Leech Heart (HE) Motor Neuron conductances contributions to NN activity (Lamb & Calabrese 2013)

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Accession:153355
"... To explore the relationship between conductances, and in particular how they influence the activity of motor neurons in the well characterized leech heartbeat system, we developed a new multi-compartmental Hodgkin-Huxley style leech heart motor neuron model. To do so, we evolved a population of model instances, which differed in the density of specific conductances, capable of achieving specific output activity targets given an associated input pattern. ... We found that the strengths of many conductances, including those with differing dynamics, had strong partial correlations and that these relationships appeared to be linked by their influence on heart motor neuron activity. Conductances that had positive correlations opposed one another and had the opposite effects on activity metrics when perturbed whereas conductances that had negative correlations could compensate for one another and had similar effects on activity metrics. "
Reference:
1 . Lamb DG, Calabrese RL (2013) Correlated conductance parameters in leech heart motor neurons contribute to motor pattern formation. PLoS One 8:e79267 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Leech;
Cell Type(s): Leech heart motor neuron (HE);
Channel(s): I Na,p; I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium; I Na, leak;
Gap Junctions: Gap junctions;
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS;
Model Concept(s): Action Potential Initiation; Activity Patterns; Bursting; Temporal Pattern Generation; Detailed Neuronal Models; Parameter sensitivity; Conductance distributions;
Implementer(s): Lamb, Damon [Damon.Lamb at neurology.ufl.edu];
Search NeuronDB for information about:  I Na,p; I A; I K; I K,leak; I K,Ca; I Sodium; I Calcium; I Na, leak;
/
LambCalabrese2013
lgenesis-noX
include
absff_func_ext.h
absff_header.h
axon_ext.h
axon_g@.h
axon_struct.h
basic_g@.h
buf_defs.h
buf_ext.h
buf_struct.h
buffer_g@.h
conc_defs.h
conc_ext.h
conc_struct.h
concen_g@.h
copyright.h
dev_ext.h
dev_struct.h
devices_g@.h
diskio_defs.h
diskio_ext.h
diskio_func_ext.h
diskio_g@.h
diskio_struct.h
fac_debug.h
fac_defs.h
fac_ext.h
fac_struct.h
FMT1.h
FMT1_ext.h
FMT1_func_ext.h
FMT1_struct.h
hash.h
header.h
hh_ext.h
hh_g@.h
hh_struct.h
hh_struct_defs.h
hines_defs.h
hines_ext.h
hines_g@.h
hines_struct.h
interface.h
iofunc.h
kin_ext.h
kin_g@.h
kin_struct.h
netcdf.h
netcdf_ext.h
netcdf_func_ext.h
netcdf_struct.h
newconn_defs.h
newconn_ext.h
newconn_g@.h
newconn_struct.h
nrutil.h
NULLArgv.h
olf_ext.h
olf_g@.h
olf_struct.h
out_defs.h
out_ext.h
out_struct.h
output_g@.h
par_ext.h
param_defs.h
param_ext.h
param_g@.h
param_struct.h
per_ext.h
per_struct.h
personal_g@.h
pore_ext.h
pore_g@.h
pore_struct.h
profile.h
seg.h
seg_defs.h
seg_ext.h
seg_struct.h
segment_g@.h
shell.h
shell_defs.h
shell_ext.h
shell_func_ext.h
shell_g@.h
shell_struct.h
sim.h
sim_defs.h
sim_ext.h
sim_func_ext.h
sim_struct.h
sim_version.h
simconn_ext.h
simconn_g@.h
simconn_struct.h *
spike_ext.h
spike_struct.h
sprng.h
sprng_f.h
struct_defs.h
syn_ext.h
syn_struct.h
synapse_g@.h
synaptic_event.h
SynGS_ext.h *
SynGS_struct.h
system_deps.h
tool_ext.h
tool_struct.h
toolconn_ext.h
toolconn_g@.h
toolconn_struct.h *
tools.h
user_ext.h
user_g@.h
user_struct.h
                            
/*
** $Id: sim_func_ext.h,v 1.2 2005/06/27 19:01:07 svitak Exp $
** $Log: sim_func_ext.h,v $
** Revision 1.2  2005/06/27 19:01:07  svitak
** Added explicit types to untyped functions and fixed return values as
** appropriate. Initialized values explicitly when it was unclear if
** they were being used uninitialized (may not apply to all files being
** checked in in this batch).
**
** Revision 1.1.1.1  2005/06/14 04:38:29  svitak
** Import from snapshot of CalTech CVS tree of June 8, 2005
**
** Revision 1.16  2001/04/25 17:17:01  mhucka
** Misc. small changes to improve portability and address compiler warnings.
**
** Revision 1.15  2000/03/27 10:34:44  mhucka
** Commented out statusline functionality, because it caused GENESIS to
** print garbage control characters upon exit, screwing up the user's
** terminal.  Also added return type declaractions for various things.
**
** Revision 1.14  1999/08/22 04:42:15  mhucka
** Various fixes, mostly for Red Hat Linux 6.0
**
** Revision 1.13  1997/07/23 21:52:47  venkat
** Added extern declaration of quitCallback()
**
** Revision 1.12  1997/05/23 01:40:49  dhb
** Added DeleteMsgReferringToData() which deletes outbound messages
** with data slots pointing to data which is no longer valid.
**
** Revision 1.11  1997/05/23 00:28:40  dhb
** Added decl for RemapMsgData().
**
** Revision 1.10  1996/05/16 21:46:31  dhb
** Change messages back to a linked structure.
**
** MsgIn and MsgOut are now unified into a single Msg structure which
** is linked on two lists (inbound and outbound).
**
** GetMsgInByMsgOut() and GetMsgOutByMsgIn() are now macros which just
** return the Msg structure.
**
** The MsgIn and MsgOut types are still supported but are now aliases
** for Msg.
**
 * Revision 1.9  1994/08/31  02:57:39  dhb
 * Added FieldNameProper().
 *
 * Revision 1.8  1994/05/27  22:26:58  dhb
 * Added all the fieldlist interface functions.
 *
 * Revision 1.7  1993/12/23  03:00:58  dhb
 * Extended Objects (mostly complete)
 *
 * Revision 1.6  1993/06/29  18:56:07  dhb
 * Extended objects (incomplete)
 *
 * Revision 1.5  1993/04/23  22:11:48  dhb
 * Added various GetMsg...By...() functions
 *
 * Revision 1.4  1993/04/23  21:52:36  dhb
 * Added extern statements for additional extended field functions.
 *
 * Revision 1.3  1993/03/10  23:15:58  dhb
 * Extended element fields.
 *
 * Revision 1.2  1992/12/18  21:19:06  dhb
 * Made AddMsgIn and AddMsgOut extern (defined in sim_msg.c) to
 * support compact messages
 *
 * Revision 1.1  1992/10/27  21:19:36  dhb
 * Initial revision
 *
*/

#ifndef SIM_FUNC_EXT_H
#define SIM_FUNC_EXT_H

#include <stdlib.h>
#include <string.h>
#include "sim_struct.h"
#include "shell_struct.h"

extern char				*ArgListToString();
extern FILE				*CurrentScriptFp();
extern FILE				*NextScriptFp();
extern float				GetVarNumData();
extern char				*GetVarStrData();
extern char				*array();
extern PFI				LoadFunction();
extern FuncTable			GetCommand();
extern PFI				GetFuncAddress();
extern char				*FindSrcLine();
extern char				*GetFuncName();
extern char				*date();
extern float				Atof();
extern double				Atod();
extern char				*ftoa();
extern char				*itoa();

/* 1999-07-16 <mhucka@bbb.caltech.edu>
 * This fix for Red Hat Linux 6.0 is courtesy of Mike Vanier
 * <mvanier@bbb.caltech.edu>.  
 */
#ifdef linux
extern char                             *strchr __P ((__const char *__s, int __c));
#else
extern char	                        *strchr();
#endif

extern void            ClearPinfo();
extern int             LocateOp();
extern char            *GetIdent();
extern char            *NextDelimiter();
extern char            *CloseDelimiter();
extern int             MatchWildcard();
extern char            *LocalPath();
extern void            GetPathInfo();
extern int             CheckOptions();
extern void            FillList();
extern ElementList     *SubWildcardGetElement();
extern ElementList     *WildcardGetElement();
extern void            Enable();
extern void            Block();
extern int             IsEnabled();
extern void            HsolveEnable();
extern void            HsolveBlock();
extern int             IsHsolved();
extern int             IsActive();
extern void            ActionHashInit();
extern int             ActionHashPut();
extern Action          *GetAction();
extern char            *GetActionName();
extern void            AddAction();
extern void            BasicActions();
extern int             AddActionToObject();
extern int             UpdateActionObjects();
extern int             DeleteActionFromObject();
extern int             ActionIsPermanent();
extern void            ActionListMakePermanent();
extern int             ActionListEqual();
extern char            *Actionname();
extern char            *CheckActionType();
extern int             CheckActionName();
extern ActionList*     GetActionListByType();
extern PFI             GetActionFunc();
extern int             CallScriptActionFunc();
extern int             CallActionsSubToBase();
extern int             CallActionsBaseToSub();
extern int             CallActionByActionList();
extern int             CallActionFunc();
extern int             CallEventActionWithTime();
extern int             CallEventAction();
extern void            SimExecuteFunction();
extern int             IndexOffset();
extern int             CalculateOffset();
extern int             StructSize();
extern int             ComputeMode();
extern int             ComputeIndirection();
extern char            *CalculateAddress();
extern int             Attach();
extern int             AttachToEnd();
extern void            OK();
extern void            FAILED();
extern void            SetSimFlags();
extern void            ValidElements();
extern void            DisplayProfile();
extern Element         *RootElement();
extern void            StartupElements();
extern void            SimStartup();
extern char            *GetBinding();
extern void            DeleteBuffer();
extern int             BufferCopy();
extern int             BufferCreate();
extern int             CallElement();
extern int             CallElementParentObject();
extern int             CallElementVirtualObject();
extern int             CallElementWithMode();
extern void            CheckSimulation();
extern int             CheckClass();
extern int             ClassListEqual();
extern void            ClassHashInit();
extern int             ClassHashPut();
extern int             ClassHashFind();
extern int             ClassID();
extern char            *GetClassName();
extern void            AddClass();
extern int             ClassIsPermanent();
extern void            ClassListMakePermanent();
extern void            BasicClasses();
extern void            CheckClocks();
extern void            CheckClocksSet();
extern void            ShowClocks();
extern void            AssignElementClock();
extern void            SetClock();
extern Event           *CopyEvents();
extern Element         *CopyElement();
extern Element         *CopyElementTree();
extern int             CopyAction();
extern int             CreateAction();
extern Element         *Create();
extern char            *CreateObject();
extern Element         *WorkingElement();
extern void            SetWorkingElement();
extern void            SetRecentElement();
extern Element         *RecentElement();
extern void            SetRecentConnection();
extern Connection      *RecentConnection();
extern void            FreeTree();
extern int             ElementReaper();
extern int             DeleteElement();
extern int             FreeElement();
extern int             DetachElement();
extern int             AddObjToDumpList();
extern void            DumpObj();
extern void            FillDumpList();
extern void            WriteDumpHeaders();
extern void            WriteDumpTail();
extern void            WriteDumpList();
extern int             ObjectSubstitute();
extern void            DumpInterpol();
extern int             IsDumpDisabled();
extern void            EnableDump();
extern void            DisableDump();
extern void            MessageSubstitute();
extern Element         *GetChildElement();
extern int             IsElementWithinRegion();
extern int             IsElementWithinRegionRel();
extern ElementList     *CreateElementList();
extern void            AddElementToList();
extern void            FreeElementList();
extern int             IsElementInList();
extern void            ClearBuffer();
extern void            ResetBuffer();
extern int             AddEventBuffer();
extern void            ReplaceEvent();
extern int             ExpandBuffer();
extern void            IncrementEnd();
extern int             InsertEvent();
extern int             AppendEvent();
extern int             PutEvent();
extern Event           *FindEvent();
extern Event           *PreviousEvent();
extern int             AddExtField();
extern int             DelExtField();
extern void            DelAllExtFields();
extern int             SetExtField();
extern char*           GetExtField();
extern int             CopyExtFields();
extern int             MemUsageExtFields();
extern void            DisplayExtFields();
extern void            AddExtFieldsToString();
extern double          ExtFieldMessageData();
extern double          IndFieldMessageData();
extern char*           GetExtFieldAdr();
extern void            FreeExtFieldAdr();
extern char*           GetExtFieldNameByAdr();
extern GenesisObject*  BaseObject();
extern int             ElementIsA();
extern void            ObjectFree();
extern void            ObjectCacheEnter();
extern GenesisObject*  ObjectCacheFind();
extern GenesisObject*  ObjectCacheCheck();
extern GenesisObject*  ObjectModify();
extern int             SetFieldListDebug();
extern int             GetFieldListDebug();
extern int             AddFieldList();
extern void            FieldListFree();
extern int             DelFieldList();
extern int             AddDefaultFieldList();
extern void*           GetFieldListInfo();
extern int             GetFieldListType();
extern int             SetFieldListType();
extern int             GetFieldListProt();
extern int             SetFieldListProt();
extern char*           GetFieldListDesc();
extern int             SetFieldListDesc();
extern int             FieldIsPermanent();
extern int             FieldListExists();
extern void            CopyFieldList();
extern void            DisplayFieldList();
extern int             FieldListEqual();
extern void            FieldListMakePermanent();
extern FLI*            FLIOpen();
extern void            FLIClose();
extern int             FLIValid();
extern void            FLINext();
extern int             FLIType();
extern int             FLIProt();
extern char*           FLIName();
extern void*           FLIInfo();
extern int             FLIFind();
extern int             GetDatatype();
extern void            DisplayOneField();
extern void            DisplayFields();
extern void            FieldFormat();
extern char            *FieldValue();
extern void            DisplayField();
extern char            *GetFieldStr();
extern char            *GetFieldAdr();
extern char            *FormatStruct();
extern void            CloseAllAsciiFiles();
extern Element         *FindElement();
extern Element         *GetElement();
extern char*           ElmFieldValue();
extern Element **      *CreateGrid();
extern int             CreateMap();
extern void            ElementHashInit();
extern int             ElementHashPut();
extern int             ElementHashPutTree();
extern void            ElementHashRemove();
extern void            ElementHashRemoveTree();
extern Element         *ElementHashFind();
extern void            hashelminfo();
extern int             GetElementIndex();
extern int             FindFreeIndex();
extern double          DirectIntegrate();
extern double          IntegrateMethod();
extern double          Gear();
extern double          AB2();
extern double          AB3();
extern double          AB4();
extern double          AB5();
extern double          Euler_Predictor_Corrector();
extern double          Runge_Kutta();
extern void            DisplayHeader();
extern void            init_smalloc();
extern int             push_element();
extern Element         *pop_element();
extern char            *smalloc();
extern char            *scalloc();
extern int             sfree();
extern int             sfreeall();
extern int             smalloc_used();
extern void            init_smalloc();
extern Element **      *CreateGrid();
extern int             CreateMap();
extern int             CountMarkers();
extern void            ClearMarkers();
extern void            SetIntMethods();
extern int             ValidHierarchy();
extern int             MsgListEqual();
extern MsgList         *GetMsgListByName();
extern double          DoubleMessageData();
extern double          FloatMessageData();
extern double          IntMessageData();
extern double          ShortMessageData();
extern double          StringMessageData();
extern double          VoidMessageData();
extern char            *GetStringMsgData();
extern int             GetSlotType();
extern void            DisplayMsgIn();
extern MsgList         *GetMsgListByType();
extern void            ShowMsgIn();
extern void            ShowMsgOut();
extern int             UnlinkMsgIn();
extern int             UnlinkMsgOut();
extern int             GetMsgOutNumber();
extern Msg             *GetMsgOutByNumber();
extern int             GetMsgInNumber();
extern Msg             *GetMsgInByNumber();
extern int             MsgInMemReq();
extern Msg*            AllocMsg();
extern void            FreeMsg();
extern void            RemapMsgData();
extern void            DeleteMsgReferringToData();
extern int             LinkMsgIn();
extern int             LinkMsgOut();
extern void            CopyMsgs();
extern int             DeleteAllMsgsByType();
extern void            DeleteAllMsgs();
extern int             DeleteMsg();
extern void            AssignSlotFunc();
extern int             MsgListMaxType();
extern int             MsgListAdd();
extern int             MsgListDelete();
extern void            MsgListMakePermanent();
extern Msg*            AddForwMsg();
extern void            DeleteForwMsg();
extern void            AddMsg();
extern int             GetMsgNumBySrcDest();
extern int             Name();
extern void            NameHashInit();
extern int             AddName();
extern int             FindName();
extern char            *GetHeader();
extern void            Notes();
extern void            ObjectHashInit();
extern int             ObjectHashEnter();
extern int             ObjectHashPut();
extern GenesisObject   *ObjectHashFind();
extern GenesisObject   *GetObject();
extern char            *getobjenv();
extern void            AddObject();
extern void            ObjectAddClass();
extern void            BasicObjects();
extern int             SetElementEnv();
extern int             SaveData();
extern int             WriteHeader();
extern int             CloseSave();
extern int             SaveString();
extern int             SaveSlot();
extern int             SaveMsg();
extern int             SaveElement();
extern int             SaveTree();
extern int             SaveArgList();
extern int             SaveActionList();
extern int             SaveMsgList();
extern int             SaveFieldList();
extern int             SaveObject();
extern int             SaveObjects();
extern int             SaveClasses();
extern int             SaveSimulation();
extern int             PositionElement();
extern void            quitCallback();
extern void            QuitStage1();
extern float           ran1();
extern float           ran3();
extern int             FreeRegionMask();
extern int             GetRegionDefinition();
extern void            SimReset();
extern void            ResetTmin();
extern void            ResetSimState();
extern void            ResetElements();
extern void            ErrorMessage();
extern void            ActionHeader();
extern void            InvalidAction();
extern void            InvalidPath();
extern void            InvalidField();
extern size_t          memusage();
extern void            sim_set_float_format();
extern int             CheckType2Header();
extern Schedule        *GetSchedule();
extern int             GetMaxTasks();
extern int             WorkingTasks();
extern Schedule        *GetWorkingTask();
extern void            InitSchedule();
extern void            ExecuteTasks();
extern void            ClearWorkingSchedule();
extern void            Reschedule();
extern int             Server();
extern int             ServerJob();
extern int             ServerArgv();
extern int             GoodBye();
extern int             Shutdown();
extern int             GenCmd();
extern int             ExecuteServerCmd();
extern int             ServerCommand();
extern int             ServerReply();
extern int             ServerLog();
extern int             CallSetActions();
extern char*           FieldNameProper();
extern int             SetElement();
extern int             DirectSetElement();
extern int             SetField();
extern void            ShowObject();
extern void            ShowSpecific();
extern void            ShowBasic();
extern void            ShowAll();
extern void            ShowField();
extern int             IsGElement();
extern void            Simulate();
extern void            ClearCheckMarkers();
extern ElementStack    *NewPutElementStack();
extern void            NewFreeElementStack();
extern Element         *NewTopOfStack();
extern Element         *NewNextElement();
extern Element         *NewFastNextElement();
extern void            PrintStatus();
extern void            SimStatus();
extern void            SetBreakFlag();
extern int             GetCurrentStep();
extern void            StepStatus();
extern void            SetCurrentStep();
extern void            StepSimulation();
extern void            TStepSimulation();
extern void            RemoveSimulationJob();
extern void            ActivateStep();
extern void            ReportStatus();
extern int             ParseConnection();
extern char            *GetNameAndIndex();
extern int             HasElementField();
extern char            *SpecificField();
extern char            *Pathname();
extern char            *GetParentComponent();
extern char            *GetBaseComponent();
extern char            *GetPathComponent();
extern char            *GetFieldComponent();
extern int             GetIndexComponent();
extern void            SetProjectionScale();
extern void            SetProjectionTranslate();
extern void            SetProjectionRotate();
extern int             GetTreeCount();
extern char            *GetTreeName();
extern char            *AdvancePathname();
extern void            ChangeWorkingElement();
extern void            ListElements();
extern int             CountChildren();
extern int             PutElementStack();
extern void            FreeElementStack();
extern Element         *TopOfStack();
extern Element         *NextElement();
extern Element         *FastNextElement();
extern int             ValidElement();
extern char            *GetValue();
extern int             PutValue();
extern void            do_initdump();
extern void            do_create();
extern int             do_add_msg();
extern int             check_method();
extern struct mask_type *GetMaskFromArgv();

#endif /* SIM_FUNC_EXT_H */

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