cnapy-org / cnapy Goto Github PK

New structure simply projects

SmallExample2 - SmallExample2.cna
              - Smallexample2-map1.map
              - scenario1.scen
              - background-map1.svg
              - verycool.modes
...

Start with $User/CNA-projects.

Needs investigation

• remove close button on tabs
• add delete map button next to add map button

Only flux ranges that exclude 0 should be painted green

• Clear scenario
• Restore scenario
• Turn heatmap coloring on
• Turn On/Off coloring on

Instead of double click on a reaction box in the map view add a entry to the context menu of the reaction box.

Elementary mode computation can consider 0 values in the scenario.
Maybe we should keep those and restore them after the ModeNavigator is closed.
Maybe make the "consider 0 values" option default.

net_conversion.m uses get_rates.m which grabs the values from the CNA map.

Don't know about this. I think it should probably only be removed if the reaction is removed. The scenario value would still be visible in the reaction list.
Related: Don't load scenario values for reactions that are not in the current model.

• We do read and show the cobra annotation for reactions.

But cobra does it's own parsing of the annotations

<reaction id="R_ULA4Ntppi" fast="false" reversible="false" name="Transport (cytoplasm to periplasm)" metaid="R_ULA4Ntppi" sboTerm="SBO:0000185" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
  <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
      <rdf:Description rdf:about="#R_ULA4Ntppi">
        <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
          <rdf:Bag>
            <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/ULA4Ntppi"/>
            <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR105114"/>
            <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn09357"/>
          </rdf:Bag>
        </bqbiol:is>
      </rdf:Description>
    </rdf:RDF>
  </sbml:annotation>

and is returning a bunch of identifiers

{'sbo': 'SBO:0000185', 'bigg.reaction': 'ULA4Ntppi', 'metanetx.reaction': 'MNXR105114', 'seed.reaction': 'rxn09357'}

I have no idea how we could get our metadata into this scheme.

The buttons are disabled for now.

• Number of reactions, metabolites
• Stoichiometric matrix infos
• conservation relations
• degrees of freedom
• smallest/largest absolute value > 0 in matrix

STOICHIOMETRIC MATRIX (without external metabolites):
     6 internal (balanced) metabolites (rows)
     10 reactions (columns), thereof 2 reversible
     Rank of stoichiometric matrix: 6
          --> No conservation relation(s) exist.
     Degrees of freedom: 4
 
     Smallest (absolute) non-zero-value: 1
     Largest (absolute) value: 1
 
     Network can be compressed to (isozymes not considered): 
          2 metabolites 
          6 reactions (thereof 2 reversible)

• Model Annotations

• CNA path
• Colors
• Shown number of digits after decimal point
• Defaultcolor : Qt.gray
• self.abs_tol : 0.0001
• Working directory should better be set to last used(open/save) directory

Not sure yet how this is done best.
In some sense the bounds on the models reaction represent itself a scenario.
Should constraints from an default scenario would overwrite these bounds?

Example: in the model has reaction R the bounds -10>=,<=5
in the scenario the bounds are set to 6>=,<=10.

I see two ways to interpret this situation and I'm not yet sure which to choose:

1. If i give both constraints there would be no solution.
2. if the scenario replaces the models constraint there are solutions

use this wiki https://github.com/ARB-Lab/CNApy/wiki/CNApy-User-Manual

Maybe use pyqtconsole?
pyqtconsole is using PyQt5 while we are using PySide2 as qt bindings also it has no conda package.
qtconsole looks like a larger more active project they also have conda packages and may work with PySide2 via qtpy.

I think this should be reimplemented in python. It looks like the glue code would be more than the current implementation.

Currently a scenario is only a set of fixed reaction rates.
In future it would be nice to allow complex constraints like in this example.

P:ex -> R3

I see 3 approaches

1. automatically remove unused species if the model changes
2. add a function to remove unused species on demand
3. add a button to remove species manually

• Last project file
• Last scenario
• Window position/size
• etc.

Basic version is working. This needs the cnapy_compute_mcs.m from CellNetAnalyzer master.

For the following cases we need a message box!

• FBA returns infeasible
• pFBA returns infeasible
• FVA returns infeasible
• EFM returns no modes
• MCS returns no cut sets

https://cobrapy.readthedocs.io/en/latest/getting_started.html#Genes

Either like cobrapy in the SBML annotations (as RDF) or in a separate file which would be included in the cna project/archive.
Here a list of CNA specific reaction attributes:

• deltaGR_0 : -35.68;
• deltaGR_Uncertainty : 7.97
• KEGG_ID : R08549
• BiGG_ID :AKGDH

and a list of CNA specific species attributes:

• BiGG_ID : 4crsol_p
• Universal_BiGG_ID : 4crsol
• KEGG_ID :
• CHEBI_ID : CHEBI:44726
• Formula : C23H34N7O17P3S
• Charge : NaN

1st case: bound do exclude 0 like (-inf,-1.0) or (1.,200)
2nd case: everything else

On = green = if v != 0

• enable text entry on checking checkbox
• set default to 100