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					LiSDAS: format version = 1.0
date: 20100409


# This file illustrates the format rule on making a model with the LiSDAS .mdl file.
# Each model context is caugh between BEGIN and END tags - <begin:xxxxx> and <end:xx
# All the tag names are case-sensitive.
# LiSDAS reads each statement as a space-separated text.

### Arbitrary model name (unused in OpenLiSDAS 2.0)
<begin:Model_Reference>
                       CircadianClock_2
<end:Model_Reference>


### Description (unused in OpenLiSDAS 2.0)
<begin:Model_Descriptions>
                       Transcriptional regulatory circuit of mammalian circadian clock
<end:Model_Descriptions>


### Definition of biochemical species in model (state variables)
     1st column        State variable ID
     2nd column        Name of variable

<begin:List_Species>
                                              1   per2
                                              2   Per2
                                              3   cry1
                                              4   Cry1
                                              5   Per2_Cry1
                                              6   rev_erbAbeta
                                              7   Rev_ErbAbeta
                                              8   clock
                                              9   Clock
                                             10   bmal1
                                             11   Bmal1
                                             12   Clock_Bmal1
                                             13   dbp
                                             14   Dbp
                                             15   per1
                                             16   Per1
                                             17   rorAlpha
                                               18 RorAlpha
                                               19 Per1_Cry1
<end:List_Species>


### Time interval on Euler discretization in the numerical simulation
<begin:Time_Interval>
                                              0.1
<end:Time_Interval>


### Start and End time points on discretized simulation time interval
<begin:Time_Simulation>
                        Start_Time_Point                                              1
                        End_Time_Point                                              700
<end:Time_Simulation>


### Definition of Reaction Elements in ODE model
The user must define a set of elementary equations in a model.
<List_ReactionModules> section in below specifies a connection of these reaction elements.
For instance, if dX/dt=F(Y)+G(Z)H(P), the following <List_ReactionElements> section indicates F(Y), G(Z), and H(P).
Then, in <List_ReactionModules> section,mutiplication of G(Z) and H(P) is deined, and F(Y) is added.


Currently-supported form of equations

Kinetic_Law             Kinetic_ID                  Description
DifferentiationOverTime                         1 This term MUST be specified once for each variable.
Baseline                                        2 Baseline
RnaDegradation                                  3 Linear function
ProteinDegradation                              3 Linear function
ProteinDegradation                              3 Linear function
Binding                                         4
TranscriptionActivation                        18 Hill function for Activation 1/(K/X)^s: the parameters K and s are spe
TranscriptionRepression                        19 Hill function for Inactivation 1/(X/K)^s: the parameters K and s are sp


<begin:List_ReactionElements>
                        Process_ID                  Product_Name
                                                1   per2
                                                2   per2
                                                3   per2
                                                4   per2
 5   per2
 6   Per2
 7   Per2
 8   Per2
 9   Per2
10   Per2
11   cry1
12   cry1
13   cry1
14   cry1
15   cry1
16   Cry1
17   Cry1
18   Cry1
19   Cry1
20   Cry1
21   Per2_Cry1
22   Per2_Cry1
23   Per2_Cry1
24   rev_erbAbeta
25   rev_erbAbeta
26   rev_erbAbeta
27   rev_erbAbeta
28   Rev_ErbAbeta
29   Rev_ErbAbeta
30   Rev_ErbAbeta
31   clock
32   clock
33   clock
34   Clock
35   Clock
36   Clock
37   Clock
38   Clock
39   bmal1
40   bmal1
41   bmal1
42   bmal1
43   bmal1
44   Bmal1
45   Bmal1
46   Bmal1
47   Bmal1
48   Bmal1
49   Clock_Bmal1
                              50   Clock_Bmal1
                              51   Clock_Bmal1
                              52   Per2_Cry1
                              53   per1
                              54   per1
                              55   per1
                              56   per1
                              57   per1
                              58   per1
                              59   per2
                              60   per2
                              61   cry1
                              62   cry1
                              63   cry1
                              64   rev_erbAbeta
                              65   rev_erbAbeta
                              66   rev_erbAbeta
                              67   clock
                              68   clock
                              69   bmal1
                              70   bmal1
                              71   rorAlpha
                              72   rorAlpha
                              73   rorAlpha
                              74   Per1
                              75   Per1
                              76   Per1
                              77   Per1
                              78   Per1
                              79   RorAlpha
                              80   RorAlpha
                              81   RorAlpha
                              82   Per1_Cry1
                              83   Per1_Cry1
                              84   Per1_Cry1
                              85   Per1_Cry1
                              86   dbp
                              87   dbp
                              88   dbp
                              89   dbp
                              90   dbp
                              91   Dbp
                              92   Dbp
                              93   Dbp
<end:List_ReactionElements>
### Definition of Reaction Modules in ODE model
Definition of mutiplicative sets of Reaction Elements specified at <List_ReactionElements>.


<begin:List_ReactionModules>
                        Module_ID                   Product_Name
                                                1   per2
                                                2   per2
                                                3   per2
                                                4   per2
                                                5   Per2
                                                6   Per2
                                                7   Per2
                                                8   Per2
                                                9   cry1
                                               10   cry1
                                               11   cry1
                                               12   cry1
                                               13   Cry1
                                               14   Cry1
                                               15   Cry1
                                               16   Cry1
                                               17   Per2_Cry1
                                               18   Per2_Cry1
                                               19   Per2_Cry1
                                               20   rev_erbAbeta
                                               21   rev_erbAbeta
                                               22   rev_erbAbeta
                                               23   rev_erbAbeta
                                               24   Rev_ErbAbeta
                                               25   Rev_ErbAbeta
                                               26   Rev_ErbAbeta
                                               27   clock
                                               28   clock
                                               29   clock
                                               30   Clock
                                               31   Clock
                                               32   Clock
                                               33   Clock
                                               34   bmal1
                                               35   bmal1
                                               36   bmal1
                                               37   bmal1
                                               38   Bmal1
                                             39   Bmal1
                                             40   Bmal1
                                             41   Bmal1
                                             42   Clock_Bmal1
                                             43   Clock_Bmal1
                                             44   Clock_Bmal1
                                             45   Cry1
                                             46   rorAlpha
                                             47   rorAlpha
                                             48   rorAlpha
                                             49   RorAlpha
                                             50   RorAlpha
                                             51   RorAlpha
                                             52   per1
                                             53   per1
                                             54   per1
                                             55   Per1
                                             56   Per1
                                             57   Per1
                                             58   Per1
                                             59   Per1_Cry1
                                             60   Per1_Cry1
                                             61   Per1_Cry1
                                             62   dbp
                                             63   dbp
                                             64   dbp
                                             65   Dbp
                                             66   Dbp
                                             67   Dbp
<end:List_ReactionModules>


### Definition of Reaction Elements in ODE model
The user must specify the explored parameters in ReactionElements.


<begin:List_ParametersInElements>
                       Process                    Product
                                             13   cry1
                                             14   cry1
                                             26   rev_erbAbeta
                                             42   bmal1
                                             43   bmal1
                                             53   per1
                                             54   per1
                                             55   per1
                                             56   per1
                                             59   per2
                                             60   per2
                                             61   cry1
                                             62   cry1
                                             63   cry1
                                             64   rev_erbAbeta
                                             65   rev_erbAbeta
                                             66   rev_erbAbeta
                                             67   clock
                                             68   clock
                                             69   bmal1
                                             70   bmal1
                                             72   rorAlpha
                                             86   dbp
                                             87   dbp
                                             88   dbp
<end:List_ParametersInElements>


### Definition of Reaction Elements in ODE model
The user must specify the explored parameters in ReactionModules, whose IDs are defined at [Module ID] in <List_Re


<begin:List_Initial_Values>
                       Species_Name               Species_ID
                       per2                                                       1
                       Per2                                                       2
                       cry1                                                       3
                       Cry1                                                       4
                       Per2_Cry1                                                  5
                       rev_erbAbeta                                               6
                       Rev_ErbAbeta                                               7
                       clock                                                      8
                       Clock                                                      9
                       bmal1                                                     10
                       Bmal1                                                     11
                       Clock_Bmal1                                               12
                       dbp                                                       13
                       Dbp                                                       14
                       per1                                                      15
                       Per1                                                      16
                       rorAlpha                                                  17
                       RorAlpha                                                  18
                       Per1_Cry1                                                 19
<end:List_Initial_Values>


### Definition of Reaction Elements in ODE model
The user must specify the explored parameters in ReactionModules, whose IDs are defined at [Module ID] in <List_Re
Means and variance of Gaussian prior distributions MUST be specfied


<begin:List_ParametersInModules>
kinetic_module_id        prior_mean                prior_variance
                    10                    0.025                                 0.9
                     8                     0.07                                 0.9
                     5                     0.06                                 0.9
                     6                       0.4                                0.9
                     1                       0.1                                0.9
                     2                       0.4                                0.9
                     3                       0.5                                0.9
                     4                       0.2                                0.9
                     7                       0.5                                0.9
                     9                       0.2                                0.9
                    11                    0.075                                 0.9
                    12                     0.05                                 0.9
                    13                       0.5                                0.9
                    14                    0.242                                 0.9
                    16                       0.5                                0.9
                    17                     0.25                                 0.9
                    19                       0.5                                0.9
                    20                    0.297                                 0.9
                    21                    0.025                                 0.9
                    22                    0.073                                 0.9
                    23                    0.075                                 0.9
                    18                     0.07                                 0.9
                    24                     0.03                                 0.9
                    25                     0.03                                 0.9
                    26                     0.03                                 0.9
                    28                     0.03                                 0.9
                    27                       0.5                                0.9
                    15                       0.2                                0.9
                    51                       0.5                                0.9
                    52                    0.075                                 0.9
                    53                     0.05                                 0.9
                    54                       0.5                                0.9
                    55                    0.242                                 0.9
                    56                       0.1                                0.9
                    57                       0.4                                0.9
                    58                       0.5                                0.9
              59                    0.2                0.9
              60                  0.07                 0.9
              61                 0.025                 0.9
              62                 0.075                 0.9
              63                  0.05                 0.9
              64                    0.5                0.9
              65                 0.242                 0.9
<end:List_ParametersInModules>


### Measurement noise variances for each variable specified by ID in the second
<begin:Variance_Noise_Observed>
                                   0.1                  1
                                   0.1                  2
                                   0.1                  3
                                   0.1                  4
                                   0.1                  5
                                   0.1                  6
                                   0.1                  7
                                   0.1                  8
                                   0.1                  9
                                   0.1                 10
                                   0.1                 11
                                   0.1                 12
                                   0.1                 13
                                   0.1                 14
                                   0.1                 15
                                   0.1                 16
                                   0.1                 17
                                   0.1                 18
                                   0.1                 19
<end:Variance_Noise_Observed>


### Measurement noise variances for each variable specified by ID in the second
<begin:Variance_Noise_System>
                                 0.001                  1
                                 0.001                  2
                                 0.001                  3
                                 0.001                  4
                                 0.001                  5
                                 0.001                  6
                                 0.001                  7
                                 0.001                  8
                              0.001    9
                              0.001   10
                              0.001   11
                              0.001   12
                              0.001   13
                              0.001   14
                              0.001   15
                              0.001   16
                              0.001   17
                              0.001   18
                              0.001   19
<end:Variance_Noise_System>
el with the LiSDAS .mdl file.
 ND tags - <begin:xxxxx> and <end:xxxxx>.




state variables)
numerical simulation




mulation time interval




 se reaction elements.
ments> section indicates F(Y), G(Z), and H(P).
H(P) is deined, and F(Y) is added.




 specified once for each variable.




vation 1/(K/X)^s: the parameters K and s are specified to [Parameter1] and [Parameter2], respectively.
tivation 1/(X/K)^s: the parameters K and s are specified to [Parameter1] and [Parameter2], respectively.



                   Product_ID            Kinetic_Law         Kinetic_Law            Reactant_Name
                                     1   DifferentiationOverTime                1   per2
                                     1   Baseline                               2        FALSE
                                     1   RnaDegradation                         3   per2
                                     1   TranscriptionActivation               18   Bmal1_Clock
 1   TranscriptionRepression   19   Per2_Cry1
 2   DifferentiationOverTime    1   Per2
 2   Translation                3   per2
 2   ProteinDegradation         3   Per2
 2   Binding                    4   Per2
 2   Binding                    4   Cry1
 3   DifferentiationOverTime    1   cry1
 3   RnaDegradation             3   cry1
 3   TranscriptionActivation   18   Bmal1_Clock
 3   TranscriptionRepression   19   Per2_Cry1
 3   Baseline                   2         FALSE
 4   DifferentiationOverTime    1   Cry1
 4   Translation                3   cry1
 4   Binding                    4   Per2
 4   Binding                    4   Cry1
 4   ProteinDegradation         3   Cry1
 5   DifferentiationOverTime    1   Per2_Cry1
 5   Binding                    4   Per2
 5   ProteinDegradation         3   Per2_Cry1
 6   DifferentiationOverTime    1   rev_erbAbeta
 6   Baseline                   2         FALSE
 6   TranscriptionRepression   19   Per2_Cry1
 6   RnaDegradation             3   rev_erbAbeta
 7   DifferentiationOverTime    1   Rev_ErbAbeta
 7   Translation                3   rev_erbAbeta
 7   ProteinDegradation         3   Rev_ErbAbeta
 8   DifferentiationOverTime    1   clock
 8   Baseline                   2         FALSE
 8   RnaDegradation             3   clock
 9   DifferentiationOverTime    1   Clock
 9   Translation                3   clock
 9   ProteinDegradation         3   Clock
 9   Binding                    4   Clock
 9   Binding                    4   Bmal1
10   DifferentiationOverTime    1   bmal1
10   Baseline                   2         FALSE
10   RnaDegradation             3   bmal1
10   TranscriptionActivation   18   Per2_Cry1
10   TranscriptionRepression   19   Rev_ErbAbeta
11   DifferentiationOverTime    1   Bmal1
11   Translation                3   bmal1
11   ProteinDegradation         3   Bmal1
11   Binding                    4   Clock
11   Binding                    4   Bmal1
12   DifferentiationOverTime    1   Clock^Bmal1
12   Binding                    4   Clock&Bmal1
12   ProteinDegradation         3   Clock^Bmal1
 5   Binding                    4   Cry1
15   TranscriptionActivation   19   Dbp
15   TranscriptionRepression   19   Per1_Cry1
15   TranscriptionRepression   19   Per2_Cry1
15   TranscriptionActivation   18   Bmal1_Clock
15   DifferentiationOverTime    1   per1
15   RnaDegradation             3   per1
 1   TranscriptionRepression   19   Dbp
 1   TranscriptionRepression   19   Per1_Cry1
 3   TranscriptionRepression   19   Dbp
 3   TranscriptionRepression   19   Per1_Cry1
 3   TranscriptionActivation   18   RorAlpha
 6   TranscriptionActivation   18   Dbp
 6   TranscriptionRepression   19   Per1_Cry1
 6   TranscriptionActivation   18   Bmal1_Clock
 8   TranscriptionRepression   19   Rev_ErbAbeta
 8   TranscriptionActivation   18   RorAlpha
10   TranscriptionActivation   18   Per1_Cry1
10   TranscriptionActivation   18   RorAlpha
17   DifferentiationOverTime    1   rorAlpha
17   TranscriptionActivation   18   Dbp
17   RnaDegradation             3   rorAlpha
16   DifferentiationOverTime    1   Per1
16   Translation                3   per1
16   ProteinDegradation         3   Per1
16   Binding                    4   Per1
16   Binding                    4   Cry1
18   DifferentiationOverTime    1   RorAlpha
18   Translation                3   rorAlpha
18   ProteinDegradation         3   RorAlpha
19   DifferentiationOverTime    1   Per1_Cry1
19   Binding                    4   Per1
19   ProteinDegradation         3   Per1_Cry1
19   Binding                    4   Cry1
13   TranscriptionRepression   19   Per1_Cry1
13   TranscriptionRepression   19   Per2_Cry1
13   TranscriptionActivation   18   Bmal1_Clock
13   DifferentiationOverTime    1   dbp
13   RnaDegradation             3   dbp
14   DifferentiationOverTime    1   Dbp
14   Translation                3   dbp
14   ProteinDegradation         3   Dbp
ReactionElements>.



                Product_ID        KineticLaw          Reactant_Name      RateParameterID
                              1                       per2
                                  DifferentiationOverTime                                0
                              1   Baseline            none                              24
                              1   RnaDegradation      per2                               1
                              1   Transcription       Bmal1_Clock^Per2_Cry1^Per1_Cry1^Dbp2
                              2                       Per2
                                  DifferentiationOverTime                                0
                              2   Translation         per2                               3
                              2   ProteinDegradation Per2                                4
                              2   Binding             Per2                               8
                              3                       cry1
                                  DifferentiationOverTime                                0
                              3   RnaDegradation      cry1                               5
                              3   Transcription                                          6
                                                      Bmal1_Clock^Per2_Cry1^Per1_Cry1^RorAlpha^Rev_ErbAbeta
                              3   Baseline            none                              25
                              4                       Cry1
                                  DifferentiationOverTime                                0
                              4   Translation         cry1                               7
                              4   Binding             Per2                               8
                              4   ProteinDegradation Cry1                                9
                              5                       Per2_Cry1
                                  DifferentiationOverTime                                0
                              5   Binding             Per2^Cry1                          8
                              5   ProteinDegradation Per2_Cry1                          10
                              6                       rev_erbAbeta
                                  DifferentiationOverTime                                0
                              6   Baseline            none                              26
                              6   Transcription                                         11
                                                      Per2_Cry1^Per1_Cry1^Bmal1_Clock^Dbp
                              6   RnaDegradation      rev_erbAbeta                      12
                              7                       Rev_ErbAbeta
                                  DifferentiationOverTime                                0
                              7   Translation         rev_erbAbeta                      13
                              7   ProteinDegradation Rev_ErbAbeta                       14
                              8                       clock
                                  DifferentiationOverTime                                0
                              8   Transcription       Rev_ErbAbeta^RorAlpha             51
                              8   RnaDegradation      clock                             15
                              9                       Clock
                                  DifferentiationOverTime                                0
                              9   Translation         clock                             16
                              9   Binding             Clock^Bmal1                       17
                              9   ProteinDegradation Clock                              18
                             10                       bmal1
                                  DifferentiationOverTime                                0
                             10   Baseline            none                              28
                             10   RnaDegradation      bmal1                             22
                             10   Transcription                                         23
                                                      Per2_Cry1^Rev_ErbAbeta^RorAlpha^Per1_Cry1
                             11                       Bmal1
                                  DifferentiationOverTime                                0
                11   Translation         bmal1                            19
                11   ProteinDegradation Bmal1                             20
                11   Binding             Clock^Bmal1                      18
                12                       Clock_Bmal1
                     DifferentiationOverTime                               0
                12   Binding             Clock^Bmal1                      18
                12   ProteinDegradation Clock_Bmal1                       21
                 4   Binding             Per1                             51
                17                       rorAlpha
                     DifferentiationOverTime                               0
                17   Transcription       Dbp                              52
                17   RnaDegradation      rorAlpha                         53
                18                       RorAlpha
                     DifferentiationOverTime                               0
                18   Translation         rorAlpha                         54
                18   ProteinDegradation RorAlpha                          55
                15                       per1
                     DifferentiationOverTime                               0
                15   RnaDegradation      per1                             57
                15   Transcription                                        58
                                         Bmal1_Clock^Per2_Cry1^Per1_Cry1^Dbp
                16                       Per1
                     DifferentiationOverTime                               0
                16   Translation         per1                             59
                16   ProteinDegradation Per1                              60
                16   Binding             Per1^Cry1                        61
                19                       Per1_Cry1
                     DifferentiationOverTime                               0
                19   Binding             Per1^Cry1                        61
                19   ProteinDegradation Per1_Cry1                         62
                13                       dbp
                     DifferentiationOverTime                               0
                13   Transcription       Per2_Cry1^Per1_Cry1^Bmal1_Clock 63
                13   RnaDegradation      dbp                              64
                14                       Dbp
                     DifferentiationOverTime                               0
                14   Translation         dbp                              65
                14   ProteinDegradation Dbp                               66




KineticLaw_ID        RelatedVariable        NumberOfParametersParameter
                18                     12                   2             0.3
                19                      5                   2             4.4
                18                      5                   2             4.7
                18                      5                   2             4.5
                19                      7                   2               8
                19                     14                   2             4.4
                19                     19                   2             4.4
                19                      5                   2             4.4
                                     18                    12                      2    0.3
                                     19                    14                      2    4.4
                                     19                    19                      2    4.4
                                     19                    14                      2    4.4
                                     19                    19                      2    4.4
                                     18                    18                      2    0.1
                                     18                    14                      2    0.3
                                     19                    19                      2    4.4
                                     18                    12                      2    0.3
                                     19                     7                      2      1
                                     18                    18                      2      1
                                     18                    19                      2    0.1
                                     18                    18                      2    0.3
                                     18                    14                      2    0.3
                                     19                    19                      2    4.4
                                     19                     5                      2    4.4
                                     18                    12                      2    0.3




whose IDs are defined at [Module ID] in <List_ReactionModules> .



                  Value                    Prior_Mean           Prior_Variance
                           0.52228072             0.52228072                   0.001
                                 0.5997                 0.5997                    0.1
                          0.954909176            0.954909176                   0.001
                                     1.3                    1.3                   0.1
                                 4.0392                 4.0392                    0.1
                                 0.9579                 0.9579                 0.001
                                 1.6507                 1.6507                    0.1
                                 2.4944                 2.4944                    0.1
                                 1.0967                 1.0967                    0.1
                          1.065381102            1.065381102                   0.001
                                 1.0967                 1.0967                    0.1
                                       1                      1                   0.1
                                    1.01                   1.01                0.001
                                    1.01                   1.01                   0.1
                              0.520123               0.520123                  0.001
                                 0.5997                 0.5997                    0.1
                               1.15282                1.15282                  0.001
                               1.15282                1.15282                     0.1
                                 4.0392                 4.0392                    0.1
whose IDs are defined at [Module ID] in <List_ReactionModules> .




                  scan_prob             comments
                                  0.8   Degradation-of-Per2_Cry1
                                  0.8   Binding-of-Per2-and-Cry1
                                  0.8   Degradation-of-cry1
                                  0.8   Transcription-of-cry1-regulated-Per2_Cry1
                                  0.8   Degradation of per2
                                  0.8   Transcription-of-per2-regulated-by-Per2_Cry1
                                  0.8   Translation-of-Per2
                                  0.8   Degradation-of-Per2
                                  0.8   Translation-of-Cry1
                                  0.8   Degradation-of-Cry1
                                  0.8   Transcription-of-rev_erbAbeta-regulated-by-Per2_Cry1
                                  0.8   Degradation-of-rev_erbAbeta
                                  0.8   Translation-of-Rev_ErbAbeta
                                  0.8   Degradation-of-rev_erbAbeta
                                  0.8   Translation-of-Clock
                                  0.8   Degradation-of-Clock
                                  0.8   Translation-of-Bmal1
                                  0.8   Degradation-of-Bmal1
                                  0.8   Degradation-of-Bmal1_Clock
                                  0.8   Degradation-of-bmal1
                                  0.8   Transcription-of-bmal1-regulated-by-Per2_Cry1-and-Bmal1_Clock
                                  0.8   Binding-of-Clock-and-Bmal1
                                  0.8   Baseline-per2
                                  0.8   Baseline-cry1
                                  0.8   Baseline-rev_erbAbeta
                                  0.8   Baseline-bmal1
                                  0.8   Baseline-clock
                                  0.8   Degradation-of-clock
                                  0.8   Transcription-of-clock-regulated-by-Rev-ErbAbeta
                                  0.8   Transcription-of-rorAlpha-regulated-by-Dbp
                                  0.8   Degradation-of-rorAlpha
                                  0.8   Translation-of-RorAlpha
                                  0.8   Degradation-of-RorAlpha
                                  0.8   Degradation-of-per1
                                  0.8   Transcription-of-per1-regulated
                                  0.8   Translation-of-Per1
                           0.8   Degradation-of-Per1
                           0.8   Binding-of-Per1-and-Cry1
                           0.8   Degradation-of-Per1Cry1
                           0.8   Transcription-of-dbp-regulated
                           0.8   Degradation-of-dbp
                           0.8   Translation-of-Dbp
                           0.8   Degradation-of-Dbp




able specified by ID in the second column

            per2
            Per2
            cry1
            Cry1
            Per2_Cry1
            rev_erbAbeta
            Rev_ErbAbeta
            clock
            Clock
            bmal1
            Bmal1
            Clock_Bmal1
            dbp
            Dbp
            per1
            Per1
            rorAlpha
            RorAlpha
            Per1_Cry1




able specified by ID in the second column

            per2
            Per2
            cry1
            Cry1
            Per2_Cry1
            rev_erbAbeta
            Rev_ErbAbeta
            clock
Clock
bmal1
Bmal1
Clock_Bmal1
dbp
Dbp
per1
Per1
rorAlpha
RorAlpha
Per1_Cry1
eter2], respectively.



                    Reactant_ID        Parameter1         Parameter2    Parameter3 Parameter4
                                   1                  0             0             0      0
                                   0                  0             0             0      0
                                   1                  0             0             0      0
                                  12                0.3            40             0      0
 5   4.4   40   0   0
 2     0    0   0   0
 1     0    0   0   0
 2     0    0   0   0
 2     0    0   0   0
 4     0    0   0   0
 3     0    0   0   0
 3     0    0   0   0
12   0.3   40   0   0
 5   4.4   40   0   0
 0     0    0   0   0
 4     0    0   0   0
 3     0    0   0   0
 2     0    0   0   0
 4     0    0   0   0
 4     0    0   0   0
 5     0    0   0   0
 2     0    0   0   0
 5     0    0   0   0
 6     0    0   0   0
 0     0    0   0   0
 5   4.7   40   0   0
 6     0    0   0   0
 7     0    0   0   0
 6     0    0   0   0
 7     0    0   0   0
 8     0    0   0   0
 0     0    0   0   0
 8     0    0   0   0
 9     0    0   0   0
 8     0    0   0   0
 9     0    0   0   0
 9     0    0   0   0
11     0    0   0   0
10     0    0   0   0
 0     0    0   0   0
10     0    0   0   0
 5     5   40   0   0
 7     8   40   0   0
11     0    0   0   0
10     0    0   0   0
11     0    0   0   0
 9     0    0   0   0
11     0    0   0   0
12     0    0   0   0
 9     0    0   0   0
12     0    0   0   0
 4     0    0   0   0
14   4.4   40   0   0
19   4.4   40   0   0
 5   4.4   40   0   0
12   0.3   40   0   0
15     0    0   0   0
15     0    0   0   0
14   4.4   40   0   0
19   4.4   40   0   0
14   4.4   40   0   0
19   4.4   40   0   0
18   0.3   40   0   0
14   4.4   40   0   0
19   4.4   40   0   0
12   0.3   40   0   0
 7   4.4   40   0   0
18   0.3   40   0   0
19   4.4   40   0   0
18   4.4   40   0   0
17     0    0   0   0
14   4.4   40   0   0
17     0    0   0   0
16     0    0   0   0
15     0    0   0   0
16     0    0   0   0
16     0    0   0   0
 3     0    0   0   0
18     0    0   0   0
17     0    0   0   0
18     0    0   0   0
19     0    0   0   0
 2     0    0   0   0
19     0    0   0   0
16     0    0   0   0
19   4.4   40   0   0
 5   4.4   40   0   0
12   0.3   40   0   0
13     0    0   0   0
13     0    0   0   0
14     0    0   0   0
13     0    0   0   0
14     0    0   0   0
RateParameter                            Num_Children Child_Process
                         SignRateParameter                         Child_Process
                     1                 1            1            1
                 0.03                  1            1            2
                   0.1                -1            1            3
                   0.4                 1            4            4        5        59
                     1                 1            1            6
                   0.5                 1            1            7
                   0.2                -1            1            8
                 0.07                 -1            2            9       10
                     1                 1            1           11
                 0.06                 -1            1           12
                 0.15                  1            5           13       14        61
                 0.03                  1            1           15
                     1                 1            1           16
                   0.5                 1            1           17
                 0.07                 -1            2           18       19
                   0.2                -1            1           20
                     1                 1            1           21
                 0.07                  1            2           22       52
                0.025                 -1            1           23
                     1                 1            1           24
                 0.03                  1            1           25
                0.075                  1            4           26       64        65
                 0.05                 -1            1           27
                     1                 1            1           28
                   0.5                 1            1           29
                0.242                 -1            1           30
                     1                 1            1           31
                   0.5                 1            2           67       68
                   0.2                -1            1           33
                     1                 1            1           34
                   0.5                 1            1           35
                 0.25                 -1            2           37       38
                   0.1                -1            1           36
                     1                 1            1           39
                 0.03                  1            1           40
                0.073                 -1            1           41
                0.075                  1            4           42       43        69
                     1                 1            1           44
               0.5                 1                1            45
            0.297                 -1                1            46
               0.1                -1                2            47        48
                 1                 1                1            49
               0.1                 1                2            47        48
            0.297                 -1                1            51
             0.07                 -1                2            19        78
                 1                 1                1            71
            0.075                  1                1            72
             0.05                 -1                1            73
                 1                 1                1            79
               0.5                 1                1            80
            0.242                 -1                1            81
                 1                 1                1            57
               0.1                -1                1            58
               0.4                 1                4            53        54        55
                 1                 1                1            74
               0.5                 1                1            75
               0.2                -1                1            76
             0.07                 -1                2            77        78
                 1                 1                1            82
             0.07                  1                2            77        78
            0.025                 -1                1            84
                 1                 1                1            89
            0.075                  1                3            86        87        88
             0.05                 -1                1            90
                 1                 1                1            91
               0.5                 1                1            92
            0.242                 -1                1            93




Parameter            PriorMean         PriorMean                                Description1
                                                        PriorVariance PriorVariance
               40                0.3               40             0.5      0.01 Clock_Bmal1
               40                4.4               40             0.5      0.01 Per2_Cry1
               40                4.7               40             0.5      0.01 Per2_Cry1
               40                4.5               40             0.5      0.01 Per2_Cry1
               40                  8               40             0.5      0.01 Rev_ErbAbeta
               40                4.4               40             0.5      0.01 Dbp
               40                4.4               40             0.5      0.01 Per1_Cry1
               40                4.4               40             0.5      0.01 Per2_Cry1
40   0.3   40   0.5   0.01   Clock_Bmal1
40   4.4   40   0.5   0.01   Dbp
40   4.4   40   0.5   0.01   Per1_Cry1
40   4.4   40   0.5   0.01   Dbp
40   4.4   40   0.5   0.01   Per1_Cry1
40   0.1   40   0.5   0.01   RorAlpha
40   0.3   40   0.5   0.01   Dbp
40   4.4   40   0.5   0.01   Per1_Cry1
40   0.3   40   0.5   0.01   Per2_Cry1
40     1   40   0.5   0.01   Rev_ErbAbeta
40     1   40   0.5   0.01   RorAlpha
40   4.4   40   0.5   0.01   Per1_Cry1
40   0.3   40   0.5   0.01   RorAlpha
40   0.3   40   0.5   0.01   Dbp
40   4.4   40   0.5   0.01   Per1_Cry1
40   4.4   40   0.5   0.01   Per2_Cry1
40   0.3   40   0.5   0.01   RorAlpha
y1-and-Bmal1_Clock
60




62   63




66




70
      56




Description2
Activator
Repressor
Activator
Activator
Repressor
Repressor
Repressor
Repressor
Activator
Repressor
Repressor
Repressor
Repressor
Activator
Activator
Repressor
Activator
Repressor
Activator
Activator
Activator
Activator
Repressor
Repressor
Activator

				
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