SymCA enhancement (see note)

Note:

This release is essentially identical to 0.8.5 with the version number being increased for technical reasons. We therefore repeat the release notes of 0.8.5 here.

Summary of changes

The main changes in this release are:

• SymCA update
• Documentation and README updates
• Bugfixes

SymCA update

For this release we have improved support for SymCA to perform symbolic control analysis on models that cannot reach a steady state. Now SymCA can yield valid control coefficient expressions even if no numerical MCA values are available (values are assigned to each control coefficient based on the assumption that species concentrations, reaction rates, and elasticity coefficients are all equal to 1).

This is useful for when information regarding the control structure of a pathway is desired for systems where only the network topology is known. However, this functionality is available for any models (regardless of their ability to reach a valid steady state).

If only the network topology is known, models must be coded as described below.

Reactions with no allosteric effectors are coded as follows in the psc model:

R1:
    S1 = S2
    v1

Where R1 catalyses the conversion of the S1 species to S2, using the dummy rate v1 (set to any non-zero number elsewhere in the model).

In the case where a reaction does have an allosteric effector it is coded as follows:

R1:
    S1 = S2
    v1*S3

Thus the only change is that the allosteric effector S3 is included by multiplying the dummy rate v1 by the S3 concentration. How it is included in the dummy rate equation (through multiplication, addition, etc.) is of no consequence as the rates in this model will be meaningless in any case. This does, however, allow PySCeS to pick the species up as an allosteric effector.

After loading a model with PySCeS, must instantiate the SymCA object with the argument python ignore_steady_state set to True as follows:

mod = pysces.model('test_model.psc')
sc = psctb.Symca(mod, ignore_steady_state=True)

Further steps are the same as previously outlined (see the documentation).

Documentation and README updates

The README has been shortened with some of its contents being moved to the documentation. The documentation now includes detailed step-by-step instructions on installing PySCeSToolbox on any of Mac OS X, Linux and Windows.

Minor bugfixes

Symca now gives the correct error message when Maxima is not installed on Linux and Mac (previously a message containing reference to Windows directories was shown).