#summary Biological Life Research
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This page is intended to create model of biological human brain based on open research results across the world.
Related findings are structured by other research themes.

<wiki:toc max_depth="2" />

= Overview =

  * *Biological Model* contains *Central Nervous System* (CNS), *Peripheral Nervous System* (PNS) and human *Target Sensors* and *Target Effectors*, connected together and systematically described in machine-readable format
  * Model data are divided into *Engine Data* (mind.xml, target.xml), *Internal Model Data* (hmind, muscles, nerves, global.xml) and *External Model Data* (circuits)
   * Engine Data are divided into 
    * *Engine Core Data* (mind.xml, mind.core.xml) - most probably universal items, independent of biological nature or phenotype
    * *Engine Lifecycle Data* (mind.lifecycle.xml) - items supporting life functions of biological organism
    * *Engine Specific Data* (mind.specific.xml, mind.integration.xml) - nervous system items responsible for handling specific human organs
    * *Engine Target Data* (target.xml) - final sets of human sensors and effectors
   * Internal Model Data provide human-readable descriptions and additional details
    * *Global Circuits* are independent overlapping groups of regions (global.xml) which shed light on specific modality of mind function across many Mind Areas
   * External Model Data provide thirdparty models, partial and sometimes contradicting, with their own visualization and schema linked with aHuman items identification
  * Detailed data are grouped using two distinct structures - *Brain Centers* and *Mind Areas*
   * Brain Centers are well-known anatomical groups existing as major solid structures or sets of nuclei or cortices, located on specific anatomical area
   * Mind Areas are aHuman functional structures grouping items implementing major mind functions
    * Every Mind Area is a set of non-overlapping *Local Circuits*
     * Local Circuit contains specific mind regions, circuits internal inter-region connections and circuit outbound connections, which establish brain area subfunction or the same function but handling specific aspect of human organism

*See further information:*
  * Description of model elements and attributes -  [BiologicalModel Biological Model Metadata]
  * Full mind hierarchy - [OverallMindMaps Mind Maps]
  * Spinal and cranial tracts - [MindTracts Mind Tracts]
  * Peripheral nervous System - [PeripheralBrain Peripheral Brain]
  * Nervous tissue types - [OverallNeuralNetworks Neural Networks]
  * Global functional circuits - [OverallCircuits Overall Circuits]
  * How brain is developed from the very beginning - [OverallBrainDevelopment Brain Development]

= Mind Areas =

*Approach of defining areas*:
  * make areas functionally named and identified
  * do not create thalamus area to avoid mixing unrelated paths, assign thalamus nuclei to other areas
  * do not create limbic area to avoid mixing unrelated functions, assign limbic components to other areas
  * take into account all subcortical nuclei and ganglia
  * all areas mapped by Brodmann placed in cortical category
  * consider only single left hemisphere
  * consider area as set of groups of regions and links which serve similar function, with area corresponging to providing this function in several circuits (groups)

|| *Area Code* || *Area Name* || *Type* || *Function* || *Comments* ||
|| <font color="red">aHuman</font> || || || || ||
|| *TSA* || [BrainAreaTSA Target Sensory Area] || target || aHuman Target Sensors || Biological Sensors ||
|| *TEA* || [BrainAreaTEA Target Effectory Area] || target || aHuman Target Effectors || Biological Motors ||
|| <font color="red">Lower Brain</font> || || || || ||
|| *LLC* || [BrainAreaLLC Locomotion Control Area] || core || Learned Rythmic Movements || Locomotion Nuclei and Cerebellum ||
|| *LAC* || [BrainAreaLAC Autonomous Control Area] || lifecycle || Autonomic Nuclei and Ganglia || Nuclei to Control Autonomic Organs and Autonomic Ganglia ||
|| *LMC* || [BrainAreaLMC Modulatory Contol Area] || lifecycle || Ascending and Descending Non-Specific Modulation || Includes Nuclei Projecting Both Up and Down ||
|| *LPC* || [BrainAreaLPC Peripheral Control Area] || specific || Conscious Control of Target || Sensory Ganglia, Conscious Sensory and Motor Nuclei ||
|| *LRC* || [BrainAreaLRC Motor Reflex Area] || specific || Reflexive Motor Behavior || Nuclei of Reflex Circuits Resulting in Motor Behavior and Posture Maintenance ||
|| <font color="red">Forebrain</font> || || || || ||
|| *FEC* || [BrainAreaFEC Execution Control Area] || core || Executing Motor Sequences || Premotor and Supplemental Sequences are Wrapped out via Basal Ganglia ||
|| *FAM* || [BrainAreaFAM Affective Motivations Area] || core || Aggregate Body and Mental Motivations || Merges Top Body Feeling and Sensory Streams ||
|| *FMM* || [BrainAreaFMM Memory Management Area] || core || Establish Hierarchical Memory || Top of Sensory Hierarchy ||
|| <font color="red">Neocortical Brain</font> || || || || ||
|| *NMA* || [BrainAreaNMA Motor Aggregation Area] || core || Motor Hierarhical Aggregation || Wrap Out Motor Sequences to Specific Motor Steps ||
|| *NDM* || [BrainAreaNDM Decision Making Area] || core || Sensory-Drive Associations with Working Memory || Choose Actions and Create Working Memory ||
|| *NCP* || [BrainAreaNCP Conscious Personality Area] || core || Produce Mental Feeling || Handle Pain and Errors ||
|| *NSA* || [BrainAreaNSA Sensory Aggregation Area] || specific || Unimodal Sensory Aggregation || Neocortical Sensory Data and Unimodal Aggregation ||
|| *NPE* || [BrainAreaNPE Unimodal Execution Area] || specific || Initiate Polymodal Execution || Aggregate polymodal data, direct to planning and decision making ||

= Brain Structure Overview =
(generated)


*Forebrain Diencephalon* (FD):
  * [BrainCenterFAM_FD_HB Habenula] (FAM.FD.HB)
  * [BrainCenterFD_HT Hypothalamus] (FD.HT)
  * [BrainRegionLPC_FD_RT Retinal Nucleus] (LPC.FD.RT)
  * [BrainCenterFEC_FD_STA Subthalamus Area] (FEC.FD.STA)
  * Thalamus
   * [BrainCenterFD_TH_CR Cognitive Thalamus] (FD.TH.CR)
   * [BrainCenterFD_TH_MR Motor Thalamus] (FD.TH.MR)
   * [BrainCenterFD_TH_SR Sensory Thalamus] (FD.TH.SR)

*Forebrain Telencephalon* (FT):
  * [BrainCenterFEC_FT_BG Basal Ganglia] (FEC.FT.BG)
  * Extended Amygdala
   * [BrainCenterFAM_FT_AM Amygdala] (FAM.FT.AM)
   * [BrainCenterFAM_FT_CEAM Central Extended Amygdala] (FAM.FT.CEAM)
   * [BrainCenterFAM_FT_SEP Septal Nuclei] (FAM.FT.SEP)
  * [BrainCenterFMM_FT_HF Hippocampal Formation] (FMM.FT.HF)
  * [BrainCenterFT_OLF Olfactory Nuclei] (FT.OLF)

*Hindbrain Myelencephalon* (HL):
  * [BrainCenterHL_RF Medullary Reticular Formation] (HL.RF)
  * [BrainCenterHL_MN Myelencephalic Motor Nuclei] (HL.MN)
  * [BrainCenterHL_PSN Myelencephalic Parasympathetic Nuclei] (HL.PSN)
  * [BrainCenterHL_SN Myelencephalic Sensory Nuclei] (HL.SN)

*Hindbrain Metencephalon* (HT):
  * [BrainCenterLLC_HT_CRC Cerebellar Complex] (LLC.HT.CRC)
  * [BrainRegionLMC_HT_LC Locus Coeruleus] (LMC.HT.LC)
  * [BrainCenterHT_MN Metencephalic Motor Nuclei] (HT.MN)
  * [BrainCenterHT_SN Metencephalic Sensory Nuclei] (HT.SN)
  * [BrainCenterHT_RF Pontine Reticular Formation] (HT.RF)
  * [BrainCenterHT_TG Pontine Tegmental Nuclei] (HT.TG)
  * [BrainCenterLPC_HT_VBN Vestibular Nuclei] (LPC.HT.VBN)

*Midbrain Mesencephalon* (MM):
  * [BrainCenterMM_RF Mesencephalic Reticular Formation] (MM.RF)
  * [BrainCenterMM_PER Perhipheral Nuclei of Midbrain Mesencephalon] (MM.PER)
  * [BrainRegionLMC_MM_PAG Periaqueductal Gray Matter] (LMC.MM.PAG)
  * [BrainCenterLLC_MM_RD Red Nucleus] (LLC.MM.RD)
  * [BrainCenterMM_REF Reflexes Nuclei of Midbrain Mesencephalon] (MM.REF)
  * [BrainRegionLMC_MM_VTA Ventral Tegmental Area] (LMC.MM.VTA)

*Cerebral Cortex* (NC):
  * Anterior Lobe
   * [BrainCenterNC_ACG Anterior Cingulate Area] (NC.ACG)
   * [BrainRegionNMA_NC_MC Motor Cortex] (NMA.NC.MC)
   * Prefrontal Cortex
    * [BrainCenterNC_AL_LPFC Lateral Prefrontal Cortex] (NC.AL.LPFC)
    * [BrainCenterNC_AL_OMPFC Orbitomedial Prefrontal Cortex] (NC.AL.OMPFC)
   * [BrainCenterNC_PMC Premotor Cortex] (NC.PMC)
   * [BrainCenterNMA_NC_SMC Supplementary Motor Cortex] (NMA.NC.SMC)
  * [BrainCenterNC_LOBE_OCC Occipital Lobe] (NC.LOBE.OCC)
  * Parahippocampal Lobe
   * Anterior Parahippocampal Gyrus
    * [BrainCenterFMM_NC_PHA_RS Retrosubicular Area] (FMM.NC.PHA.RS)
    * [BrainCenterNC_PHA_RH Rhinal Cortex] (NC.PHA.RH)
   * [BrainCenterFMM_NC_PHP Posterior Parahippocampal Gyrus] (FMM.NC.PHP)
  * Parietal Lobe
   * [BrainCenterNC_IPL Inferior Parietal Lobule] (NC.IPL)
   * [BrainCenterNSA_NC_IPS Intraparietal Sulcus] (NSA.NC.IPS)
   * [BrainCenterNC_MPL Medial Parietal Lobule] (NC.MPL)
   * Postcentral Gyrus
    * [BrainCenterNC_PG_APC Anterior Parietal Cortex] (NC.PG.APC)
    * [BrainCenterNC_PG_LPC Lateral Parietal Cortex] (NC.PG.LPC)
    * [BrainCenterNC_PO Parietal Operculum] (NC.PO)
   * [BrainCenterNC_SPL Superior Parietal Lobule] (NC.SPL)
  * Temporal Lobe
   * [BrainCenterNSA_NC_IT Inferotemporal Area] (NSA.NC.IT)
   * [BrainCenterNC_INS Insular Cortex] (NC.INS)
   * [BrainCenterNC_STG Superior Temporal Gyrus] (NC.STG)
   * [BrainCenterNSA_NC_TTG Transverse Temporal Gyrus] (NSA.NC.TTG)

*Peripheral Nervous System* (PNS):
  * Parasympathetic Ganglia
   * [BrainCenterPN_PSYM_BD Body Parasympathetic Ganglia] (PN.PSYM.BD)
   * [BrainCenterPN_PSYM_HD Head and Neck Parasympathetic Ganglia] (PN.PSYM.HD)
  * Sensory Ganglia
   * [BrainCenterLPC_PN_SG_DRG Dorsal Root Ganglia] (LPC.PN.SG.DRG)
   * [BrainCenterPN_SG_SE Sensory Exteroception Ganglia] (PN.SG.SE)
   * [BrainCenterPN_SG_SI Sensory Interoception Ganglia] (PN.SG.SI)
   * [BrainCenterLPC_PN_SG_VB Vestibular Ganglion] (LPC.PN.SG.VB)
  * Sympathetic Ganglia
   * [BrainCenterLAC_PN_SYM_PA Paravertebral Sympathetic Ganglia] (LAC.PN.SYM.PA)
   * [BrainCenterLAC_PN_SYM_PR Prevertebral Sympathetic Ganglia] (LAC.PN.SYM.PR)

*Spinal Cord* (SC):
  * [BrainCenterSC_VH Anterior/Ventral Horn] (SC.VH)
  * [BrainCenterAVA_SC_CC Central canal] (AVA.SC.CC)
  * [BrainCenterSC_IZ Intermediate Zone] (SC.IZ)
  * [BrainCenterBMA_SC_LH Lateral Horn/Funiculus] (BMA.SC.LH)
  * [BrainCenterBMA_SC_PH Posterior/Dorsal Horn] (BMA.SC.PH)

*Target* (TG):
  * Human Effectors
   * [BrainRegionTARGET_TEA_VESSELS Blood vessels] (TARGET.TEA.VESSELS)
   * [BrainRegionTARGET_TEA_BREAST Breast] (TARGET.TEA.BREAST)
   * [BrainRegionTARGET_TEA_ENDOCRINE Endocrine Glands] (TARGET.TEA.ENDOCRINE)
   * [BrainRegionTARGET_TEA_FACE Face] (TARGET.TEA.FACE)
   * [BrainRegionTARGET_TEA_GENITALIA Genitalia] (TARGET.TEA.GENITALIA)
   * [BrainRegionTARGET_TEA_HAND Hand] (TARGET.TEA.HAND)
   * [BrainRegionTARGET_TEA_HEART Heart] (TARGET.TEA.HEART)
   * [BrainRegionTARGET_TEA_PROTECTOR Immunity glands and meninges] (TARGET.TEA.PROTECTOR)
   * [BrainRegionTARGET_TEA_LEG Leg] (TARGET.TEA.LEG)
   * [BrainRegionTARGET_TEA_LIVER Liver] (TARGET.TEA.LIVER)
   * [BrainRegionTARGET_TEA_LUNG Lung] (TARGET.TEA.LUNG)
   * [BrainRegionTARGET_TEA_FEEDER Mouth feeder] (TARGET.TEA.FEEDER)
   * [BrainRegionTARGET_TEA_SPEAKER Mouth speaker] (TARGET.TEA.SPEAKER)
   * [BrainRegionTARGET_TEA_NECK Neck] (TARGET.TEA.NECK)
   * [BrainRegionTARGET_TEA_RECTUM Rectum] (TARGET.TEA.RECTUM)
   * [BrainRegionTARGET_TEA_STOMACH Stomach] (TARGET.TEA.STOMACH)
   * [BrainRegionTARGET_TEA_TRUNK Trunk] (TARGET.TEA.TRUNK)
   * [BrainRegionTARGET_TEA_URETER Ureter] (TARGET.TEA.URETER)
  * Human Sensors
   * [BrainRegionTARGET_TSA_EAR Ear] (TARGET.TSA.EAR)
   * [BrainRegionTARGET_TSA_EYE Eye] (TARGET.TSA.EYE)
   * [BrainRegionTARGET_TSA_NOSE Nose] (TARGET.TSA.NOSE)

= Circuits =
(generated)