aresio / lassie Goto Github PK

Hi all,
I just read the LASSIE paper and wanted to compare the results to libroadrunner I was involved with
See:
https://www.ncbi.nlm.nih.gov/pubmed/26085503
which achieves in my own experience ~5-10x speedup for large system compared to COPASI (which uses LSODA) and has no problem running reaction kinetics with arbitrary math on large systems (~3000 reactions and species).

I tried to run the provided 4096x4096 SBML model, but there seems to be an issue with the model equations because around ~10 seconds of simulation the concentrations run against infinity (i.e. step sizes cannot be fullfilled any more). Also before some of the concentrations have negative values, like X454, which than stops the integrator around 9.064 s
See for instance X454 which runs against negative infinity shortly before the simulation aborts.

	time	[X454]
0	0	0.07
1	0.453	0.0426487581
2	0.906	0.0143706688
3	1.359	-0.0134872222
4	1.812	-0.0406795254
5	2.265	-0.0677183225
6	2.718	-0.0956023649
7	3.171	-0.1256590949
8	3.624	-0.1595044889
9	4.077	-0.1991152275
10	4.53	-0.2470183384
11	4.983	-0.3066406604
12	5.436	-0.3829256622
13	5.889	-0.4834716336
14	6.342	-0.6207917802
15	6.795	-0.8172666296
16	7.248	-1.1174850204
17	7.701	-1.625187808
18	8.154	-2.6505199791
19	8.607	-5.7315926781
20	9.06	-633.5137869673

In my opinion there should be no negative concentrations which seems to be an indicator for either wrong kinetics or initial values.

Are you sure that the kinetics are correctly encoded in the SBML file? I could imagine that the reason COPASI could not handle the file is that it is a non-integratable system (running to infinity) due to some encoding error of the ODEs. Could you check that the SBML has the correct kinetics?
Could you provide a reference solution for the 4096x4096 SBML model simulated with LASSIE (do you see negative values)?
Could you provide SBML files for the smaller examples in Table 1, i.e the 64x64 up to the 8192x8192 models, so I could run a full benchmark comparison of LASSIE against libroadrunner.

Thanks for any help
Matthias