[JAMESII-302] Invalid parameterization of text-based species-reactions models (depending on context) Created: 10/Jan/13  Updated: 11/Jan/13  Resolved: 11/Jan/13

Status: Resolved
Project: James II
Component/s: SR
Affects Version/s: James II 0.8.8, James II 0.9, James II 0.9.1
Fix Version/s: James II 0.9.1
Security Level: public (Visible to EVERYONE.)

Type: Bug Priority: Blocker
Reporter: re027 Assignee: Stefan Rybacki
Resolution: Fixed Votes: 0
Labels: parameters, testing
Σ Remaining Estimate: 0 minutes Remaining Estimate: 0 minutes
Σ Time Spent: Not Specified Time Spent: Not Specified
Σ Original Estimate: 0 minutes Original Estimate: 0 minutes

Attachments: JPEG File correct_trajectories.jpg     JPEG File incorrect_trajectories.jpg    
JAMESII-303 Parameters for an {{SRModel}} can onl... Technical task Open  


When executing a text-based SR-model with parameters, such as the following Lotka-Volterra model:

S: Food, Sheep, Wolf;
	r1 = 1Food + 1Sheep -> 2Sheep + 1Food,
	r2 = 1Sheep + 1Wolf -> 2Wolf,
	r3 = 1Wolf -> 0Wolf;
reference: http://dx.doi.org/10.1021/ja01453a010;
name: LotkaVolterra;

V: 10;
X_0: Food:10, Sheep:1000, Wolf:1000;
Rc: r1:10, r2:0.01, r3:100;

the parameters seem to be set in differing ways, depending on the way the model is executed.

For example, if you execute it from code like this (see test.sr.ssa.TestLotkaVolterra):

BaseExperiment exp = new BaseExperiment();
exp.setModelLocation(new URI("file-sr:/./LotkaVolterra.sr"));

or via New > Experiment or Workflow > Start simulation in the James II GUI, the Wolves will die out immediately (this is reproducible, see fig. 'incorrect_trajectories'), although the correct behaviour seems to be that both populations oscillate, as it can be observed when executing the experiment via Workflow > Start simple M&S (see fig. 'correct_trajectories').

Comment by Stefan Rybacki [ 11/Jan/13 ]

Problem was, that the SRLStringConverter used when storing the SR-Model from a text editor, did not parse the Volume parameter correctly (ignored it) and set it to 1.0, which was different from the value actually set.

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