colomoto / biolqm Goto Github PK

When showing the stable states for a model, a header line should give component names as well

Hi,

Is Avatar implemented in bioLQM? I couldn't find any info on the colomoto site or command-line descriptions.

I would like to run many mutations using avatar and automate the process, if possible.

Best,
y

The trapspace tool could optionally show the computed values of the extra model components

A bioLQM model has a list of "core" components, but also some "extra" components: they have functions, but they can not be used in the functions of others. When loading a model, this list is empty, but it is filled with "reduced" components to be able to retrieve their value when we need it. This issue lists various places which could make use of these extra components.

• Fixpoint tool #13
• Trapspace tool #14
• Strip (some) extra components

the exports to cnet and bnet only work for boolean models but it is not tested whether the model is boolean or not.

The SBML qual format can contain layout information through the layout and render extensions. Currently, this information is lost during SBML -> SBML conversion (even without intermediate modification steps).

• Add layout information on top of the model
• Load and save this layout information in SBML qual formats
• Preserve it across model modifications

Stochastic simulations can yield different results depending on a random seed. While this seed should not be manually selected for most analyses, it can be useful to specify it during testing.

We currently have updaters for the classical (a)synchronous methods, as well as for the (block-)sequential, we should also handle GINsim's priority classes.

Hi,

I am using BioLQM to convert an SBMLqual file to bnet.

The input SBMLqual file describes a system of 3 nodes sA, sB, sX, and the only transition is sX = sA | sB. Here is the content of the math tag of the SBML describing this transition :

            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <apply><or/>
                <apply><eq/>
                  <ci>sA</ci>
                  <cn type="integer">1</cn>
                </apply>
                <apply><eq/>
                  <ci>sB</ci>
                  <cn type="integer">1</cn>
                </apply>
              </apply>
            </math>

In the resulting bnet file, I obtained sX, !sB&sA | sB.

I know that (!B&A) | B is equivalent to A | B, but I am wondering why I don't obtain the exact equivalent of what is wrote in the SBMLqual. Is there any reason to have picked this form, or is it a weird bug ?

The fixpoint tool could optionally show the computed values of the extra model components

While they are not used for dynamical analysis, model annotation are a crucial part of the modelling process. BioLQM should be able to load and save annotations for the SBML format.

SBML qual supports annotation in any format, attached to any element of a model. The full scope of possible annotations will not be supported, but bioLQM aims to encourage good practices.

We plan to start with basic MIRIAM annotations on the model itself and on it's components before extending the support to follow the needs of the community.

Currently, when a qualitativeSpecies has no maxLevel, it gets a max of 1 by default. In this case, the max should be extracted from the logical functions instead.

Hi Aurelien,
I want to use your tool to test a lot of perturbations (mostly more than one at a time) on my model. One perturbation worked fine for me, but double doesn't, it just gives me the unperturbed attractors. So when I say "A%1" that works, but "A%1,B%1" even A and B are not restricted.
I noticed that your example in the colomoto notebook "bioLQM_tutorial.ipynb" does the same thing, when you set "CycD%1" it only gives you the cyclic attractor with CycD=1, but if you do the combination "CycD%1,Rb%1" you get your original unperturbed attractors.

What does work is redefining the model twice:
pert = biolqm.perturbation(model, "A%1")
pert2 = biolqm.perturbation(pert, "B%1")

But that would be much more complicated, when trying to automate testing for > 100 perturbations with varying numbers of alterations.

Cheers, Kirsten

When applying "booleanize" modification and then "perturbation" on the resulting model, an infinite recursion occurs leading to stack overlowing.
Here is a notebook showing the behaviour:
https://nbviewer.jupyter.org/gist/pauleve/b413da4ffeeddddb7563799b0a8c02c9

The IDs of inputs should be recognised as valid threshold values in the SBML import (now they trigger exception).

Hi, I saw that bioLQM is supporting the SIF format.
I've been switching from SIF to CIF (complex interaction format) for my application.
To enhance the interoperability with other tools that use SIF i was thinking about writing a CIF2SIF converter.
I saw that you also support Boolean formats which are very close to CIF.
So i was wondering whether you are interested in implementing CIF support in bioLQM?

if I use punctutions like ? " . in comments the parser currently throws an token recognition error at error. this booleannet file

# this is a comment?
EGF *= 1
ERBB1 *= EGF

does not parse

When converting a sbml-qual model to bnet, pint, etc., bioLQM uses the nodeID as variable name. It would be useful to be able to choose to use the name instead.

Here is a test model:
model.sbml.txt

The conversion will output nodes with names of the form S_X, whereas pretty name are also loaded.

the current SBML import supports very few logical operations in the function import. Extra comparisons must be added