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NeuroML2 improvements #396

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695d75b
saving data to npy format in streamer is now bug free. Added three te…
Mar 9, 2020
182b705
boost::filesystem is no longer used even when boost is used.
Mar 10, 2020
f25469a
Default tick for Streamer is 10s.
Mar 10, 2020
a10abc9
Able to run nml2 example with python3 (BhallaLab/moose#253).
Mar 10, 2020
6fce93b
Able to run nml2 example with python3 (BhallaLab/moose#253).
Mar 10, 2020
d1b0662
moose.server uses the standard logger and does not set global logging to
Mar 10, 2020
fd77d8e
Got reader.py from https://raw.githubusercontent.com/pgleeson/moose-c…
Mar 10, 2020
2143a04
Pulled changes from https://github.com/pgleeson/moose-core/commit/29e…
Mar 10, 2020
ee7eaa1
Merge branch 'neuroml2' of github.com:dilawar/moose-core into neuroml2
Mar 10, 2020
74de3b1
Fixes after merge.
Mar 10, 2020
f2bc3aa
Merge remote-tracking branch 'bhallalab/master' into neuroml2
Mar 11, 2020
1af4b64
Some more tweaks to get CaConc working with NML.
Mar 11, 2020
8a0bd8e
- If nml user has set id of the gate to be 'x', 'y' or 'z' then load …
Mar 12, 2020
d576049
- If channels are named 'm', 'n', load them into 'X', 'Y', 'Z' in the
Mar 13, 2020
dd7caea
pylint fixes.
Mar 13, 2020
fdedfb2
Added missing nml2 files.
Mar 13, 2020
5324a3c
Needs a xml convertor to conver NML to MOOSEML.
Mar 13, 2020
b199f5c
Added some more tests. Basically parsing NML2 files. Whether they work
Mar 13, 2020
150d9f7
Merge branch 'master' into neuroml2
dilawar Apr 6, 2020
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205 changes: 104 additions & 101 deletions biophysics/CaConc.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -14,43 +14,43 @@

const Cinfo* CaConc::initCinfo()
{
static string doc[] =
{
"Name", "CaConc \n",
"Author", "Upinder S. Bhalla, 2014, NCBS \n",
"Description", "CaConc: Calcium concentration pool. Takes current from a \n"
"channel and keeps track of calcium buildup and depletion by a \n"
"single exponential process. \n",
};

static Dinfo< CaConc > dinfo;

static Cinfo CaConcCinfo(
"CaConc",
CaConcBase::initCinfo(),
0,
0,
&dinfo,
doc,
sizeof(doc)/sizeof(string)
);

return &CaConcCinfo;
static string doc[] =
{
"Name", "CaConc \n",
"Author", "Upinder S. Bhalla, 2014, NCBS \n",
"Description", "CaConc: Calcium concentration pool. Takes current from a \n"
"channel and keeps track of calcium buildup and depletion by a \n"
"single exponential process. \n",
};

static Dinfo< CaConc > dinfo;

static Cinfo CaConcCinfo(
"CaConc",
CaConcBase::initCinfo(),
0,
0,
&dinfo,
doc,
sizeof(doc)/sizeof(string)
);

return &CaConcCinfo;
}
///////////////////////////////////////////////////

static const Cinfo* caConcCinfo = CaConc::initCinfo();

CaConc::CaConc()
: CaConcBase(),
Ca_( 0.0 ),
CaBasal_( 0.0 ),
tau_( 1.0 ),
B_( 1.0 ),
c_( 0.0 ),
activation_( 0.0 ),
ceiling_( 1.0e9 ),
floor_( 0.0 )
: CaConcBase(),
Ca_( 0.0 ),
CaBasal_( 0.0 ),
tau_( 1.0 ),
B_( 1.0 ),
c_( 0.0 ),
activation_( 0.0 ),
ceiling_( 1.0e9 ),
floor_( 0.0 )
{;}

///////////////////////////////////////////////////
Expand All @@ -59,46 +59,46 @@ CaConc::CaConc()

void CaConc::vSetCa( const Eref& e, double Ca )
{
Ca_ = Ca;
Ca_ = Ca;
}
double CaConc::vGetCa( const Eref& e ) const
{
return Ca_;
return Ca_;
}

void CaConc::vSetCaBasal( const Eref& e, double CaBasal )
{
CaBasal_ = CaBasal;
CaBasal_ = CaBasal;
}
double CaConc::vGetCaBasal( const Eref& e ) const
{
return CaBasal_;
return CaBasal_;
}

void CaConc::vSetTau( const Eref& e, double tau )
{
tau_ = tau;
tau_ = tau;
}
double CaConc::vGetTau( const Eref& e ) const
{
return tau_;
return tau_;
}

void CaConc::vSetB( const Eref& e, double B )
{
B_ = B;
B_ = B;
}
double CaConc::vGetB( const Eref& e ) const
{
return B_;
return B_;
}
void CaConc::vSetCeiling( const Eref& e, double ceiling )
{
ceiling_ = ceiling;
}
double CaConc::vGetCeiling( const Eref& e ) const
{
return ceiling_;
return ceiling_;
}

void CaConc::vSetFloor( const Eref& e, double floor )
Expand All @@ -107,7 +107,7 @@ void CaConc::vSetFloor( const Eref& e, double floor )
}
double CaConc::vGetFloor( const Eref& e ) const
{
return floor_;
return floor_;
}

///////////////////////////////////////////////////
Expand All @@ -116,45 +116,48 @@ double CaConc::vGetFloor( const Eref& e ) const

void CaConc::vReinit( const Eref& e, ProcPtr p )
{
activation_ = 0.0;
c_ = 0.0;
Ca_ = CaBasal_;
concOut()->send( e, Ca_ );
activation_ = 0.0;
c_ = 0.0;
Ca_ = CaBasal_;
concOut()->send( e, Ca_ );
}

void CaConc::vProcess( const Eref& e, ProcPtr p )
{
double x = exp( -p->dt / tau_ );
Ca_ = CaBasal_ + c_ * x + ( B_ * activation_ * tau_ ) * (1.0 - x);
if ( ceiling_ > 0.0 && Ca_ > ceiling_ ) {
Ca_ = ceiling_;
} else if ( Ca_ < floor_ ){
Ca_ = floor_;
}
c_ = Ca_ - CaBasal_;
concOut()->send( e, Ca_ );
activation_ = 0;
double x = exp( -p->dt / tau_ );
Ca_ = CaBasal_ + c_ * x + ( B_ * activation_ * tau_ ) * (1.0 - x);
if ( ceiling_ > 0.0 && Ca_ > ceiling_ )
{
Ca_ = ceiling_;
}
else if ( Ca_ < floor_ )
{
Ca_ = floor_;
}
c_ = Ca_ - CaBasal_;
concOut()->send( e, Ca_ );
activation_ = 0;
}


void CaConc::vCurrent( const Eref& e, double I )
{
activation_ += I;
activation_ += I;
}

void CaConc::vCurrentFraction( const Eref& e, double I, double fraction )
{
activation_ += I * fraction;
activation_ += I * fraction;
}

void CaConc::vIncrease( const Eref& e, double I )
{
activation_ += fabs( I );
activation_ += fabs( I );
}

void CaConc::vDecrease( const Eref& e, double I )
{
activation_ -= fabs( I );
activation_ -= fabs( I );
}

///////////////////////////////////////////////////
Expand All @@ -165,52 +168,52 @@ void CaConc::vDecrease( const Eref& e, double I )
void testCaConc()
{
/*
CaConc cc;
double tau = 0.10;
double basal = 0.0001;

cc.setCa( basal );
cc.setCaBasal( basal );
cc.setTau( tau );
// Here we use a volume of 1e-15 m^3, i.e., a 10 micron cube.
cc.setB( 5.2e-6 / 1e-15 );
// Faraday constant = 96485.3415 s A / mol
// Use a 1 pA input current. This should give (0.5e-12/F) moles/sec
// influx, because Ca has valence of 2.
// So we get 5.2e-18 moles/sec coming in.
// Our volume is 1e-15 m^3
// So our buildup should be at 5.2e-3 moles/m^3/sec = 5.2 uM/sec
double curr = 1e-12;
// This will settle when efflux = influx
// dC/dt = B*Ik - C/tau = 0.
// so Ca = CaBasal + tau * B * Ik =
// 0.0001 + 0.1 * 5.2e-6 * 1e3 = 0.000626

ProcInfo p;
p.dt = 0.001;
p.currTime = 0.0;
CaConc cc;
double tau = 0.10;
double basal = 0.0001;

cc.setCa( basal );
cc.setCaBasal( basal );
cc.setTau( tau );
// Here we use a volume of 1e-15 m^3, i.e., a 10 micron cube.
cc.setB( 5.2e-6 / 1e-15 );
// Faraday constant = 96485.3415 s A / mol
// Use a 1 pA input current. This should give (0.5e-12/F) moles/sec
// influx, because Ca has valence of 2.
// So we get 5.2e-18 moles/sec coming in.
// Our volume is 1e-15 m^3
// So our buildup should be at 5.2e-3 moles/m^3/sec = 5.2 uM/sec
double curr = 1e-12;
// This will settle when efflux = influx
// dC/dt = B*Ik - C/tau = 0.
// so Ca = CaBasal + tau * B * Ik =
// 0.0001 + 0.1 * 5.2e-6 * 1e3 = 0.000626

ProcInfo p;
p.dt = 0.001;
p.currTime = 0.0;
Eref sheller(Id().eref());
Shell * shell = reinterpret_cast<Shell*> (sheller.data());
Id temp = shell->doCreate("CaConc", Id(), "caconc", 1);
assert(temp.element()->getName() == "caconc");
// Id tempId = Id::nextId();
// Element temp( tempId, CaConc::initCinfo(), "temp", 0 );
Eref er( &temp, 0 );
cc.reinit( er, &p );

double y;
double conc;
double delta = 0.0;
for ( p.currTime = 0.0; p.currTime < 0.5; p.currTime += p.dt )
{
cc.current( curr );
cc.process( er, &p );
y = basal + 526.0e-6 * ( 1.0 - exp( -p.currTime / tau ) );
conc = cc.getCa();
delta += ( y - conc ) * ( y - conc );
}
assert( delta < 1e-6 );
cout << "." << flush;
// Id tempId = Id::nextId();
// Element temp( tempId, CaConc::initCinfo(), "temp", 0 );
Eref er( &temp, 0 );
cc.reinit( er, &p );

double y;
double conc;
double delta = 0.0;
for ( p.currTime = 0.0; p.currTime < 0.5; p.currTime += p.dt )
{
cc.current( curr );
cc.process( er, &p );
y = basal + 526.0e-6 * ( 1.0 - exp( -p.currTime / tau ) );
conc = cc.getCa();
delta += ( y - conc ) * ( y - conc );
}
assert( delta < 1e-6 );
cout << "." << flush;
*/
}
#endif
76 changes: 38 additions & 38 deletions biophysics/CaConc.h
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@
* without diffusion. It uses a simple exponential return of Ca
* to baseline, with influxes from ion channels. It solves the
* equation:
* dC/dt = B*Ik - C/tau
* where Ca = Ca_base + C.
*
* dC/dt = B*Ik - C/tau, where Ca = Ca_base + C.
*
* From the GENESIS notes:
* In SI units, where concentration is moles/m^3
Expand All @@ -35,44 +35,44 @@

class CaConc: public CaConcBase
{
public:
CaConc();
///////////////////////////////////////////////////////////////
// Message handling functions
///////////////////////////////////////////////////////////////
void vReinit( const Eref&, ProcPtr info );
void vProcess( const Eref&, ProcPtr info );
public:
CaConc();
///////////////////////////////////////////////////////////////
// Message handling functions
///////////////////////////////////////////////////////////////
void vReinit( const Eref&, ProcPtr info );
void vProcess( const Eref&, ProcPtr info );

void vCurrent( const Eref& e, double I );
void vCurrentFraction( const Eref& e, double I, double fraction );
void vIncrease( const Eref& e, double I );
void vDecrease( const Eref& e, double I );
///////////////////////////////////////////////////////////////
// Field handling functions
///////////////////////////////////////////////////////////////
void vSetCa( const Eref& e, double val );
double vGetCa( const Eref& e ) const;
void vSetCaBasal( const Eref& e, double val );
double vGetCaBasal( const Eref& e ) const;
void vSetTau( const Eref& e, double val );
double vGetTau( const Eref& e ) const;
void vSetB( const Eref& e, double val );
double vGetB( const Eref& e ) const;
void vSetCeiling( const Eref& e, double val );
double vGetCeiling( const Eref& e ) const;
void vSetFloor( const Eref& e, double val );
double vGetFloor( const Eref& e ) const;
void vCurrent( const Eref& e, double I );
void vCurrentFraction( const Eref& e, double I, double fraction );
void vIncrease( const Eref& e, double I );
void vDecrease( const Eref& e, double I );
///////////////////////////////////////////////////////////////
// Field handling functions
///////////////////////////////////////////////////////////////
void vSetCa( const Eref& e, double val );
double vGetCa( const Eref& e ) const;
void vSetCaBasal( const Eref& e, double val );
double vGetCaBasal( const Eref& e ) const;
void vSetTau( const Eref& e, double val );
double vGetTau( const Eref& e ) const;
void vSetB( const Eref& e, double val );
double vGetB( const Eref& e ) const;
void vSetCeiling( const Eref& e, double val );
double vGetCeiling( const Eref& e ) const;
void vSetFloor( const Eref& e, double val );
double vGetFloor( const Eref& e ) const;

static const Cinfo* initCinfo();
private:
double Ca_;
double CaBasal_;
double tau_;
double B_;
double c_;
double activation_;
double ceiling_;
double floor_;
static const Cinfo* initCinfo();
private:
double Ca_;
double CaBasal_;
double tau_;
double B_;
double c_;
double activation_;
double ceiling_;
double floor_;
};


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