public static void Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("Need one argument, the SBML file to solve");
Environment.Exit(-1);
}
string sbmlContent = File.ReadAllText(args[0]);
FluxBalance fluxBalance = new FluxBalance();
fluxBalance.LoadSBML(sbmlContent);
fluxBalance.Constraints = new List<LPsolveConstraint>(new LPsolveConstraint[] {
new LPsolveConstraint("J1", lpsolve_constr_types.EQ, 10.0),
new LPsolveConstraint("J5", lpsolve_constr_types.EQ, 6.0),
new LPsolveConstraint("J3", lpsolve_constr_types.GE, 1.0)
});
fluxBalance.Objectives = new List<LPsolveObjective>(new LPsolveObjective[] {
new LPsolveObjective("J9", 0.5),
new LPsolveObjective("J8", 0.75)
});
LPsolveSolution result = fluxBalance.Solve();
result.WriteTo(Console.Out);
Console.WriteLine("(any key to continue)");
Console.ReadKey();
}
private static string ConvertSBML(string sbmlContent)
{
FluxBalance fluxBalance = new FluxBalance();
fluxBalance.Mode = FBA_Mode.maximize;
// read SBML
NOM.loadSBML(sbmlContent);
// fix boundary flags
var model = NOM.SbmlModel;
for (int i = 0; i < model.getNumSpecies(); i++)
{
Species species = model.getSpecies(i);
if (species.getId().EndsWith("_b"))
species.setBoundaryCondition(true);
}
// find objective
for (int i = 0; i < model.getNumReactions(); i++)
{
Reaction reaction = model.getReaction(i);
if (reaction.isSetKineticLaw())
{
KineticLaw law = reaction.getKineticLaw();
var parameter = law.getParameter("OBJECTIVE_COEFFICIENT");
if (parameter == null || parameter.getValue() != 1.0)
continue;
fluxBalance.Objectives.Add(new LPsolveObjective(reaction.getId(), 1.0));
reaction.unsetKineticLaw();
}
}
// build constraints
for (int i = 0; i < model.getNumReactions(); i++)
{
Reaction reaction = model.getReaction(i);
if (reaction.isSetKineticLaw())
{
KineticLaw law = reaction.getKineticLaw();
var lowerBound = law.getParameter("LOWER_BOUND");
var upperBound = law.getParameter("UPPER_BOUND");
if (lowerBound == null || upperBound == null) continue;
fluxBalance.Constraints.Add(new LPsolveConstraint(reaction.getId(), lpsolve_constr_types.LE, lowerBound.getValue()));
fluxBalance.Constraints.Add(new LPsolveConstraint(reaction.getId(), lpsolve_constr_types.GE, upperBound.getValue()));
reaction.unsetKineticLaw();
}
}
string newSBML = libsbml.writeSBMLToString(NOM.SbmlDocument);
fluxBalance.SBML = newSBML;
return fluxBalance.WriteSBML();
}
public void loadSBML(string sbmlContent)
{
SBML = Encoding.ASCII.GetString(Encoding.UTF8.GetBytes(sbmlContent));
reactionTextTable = new Hashtable();
_FluxBalance = new FluxBalance(SBML);
if (_FluxBalance.Warnings.Count > 0)
{
MessageBox.Show(this,
_FluxBalance.Warnings[0],
"Warnings occured...", MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
if (_FluxBalance.IsEmpty)
{
MessageBox.Show(this,
"The model you have loaded has an empty Stoichiometry Matrix. As such the model is not suited for Flux Balance Analysis. Please ensure that you loaded a model that uses SBML non-boundary species and reactions.",
"Model not suitable", MessageBoxButtons.OK, MessageBoxIcon.Warning);
}
bool doLayout = true;
if (_FluxBalance.SpeciesNames.Count > 100 || _FluxBalance.ReactionNames.Count > 100)
{
if (MessageBox.Show(this,
string.Format(
"The model you have loaded has {0} species and {1} reactions. Would you still like to generate an image for it? The image is unlikely to provide much information.",
_FluxBalance.SpeciesNames.Count, _FluxBalance.ReactionNames.Count),
"Generate Layout?", MessageBoxButtons.YesNo, MessageBoxIcon.Question) == DialogResult.No)
doLayout = false;
}
if (doLayout)
InitializeLayout(SBML, _FluxBalance);
if (SBMLLayout.Instance.hasLayout())
{
splitContainer2.Panel1Collapsed = false;
SetImage();
}
else
{
splitContainer2.Panel1Collapsed = true;
}
controlSetup1.InitializeFromReactionNames(_FluxBalance.ReactionNames);
controlSetup1.Maximize = _FluxBalance.Mode == FBA_Mode.maximize;
controlSetup1.Minimize = _FluxBalance.Mode == FBA_Mode.minimize;
controlSetup1.Constraints = _FluxBalance.Constraints;
controlSetup1.Objectives = _FluxBalance.Objectives;
}
private void InitializeLayout(string sbmlContent, FluxBalance fluxBalance)
{
// load Layout
SBMLLayout.Instance.loadSBML(sbmlContent);
if (!SBMLLayout.Instance.hasLayout())
{
GenerateLayout();
return;
}
reactionTextTable = new Hashtable();
int reactionCount = 0;
// foreach reaction add a reaction label
foreach (ReactionGlyph reactionGlyph in SBMLLayout.Instance.CurrentLayout.ReactionGlyphs)
{
var dimension = new[] {100.0, 100.0};
double[] position = GetPosition(reactionGlyph);
position[0] = position[0] - 50;
string currentLabel = reactionGlyph.Name;
Text text2 = CreateTextLabel(currentLabel);
text2.Stroke = "FFFFFF";
text2.FontSize = "22";
text2.TextAnchor = "middle";
Text text = CreateTextLabel(currentLabel);
text.TextAnchor = "middle";
var style = new LocalStyle();
style.Group.Children.Add(text2);
style.Group.Children.Add(text);
style.IdList = "fb_label_" + reactionCount;
SBMLLayout.Instance.CurrentLayout.EmlDefault.Styles.Add(style);
SBMLLayout.Instance.addTextGlyph("fb_label_" + reactionCount, currentLabel, currentLabel, position,
dimension);
TextGlyph textGlyph = SBMLLayout.Instance.CurrentLayout.findTextGlyphById("fb_label_" + reactionCount);
reactionTextTable[currentLabel] = new TempLabel(textGlyph, text, style);
reactionCount++;
}
}
