Boolean network-based analysis of the apoptosis network (Mai and Liu 2009)

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Accession:144586
"To understand the design principles of the molecular interaction network associated with the irreversibility of cell apoptosis and the stability of cell surviving, we constructed a Boolean network integrating both the intrinsic and extrinsic pro-apoptotic pathways with pro-survival signal transduction pathways. We performed statistical analyses of the dependences of cell fate on initial states and on input signals. The analyses reproduced the well-known pro- and anti-apoptotic effects of key external signals and network components. We found that the external GF signal by itself did not change the apoptotic ratio from randomly chosen initial states when there is no external TNF signal, but can significantly offset apoptosis induced by the TNF signal. ..."
Reference:
1 . Mai Z, Liu H (2009) Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving J Theor Biol 259(4):760-9 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network;
Brain Region(s)/Organism: Generic;
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Methods; Signaling pathways; Boolean network; Apoptosis;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu];
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anetdemo
readme.html
bnet.mod
misc.mod *
stats.mod *
vecst.mod *
apopnames.txt
apoprules.txt
bnet.py
dbgnames.txt
dbgrules.txt
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
grvec.hoc *
init.hoc
local.hoc *
misc.h *
misc.py *
mosinit.py
netstate.gif
network.py
nqs.hoc *
nrnoc.hoc *
pyinit.py *
python.hoc
pywrap.hoc *
simctrl.hoc *
snutils.py
                            
// $Id: misc.h,v 1.38 2011/11/02 15:26:48 billl Exp $

#include <stdlib.h>
#include <math.h>
#include <limits.h> /* contains LONG_MAX */
#include <time.h>
#include <sys/time.h> 
#include <float.h>
#include <pthread.h>

#if !defined(t)
  #define _pval pval
#endif

typedef struct LISTVEC {
  int isz;
  Object* pL;
  double** pv;
  unsigned int* plen;
  unsigned int* pbuflen;
} ListVec;

typedef struct BVEC {
 int size;
 int bufsize;
 short *x;
 Object* o;
} bvec;

#define BYTEHEADER int _II__;  char *_IN__; char _OUT__[16]; int BYTESWAP_FLAG=0;
#define BYTESWAP(_X__,_TYPE__) \
    if (BYTESWAP_FLAG == 1) { \
    _IN__ = (char *) &(_X__); \
    for (_II__=0;_II__<sizeof(_TYPE__);_II__++) { \
        _OUT__[_II__] = _IN__[sizeof(_TYPE__)-_II__-1]; } \
    (_X__) = *((_TYPE__ *) &_OUT__); \
    }

#define UNCODE(_X_,_J_,_Y_) {(_Y_)=floor((_X_)/sc[(_J_)])/sc[4]; \
                             (_Y_)=floor(sc[4]*((_Y_)-floor(_Y_))+0.5);}
#define MIN(X,Y) ((X) < (Y) ? (X) : (Y))
#define MAX(X,Y) ((X) > (Y) ? (X) : (Y))

//square root of 2 * PI
#define SQRT2PI 2.5066282746310002416
//ln(2), base e log of 2
#define LG2 0.69314718055994530941723212145818
#define VRRY 200
#define ISVEC(_OB__) (strncmp(hoc_object_name(_OB__),"Vector",6)==0)
#define dmaxuint 4294967295. // for 32 bits

// Andre Fentons cast designations
typedef unsigned char   ui1;    /* one byte unsigned integer */
typedef char        si1;    /* one byte signed integer */
typedef unsigned short  ui2;    /* two byte unsigned integer */
typedef short       si2;    /* two byte signed integer */
typedef unsigned int    ui4;    /* four byte unsigned integer */ 
typedef int     si4;    /* four byte signed integer */ 
typedef float       sf4;    /* four byte signed floating point number */ 
typedef double      sf8;    /* eight byte signed floating point number */ 

extern double ERR,GET,SET,OK,NOP,ALL,NEG,POS,CHK,NOZ,GTH,GTE,LTH,LTE,EQU;
extern double EQV,EQW,EQX,NEQ,SEQ,RXP,IBE,EBI,IBI,EBE;

extern double *vector_newsize();
extern unsigned int  dcrsz;
extern double       *dcr;
extern double       *dcrset(int);
extern unsigned int  scrsz;
extern unsigned int *scr;
extern unsigned int *scrset(int);
extern unsigned int  iscrsz;
extern int *iscr;
extern int *iscrset(int);
extern double BVBASE;
extern double* hoc_pgetarg();
extern void hoc_notify_iv();
extern double hoc_call_func(Symbol*, int narg);
extern FILE* hoc_obj_file_arg(int narg);
extern Object** hoc_objgetarg();
char *gargstr();
char** hoc_pgargstr();
extern void vector_resize();
extern int vector_instance_px();
extern void* vector_arg();
extern double* vector_vec();
extern int vector_buffer_size(void*);
extern double hoc_epsilon;
extern int stoprun;
extern void set_seed();
extern void dshuffle(double* x,int nx);
extern void mcell_ran4_init(u_int32_t);
extern double mcell_ran4(u_int32_t *idx1, double *x, unsigned int n, double range);
extern int nrn_mlh_gsort();
extern int ivoc_list_count(Object*);
extern Object* ivoc_list_item(Object*, int);
extern int list_vector_px2();
extern int hoc_is_double_arg(int narg);
extern int hoc_is_str_arg(int narg);
extern int hoc_is_object_arg(int narg);
extern int hoc_is_pdouble_arg(int narg);
extern Symbol *hoc_get_symbol(char *);
extern Symbol *hoc_lookup(const char*);
extern Point_process* ob2pntproc(Object*);

extern char* hoc_object_name(Object*);
extern int cmpdfn();
extern int openvec(int, double **);
int list_vector_px();
double *list_vector_resize();
static void hxe() { hoc_execerror("",0); }
extern void FreeListVec(ListVec** pp);
extern ListVec* AllocListVec(Object* p);
extern ListVec* AllocILV(Object*, int, double *);
void FillListVec(ListVec* p,double dval);
void ListVecResize(ListVec* p,int newsz);
extern short *nrn_artcell_qindex_;
extern double nrn_event_queue_stats(double*);
extern void clear_event_queue();

static double sc[6];
static FILE*  testout;

//* in vecst.mod
extern int** getint2D(int rows,int cols);
extern void freeint2D(int*** ppp,int rows);
extern double** getdouble2D(int rows,int cols);
extern void freedouble2D(double*** ppp,int rows);
extern double ismono1 (double *x, int n, int flag);

//* in stats.mod
double kcorfast(double* input1, double* input2, double* i1d , double* i2d,int n,double* ps);
double Rktau (double* x, double* y, int n); // R version
double kcorfast (double* input1, double* input2, double* i1d , double* i2d,int n,double* ps);