='', format='')[source]¶

Plot a surface data[z] vs data[y] vs data[x] where:

data the data array
x x column index
y y column index
z z column index
title is the surface key
format is the XXX format string (default=’’)

Format can also be the CommonStyle ‘lines’ or ‘points’.

splotSurfaces(data, x, y, z=[], titles=[], formats=[''])[source]¶

Plot data[z1, z2, ] vs data[y] vs data[x] where:

data the data array
x x column index
y y column index
z list of z column indexes, if empty all of z not including x, y are plotted
titles is a list of surface keys, if empty Surf1, Surf2, Surf3 is used
formats is a list (per line) of XXX format strings (default=’’).

If formats only contains a single item, this format is used for all surfaces and can also be the CommonStyle ‘lines’ or ‘points’.

wait(seconds=3)[source]¶: Wait seconds (default = 3) or until enter is pressed (seconds = -1)

class pysces.PyscesPlot2.PyscesUPI[source]¶

This is the frontend to the PySCeS Unified Plotting Interface (pysces.plt.*) that allows one to specify which backend should be used to plot when a UPI method is called. More than one interface can be active at the same time and so far the Matplotlib and GnuPlot backends are available for use.

This is an experiment which must be refactored into a more general way of doing things. Basically, I want an instance of the abstract plotting class which will plot to one, any or all currently available backends. If anybody has an idea how I can generate this class automatically please let me know ;-)

closeAll()[source]¶: Close all active Matplolib figures

export(name, directory=None, outtype='png')[source]¶

Export the current plot as a <format> file.

filename the filename
directory optional (default = current working directory)
outtype the file format (default=’png’).

Currently only PNG is guaranteed to be available in all interfaces.

g = None¶

m = None¶

p_activateInterface(interface)[source]¶

Activate an interface that has been set with p_setInterface() but deactivated with p_deactivateInterface

interface one of [‘matplotlib’,’gnuplot’]

p_deactivateInterface(interface)[source]¶

Deactivate the interface. This does not delete the interface and it is possible to reactivate the deactivated interface with p_activateInterface.

interface one of [‘matplotlib’,’gnuplot’]

p_setInterface(name, instance)[source]¶

Add an interface to the backend selector

name the interface name currently one of [‘matplotlib’,’gnuplot’]
instance an instance of a PlotBase derived (UPI) interface

plot(data, x, y, title='', format='')[source]¶

Plot a single line data[y] vs data[x] where:

data the data array
x x column index
y y column index
title is the line key
format is the backend format string (default=’’)

plotLines(data, x, y=[], titles=[], formats=[''])[source]¶

Plot a multiple lines data[y1, y2, ] vs data[x] where:

data the data array
x x column index
y is a list of line indexes, if empty all of y not including x is plotted
titles is a list of line keys, if empty Line1,Line2,Line3 is used
formats is a list (per line) of XXX format strings.

If formats only contains a single item, this format is used for all lines.

replot()[source]¶: Replot the current figure for all active interfaces

save(name, directory=None, dfmt='%.8e')[source]¶

Save the plot data and (optionally) XXX format file

filename the filename
directory optional (default = current working directory)
dfmt the data format string (default=’%.8e’)

setAxisLabel(axis, label='')[source]¶

Set the axis label:

axis = x, y, z, xy, xz, yz, zyx
label = string (default=None)

Called with only the axis argument clears the axis label.

setGraphTitle(title='PySCeS Plot')[source]¶

Set the graph title, unset if title=None

title (string, default=’PySCeS Plot’) the graph title

setGrid(value)[source]¶

Display or remove graph grid.

value (boolean) True (on) or False (off)

setKey(value=False)[source]¶

Enable or disable the current plot key, no arguments removes key.

value boolean (default = False)

setLogScale(axis)[source]¶

Set axis to logscale where:

axis = x, y, z, xy, xz, yz, zyx

setNoLogScale(axis)[source]¶

Set axis to a linear scale where:

axis = x, y, z, xy, xz, yz, zyx

setRange(axis, min=None, max=None)[source]¶

Set axis range where

axis = x, y, z, xy, xz, yz, zyx
min = range(s) lower bound (default=None) autoscale
max = range(s) upper bound (default=None) autoscale

splot(data, x, y, z, titles='', format='')[source]¶

Plot a surface data[z] vs data[y] vs data[x] where:

data the data array
x x column index
y y column index
z z column index
titles is a list of surface keys whose len matches data columns
format is the XXX format string (default=’’)

splotSurfaces(data, x, y, z=[], titles=[], formats=[''])[source]¶

Plot data[z1, z2, ] vs data[y] vs data[x] where:

data the data array
x x column index
y y column index
z list of z column indexes, if empty all of z not including x, y are plotted
titles is a list of surface keys, if empty Surf1, Surf2, Surf3 is used
formats is a list (per line) of XXX format strings (default=’’).

If formats only contains a single item, this format is used for all surfaces.

PyscesModel¶

This module contains the core PySCeS classes which create the model and associated data objects

class pysces.PyscesModel.BagOfStuff(matrix, row, col)[source]¶

A collection of attributes defined by row and column lists used by Response coefficients etc matrix is an array of values while row/col are lists of row colummn name strings

col = None¶

get(attr1, attr2)[source]¶: Returns a single attribute “attr1_attr2” or None

list()[source]¶: Return all attributes as a attr:val dictionary

listAllOrdered(order='descending', absolute=True)[source]¶

Return an ordered list of (attr, value) tuples

order [default=’descending’] the order to return as: ‘descending’ or ‘ascending’

absolute [default=True] use the absolute value

load()[source]¶

matrix = None¶

row = None¶

select(attr, search='a')[source]¶: Return a dictionary of <attr>_<name>, <name>_<attr> : val or {} if none If attr exists as an index for both left and right attr then: search=’a’ : both left and right attributes (default) search=’l’ : left attributes only search=’r’ : right attributes

class pysces.PyscesModel.Event(name, mod)[source]¶

Events have triggers and fire EventAssignments when required. Ported from Core2.

assignments = None¶

code_string = None¶

delay = 0.0¶

formula = None¶

mod = None¶

piecewises = None¶

reset()[source]¶

setAssignment(var, formula)[source]¶

setTrigger(formula, delay=0.0)[source]¶

state = False¶

state0 = False¶

symbols = None¶

trigger = None¶

xcode = None¶

class pysces.PyscesModel.EventAssignment(name, mod)[source]¶

Event assignments are actions that are triggered by an event. Ported from Core2 to build an event handling framework fro PySCeS

code_string = None¶

evaluateAssignment()[source]¶

formula = None¶

mod = None¶

piecewises = None¶

setFormula(formula)[source]¶

setVariable(var)[source]¶

symbols = None¶

variable = None¶

xcode = None¶

class pysces.PyscesModel.Function(name, mod)[source]¶

Function class ported from Core2 to enable the use of functions in PySCeS.

addFormula(formula)[source]¶

argsl = None¶

code_string = None¶

formula = None¶

functions = None¶

mod = None¶

piecewises = None¶

setArg(var, value=None)[source]¶

symbols = None¶

value = None¶

xcode = None¶

class pysces.PyscesModel.IntegrationDataObj[source]¶

This class is specifically designed to store the results of a time simulation It has methods for setting the Time, Labels, Species and Rate data and getting Time, Species and Rate (including time) arrays. However, of more use:

getOutput(*args) feed this method species/rate labels and it will return an array of [time, sp1, r1, ….]
getDataAtTime(time) the data generated at time point “time”.
getDataInTimeInterval(time, bounds=None) more intelligent version of the above returns an array of all data points where: time-bounds <= time <= time+bounds

HAS_RATES = False¶

HAS_RULES = False¶

HAS_SPECIES = False¶

HAS_TIME = False¶

HAS_XDATA = False¶

IS_VALID = True¶

TYPE_INFO = 'Deterministic'¶

getAllSimData(lbls=False)[source]¶: Return all available data as time+species+rates+rules if lbls=True returns (array,lables) else just array

getDataAtTime(time)[source]¶: Return all data generated at “time”

getDataInTimeInterval(time, bounds=None)[source]¶: getDataInTimeInterval(time, bounds=None) returns an array of all data points where: time-bounds <= time <= time+bounds where bound defaults to stepsize

getOutput(*args, **kwargs)[source]¶: Old alias for getSimData() getOutput(*args) feed this method species/rate labels and it will return an array of [time, sp1, r1, ….]

getRates(lbls=False)[source]¶: return time+rate array

getRules(lbls=False)[source]¶: Return time+rule array

getSimData(*args, **kwargs)[source]¶: getSimData(*args) feed this method species/rate labels and it will return an array of [time, sp1, r1, ….]

getSpecies(lbls=False)[source]¶: return time+species array

getTime(lbls=False)[source]¶: return the time vector

getXData(lbls=False)[source]¶: Return time+xdata array

rate_labels = None¶

rates = None¶

rules = None¶

rules_labels = None¶

setLabels(species=None, rates=None, rules=None)[source]¶: set the species, rate and rule label lists

setRates(rates, lbls=None)[source]¶: set the rate array

setRules(rules, lbls=None)[source]¶: Set the results of rate rules

setSpecies(species, lbls=None)[source]¶: Set the species array

setTime(time, lbl=None)[source]¶: Set the time vector

setXData(xdata, lbls=None)[source]¶: Sets extra simulation data

species = None¶

species_labels = None¶

time = None¶

time_label = 'Time'¶

xdata = None¶

xdata_labels = None¶

class pysces.PyscesModel.NewCoreBase[source]¶

Core2 base class, needed here as we use Core2 derived classes in PySCes

get(attr)[source]¶: Return an attribute whose name is str(attr)

getName()[source]¶

name = None¶

setName(name)[source]¶

class pysces.PyscesModel.NumberBase[source]¶

Derived Core2 number class.

getValue()[source]¶

setValue(v)[source]¶

value = None¶

value_initial = None¶

class pysces.PyscesModel.PieceWise(pwd, mod)[source]¶

Generic piecewise class adapted from Core2 that generates a compiled Python code block that allows evaluation of arbitrary length piecewise functions. Piecewise statements should be defined in assignment rules as piecewise(<Piece>, <Conditional>, <OtherValue>) where there can be an arbitrary number of <Piece>, <Conditional> pairs.

args a dictionary of piecewise information generated by the InfixParser as InfixParser.piecewises

code_string = None¶

formula = None¶

name = None¶

value = None¶

xcode = None¶

class pysces.PyscesModel.PysMod(File=None, dir=None, loader='file', fString=None, autoload=True)[source]¶

Create a model object and instantiate a PySCeS model so that it can be used for further analyses. PySCeS model descriptions can be loaded from files or strings (see the loader argument for details).

File the name of the PySCeS input file if not explicit a *.psc extension is assumed.
dir if specified, the path to the input file otherwise the default PyscesModel directory (defined in the pys_config.ini file) is assumed.
autoload autoload the model, pre 0.7.1 call mod.doLoad(). (default=True) new
loader the default behaviour is to load PSC file, however, if this argument is set to ‘string’ an input file can be supplied as the fString argument (default=’file’)
fString a string containing a PySCeS model file (use with loader=’string’) the File argument now sepcifies the new input file name.

CVODE(initial)[source]¶

PySCeS interface to the CVode integration algorithm. Given a set of initial conditions.

Arguments:

initial: vector containing initial species concentrations

CVODE_VPYTHON(s)[source]¶: Future VPython hook for CVODE

CVODE_continue(tvec)[source]¶

Experimental: continues a simulation over a new time vector, the CVODE memobj is reused and not reinitialised and model parameters can be changed between calls to this method. The mod.data_sim objects from the initial simulation and all calls to this method are stored in the list mod.CVODE_continuous_result.

tvec a numpy array of time points

CVODE_continuous_result = None¶

CleanNaNsFromArray(arr, replace_val=0.0)[source]¶

Scan a matrix for NaN’s and replace with zeros:

arr the array to be cleaned

EvalCC()[source]¶

Calculate the MCA control coefficients using the current steady-state solution.

mod.__settings__[“mca_ccj_upsymb”] = 1 attach the flux control coefficients to the model instance mod.__settings__[“mca_ccs_upsymb”] = 1 attach the concentration control coefficients to the model instance

Arguments: None

EvalEigen()[source]¶

Calculate the eigenvalues or vectors of the unscaled Jacobian matrix and thereby analyse the stability of a system

Arguments: None

EvalEpar(input=None, input2=None)[source]¶

Calculate reaction elasticities towards the parameters.

Both inputs (input1=species,input2=rates) should be valid (steady state for MCA) solutions and given in the correct order for them to be used. If either or both are missing the last state values are used automatically. Elasticities are scaled using input 1 and 2.

Arguments:

input [default=None]: species concentration vector

input2 [default=None]: reaction rate vector

Settings, set in mod.__settings__:

- elas_epar_upsymb   [default = 1] attach individual elasticity symbols to model instance
- elas_scaling_div0_fix [default=False] if NaN's are detected in the variable and parameter elasticity matrix replace with zero

EvalEvar(input=None, input2=None)[source]¶

Calculate reaction elasticities towards the variable species.

Both inputs (input1=species,input2=rates) should be valid (steady state for MCA) solutions and given in the correct order for them to be used. If either or both are missing the last state values are used automatically. Elasticities are scaled using input 1 and 2.

Arguments:

- input [default=None]:  species concentration vector
- input2 [default=None]: reaction rate vector

Settings, set in mod.__settings__:

- elas_evar_upsymb   [default = 1] attach individual elasticity symbols to model instance
- elas_zero_conc_fix [default=False] if zero concentrations are detected in a steady-state solution make it a very small number
- elas_zero_flux_fix [default=False] if zero fluxes are detected in a steady-state solution make it a very small number
- elas_scaling_div0_fix [default=False] if INf's are detected after scaling set to zero

EvalRC()[source]¶

Calculate the MCA response coefficients using the current steady-state solution.

Arguments: None

EvalRCT()[source]¶

Calculate the MCA response coefficients using the current steady-state solution.

Responses to changes in the sums of moiety conserved cycles are also calculated.

Arguments: None

FINTSLV(initial)[source]¶

Forward integration steady-state solver. Finds a steady state when the maximum change in species concentration falls within a specified tolerance. Returns the steady-state solution and a error flag. Algorithm controls are available as mod.fintslv_<control>

Arguments:

initial: vector of initial concentrations

Fix_S_fullinput(s_vec)[source]¶

Using the full concentration vector evaluate the dependent species

Arguments:

s_vec: a full length concentration vector

Fix_S_indinput(s_vec, amounts=True)[source]¶

whether to use self.__tvec_a__ (default) or self.__tvec_c__

Given a vector of independent species evaluate and return a full concentration vector.

Arguments:

s_vec: vector of independent species

Fix_Sim(metab, flux=0, par=0)[source]¶: Deprecated

FluxGenSim(s)[source]¶: Deprecated

Forcing_Function()[source]¶

User defined forcing function either defined in the PSC input file as !F or by overwriting this method. This method is evaluated prior to every rate equation evaluation.

Arguments: None

HYBRD(initial)[source]¶

PySCeS interface to the HYBRD solver. Returns a steady-state solution and error flag. Good general purpose solver. Algorithm controls are available as mod.hybrd_<control>

Arguments:

initial: vector of initial species concentrations

InitialiseCompartments()[source]¶

InitialiseConservationArrays()[source]¶: Initialise conservation related vectors/array was in InitialiseModel but has been moved out so is can be called by when the stoichiometry is reanalysed

InitialiseEvents()[source]¶

InitialiseFunctions()[source]¶

InitialiseInputFile()[source]¶

Parse the input file associated with the PySCeS model instance and assign the basic model attributes

Arguments: None

InitialiseModel()[source]¶

Initialise and set up dynamic model attributes and methods using the model defined in the associated PSC file

Arguments: None

InitialiseOldFunctions()[source]¶

Parse and initialise user defined functions specified by !T !U in the PSC input file

Arguments: None

InitialiseRuleChecks()[source]¶

InitialiseRules()[source]¶

LSODA(initial)[source]¶

PySCeS interface to the LSODA integration algorithm. Given a set of initial conditions LSODA returns an array of species concentrations and a status flag. LSODA controls are accessible as mod.lsoda_<control>

Arguments:

initial: vector containing initial species concentrations

LoadFromFile(File=None, dir=None)[source]¶

__init__(File=None,dir=None)

Initialise a PySCeS model object with PSC file that can be found in optional directory. If a a filename is not supplied the pysces.model_dir directory contents is displayed and the model name can be entered at the promp (<ctrl>+C exits the loading process).

Arguments:

File [default=None]: the name of the PySCeS input file dir [default=pysces.model_dir]: the optional directory where the PSC file can be found

LoadFromString(File=None, fString=None)[source]¶: Docstring required

ModelLoad(stoich_load=0)[source]¶

Load and instantiate a PySCeS model so that it can be used for further analyses. This function replaces the pre-0.7.1 doLoad() method.

stoich_load try to load a structural analysis saved with Stoichiometry_Save_Serial() (default=0)

NLEQ2(initial)[source]¶

PySCeS interface to the (optional) NLEQ2 algorithm. This is a powerful steady-state solver that can usually find a solution for when HYBRD() fails. Algorithm controls are available as: mod.nleq2_<control> Returns as steady-state solution and error flag.

Arguments:

initial: vector of initial species concentrations

PITCON(scanpar, scanpar3d=None)[source]¶

PySCeS interface to the PITCON continuation algorithm. Single parameter continuation has been implemented as a “scan” with the continuation being initialised in mod.pitcon_par_space. The second argument does not affect the continuation but can be used to insert a third axis parameter into the results. Returns an array containing the results. Algorithm controls are available as mod.pitcon_<control>

Arguments:

scanpar: the model parameter to scan (x5) scanpar3d [default=None]: additional output parameter for 3D plots

ParGenSim()[source]¶: Deprecated

ReloadInitFunc()[source]¶

Recompile and execute the user initialisations (!I) as defined in the PSC input file. and in mod.__InitFuncs__.

UPDATE 2015: can now be used to define InitialAssignments (no need for self.* prefix in input file)

Arguments: None

ReloadUserFunc()[source]¶

Recompile and execute the user function (!U) from the input file.

Arguments: None

ResetNumberFormat()[source]¶

Reset PySCeS default number format stored as mod.mode_number format to %2.4e

Arguments: None

ScaleKL(input, input2)[source]¶

Scale the K and L matrices with current steady state (if either input1 or 2 == None) or user input.

Arguments:

input: vector of species concentrations input2: vector of reaction rates

Scan1(range1=[], runUF=0)[source]¶

Perform a single dimension parameter scan using the steady-state solvers. The parameter to be scanned is defined (as a model attribute “P”) in mod.scan_in while the required output is entered into the list mod.scan_out. Results of a parameter scan can be easilly viewed with Scan1Plot().

mod.scan_in - a model attribute written as in the input file (eg. P, Vmax1 etc) mod.scan_out - a list of required output [‘A’,’T2’, ‘ecR1_s1’, ‘ccJR1_R1’, ‘rcJR1_s1’, …] mod.scan_res - the results of a parameter scan mod.scan - numpy record array with the scan results (scan_in and scan_out), call as mod.scan.Vmax, mod.scan.A_ss, mod.scan.J_R1, etc. mod.__settings__[“scan1_mca_mode”] - force the scan algorithm to evaluate the elasticities (1) and control coefficients (2) (this should also be auto-detected by the Scan1 method).

Arguments:

range1 [default=[]]: a predefined range over which to scan. runUF [default=0]: run (1) the user defined function mod.User_Function (!U) before evaluating the steady state.

Scan1Plot(plot=[], title=None, log=None, format='lines', filename=None)[source]¶

Plot the results of a parameter scan generated with Scan1()

plot if empty mod.scan_out is used, otherwise any subset of mod.scan_out (default=[])
filename the filename of the PNG file (default=None, no export)
title the plot title (default=None)
log if None a linear axis is assumed otherwise one of [‘x’,’xy’,’xyz’] (default=None)
format the backend dependent line format (default=’lines’) or the CommonStyle ‘lines’ or ‘points’.

Scan2D(p1, p2, output, log=False)[source]¶

Generate a 2 dimensional parameter scan using the steady-state solvers.

p1 is a list of [parameter1, start, end, points]
p2 is a list of [parameter2, start, end, points]
output steady-state variable/properties e.g. ‘J_R1’, ‘A_ss’, ‘ecR1_s1’
log scan using log ranges for both axes

Scan2DPlot(title=None, log=None, format='lines', filename=None)[source]¶

Plot the results of a 2D scan generated with Scan2D

filename the filename of the PNG file (default=None, no export)
title the plot title (default=None)
log if None a linear axis is assumed otherwise one of [‘x’,’xy’,’xyz’] (default=None)
format the backend dependent line format (default=’lines’) or the CommonStyle ‘lines’ or ‘points’.

SerialDecode(filename)[source]¶

Decode and return a serialised object saved with SerialEncode.

Arguments:

filename: the filename (.pscdat is assumed)

SerialEncode(data, filename)[source]¶

Serialise and save a Python object using a binary pickle to file. The serialised object is saved as <filename>.pscdat in the directory defined by mod.model_serial.

Arguments:

data: pickleable Python object filename: the ouput filename

SetLoud()[source]¶

Turn on as much solver reporting noise as possible: mod.__settings__[‘hybrd_mesg’] = 1 mod.__settings__[‘nleq2_mesg’] = 1 mod.__settings__[“lsoda_mesg”] = 1 mod.__settings__[‘mode_state_mesg’] = 1 mod.__settings__[‘scan1_mesg’] = 1 mod.__settings__[‘solver_switch_warning’] = True

Arguments: None

SetQuiet()[source]¶

Turn off as much solver reporting noise as possible: mod.__settings__[‘hybrd_mesg’] = 0 mod.__settings__[‘nleq2_mesg’] = 0 mod.__settings__[“lsoda_mesg”] = 0 mod.__settings__[‘mode_state_mesg’] = 0 mod.__settings__[‘scan1_mesg’] = 0 mod.__settings__[‘solver_switch_warning’] = False

Arguments: None

SetStateSymb(flux, metab)[source]¶

Sets the individual steady-state flux and concentration attributes as mod.J_<reaction> and mod.<species>_ss

Arguments:

flux: the steady-state flux array metab: the steady-state concentration array

SimPlot(plot='species', filename=None, title=None, log=None, format='lines')[source]¶

Plot the simulation results, uses the new UPI pysces.plt interface:

plot: output to plot (default=’species’)

‘all’ rates and species

‘species’ species

‘rates’ reaction rates

[‘S1’, ‘R1’, ] a list of model attributes (species, rates)

filename if not None file is exported to filename (default=None)
title the plot title (default=None)
log use log axis for ‘x’, ‘y’, ‘xy’ (default=None)
format line format, backend dependant (default=’’)

Simulate(userinit=0)[source]¶

PySCeS integration driver routine that evolves the system over the time. Resulting array of species concentrations is stored in the mod.data_sim object Initial concentrations can be selected using mod.__settings__[‘mode_sim_init’] (default=0):

0 initialise with intial concentrations
1 initialise with a very small (close to zero) value
2 initialise with results of previously calculated steady state
3 initialise with final point of previous simulation

userinit values can be (default=0):

0: initial species concentrations intitialised from (mod.S_init),
time array calculated from sim_start/sim_end/sim_points
1: intial species concentrations intitialised from (mod.S_init) existing
“mod.sim_time” used directly
2: initial species concentrations read from “mod.__inspec__”,
“mod.sim_time” used directly

State()[source]¶

PySCeS non-linear solver driver routine. Solve for a steady state using HYBRD/NLEQ2/FINTSLV algorithms. Results are stored in mod.state_species and mod.state_flux. The results of a steady-state analysis can be viewed with the mod.showState() method.

The solver can be initialised in 3 ways using the mode_state_init switch. mod.mode_state_init = 0 initialize with species initial values mod.mode_state_init = 1 initialize with small values mod.mode_state_init = 2 initialize with the final value of a 10-logstep simulation numpy.logspace(0,5,18)

Arguments: None

Stoich_nmatrix_SetValue(species, reaction, value)[source]¶

Change a stoichiometric coefficient’s value in the N matrix. Only a coefficients magnitude may be set, in other words a a coefficient’s value must remain negative, positive or zero. After changing a coefficient it is necessary to Reanalyse the stoichiometry.

Arguments:

species: species name (s0) reaction: reaction name (R4) value: new coefficient value

Stoichiometry_Analyse(override=0, load=0)[source]¶

Perform a structural analyses. The default behaviour is to construct and analyse the model from the parsed model information. Overriding this behaviour analyses the stoichiometry based on the current stoichiometric matrix. If load is specified PySCeS tries to load a saved stoichiometry, otherwise the stoichiometric analysis is run. The results of the analysis are checked for floating point error and nullspace rank consistancy.

Arguments:

override [default=0]: override stoichiometric analysis intialisation from parsed data load [default=0]: load a presaved stoichiometry

Stoichiometry_Init(nmatrix, load=0)[source]¶

Initialize the model stoichiometry. Given a stoichiometric matrix N, this method will return an instantiated PyscesStoich instance and status flag. Alternatively, if load is enabled, PySCeS will attempt to load a previously saved stoichiometric analysis (saved with Stoichiometry_Save_Serial) and test it’s correctness. The status flag indicates 0 = reanalyse stoichiometry or 1 = complete structural analysis preloaded.

Arguments:

nmatrix: The input stoichiometric matrix, N load [default=0]: try to load a saved stoichiometry (1)

Stoichiometry_Load_Serial()[source]¶

Load a saved stoichiometry saved with mod.Stoichiometry_Save_Serial() and return a stoichiometry instance.

Arguments: None

Stoichiometry_ReAnalyse()[source]¶

Reanalyse the stoichiometry using the current N matrix ie override=1 (for use with mod.Stoich_matrix_SetValue)

Arguments: None

Stoichiometry_Save_Serial()[source]¶

Serialize and save a Stoichiometric instance to binary pickle Stoichiometry_Save_Serial()

Serilaise and save the current model stoichiometry to a file with name <model>_stoichiometry.pscdat in the mod.__settings__[‘serial_dir’] directory (default: mod.model_output/pscdat)

Arguments: None

TestSimState(endTime=10000, points=101, diff=1e-05)[source]¶: Deprecated

User_Function()[source]¶: Deprecated

Write_array(input, File=None, Row=None, Col=None, close_file=0, separator=' ')[source]¶

Write an array to File with optional row/col labels. A ‘,’ separator can be specified to create a CSV style file.

mod.__settings__[‘write_array_header’]: add <filename> as a header line (1 = yes, 0 = no) mod.__settings__[‘write_array_spacer’]: add a space after the header line (1 = yes, 0 = no) mod.__settings__[‘write_arr_lflush’]: set the flush rate for large file writes

Arguments:

input: the array to be written File [default=None]: an open, writable Python file object Row [default=None]: a list of row labels Col [default=None]: a list of column labels close_file [default=0]: close the file after write (1) or leave open (0) separator [default=’ ‘]: the column separator to use

Write_array_html(input, File=None, Row=None, Col=None, name=None, close_file=0)[source]¶

Write an array as an HTML table (no header/footer) or complete document. Tables are formatted with coloured columns if they exceed a specified size.

mod.__settings__[‘write_array_html_header’]: write the HTML document header mod.__settings__[‘write_array_html_footer’]: write the HTML document footer

Arguments:

input: the array to be written File [default=None]: an open, writable Python file object Row [default=None]: a list of row labels Col [default=None]: a list of column labels name [default=None]: an HTML table description line close_file [default=0]: close the file after write (1) or leave open (0)

Write_array_latex(input, File=None, Row=None, Col=None, close_file=0)[source]¶

Write an array to an open file as a ‘LaTeX’ {array}

Arguments:

input: the array to be written File [default=None]: an open, writable Python file object Row [default=None]: a list of row labels Col [default=None]: a list of column labels close_file [default=0]: close the file after write (1) or leave open (0)

clone()[source]¶: Returns a deep copy of this model object (experimental!)

doEigen()[source]¶

Calculate the eigenvalues, automatically performs a steady state and elasticity analysis.

Calls: State() EvalEvar() Evaleigen()

Arguments: None

doEigenMca()[source]¶

Calculate a full Control Analysis and eigenvalues, automatically performs a steady state, elasticity, control analysis.

Calls: State() EvalEvar() EvalCC() Evaleigen()

Arguments: None

doEigenShow()[source]¶

Calculate the eigenvalues, automatically performs a steady state and elasticity analysis and displays the results.

Calls: doEigen() showEigen()

Arguments: None

doElas()[source]¶

Calculate the model elasticities, this method automatically calculates a steady state.

Calls: State() EvalEvar() EvalEpar()

Arguments: None

doLoad(stoich_load=0)[source]¶

Load and instantiate a PySCeS model so that it can be used for further analyses. This function is being replaced by the ModelLoad() method.

stoich_load try to load a structural analysis saved with Stoichiometry_Save_Serial() (default=0)

doMca()[source]¶

Perform a complete Metabolic Control Analysis on the model, automatically calculates a steady state.

Calls: State() EvalEvar() EvalEpar() EvalCC()

Arguments: None

doMcaRC()[source]¶

doMca()

Perform a complete Metabolic Control Analysis on the model, automatically calculates a steady state.

Calls: State() EvalEvar() EvalEpar() EvalCC() EvalRC()

Arguments: None

doMcaRCT()[source]¶

Perform a complete Metabolic Control Analysis on the model, automatically calculates a steady state.

In additional, response coefficients to the sums of moiety-conserved cycles are calculated.

Calls: State() EvalEvar() EvalEpar() EvalCC() EvalRC() EvalRCT()

Arguments: None

doSim(end=10.0, points=20.0)[source]¶

Run a time simulation from t=0 to t=sim_end with sim_points.

Calls: Simulate()

Arguments:

end [default=10.0]: simulation end time points [default=20.0]: number of points in the simulation

doSimPerturb(pl, end)[source]¶: Deprecated: use events instead

doSimPlot(end=10.0, points=21, plot='species', fmt='lines', filename=None)[source]¶

Run a time simulation from t=0 to t=sim_end with sim_points and plot the results. The required output data and format can be set:

end the end time (default=10.0)
points the number of points in the simulation (default=20.0)
plot (default=’species’) select output data

‘species’

‘rates’

‘all’ both species and rates

fmt plot format, UPI backend dependent (default=’’) or the CommonStyle ‘lines’ or ‘points’.
filename if not None (default) then the plot is exported as filename.png

Calls: - Simulate() - SimPlot()

doState()[source]¶

Calculate the steady-state solution of the system.

Calls: State()

Arguments: None

doStateShow()[source]¶

Calculate the steady-state solution of a system and show the results.

Calls: State() showState()

Arguments: None

exportSimAsSedML(output='files', return_sed=False, vc_given='PySCeS', vc_family='Software', vc_email='', vc_org='pysces.sourceforge.net')[source]¶

Exports the current simulation as SED-ML in various ways it creates and stores the SED-ML files in a folder generated from the model name.

output [default=’files’] the SED-ML export type can be one or more comma separated e.g. ‘files,combine’

files export the plain SBML and SEDML XML files

archive export as a SED-ML archive <file>.sedx containing the SBML and SEDML xml files

combine export as a COMBINE archive <file>.omex containing the SBML, SEDML, manifest (XML) and metadata (RDF) - vc_given [default=’PySCeS’] - vc_family [default=’Software’] - vc_email [default=’bgoli@users.sourceforge.net’] - vc_org [default=’<pysces.sourceforge.net>’]

random = <module 'pysces.PyscesRandom' from '../../pysces/PyscesRandom.py'>¶

reLoad(stoich_load=0)[source]¶

Re-load and instantiate a PySCeS model so that it can be used for further analyses. This is just a convenience call to the ModelLoad() method.

stoich_load try to load a structural analysis saved with Stoichiometry_Save_Serial() (default=0)

property scan¶

showCC(File=None)[source]¶

Print all control coefficients as ‘LaTex’ formatted strings to the screen or file.

Arguments:

File [default=None]: an open, writable Python file object

showConserved(File=None, screenwrite=1, fmt='%2.3f')[source]¶

Print the moiety conserved cycles present in the system.

Arguments:

File [default=None]: an open writable Python file object screenwrite [default=1]: write results to console (0 means no reponse) fmt [default=’%2.3f’]: the output number format string

showEigen(File=None)[source]¶

Print the eigenvalues and stability analysis of a system generated with EvalEigen() to the screen or file.

Arguments:

File [default=None]: an open, writable Python file object

showElas(File=None)[source]¶

Print all elasticities to screen or file as ‘LaTeX’ compatible strings. Calls showEvar() and showEpar()

Arguments:

File [default=None]: an open writable Python file object

showEpar(File=None)[source]¶

Write out all nonzero parameter elasticities as ‘LaTeX’ formatted strings, alternatively write to file.

Arguments:

File [default=None]: an open writable Python file object

showEvar(File=None)[source]¶

Write out all variable elasticities as ‘LaTeX’ formatted strings, alternatively write results to a file.

Arguments:

File [default=None]: an open writable Python file object

showFluxRelationships(File=None)[source]¶

showConserved(File=None)

Print the flux relationships present in the system.

Arguments:

File [default=None]: an open writable Python file object

showK(File=None, fmt='%2.3f')[source]¶

Print the Kernel matrix (K), including row and column labels to screen or File.

Arguments:

File [default=None]: an open, writable Python file object fmt [default=’%2.3f’]: output number format

showL(File=None, fmt='%2.3f')[source]¶

Print the Link matrix (L), including row and column labels to screen or File.

Arguments:

File [default=None]: an open, writable Python file object fmt [default=’%2.3f’]: output number format

showModel(filename=None, filepath=None, skipcheck=0)[source]¶

The PySCeS ‘save’ command, prints the entire model to screen or File in a PSC format. (Currently this only applies to basic model attributes, ! functions are not saved).

Arguments:

filename [default=None]: the output PSC file filepath [default=None]: the output directory skipcheck [default=0]: skip check to see if the file exists (1) auto-averwrite

showModifiers(File=None)[source]¶

Prints the current value of the model’s modifiers per reaction to screen or file.

Arguments:

File [default=None]: an open, writable Python file object

showN(File=None, fmt='%2.3f')[source]¶

Print the stoichiometric matrix (N), including row and column labels to screen or File.

Arguments:

File [default=None]: an open, writable Python file object fmt [default=’%2.3f’]: output number format

showNr(File=None, fmt='%2.3f')[source]¶

Print the reduced stoichiometric matrix (Nr), including row and column labels to screen or File.

Arguments:

File [default=None]: an open, writable Python file object fmt [default=’%2.3f’]: output number format

showODE(File=None, fmt='%2.3f')[source]¶

Print a representation of the full set of ODE’s generated by PySCeS to screen or file.

Arguments:

File [default=None]: an open, writable Python file object fmt [default=’%2.3f’]: output number format

showODEr(File=None, fmt='%2.3f')[source]¶

Print a representation of the reduced set of ODE’s generated by PySCeS to screen or file.

Arguments:

File [default=None]: an open, writable Python file object fmt [default=’%2.3f’]: output number format

showPar(File=None)[source]¶

Prints the current value of the model’s parameter values (mod.P) to screen or file.

Arguments:

File [default=None]: an open, writable Python file object

showRate(File=None)[source]¶

Prints the current rates of all the reactions using the current parameter values and species concentrations

File an open, writable Python file object (default=None)

showRateEq(File=None)[source]¶

Prints the reaction stoichiometry and rate equations to screen or File.

Arguments:

File [default=None]: an open, writable Python file object

showSpecies(File=None)[source]¶

Prints the current value of the model’s variable species (mod.X) to screen or file.

Arguments:

File [default=None]: an open, writable Python file object

showSpeciesFixed(File=None)[source]¶

Prints the current value of the model’s fixed species values (mod.X) to screen or file.

Arguments:

File [default=None]: an open, writable Python file object

showSpeciesI(File=None)[source]¶

Prints the current value of the model’s variable species initial values (mod.X_init) to screen or file.

Arguments:

File [default=None]: an open, writable Python file object

showState(File=None)[source]¶

Prints the result of the last steady-state analyses. Both steady-state flux’s and species concentrations are shown.

Arguments:

File [default=None]: an open, writable Python file object

property sim¶

class pysces.PyscesModel.ReactionObj(mod, name, kl, klrepl='self.')[source]¶

Defines a reaction with a KineticLaw kl8, *formula and name bound to a model instance, mod.

code_string = None¶

compartment = None¶

formula = None¶

mod = None¶

piecewises = None¶

rate = None¶

setKineticLaw(kl, klrepl='self.')[source]¶

symbols = None¶

xcode = None¶

class pysces.PyscesModel.ScanDataObj(par_label)[source]¶

New class used to store parameter scan data (uses StateDataObj)

ALL_VALID = True¶

HAS_FLUXES = False¶

HAS_MOD_DATA = False¶

HAS_RULES = False¶

HAS_SET_LABELS = False¶

HAS_SPECIES = False¶

HAS_XDATA = False¶

OPEN = True¶

addModData(mod, *args)[source]¶

addPoint(ipar, ssdata)[source]¶: takes a list/array of input parameter values and the associated ssdata object

closeScan()[source]¶

flux_labels = None¶

fluxes = None¶

getAllScanData(lbls=False)[source]¶

getFluxes(lbls=False)[source]¶

getModData(lbls=False)[source]¶

getRules(lbls=False)[source]¶

getScanData(*args, **kwargs)[source]¶: getScanData(*args) feed this method species/flux/rule/mod labels and it will return an array of [parameter(s), sp1, f1, ….]

getSpecies(lbls=False)[source]¶

getXData(lbls=False)[source]¶

invalid_states = None¶

mod_data = None¶

mod_data_labels = None¶

parameter_labels = None¶

parameters = None¶

rules = None¶

rules_labels = None¶

setLabels(ssdata)[source]¶

species = None¶

species_labels = None¶

xdata = None¶

xdata_labels = None¶

class pysces.PyscesModel.StateDataObj[source]¶

New class used to store steady-state data.

HAS_FLUXES = False¶

HAS_RULES = False¶

HAS_SPECIES = False¶

HAS_XDATA = False¶

IS_VALID = True¶

flux_labels = None¶

fluxes = None¶

getAllStateData(lbls=False)[source]¶: Return all available data as species+fluxes+rules if lbls=True returns (array,labels) else just array

getFluxes(lbls=False)[source]¶: return flux array

getRules(lbls=False)[source]¶: Return rule array

getSpecies(lbls=False)[source]¶: return species array

getStateData(*args, **kwargs)[source]¶: getSimData(*args) feed this method species/rate labels and it will return an array of [time, sp1, r1, ….]

getXData(lbls=False)[source]¶: Return xdata array

rules = None¶

rules_labels = None¶

setFluxes(fluxes, lbls=None)[source]¶: set the flux array

setRules(rules, lbls=None)[source]¶: Set the results of rate rules

setSpecies(species, lbls=None)[source]¶: Set the species array

setXData(xdata, lbls=None)[source]¶: Sets extra simulation data

species = None¶

species_labels = None¶

xdata = None¶

xdata_labels = None¶

class pysces.PyscesModel.WasteManagement[source]¶

pysces.PyscesModel.chkmdir()[source]¶

Import and grab pysces.model_dir

Arguments: None

pysces.PyscesModel.chkpsc(File)[source]¶

Chekc whether the filename “File” has a ‘.psc’ extension and adds one if not.

Arguments:

File: filename string

PyscesScan¶

PySCeS classes for continuations and multi-dimensional parameter scans

class pysces.PyscesScan.PITCONScanUtils(model)[source]¶

Static Bifurcation Scanning utilities using PITCON, call with loaded model object. Hopefully nobody else was trying to use the older class as it was horrible. This new one is is leaner, meaner and pretty cool ;-)

analyseData(analysis='elas')[source]¶

Performs “analysis” on the PITCON generated set of steady-state results where analysis is:

‘elasv’ = variable elasticities
‘elasp’ = parameter elasticities
‘elas’ = all elasticities
‘mca’ = control coefficients
‘resp’ = response coefficients
‘eigen’ = eigen values
‘all’ = all of the above

Higher level analysis types automatically enable the lower level analysis needed e.g. selecting ‘mca’ implies ‘elasv’ etc. User output defined with mod.setUserOutput() is stored in the mod.res_user array.

getArrayListAsArray(array_list)[source]¶: Stack (concatenate) the list of arrays into a single array.

model = None¶

pitcon_range_high = None¶

pitcon_range_low = None¶

pitcon_res = None¶

pitcon_scan_density = None¶

pitcon_scan_parameter = None¶

pitcon_scan_parameter_3d = None¶

res_eigen = None¶

res_flux = None¶

res_idx = None¶

res_metab = None¶

res_user = None¶

runContinuation(parameter, low, high, density, par3d=None, logrange=True, runQuiet=True)[source]¶

Run the continuation using the following parameters:

Args:

parameter = str(the parameter to be scanned)
low = float(lower bound)
high = float(upper bound)
density = int(the number of initial points)
par3d = float(extra 3d parameter to insert into the output array) this parameter is not set ONLY used in output
logrange = boolean [default = True], if True generate the result using logspace(log10(low), log10(high), density) otherwise use a linear range
runQuiet = boolean [default = True], if True do not display intermediate results to screen, disable for debugging

After running the continuation the results are stored in numpy arrays

mod.res_idx = scan parameter values (and optionally par3d)
mod.res_metab = steady-state species concentrations
mod.res_flux = steady-state flux values

setUserOuput(*args)[source]¶: Set the user output required as n string arguments.

timer = None¶

user_output = None¶

class pysces.PyscesScan.Scanner(mod)[source]¶

Arbitrary dimension generic scanner. This class is initiated with a loaded PySCeS model and then allows the user to define scan parameters see self.addScanParameter() and user output see self.addUserOutput(). Steady-state results are always stored in self.SteadyStateResults while user output can be found in self.UserOutputResults - brett 2007.

Analyze()[source]¶: The analysis method, the mode is automatically set by the self.addUserOutput() method but can be reset by the user.

HAS_STATE_OUTPUT = True¶

HAS_USER_OUTPUT = False¶

MSG_PRINT_INTERVAL = 500¶

Run(ReRun=False)[source]¶: Run the parameter scan

RunAgain()[source]¶: While it is impossible to change the generator/range structure of a scanner (just build another one) you can ‘in principle’ change the User Output and run it again.

StoreData()[source]¶: Internal function which concatenates and stores the data generated by Analyze.

addScanParameter(name, start, end, points, log=False, follower=False)[source]¶

Add a parameter to scan (an axis if you like) input is:

str(name) = model parameter name
float(start) = lower bound of scan
float(end) = upper bound of scan
int(points) = number of points in scan range
bool(log) = Use a logarithmic (base10) range
bool(follower) = Scan parameters can be leaders i.e. an independent axis or a “follower” which moves synchronously with the previously defined parameter range.

The first ScanParameter cannot be a follower.

addUserOutput(*kw)[source]¶: Add output parameters to the scanner as a collection of one or more string arguments (‘O1’,’O2’,’O3’, ‘On’). These are evaluated at each iteration of the scanner and stored in the self.UserOutputResults array. The list of output is stored in self.UserOutputList.

genOn = True¶

getOutput()[source]¶: Will be the new output function.

getResultMatrix(stst=False, lbls=False)[source]¶

Returns an array of result data. I’m keepin this for backwards compatibility but it will be replaced by a getOutput() method when this scanner is updated to use the new data_scan object.

stst add steady-state data to output array
lbls return a tuple of (array, column_header_list)

If stst is True output has dimensions [scan_parameters]+[state_species+state_flux]+[Useroutput] otherwise [scan_parameters]+[Useroutput].

invalid_state_list = None¶

invalid_state_list_idx = None¶

makeRange(start, end, points, log)[source]¶

Should be pretty self evident it defines a range:

float(start)
float(end)
int(points)
bool(log)

nan_on_bad_state = True¶

quietRun = False¶

rangeGen(name, start, end, points, log)[source]¶

This is where things get more interesting. This function creates a cycling generator which loops over a parameter range.

parameter name
start value
end value
points
log scale

resetInputParameters()[source]¶: Just remembered what this does, I think it resets the input model parameters after a scan run.

setModValue(name, value)[source]¶: An easy one, assign value to name of the instantiated PySCeS model attribute

stepGen(offset)[source]¶: Another looping generator function. The idea here is to create a set of generators for the scan parameters. These generators then all fire together and determine whether the range generators should advance or not. Believe it or not this dynamically creates the matrix of parameter values to be evaluated.

testInputParameter(name)[source]¶: This tests whether a str(name) is an attribute of the model

PyscesInterfaces¶

Interfaces converting to and from PySCeS models - makes use of Brett’s Core2

class pysces.PyscesInterfaces.Core2interfaces[source]¶

Defines interfaces for translating PySCeS model objects into and from other formats.

convertSBML2PSC(sbmlfile, sbmldir=None, pscfile=None, pscdir=None)[source]¶

Convert an SBML file to a PySCeS MDL input file.

sbmlfile: the SBML file name
sbmldir: the directory of SBML files (if None current working directory is assumed)
pscfile: the output PSC file name (if None sbmlfile.psc is used)
pscdir: the PSC output directory (if None the pysces.model_dir is used)

core = None¶

core2psc = None¶

core2sbml = None¶

readMod2Core(mod, iValues=True)[source]¶

Convert a PySCeS model object to core2

iValues: if True then the models initial values are used (or the current values if False).

readSBMLToCore(filename, directory=None)[source]¶

Reads the SBML file specified with filename and converts it into a core2 object pysces.interface.core

filename: the SBML file
directory: (optional) the SBML file directory None means try the current working directory

sbml = None¶

sbml2core = None¶

sbml_level = 2¶

sbml_version = 1¶

writeCore2PSC(filename=None, directory=None, getstrbuf=False)[source]¶

Writes a Core2 object to a PSC file.

filename: writes <filename>.xml or <model_name>.xml if None
directory: (optional) an output directory
getstrbuf: if True a StringIO buffer is returned instead of writing to disk

writeCore2SBML(filename=None, directory=None, getdocument=False)[source]¶

Writes Core2 object to an SBML file.

filename: writes <filename>.xml or <model_name>.xml if None
directory: (optional) an output directory
getdocument: if True an SBML document object is returned instead of writing to disk or

writeMod2PSC(mod, filename=None, directory=None, iValues=True, getstrbuf=False)[source]¶

Writes a PySCeS model object to a PSC file.

filename: writes <filename>.psc or <model_name>.psc if None
directory: (optional) an output directory
iValues: if True then the models initial values are used (or the current values if False).
getstrbuf: if True a StringIO buffer is returned instead of writing to disk

writeMod2SBML(mod, filename=None, directory=None, iValues=True, getdocument=False, getstrbuf=False)[source]¶

Writes a PySCeS model object to an SBML file.

filename: writes <filename>.xml or <model_name>.xml if None
directory: (optional) an output directory
iValues: if True then the models initial values are used (or the current values if False).
getdocument: if True an SBML document object is returned instead of writing to disk or
getstrbuf: if True a StringIO buffer is returned instead of writing to disk

PyscesStoich¶

PySCeS stoichiometric analysis classes.

class pysces.PyscesStoich.MathArrayFunc[source]¶

PySCeS array functions - used by Stoich

LinAlgError = 'LinearAlgebraError'¶

MatrixFloatFix(mat, val=1e-15)[source]¶

Clean an array removing any floating point artifacts defined as being smaller than a specified value. Processes an array inplace

Arguments:

mat: the input 2D array val [default=1.e-15]: the threshold value (effective zero)

MatrixValueCompare(matrix)[source]¶

Finds the largest/smallest abs(value) > 0.0 in a matrix. Returns a tuple containing (smallest,largest) values

Arguments:

matrix: the input 2D array

SwapCol(res_a, r1, r2)[source]¶

Swap two columns using BLAS swap, arrays can be (or are upcast to) type double (d) or double complex (D). Returns the colswapped array

Arguments:

res_a: the input array r1: the first column to be swapped r2: the second column to be swapped

SwapCold(res_a, c1, c2)[source]¶

Swaps two double (d) columns in an array using BLAS DSWAP. Returns the colswapped array.

Arguments:

res_a: input array c1: column index 1 c2: column index 2

SwapColz(res_a, c1, c2)[source]¶

Swaps two double complex (D) columns in an array using BLAS ZSWAP. Returns the colswapped array.

Arguments:

res_a: input array c1: column index 1 c2: column index 2

SwapElem(res_a, r1, r2)[source]¶

Swaps two elements in a 1D vector

Arguments:

res_a: the input vector r1: index 1 r2: index 2

SwapRow(res_a, r1, r2)[source]¶

Swaps two rows using BLAS swap, arrays can be (or are upcast to) type double (d) or double complex (D). Returns the rowswapped array.

Arguments:

res_a: the input array r1: the first row index to be swapped r2: the second row index to be swapped

SwapRowd(res_a, c1, c2)[source]¶

Swaps two double (d) rows in an array using BLAS DSWAP. Returns the rowswapped array.

Arguments:

res_a: input array c1: row index 1 c2: row index 2

SwapRowz(res_a, c1, c2)[source]¶

Swaps two double complex (D) rows in an array using BLAS ZSWAP. Returns the rowswapped array.

Arguments:

res_a: input array c1: row index 1 c2: row index 2

array_kind = {'D': 1, 'F': 1, 'd': 0, 'f': 0, 'i': 0, 'l': 0}¶

array_precision = {'D': 1, 'F': 0, 'd': 1, 'f': 0, 'i': 1, 'l': 1}¶

array_type = [['f', 'd'], ['F', 'D']]¶

assertRank2(\*arrays)[source]¶

Check that we are using a 2D array

Arguments:

*arrays: input array(s)

castCopyAndTranspose(type, \*arrays)[source]¶

Cast numeric arrays to required type and transpose

Arguments:

type: the required type to cast to *arrays: the arrays to be processed

commonType(\*arrays)[source]¶

Numeric detect and set array precision (will be replaced with new scipy.core compatible code when ready)

Arguments:

*arrays: input arrays

class pysces.PyscesStoich.Stoich(input)[source]¶

PySCeS stoichiometric analysis class: initialized with a stoichiometric matrix N (input)

AnalyseK()[source]¶

Evaluate the stoichiometric matrix and calculate the nullspace using LU decomposition and backsubstitution . Generates the MCA K and Ko arrays and associated row and column vectors

Arguments: None

AnalyseL()[source]¶

Evaluate the stoichiometric matrix and calculate the left nullspace using LU factorization and backsubstitution. Generates the MCA L, Lo, Nr and Conservation matrix and associated row and column vectors

Arguments: None

BackSubstitution(res_a, row_vector, column_vector)[source]¶

Jordan reduction of a scaled upper triangular matrix. The returned array is now in the form [I R] and can be used for nullspace determination. Modified row and column tracking vetors are also returned.

Arguments:

res_a: unitary pivot upper triangular matrix row_vector: row tracking vector column_vector: column tracking vector

GetUpperMatrix(a)[source]¶

Core analysis algorithm; an input is preconditioned using PivotSort_initial and then cycles of PLUfactorize and PivotSort are run until the factorization is completed. During this process the matrix is reordered by column swaps which emulates a full pivoting LU factorization. Returns the pivot matrix P, upper factorization U as well as the row/col tracking vectors.

Arguments:

a: a stoichiometric matrix

GetUpperMatrixUsingQR(a)[source]¶

GetUpperMatrix(a)

Core analysis algorithm; an input is preconditioned using PivotSort_initial and then cycles of PLUfactorize and PivotSort are run until the factorization is completed. During this process the matrix is reordered by column swaps which emulates a full pivoting LU factorization. Returns the pivot matrix P, upper factorization U as well as the row/col tracking vectors.

Arguments:

a: a stoichiometric matrix

K_split_R(R_a, row_vector, column_vector)[source]¶

Using the R factorized form of the stoichiometric matrix we now form the K and Ko matrices. Returns the r_ipart,Komatrix,Krow,Kcolumn,Kmatrix,Korow,info

Arguments:

R_a: the Gauss-Jordan reduced stoichiometric matrix row_vector: row tracking vector column_vector: column tracking vector

L_split_R(Nfull, R_a, row_vector, column_vector)[source]¶

Takes the Gauss-Jordan factorized N^T and extract the L, Lo, conservation (I -Lo) and reduced stoichiometric matrices. Returns: lmatrix_col_vector, lomatrix, lomatrix_row, lomatrix_co, nrmatrix, Nred_vector_row, Nred_vector_col, info

Arguments:

Nfull: the original stoichiometric matrix N R_a: gauss-jordan factorized form of N^T row_vector: row tracking vector column_vector: column tracking vector

PLUfactorize(a_in)[source]¶

Performs an LU factorization using LAPACK D/ZGetrf. Now optimized for FLAPACK interface. Returns LU - combined factorization, IP - rowswap information and info - Getrf error control.

Arguments:

a_in: the matrix to be factorized

PivotSort(a, row_vector, column_vector)[source]¶

This is a sorting routine that accepts a matrix and row/colum vectors and then sorts them so that: there are no zero rows (by swapping with first non-zero row) The abs(largest) pivots are moved onto the diagonal to maintain numerical stability. Row and column swaps are recorded in the tracking vectors.

Arguments:

a: the input array row_vector: row tracking vector column_vector: column tracking vector

PivotSort_initial(a, row_vector, column_vector)[source]¶

This is a sorting routine that accepts a matrix and row/colum vectors and then sorts them so that: the abs(largest) pivots are moved onto the diagonal to maintain numerical stability i.e. the matrix diagonal is in descending max(abs(value)). Row and column swaps are recorded in the tracking vectors.

Arguments:

a: the input array row_vector: row tracking vector column_vector: column tracking vector

SVD_Rank_Check(matrix=None, factor=10000.0, resultback=0)[source]¶

Calculates the dimensions of L/L0/K/K) by way of SVD and compares them to the Guass-Jordan results. Please note that for LARGE ill conditioned matrices the SVD can become numerically unstable when used for nullspace determinations

Arguments:

matrix [default=None]: the stoichiometric matrix default is self.Nmatrix factor [default=1.0e4]: factor used to calculate the ‘zero pivot’ mask = mach_eps*factor resultback [default=0]: return the SVD results, U, S, vh

ScalePivots(a_one)[source]¶

Given an upper triangular matrix U, this method scales the diagonal (pivot values) to one.

Arguments:

a_one: an upper triangular matrix U

SplitLU(plu, row, col, t)[source]¶

PLU takes the combined LU factorization computed by PLUfactorize and extracts the upper matrix. Returns U.

Arguments:

plu: LU factorization row: row tracking vector col: column tracking vector t [default=None)]: typecode argument (currently not used)

USE_QR = False¶

info_moiety_conserve = False¶

class pysces.PyscesStoich.StructMatrix(array, ridx, cidx, row=None, col=None)[source]¶

This class is specifically designed to store structural matrix information give it an array and row/col index permutations it can generate its own row/col labels given the label src.

array = None¶

cidx = None¶

col = None¶

getByIdx(row, col)[source]¶

getByName(row, col)[source]¶

getColsByIdx(*args)[source]¶: Return the columns referenced by index (1,3,5)

getColsByName(*args)[source]¶: Return the columns referenced by label (‘s’,’x’,’d’)

getIndexes(axis='all')[source]¶: Return the matrix indexes ([rows],[cols]) where axis=’row’/’col’/’all’

getLabels(axis='all')[source]¶: Return the matrix labels ([rows],[cols]) where axis=’row’/’col’/’all’

getRowsByIdx(*args)[source]¶: Return the rows referenced by index (1,3,5)

getRowsByName(*args)[source]¶: Return the rows referenced by label (‘s’,’x’,’d’)

ridx = None¶

row = None¶

setByIdx(row, col, val)[source]¶

setByName(row, col, val)[source]¶

setCol(src)[source]¶: Assuming that the col index array is a permutation (full/subset) of a source label array by supplying that src to setCol maps the row labels to cidx and creates self.col (col label list)

setRow(src)[source]¶: Assuming that the row index array is a permutation (full/subset) of a source label array by supplying that source to setRow it maps the row labels to ridx and creates self.row (row label list)

shape = None¶

PyscesLink¶

Interfaces to external software and API’s, has replaced the PySCeS contrib classes.

class pysces.PyscesLink.METATOOLlink(mod, __metatool_path__=None)[source]¶

New interface to METATOOL binaries

doEModes()[source]¶

Calculate the elementary modes by way of an interface to MetaTool.

METATOOL is a C program developed from 1998 to 2000 by Thomas Pfeiffer (Berlin) in cooperation with Stefan Schuster and Ferdinand Moldenhauer (Berlin) and Juan Carlos Nuno (Madrid). http://www.biologie.hu-berlin.de/biophysics/Theory/tpfeiffer/metatool.html

Arguments: None

getEModes()[source]¶: Returns the elementary modes as a linked list of fluxes

showEModes(File=None)[source]¶

Print the results of an elementary mode analysis, generated with doEModes(), to screen or file.

Arguments: File [default=None]: Boolean, if True write parsed elementary modes to file

class pysces.PyscesLink.SBWLayoutWebLink[source]¶

Enables access to DrawNetwork and SBMLLayout web services at www.sys-bio.org

DEBUGLEVEL = 1¶

DEBUGMODE = False¶

DRAWNETWORKLOADED = False¶

LAYOUTMODULELOADED = False¶

drawNetworkGetSBMLwithLayout()[source]¶

drawNetworkLoadSBML()[source]¶

getSBML()[source]¶

getSBMLlayout()[source]¶

getSVG()[source]¶

getVersion()[source]¶

layoutModuleGetSVG()[source]¶

layoutModuleLoadSBML()[source]¶

loadSBMLFileFromDisk(File, Dir=None)[source]¶

loadSBMLFromString(str)[source]¶

sbml = None¶

sbmllayout = None¶

sbwhost = '128.208.17.26'¶

setProxy(**kwargs)[source]¶

Set as many proxy settings as you need. You may supply a user name without a password in which case you will be prompted to enter one (once) when required (NO guarantees, implied or otherwise, on password security AT ALL). Arguments can be:

user = ‘daUser’, pwd = ‘daPassword’, host = ‘proxy.paranoid.net’, port = 3128

svg = None¶

urlGET(host, urlpath)[source]¶

urlPOST(host, urlpath, data)[source]¶

class pysces.PyscesLink.SBWlink[source]¶

Generic access for local SBW services using SBWPython

SBW_exposeAll(module)[source]¶

SBW_getActiveModules()[source]¶

SBW_loadModule(module_name)[source]¶

moduleDict = None¶

modules = None¶

psbw = None¶

sbw = None¶

sbwModuleProxy = None¶

PySCeS User Guide¶

Introduction¶

Getting started¶

Loading PySCeS¶

Creating a PySCeS model object¶

Advanced¶

Loading the model object¶

Basic model attributes¶

Groups of model properties (either tuples, lists or dictionaries)¶

Advanced¶

Modelling¶

Structural Analysis¶

Structural Analysis - new objects¶

Structural Analysis - legacy¶

Time simulation¶

Simulation results¶

Advanced¶

Steady-state analysis¶

The steady-state data object¶

Stability analysis¶

Metabolic Control Analysis¶

Elasticities¶

Control coefficients¶

Response coefficients¶

Response coefficients with respect to moiety-conserved sums¶

Parameter scanning¶

Single dimension parameter scans¶

Two-dimensional parameter scans¶

Multi-dimensional parameter scans¶

Parallel parameter scans¶

Plotting¶

Displaying data¶

Displaying/saving model attributes¶

Writing formatted arrays¶

Write_array()¶

Write_array_latex()¶

Installing and configuring¶

General requirements¶

Installation¶

Compilation from source¶

Windows build¶

Linux build¶

macOS build¶

Configuration¶

References¶

Input file guide¶

The PySCeS Model Description Language¶

Defining a PySCeS model¶

A kinetic model¶

Model keywords¶

Global unit definition¶

Symbol names and comments¶

Compartment definition¶

Function definitions¶

Defining fixed species¶

Reaction stoichiometry and rate equations¶

Species and parameter initialisation¶

Advanced model construction¶

Assignment rules¶

Rate rules¶

Events¶

Piecewise¶

Reagent placeholder¶

Example PySCeS input files¶

Basic model definition¶

Advanced example¶

Module documentation¶

PySCeS Module documentation¶

PyscesUtils¶

PyscesPlot2¶

PyscesModel¶

PyscesScan¶

PyscesInterfaces¶

PyscesStoich¶

PyscesLink¶

Indices and tables¶

`Write_array()`¶

`Write_array_latex()`¶