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]
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
                            
//  $Header: /usr/site/nrniv/simctrl/hoc/RCS/local.hoc,v 1.15 2003/02/13 15:32:06 billl Exp $
//
//  This file contains local modifications to nrnoc.hoc and default.hoc
//
//  Users should not edit nrnoc.hoc or default.hoc.  Any local 
//  changes to these files should be made in this file.

// ------------------------------------------------------------
//* MODIFICATIONS TO NRNOC.HOC
// The procedures declared here will overwrite any duplicate
// procedures in nrnoc.hoc.
// ------------------------------------------------------------

//*MODIFICATIONS TO DEFAULT.HOC
//
// Vars added here may not be handled properly within nrnoc.hoc
//------------------------------------------------------------

//** String defaults

//** Simulation defaults

long_dt     = .001      // msec 

objref sfunc,tmpfile
sfunc = hoc_sf_   // needed to use is_name()
tmpfile = new File()  // check for existence before opening a user's local.hoc file

proc write_comment () {
  tmpfile.aopen("index")
  tmpfile.printf("%s\n",$s1)
  tmpfile.close()  
}

func asin () { return atan($1/sqrt(1-$1*$1)) }
func acos () { return atan(sqrt(1-$1*$1)/$1) }

objref mt[2]
mt = new MechanismType(0)
proc uninsert_all () { local ii
  forall for ii=0,mt.count()-1 {
    mt.select(ii)
    mt.selected(temp_string_)
    if (strcmp(temp_string_,"morphology")==0) continue
    if (strcmp(temp_string_,"capacitance")==0) continue
    if (strcmp(temp_string_,"extracellular")==0) continue
    if (sfunc.substr(temp_string_,"_ion")!=-1) continue
    mt.remove()
    // print ii,temp_string_
  }
}

condor_run = 0  // define for compatability

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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