nesting of if-then-else statements in global functions

[wshlavacek]

The level of nesting of if-then-else statements allowed in NFsim is different than in BioNetGen. It seems that 50 levels deep is the max, whereas deeper nesting is possible in BioNetGen. This causes problems when switching from the ODE solver simulation method to the NFsim simulation method. There is probably a setting for the max level of nesting in the NFsim code. Could this setting be modified for consistency with BioNetGen? Below is an example of a function definition that involves nested if-then-else statements.

Data_DailyCases()=if(t<=38,0,
if(t<=39,1,
if(t<=40,0,
if(t<=41,1,
if(t<=42,9,
if(t<=43,11,
if(t<=44,22,
if(t<=45,45,
if(t<=46,17,
if(t<=47,36,
if(t<=48,31,
if(t<=49,44,
if(t<=50,109,
if(t<=51,95,
if(t<=52,189,
if(t<=53,122,
if(t<=54,218,
if(t<=55,425,
if(t<=56,1012,
if(t<=57,1774,
if(t<=58,2952,
if(t<=59,3258,
if(t<=60,4817,
if(t<=61,5711,
if(t<=62,4805,
if(t<=63,7413,
if(t<=64,5941,
if(t<=65,5688,
if(t<=66,8771,
if(t<=67,6266,
if(t<=68,7721,
if(t<=69,8707,
if(t<=70,8153,
if(t<=71,8996,
if(t<=72,10329,
if(t<=73,12274,
if(t<=74,8122,
if(t<=75,9304,
if(t<=76,8314,
if(t<=77,9568,
if(t<=78,10765,
if(t<=79,10794,
if(t<=80,10160,
if(t<=81,8435,
if(t<=82,6548,
if(t<=83,7402,
if(t<=84,11755,
if(t<=85,8631,
if(t<=86,7532,
if(t<=87,7249,
if(t<=88,6199,
if(t<=89,4867,
if(t<=90,4324,
if(t<=91,5659,
if(t<=92,6341,
if(t<=93,8286,
if(t<=94,10683,
if(t<=95,6013,
if(t<=96,4077,
if(t<=97,3285,
if(t<=98,4718,
if(t<=99,4702,
if(t<=100,3879,
if(t<=101,4559,
if(t<=102,3699,
if(t<=103,2524,
if(t<=104,2302,
if(t<=105,2746,
if(t<=106,3526,
if(t<=107,2873,
if(t<=108,2715,
if(t<=109,2138,
if(t<=110,1610,
if(t<=111,1438,
if(t<=112,2123,
if(t<=113,2364,
if(t<=114,2759,
if(t<=115,2185,
if(t<=116,1901,
if(t<=117,1241,
if(t<=118,1479,
if(t<=119,1478,
if(t<=120,2078,
0)))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))

[jrfaeder]

Hi Bill,

We will look into implementing the change you are requesting to ensure compatibility between BNG and NFsim models. In the meantime, the fuctionality you are looking to implement can be obtained by using a time-dependent function (TFUN) in NFsim. See here for more details.

[wshlavacek]

Thanks Jim!Sent from my iPhoneOn Apr 30, 2024, at 12:39 PM, Jim Faeder ***@***.***> wrote: Hi Bill, We will look into implementing the change you are requesting to ensure compatibility between BNG and NFsim models. In the meantime, the fuctionality you are looking to implement can be obtained by using a time-dependent function (TFUN) in NFsim. See here for more details. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[wshlavacek]

I’m trying to use the TFUN feature.Is there a working example available somewhere? I don’t see info about the format of the DAT fileSent from my iPhoneOn Apr 30, 2024, at 12:39 PM, Jim Faeder ***@***.***> wrote: Hi Bill, We will look into implementing the change you are requesting to ensure compatibility between BNG and NFsim models. In the meantime, the fuctionality you are looking to implement can be obtained by using a time-dependent function (TFUN) in NFsim. See here for more details. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[jrfaeder]

Additional detail and a link to an example .dat file are here.

[jrfaeder]

There is a full example in the Validate folder of the bng2 subdirectory: https://github.com/RuleWorld/bionetgen/blob/master/bng2/Validate/test_tfun.bngl

[wshlavacek]

I'm getting an error when I try to run the TFUN example - details are below. I get the same error message when trying to run my own test: Error preparing function NAME_OF_FUNCTION in class GlobalFunction!! File doesn't look like it exists Quitting Any ideas on what's going on? --Bill BNGL file: begin model begin parameters k_t 2 end parameters begin molecule types A() B() C() D() dummy() end molecule types begin species A() 1000 B() 1000 C() 1000 D() 1000 end species begin observables Molecules A A() Molecules B B() Molecules C C() Molecules D D() Molecules dum dummy() end observables begin functions mctr = dum/1e4 # various tests on TFUN k1 = TFUN(mctr,'test.dat') k2 = (TFUN(mctr, "test.dat")/1e1) k3 = (TFUN(mctr, "test.dat")/k_t) k4 = (TFUN(mctr, "test.dat")/mctr) end functions begin reaction rules dummy: 0 -> dummy() 1e4 Ad: A() -> 0 k1 Bd: B() -> 0 k2 Cd: C() -> 0 k3 Dd: D() -> 0 k4 end reaction rules end model simulate({method=>"nf",t_end=>20,n_steps=>1000,print_functions=>1,param=>"-v -gml 1000000"}) DAT file (located in the same folder as the BNGL file): 1.000000000000000000e+01 1.000000000000000000e+00 2.000000000000000000e+01 2.000000000000000000e+00 3.000000000000000000e+01 3.000000000000000000e+00 4.000000000000000000e+01 4.000000000000000000e+00 5.000000000000000000e+01 5.000000000000000000e+00 6.000000000000000000e+01 6.000000000000000000e+00 7.000000000000000000e+01 7.000000000000000000e+00 8.000000000000000000e+01 8.000000000000000000e+00 9.000000000000000000e+01 9.000000000000000000e+00 LOG file: BioNetGen version 2.8.4 Reading from file /Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/test_tfun.bngl (level 0) Read 1 parameters. Read 5 molecule types. Read 4 species. Read 5 observable(s). Read 5 functions. Read 5 reaction rule(s). ACTION: simulate( method=>"nf" ) NetworkFree simulation using nf ACTION: simulate_nf( ) Wrote model in xml format to /Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/results/test_tfun/2024-05-06_14-31-20/test_tfun.xml. Running NFsim on pn2300722.lanl.gov full command: /Users/hlavacek/Simulations/BioNetGen-2.8.4/bin/NFsim -xml /Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/results/test_tfun/2024-05-06_14-31-20/test_tfun.xml -o /Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/results/test_tfun/2024-05-06_14-31-20/test_tfun.gdat -sim 20 -oSteps 1000 -cb -seed 324496329 -ogf -ss /Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/results/test_tfun/2024-05-06_14-31-20/test_tfun.species -v -gml 1000000 [simulation PID is: 61266] starting NFsim v1.2.2... Seeding random number generator with: 324496329 Trying to read xml model specification file: '/Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/results/test_tfun/2024-05-06_14-31-20/test_tfun.xml' read was successful... beginning parse... Creating system: test_tfun Reading parameter list... Identified parameter: k_t Value:2 Identified parameter: _rateLaw1 Value:10000 Reading list of MoleculeTypes... Reading and Creating MoleculeType: A() Reading and Creating MoleculeType: B() Reading and Creating MoleculeType: C() Reading and Creating MoleculeType: D() Reading and Creating MoleculeType: dummy() Reading list of Species... Creating 1000 instances of the Species: S1 Including Molecule of type: A with local id: S1_M1 Creating 1000 instances of the Species: S2 Including Molecule of type: B with local id: S2_M1 Creating 1000 instances of the Species: S3 Including Molecule of type: C with local id: S3_M1 Creating 1000 instances of the Species: S4 Including Molecule of type: D with local id: S4_M1 Reading list of Observables... Creating Observable: 'A' of type: 'Molecules' Including Molecule of type: A with local id: O1_P1_M1 => Final processed pattern: A() Creating Observable: 'B' of type: 'Molecules' Including Molecule of type: B with local id: O2_P1_M1 => Final processed pattern: B() Creating Observable: 'C' of type: 'Molecules' Including Molecule of type: C with local id: O3_P1_M1 => Final processed pattern: C() Creating Observable: 'D' of type: 'Molecules' Including Molecule of type: D with local id: O4_P1_M1 => Final processed pattern: D() Creating Observable: 'dum' of type: 'Molecules' Including Molecule of type: dummy with local id: O5_P1_M1 => Final processed pattern: dummy() Reading list of Functions... Reading Function: mctr() = dum/1e4 Reference: Observable dum Reading Function: k1() = __TFUN__VAL__ Reference: Constant __TFUN__VAL__ Reference: Function mctr Error preparing function k1 in class GlobalFunction!! File doesn't look like it exists Quitting. SpeciesLabel max molecule threshold set to 20. WARNING: Species with more than 20 molecules will be labeled with the Quasi method. readNFspecies::Reading from file /Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/results/test_tfun/2024-05-06_14-31-20/test_tfun.species ABORT: Couldn't read from file /Users/hlavacek/Simulations/RuleBender-workspace/NFsim_TFUN_test/results/test_tfun/2024-05-06_14-31-20/test_tfun.species: No such file or directory at line 49

…

On Tue, Apr 30, 2024 at 7:05 PM Jim Faeder ***@***.***> wrote: There is a full example in the Validate folder of the bng2 subdirectory: https://github.com/RuleWorld/bionetgen/blob/master/bng2/Validate/test_tfun.bngl — Reply to this email directly, view it on GitHub <#38 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETOR5ZYHWVHIKKHEQW6FSLZAA5W5AVCNFSM6AAAAABHAWG34SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBXG44TKOJTGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[wshlavacek]

So... I haven't been able to get TFUN to work but even if it did work, it doesn't seem to be a good solution to my problem. Recall that I am using nested if-then-else statements to define a function. I'd like this function to work regardless of whether I am using method=>"ode" or method=>"nf" and the problem is that NFsim and BioNetGen have different max nesting depths. My function works with BioNetGen but not NFsim. I have more than 50 nested if-then-else statements in my function. This is OK with BioNetGen but NFsim does not allow more than 50.

…

On Tue, Apr 30, 2024 at 12:39 PM Jim Faeder ***@***.***> wrote: Hi Bill, We will look into implementing the change you are requesting to ensure compatibility between BNG and NFsim models. In the meantime, the fuctionality you are looking to implement can be obtained by using a time-dependent function (TFUN) in NFsim. See here <https://github.com/RuleWorld/nfsim/releases/tag/v1.2.0> for more details. — Reply to this email directly, view it on GitHub <#38 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETOR5YY5H2WDQPGVE2PMFLY77QPHAVCNFSM6AAAAABHAWG34SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBWGUYTAMJZGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jrfaeder]

We agree that this should work in NFsim and are still working toward a fix. If you could email me the model that is causing the NFsim failure, that would expedite the process.

[wshlavacek]

I get the error with the example model file in the BNG distribution, which is in the validate subfolder, I think I only moved the BNGL and DAT file to my local workspace folder and modified the DAT file path accordingly in the TFUN lineSent from my iPhoneOn May 7, 2024, at 8:03 AM, Jim Faeder ***@***.***> wrote: We agree that this should work in NFsim and are still working toward a fix. If you could email me the model that is causing the NFsim failure, that would expedite the process. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[jrfaeder]

I was referring to the model with nested if's.
For the TFUN model, please make sure you are using the latest BioNetGen distribution.

[wshlavacek]

I have version 2.8.4 for the distribution, which includes version 1.2.2 for NFsimThat’s current? I’ll try to get the BNGL file to you soonSent from my iPhoneOn May 7, 2024, at 10:06 AM, Jim Faeder ***@***.***> wrote: I was referring to the model with nested if's. For the TFUN model, please make sure you are using the latest BioNetGen distribution. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[wshlavacek]

begin model # example of NFsim error caused by too deep nesting of if-then-else statements in function definition begin parameters end parameters begin molecule types V() counter() end molecule types begin seed species V() 0 counter() 0 end seed species begin observables Molecules t counter() Molecules V V() end observables begin functions # CASE 1: constant rate #v_rate()=1e-6 # CASE 2: variable rate defined in terms of nested if-then-else statements v_rate()=if(t<=297,1e-6,if(t<=298,1.12314383e-05,if(t<=299,9.94451901e-06,if (t<=300,4.74735912e-05,if(t<=301,2.11759573e-05,if(t<=302,0,if(t <=303,8.68001985e-05,if(t<=304,3.62421529e-05,if(t<=305,8.93918412e-05,if(t <=306,0.000146015146,if(t<=307,0.00010497702,if(t<=308,7.94473222e-05,if(t <=309,6.05025646e-05,if(t<=310,0.000364352105,if(t<=311,0.000201739564,if(t <=312,0.000357759509,if(t<=313,0.000269842203,if(t<=314,0.000257166618,if(t <=315,0.000470011593,if(t<=316,0.000451941228,if(t<=317,0.000253944211,if(t <=318,0.0006239742879999999,if(t<=319,0.00066809744,if(t <=320,0.000499101616,if(t<=321,0.000321104073,if(t<=322,0.000519506807,if(t <=323,0.000424076528,if(t<=324,0.000449397629,if(t<=325,0.000884025501,if(t <=326,0.000654416186,if(t<=327,0.00064374717,if(t<=328,0.000789273122,if(t <=329,0.000803543557,if(t<=330,0.000638530434,if(t<=331,0.00100160898,if(t <=332,0.000993807258,if(t<=333,0.00124114925,if(t<=334,0.00123426412,if(t <=335,0.00141321826,if(t<=336,0.00118332628,if(t<=337,0.00109470055,if(t <=338,0.00125019427,if(t<=339,0.00135455371,if(t<=340,0.0019431852,if(t <=341,0.00205543168,if(t<=342,0.00197207562,if(t<=343,0.0022614449,if(t <=344,0.00211490243,if(t<=345,0.00210695833,if(t<=346,0.00249495193,if(t <=347,0.00234941068,if(t<=348,0.00226462926,if(t<=349,0.00192793935,if(t <=350,0.002307822,if(t<=351,0.00177314607,if(t<=352,0.00204756246,if(t <=353,0.00223537455,if(t<=354,0.00265125171,if(t<=355,0.00215845046,if(t <=356,0.00219770402,if(t<=357,0.00178428238,if(t<=358,0.00184590186,if(t <=359,0.0018605743,if(t<=360,0.00184659497,if(t<=361,0.00229017668,if(t <=362,0.00253196493,if(t<=363,0.00239098899,if(t<=364,0.00211185421,if(t <=365,0.00219407719,if(t<=366,0.00212246707,if(t<=367,0.00269861999,if(t <=368,0.00266277044,if(t<=369,0.0022864101,if(t<=370,0.00238106143,if(t <=371,0.00288706782,if(t<=372,0.00241887213,if(t<=373,0.00264944029,if(t <=374,0.00283053906,if(t<=375,0.00324595184,if(t<=376,0.00288717874,if(t <=377,0.00276439946,if(t<=378,0.00244384282,if(t<=379,0.00233597338,if(t <=380,0.00279352064,if(t<=381,0.00286037951,if(t<=382,0.00328170603,if(t <=383,0.002822949,if(t<=384,0.00278954494,if(t<=385,0.00312619711,if(t <=386,0.00324124337,if(t<=387,0.00365400495,if(t<=388,0.00402022148,if(t <=389,0.00451327855,if(t<=390,0.00463343495,if(t<=391,0.00361972256,if(t <=392,0.00421404306,if(t<=393,0.00450737728,if(t<=394,0.00385689985,if(t <=395,0.00706347035,if(t<=396,0.00548992622,if(t<=397,0.00561269851,if(t <=398,0.00565157042,if(t<=399,0.00465943143,if(t<=400,0.00360607661,if(t <=401,0.00424833829,if(t<=402,0.00506165543,if(t<=403,0.00554584679,if(t <=404,0.00567074572,if(t<=405,0.00521791533,if(t<=406,0.00511027778,if(t <=407,0.00463445002,if(t<=408,0.0048334687,if(t<=409,0.00495195688,if(t <=410,0.00549367799,if(t<=411,0.00563900702,if(t<=412,0.00467717288,if(t <=413,0.00464379518,if(t<=414,0.00459904476,if(t<=415,0.00454237307,if(t <=416,0.00500574242,if(t<=417,0.00531713904,if(t<=418,0.00561133477,if(t <=419,0.00533865191,if(t<=420,0.00495078846,if(t<=421,0.00463678844,if(t <=422,0.00473844747,if(t<=423,0.0054393895,if(t<=424,0.00545525246,if(t <=425,0.00541193326,if(t<=426,0.00509452208,if(t<=427,0.00660187229,if(t <=428,0.00417453135,if(t<=429,0.00467057068,if(t<=430,0.00516133914,if(t <=431,0.00579060434,if(t<=432,0.00527368183,if(t<=433,0.0046510559,if(t 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reaction rules # timer 0->counter() 1 0->V() 1e4*v_rate() end reaction rules end model begin actions saveConcentrations() generate_network({overwrite=>1}) simulate({suffix=>"ODE",method=>"ode",t_start=>0,t_end=>1000,n_steps=>1000, print_functions=>1}) # works for cases 1 and 2 resetConcentrations() simulate({suffix=>"NF",method=>"nf",t_start=>0,t_end=>1000,n_steps=>1000, print_functions=>1}) # works for case 1, fails for case 2 end actions

…

On Tue, May 7, 2024 at 10:06 AM Jim Faeder ***@***.***> wrote: I was referring to the model with nested if's. For the TFUN model, please make sure you are using the latest BioNetGen distribution. — Reply to this email directly, view it on GitHub <#38 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AETOR565PDBION3TXKZOMZTZBD3ZBAVCNFSM6AAAAABHAWG34SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJYHAYTEOJWGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[jrfaeder]

Our initial tests showed the NFsim is able to read in the nested if function from the xml file using muParser, but then crashes when checking that the function has been correctly defined. In looking through the code, we discovered that NFsim is using an older version of the muParser code (1.30) than the bionetgen Network3 code (2.2.4). We will investigate whether updating to a more recent version of muParser (either 2.2.4 or 2.3.4 (the latest)) enables the function to work correctly in NFsim.