GENENET8 update

17 files changed, 1011 insertions, 0 deletions

diff --git a/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input.txt b/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input.txt
new file mode 100644
index 00000000..cf674ffd
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input.txt
@@ -0,0 +1,44 @@
+Ctrq3	MAS	Neutrophil	Load	Weight
+2	1	1	1	1
+2	0.969230769	3	3.252367514	1
+2	0.925170068	1.6	2.46322088	1.033472803
+1	0.427272727	33.8	4.206610024	0.831372549
+2	0.877835951	8.3	3.764250875	0.967153285
+2	0.914862915	4.4	3.691700208	1.046025105
+2	0.560334528	4.9	2.604550033	0.98046875
+1	0.383073497	13.1	4.273556814	0.812316716
+1	0.101010101	18.6	5.089640217	0.771929825
+1	0.106719368	18.9	4.915125346	0.80994152
+2	0.894736842	2.5	2.691700208	0.995515695
+1	0.067226891	19.8	4.878194228	0.846153846
+2	0.921022067	2.9	4.127428778	1.03875969
+2	0.938701923	0.7	4.366310867	0.984732824
+1	0.658008658	15.7	4.531121115	0.884210526
+2	0.9	4.8	2.604550033	0.913194444
+2	0.790923825	10.4	2.390670213	0.892857143
+1	0.295539033	8.6	4.24137213	0.85840708
+2	0.317757009	12.2	4.449648073	0.889830508
+1	0.032418953	20.2	5.053428044	0.811320755
+1	0.603960396	23.4	4.283775979	0.805460751
+2	0.939351199	3.6	2.349277527	0.952380952
+1	0.978448276	0.4	3.495405563	0.8875
+1	0.1	23.2	4.675613388	0.766101695
+1	0.036363636	32.6	4.938109253	0.828125
+1	0.660247593	9.2	3.826398782	0.921052632
+1	0.078651685	35.8	4.513630383	0.852112676
+1	0.186915888	20.7	5.048247532	0.779761905
+1	0.071578947	35.6	4.574586809	0.797356828
+1	0.239520958	15.4	4.331548761	0.941176471
+1	0.205741627	24.5	5.058547488	0.774193548
+1	0.062300319	13.4	4.594790195	0.832236842
+2	0.599675851	5	4.18178644	0.969348659
+1	0.324246772	13.5	4.252367514	0.858585859
+1	0.87628866	14.2	2.929061124	0.869863014
+1	0.146103896	15.6	4.579726449	0.9
+1	0.257383966	22.5	5.210214148	0.75
+1	0.033333333	31.1	4.632578756	0.718644068
+1	0.29739777	36.1	3.880756445	0.798353909
+2	0.872979215	4.2	4.097465554	0.856756757
+2	0.909221902	4.3	3.650307523	0.976
+1	0.10041841	28.3	4.46322088	0.757462687
+
diff --git a/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input_orig.txt b/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input_orig.txt
new file mode 100644
index 00000000..62705bb9
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRcontinuous_input_orig.txt
@@ -0,0 +1,42 @@
+Ctrq3	MAS	Neutrophil	Load	Weight
+2	0.969230769	3	3.252367514	1
+2	0.925170068	1.6	2.46322088	1.033472803
+1	0.427272727	33.8	4.206610024	0.831372549
+2	0.877835951	8.3	3.764250875	0.967153285
+2	0.914862915	4.4	3.691700208	1.046025105
+2	0.560334528	4.9	2.604550033	0.98046875
+1	0.383073497	13.1	4.273556814	0.812316716
+1	0.101010101	18.6	5.089640217	0.771929825
+1	0.106719368	18.9	4.915125346	0.80994152
+2	0.894736842	2.5	2.691700208	0.995515695
+1	0.067226891	19.8	4.878194228	0.846153846
+2	0.921022067	2.9	4.127428778	1.03875969
+2	0.938701923	0.7	4.366310867	0.984732824
+1	0.658008658	15.7	4.531121115	0.884210526
+2	0.9	4.8	2.604550033	0.913194444
+2	0.790923825	10.4	2.390670213	0.892857143
+1	0.295539033	8.6	4.24137213	0.85840708
+2	0.317757009	12.2	4.449648073	0.889830508
+1	0.032418953	20.2	5.053428044	0.811320755
+1	0.603960396	23.4	4.283775979	0.805460751
+2	0.939351199	3.6	2.349277527	0.952380952
+1	0.978448276	0.4	3.495405563	0.8875
+1	0.1	23.2	4.675613388	0.766101695
+1	0.036363636	32.6	4.938109253	0.828125
+1	0.660247593	9.2	3.826398782	0.921052632
+1	0.078651685	35.8	4.513630383	0.852112676
+1	0.186915888	20.7	5.048247532	0.779761905
+1	0.071578947	35.6	4.574586809	0.797356828
+1	0.239520958	15.4	4.331548761	0.941176471
+1	0.205741627	24.5	5.058547488	0.774193548
+1	0.062300319	13.4	4.594790195	0.832236842
+2	0.599675851	5	4.18178644	0.969348659
+1	0.324246772	13.5	4.252367514	0.858585859
+1	0.87628866	14.2	2.929061124	0.869863014
+1	0.146103896	15.6	4.579726449	0.9
+1	0.257383966	22.5	5.210214148	0.75
+1	0.033333333	31.1	4.632578756	0.718644068
+1	0.29739777	36.1	3.880756445	0.798353909
+2	0.872979215	4.2	4.097465554	0.856756757
+2	0.909221902	4.3	3.650307523	0.976
+1	0.10041841	28.3	4.46322088	0.757462687
diff --git a/sourcecodes/data/example_chl/old_gn/bWRgraphviz.txt b/sourcecodes/data/example_chl/old_gn/bWRgraphviz.txt
new file mode 100644
index 00000000..2cd4e8cd
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRgraphviz.txt
@@ -0,0 +1,11 @@
+digraph G {
+size="10,10";  ratio = fill;
+node [shape=square,width=1.5];
+Ctrq3 -> MAS;
+Ctrq3 -> Neutrophil;
+Ctrq3 -> Load;
+Ctrq3 -> Weight;
+MAS -> Neutrophil;
+MAS -> Load;
+Neutrophil -> Weight;
+}
\ No newline at end of file
diff --git a/sourcecodes/data/example_chl/old_gn/bWRmap.txt b/sourcecodes/data/example_chl/old_gn/bWRmap.txt
new file mode 100644
index 00000000..b24eae2f
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRmap.txt
@@ -0,0 +1,5 @@
+Ctrq3	0.487652	1.365854
+MAS	0.355012	0.479560
+Neutrophil	10.929756	15.048780
+Load	0.825354	4.077143
+Weight	0.088036	0.877077
diff --git a/sourcecodes/data/example_chl/old_gn/bWRmapdata.txt b/sourcecodes/data/example_chl/old_gn/bWRmapdata.txt
new file mode 100644
index 00000000..ce5416ce
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRmapdata.txt
@@ -0,0 +1 @@
+Ctrq3	MAS	Load	Neutrophil	Weight
diff --git a/sourcecodes/data/example_chl/old_gn/bWRname.txt b/sourcecodes/data/example_chl/old_gn/bWRname.txt
new file mode 100644
index 00000000..48018335
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRname.txt
@@ -0,0 +1 @@
+Ctrq3	MAS	Neutrophil	Load	Weight
diff --git a/sourcecodes/data/example_chl/old_gn/bWRnet_figure.txt b/sourcecodes/data/example_chl/old_gn/bWRnet_figure.txt
new file mode 100644
index 00000000..6a3a1dbc
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRnet_figure.txt
@@ -0,0 +1,433 @@
+5
+1200	1200	
+Ctrq3	200	0
+MAS	320	240
+Load	0	480
+Neutrophil	400	480
+Weight	320	720
+Ctrq3	2
+250	150
+0
+4	2	3	4	5
+1	0.6341
+2	0.3659
+MAS	1
+250	150
+1	1
+2	3	4
+-0.3226	0.0292
+-0.3060	0.0326
+-0.2895	0.0362
+-0.2729	0.0401
+-0.2564	0.0443
+-0.2398	0.0489
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+1.2838	0.0288
+1.3003	0.0258
+1.3169	0.0231
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+Load	1
+250	150
+2	1	2
+0
+1.5239	0.0030
+1.5690	0.0036
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+Neutrophil	1
+250	150
+2	1	2
+1	5
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+1.0384	0.0734
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+1.0585	0.0468
+1.0636	0.0414
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+1.1240	0.0075
+1.1290	0.0064
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diff --git a/sourcecodes/data/example_chl/old_gn/bWRnet_figure_new.txt b/sourcecodes/data/example_chl/old_gn/bWRnet_figure_new.txt
new file mode 100644
index 00000000..9b493660
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRnet_figure_new.txt
@@ -0,0 +1,433 @@
+1	
+5
+1200	1200	
+Ctrq3	200	0
+MAS	320	240
+Load	0	480
+Neutrophil	400	480
+Weight	320	720
+Ctrq3	2
+250	150
+0
+4	2	3	4	5
+1.0000	1.0000
+MAS	1
+250	150
+1	1
+2	3	4
+-2.2595	0.0066
+-2.2129	0.0085
+-2.1662	0.0109
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+0
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diff --git a/sourcecodes/data/example_chl/old_gn/bWRnlevels.txt b/sourcecodes/data/example_chl/old_gn/bWRnlevels.txt
new file mode 100644
index 00000000..9f618060
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRnlevels.txt
@@ -0,0 +1,2 @@
+Ctrq3	1	2
+
diff --git a/sourcecodes/data/example_chl/old_gn/bWRnnode.txt b/sourcecodes/data/example_chl/old_gn/bWRnnode.txt
new file mode 100644
index 00000000..7ed6ff82
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRnnode.txt
@@ -0,0 +1 @@
+5
diff --git a/sourcecodes/data/example_chl/old_gn/bWRparameters.txt b/sourcecodes/data/example_chl/old_gn/bWRparameters.txt
new file mode 100644
index 00000000..6d6eabf6
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRparameters.txt
@@ -0,0 +1,21 @@
+Ctrq3
+Discrete node with 2 states
+1	0.6341
+2	0.3659
+
+MAS
+Continuous node
+0.4796	0.3499
+
+Neutrophil
+Continuous node
+15.0488	10.8026
+
+Load
+Continuous node
+4.0771	0.8165
+
+Weight
+Continuous node
+0.8771	0.0875
+
diff --git a/sourcecodes/data/example_chl/old_gn/bWRstructure_input.txt b/sourcecodes/data/example_chl/old_gn/bWRstructure_input.txt
new file mode 100644
index 00000000..efa98e06
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRstructure_input.txt
@@ -0,0 +1,7 @@
+Ctrq3	MAS	Neutrophil	Load	Weight
+0	1	1	1	1
+0	0	1	1	0
+0	0	0	0	1
+0	0	0	0	0
+0	0	0	0	0
+
diff --git a/sourcecodes/data/example_chl/old_gn/bWRstructure_old.txt b/sourcecodes/data/example_chl/old_gn/bWRstructure_old.txt
new file mode 100644
index 00000000..a6aed858
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRstructure_old.txt
@@ -0,0 +1,5 @@
+Ctrq3	0.6341	0.3659
+MAS	0.0292	0.0326	0.0362	0.0401	0.0443	0.0489	0.0539	0.0592	0.0648	0.0709	0.0774	0.0842	0.0915	0.0992	0.1072	0.1157	0.1246	0.1338	0.1434	0.1534	0.1636	0.1742	0.1850	0.1961	0.2074	0.2188	0.2303	0.2419	0.2535	0.2651	0.2766	0.2879	0.2991	0.3099	0.3205	0.3307	0.3404	0.3496	0.3583	0.3663	0.3737	0.3804	0.3864	0.3916	0.3959	0.3994	0.4021	0.4038	0.4047	0.4046	0.4037	0.4018	0.3991	0.3954	0.3910	0.3857	0.3797	0.3729	0.3654	0.3572	0.3485	0.3392	0.3294	0.3192	0.3086	0.2977	0.2865	0.2752	0.2637	0.2521	0.2405	0.2289	0.2173	0.2059	0.1947	0.1837	0.1729	0.1623	0.1521	0.1422	0.1326	0.1234	0.1146	0.1062	0.0982	0.0906	0.0834	0.0765	0.0701	0.0641	0.0585	0.0532	0.0483	0.0438	0.0396	0.0357	0.0321	0.0288	0.0258	0.0231	0.0206
+Neutrophil	0.0245	0.0277	0.0313	0.0353	0.0396	0.0444	0.0496	0.0552	0.0613	0.0679	0.0750	0.0825	0.0906	0.0992	0.1083	0.1180	0.1281	0.1386	0.1496	0.1611	0.1729	0.1851	0.1975	0.2102	0.2231	0.2361	0.2491	0.2621	0.2750	0.2878	0.3002	0.3124	0.3240	0.3352	0.3458	0.3557	0.3648	0.3731	0.3806	0.3870	0.3925	0.3969	0.4002	0.4025	0.4035	0.4035	0.4022	0.3999	0.3964	0.3919	0.3863	0.3797	0.3722	0.3637	0.3545	0.3445	0.3339	0.3226	0.3109	0.2987	0.2862	0.2735	0.2605	0.2475	0.2345	0.2215	0.2086	0.1960	0.1835	0.1714	0.1597	0.1483	0.1373	0.1268	0.1167	0.1072	0.0981	0.0896	0.0816	0.0741	0.0670	0.0605	0.0545	0.0489	0.0438	0.0391	0.0348	0.0308	0.0273	0.0241	0.0212	0.0186	0.0163	0.0142	0.0123	0.0107	0.0093	0.0080	0.0069	0.0059	0.0050
+Load	0.0030	0.0036	0.0043	0.0050	0.0059	0.0069	0.0081	0.0094	0.0110	0.0127	0.0147	0.0169	0.0194	0.0222	0.0253	0.0287	0.0326	0.0368	0.0415	0.0466	0.0522	0.0583	0.0649	0.0720	0.0797	0.0879	0.0966	0.1059	0.1158	0.1261	0.1370	0.1484	0.1602	0.1724	0.1850	0.1979	0.2111	0.2244	0.2379	0.2514	0.2649	0.2782	0.2914	0.3042	0.3166	0.3285	0.3398	0.3504	0.3603	0.3693	0.3774	0.3845	0.3905	0.3954	0.3992	0.4017	0.4031	0.4032	0.4021	0.3997	0.3962	0.3915	0.3857	0.3788	0.3709	0.3620	0.3523	0.3418	0.3306	0.3188	0.3065	0.2937	0.2807	0.2674	0.2539	0.2404	0.2269	0.2135	0.2003	0.1874	0.1747	0.1624	0.1505	0.1391	0.1281	0.1176	0.1077	0.0983	0.0894	0.0811	0.0734	0.0662	0.0595	0.0533	0.0476	0.0424	0.0377	0.0333	0.0294	0.0259	0.0227
+Weight	0.0076	0.0089	0.0105	0.0122	0.0142	0.0164	0.0190	0.0218	0.0250	0.0286	0.0326	0.0370	0.0419	0.0473	0.0531	0.0596	0.0665	0.0741	0.0822	0.0909	0.1002	0.1101	0.1206	0.1316	0.1432	0.1553	0.1678	0.1808	0.1941	0.2076	0.2215	0.2354	0.2494	0.2633	0.2772	0.2907	0.3040	0.3168	0.3290	0.3406	0.3514	0.3614	0.3704	0.3784	0.3853	0.3910	0.3955	0.3988	0.4007	0.4013	0.4006	0.3985	0.3952	0.3906	0.3847	0.3778	0.3697	0.3605	0.3505	0.3396	0.3280	0.3157	0.3028	0.2896	0.2759	0.2621	0.2481	0.2342	0.2202	0.2064	0.1929	0.1796	0.1667	0.1542	0.1422	0.1306	0.1197	0.1092	0.0994	0.0901	0.0815	0.0734	0.0659	0.0590	0.0526	0.0468	0.0414	0.0366	0.0322	0.0283	0.0247	0.0215	0.0187	0.0162	0.0140	0.0120	0.0103	0.0088	0.0075	0.0064	0.0054
diff --git a/sourcecodes/data/example_chl/old_gn/bWRtype.txt b/sourcecodes/data/example_chl/old_gn/bWRtype.txt
new file mode 100644
index 00000000..03b402ee
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRtype.txt
@@ -0,0 +1,2 @@
+Ctrq3	MAS	Neutrophil	Load	Weight
+2	1	1	1	1	
diff --git a/sourcecodes/data/example_chl/old_gn/bWRvar.txt b/sourcecodes/data/example_chl/old_gn/bWRvar.txt
new file mode 100644
index 00000000..56a6051c
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRvar.txt
@@ -0,0 +1 @@
+1
\ No newline at end of file
diff --git a/sourcecodes/data/example_chl/old_gn/bWRvardata.txt b/sourcecodes/data/example_chl/old_gn/bWRvardata.txt
new file mode 100644
index 00000000..56a6051c
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRvardata.txt
@@ -0,0 +1 @@
+1
\ No newline at end of file
diff --git a/sourcecodes/data/example_chl/old_gn/bWRvarname.txt b/sourcecodes/data/example_chl/old_gn/bWRvarname.txt
new file mode 100644
index 00000000..6ef2df09
--- /dev/null
+++ b/sourcecodes/data/example_chl/old_gn/bWRvarname.txt
@@ -0,0 +1 @@
+Ctrq3
\ No newline at end of file