Large-scale neural model of visual short-term memory (Ulloa, Horwitz 2016; Horwitz, et al. 2005,...)

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Accession:206337
Large-scale neural model of visual short term memory embedded into a 998-node connectome. The model simulates electrical activity across neuronal populations of a number of brain regions and converts that activity into fMRI and MEG time-series. The model uses a neural simulator developed at the Brain Imaging and Modeling Section of the National Institutes of Health.
References:
1 . Tagamets MA, Horwitz B (1998) Integrating electrophysiological and anatomical experimental data to create a large-scale model that simulates a delayed match-to-sample human brain imaging study. Cereb Cortex 8:310-20 [PubMed]
2 . Ulloa A, Horwitz B (2016) Embedding Task-Based Neural Models into a Connectome-Based Model of the Cerebral Cortex. Front Neuroinform 10:32 [PubMed]
3 . Horwitz B, Warner B, Fitzer J, Tagamets MA, Husain FT, Long TW (2005) Investigating the neural basis for functional and effective connectivity. Application to fMRI. Philos Trans R Soc Lond B Biol Sci 360:1093-108 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Prefrontal cortex (PFC);
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: Python;
Model Concept(s): Working memory;
Implementer(s): Ulloa, Antonio [antonio.ulloa at alum.bu.edu];
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lsnm_in_python-master
visual_model
subject_9
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weightslist.txt
                            
% Fri Aug 21 23:03:58 2015

% Input layer: (9, 9)
% Output layer: (9, 9)
% Fanout size: (5, 1)
% Fanout spacing: (1, 1)
% Specified fanout weights

Connect(ev1v, ev4v)  {
  From:  (1, 1)  {
    |              | 
    ([ 9, 1]  0.044926) 
    ([ 1, 1]  0.046006) 
    ([ 2, 1]  0.031420) 
    ([ 3, 1]  0.030755) 
  }
  From:  (1, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 2]  0.038494) 
    ([ 3, 2]  0.030162) 
  }
  From:  (1, 3)  {
    ([ 8, 3]  0.047814) 
    ([ 9, 3]  0.030629) 
    ([ 1, 3]  0.040535) 
    ([ 2, 3]  0.047965) 
    ([ 3, 3]  0.042386) 
  }
  From:  (1, 4)  {
    |              | 
    ([ 9, 4]  0.046815) 
    |              | 
    |              | 
    ([ 3, 4]  0.032357) 
  }
  From:  (1, 5)  {
    |              | 
    ([ 9, 5]  0.045543) 
    ([ 1, 5]  0.040928) 
    ([ 2, 5]  0.048999) 
    ([ 3, 5]  0.038957) 
  }
  From:  (1, 6)  {
    ([ 8, 6]  0.047602) 
    ([ 9, 6]  0.046028) 
    ([ 1, 6]  0.043559) 
    ([ 2, 6]  0.043693) 
    ([ 3, 6]  0.042322) 
  }
  From:  (1, 7)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 7]  0.034206) 
    ([ 3, 7]  0.034361) 
  }
  From:  (1, 8)  {
    |              | 
    |              | 
    ([ 1, 8]  0.034930) 
    ([ 2, 8]  0.041834) 
    |              | 
  }
  From:  (1, 9)  {
    ([ 8, 9]  0.047688) 
    |              | 
    ([ 1, 9]  0.044465) 
    |              | 
    |              | 
  }
  From:  (2, 1)  {
    |              | 
    ([ 1, 1]  0.043937) 
    |              | 
    ([ 3, 1]  0.031698) 
    ([ 4, 1]  0.043791) 
  }
  From:  (2, 2)  {
    ([ 9, 2]  0.048196) 
    |              | 
    |              | 
    ([ 3, 2]  0.049055) 
    ([ 4, 2]  0.043003) 
  }
  From:  (2, 3)  {
    ([ 9, 3]  0.042524) 
    |              | 
    |              | 
    |              | 
    ([ 4, 3]  0.047760) 
  }
  From:  (2, 4)  {
    |              | 
    ([ 1, 4]  0.030718) 
    ([ 2, 4]  0.047228) 
    ([ 3, 4]  0.042350) 
    |              | 
  }
  From:  (2, 5)  {
    ([ 9, 5]  0.044721) 
    |              | 
    |              | 
    ([ 3, 5]  0.046833) 
    ([ 4, 5]  0.033291) 
  }
  From:  (2, 6)  {
    ([ 9, 6]  0.041182) 
    |              | 
    |              | 
    |              | 
    ([ 4, 6]  0.043000) 
  }
  From:  (2, 7)  {
    |              | 
    |              | 
    ([ 2, 7]  0.036931) 
    ([ 3, 7]  0.049544) 
    ([ 4, 7]  0.042006) 
  }
  From:  (2, 8)  {
    ([ 9, 8]  0.030039) 
    |              | 
    |              | 
    ([ 3, 8]  0.031828) 
    |              | 
  }
  From:  (2, 9)  {
    ([ 9, 9]  0.039106) 
    ([ 1, 9]  0.043512) 
    ([ 2, 9]  0.033688) 
    ([ 3, 9]  0.047201) 
    ([ 4, 9]  0.045511) 
  }
  From:  (3, 1)  {
    |              | 
    ([ 2, 1]  0.046191) 
    |              | 
    |              | 
    |              | 
  }
  From:  (3, 2)  {
    ([ 1, 2]  0.042822) 
    |              | 
    |              | 
    ([ 4, 2]  0.033183) 
    |              | 
  }
  From:  (3, 3)  {
    |              | 
    |              | 
    ([ 3, 3]  0.048270) 
    ([ 4, 3]  0.049515) 
    |              | 
  }
  From:  (3, 4)  {
    ([ 1, 4]  0.048488) 
    ([ 2, 4]  0.038235) 
    ([ 3, 4]  0.046118) 
    |              | 
    |              | 
  }
  From:  (3, 5)  {
    ([ 1, 5]  0.035552) 
    ([ 2, 5]  0.044683) 
    ([ 3, 5]  0.044226) 
    ([ 4, 5]  0.040534) 
    ([ 5, 5]  0.035124) 
  }
  From:  (3, 6)  {
    |              | 
    ([ 2, 6]  0.037719) 
    |              | 
    ([ 4, 6]  0.048563) 
    |              | 
  }
  From:  (3, 7)  {
    ([ 1, 7]  0.041000) 
    |              | 
    |              | 
    |              | 
    ([ 5, 7]  0.044756) 
  }
  From:  (3, 8)  {
    |              | 
    ([ 2, 8]  0.036851) 
    ([ 3, 8]  0.047983) 
    |              | 
    ([ 5, 8]  0.046329) 
  }
  From:  (3, 9)  {
    ([ 1, 9]  0.038319) 
    ([ 2, 9]  0.048592) 
    |              | 
    ([ 4, 9]  0.043048) 
    |              | 
  }
  From:  (4, 1)  {
    ([ 2, 1]  0.040043) 
    ([ 3, 1]  0.030663) 
    ([ 4, 1]  0.033324) 
    |              | 
    |              | 
  }
  From:  (4, 2)  {
    |              | 
    |              | 
    ([ 4, 2]  0.046416) 
    |              | 
    |              | 
  }
  From:  (4, 3)  {
    |              | 
    ([ 3, 3]  0.037794) 
    |              | 
    |              | 
    ([ 6, 3]  0.037463) 
  }
  From:  (4, 4)  {
    ([ 2, 4]  0.034017) 
    ([ 3, 4]  0.042555) 
    ([ 4, 4]  0.037494) 
    ([ 5, 4]  0.035258) 
    ([ 6, 4]  0.030787) 
  }
  From:  (4, 5)  {
    |              | 
    ([ 3, 5]  0.036497) 
    |              | 
    ([ 5, 5]  0.033806) 
    ([ 6, 5]  0.040942) 
  }
  From:  (4, 6)  {
    |              | 
    ([ 3, 6]  0.037856) 
    ([ 4, 6]  0.043239) 
    ([ 5, 6]  0.043599) 
    |              | 
  }
  From:  (4, 7)  {
    ([ 2, 7]  0.035175) 
    ([ 3, 7]  0.045577) 
    ([ 4, 7]  0.042172) 
    ([ 5, 7]  0.047171) 
    |              | 
  }
  From:  (4, 8)  {
    |              | 
    |              | 
    ([ 4, 8]  0.040687) 
    |              | 
    ([ 6, 8]  0.033285) 
  }
  From:  (4, 9)  {
    |              | 
    ([ 3, 9]  0.030402) 
    ([ 4, 9]  0.038881) 
    |              | 
    |              | 
  }
  From:  (5, 1)  {
    ([ 3, 1]  0.043129) 
    |              | 
    ([ 5, 1]  0.046876) 
    ([ 6, 1]  0.038478) 
    ([ 7, 1]  0.031223) 
  }
  From:  (5, 2)  {
    |              | 
    |              | 
    ([ 5, 2]  0.033751) 
    ([ 6, 2]  0.042282) 
    |              | 
  }
  From:  (5, 3)  {
    |              | 
    |              | 
    ([ 5, 3]  0.037819) 
    ([ 6, 3]  0.044298) 
    ([ 7, 3]  0.035679) 
  }
  From:  (5, 4)  {
    ([ 3, 4]  0.049238) 
    |              | 
    ([ 5, 4]  0.041577) 
    ([ 6, 4]  0.048214) 
    ([ 7, 4]  0.031345) 
  }
  From:  (5, 5)  {
    ([ 3, 5]  0.045127) 
    |              | 
    ([ 5, 5]  0.044168) 
    |              | 
    |              | 
  }
  From:  (5, 6)  {
    |              | 
    ([ 4, 6]  0.045162) 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.048705) 
    ([ 4, 7]  0.038332) 
    ([ 5, 7]  0.048157) 
    ([ 6, 7]  0.036176) 
    |              | 
  }
  From:  (5, 8)  {
    ([ 3, 8]  0.045947) 
    |              | 
    ([ 5, 8]  0.047883) 
    |              | 
    |              | 
  }
  From:  (5, 9)  {
    |              | 
    |              | 
    ([ 5, 9]  0.045243) 
    |              | 
    |              | 
  }
  From:  (6, 1)  {
    ([ 4, 1]  0.035926) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.035484) 
    ([ 5, 2]  0.038837) 
    |              | 
    ([ 7, 2]  0.040773) 
    |              | 
  }
  From:  (6, 3)  {
    ([ 4, 3]  0.048466) 
    |              | 
    |              | 
    ([ 7, 3]  0.036979) 
    |              | 
  }
  From:  (6, 4)  {
    ([ 4, 4]  0.031135) 
    ([ 5, 4]  0.043816) 
    ([ 6, 4]  0.038013) 
    ([ 7, 4]  0.047061) 
    ([ 8, 4]  0.044567) 
  }
  From:  (6, 5)  {
    ([ 4, 5]  0.044419) 
    ([ 5, 5]  0.034926) 
    |              | 
    |              | 
    ([ 8, 5]  0.038575) 
  }
  From:  (6, 6)  {
    ([ 4, 6]  0.049655) 
    |              | 
    ([ 6, 6]  0.039505) 
    |              | 
    ([ 8, 6]  0.039345) 
  }
  From:  (6, 7)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.037203)   }
  From:  (6, 8)  {
    ([ 4, 8]  0.043030) 
    |              | 
    |              | 
    ([ 7, 8]  0.044012) 
    ([ 8, 8]  0.047311) 
  }
  From:  (6, 9)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 8, 9]  0.033940) 
  }
  From:  (7, 1)  {
    ([ 5, 1]  0.044501) 
    ([ 6, 1]  0.036003) 
    ([ 7, 1]  0.032608) 
    |              | 
    |              | 
  }
  From:  (7, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 8, 2]  0.040322) 
    ([ 9, 2]  0.045952) 
  }
  From:  (7, 3)  {
    ([ 5, 3]  0.044341) 
    |              | 
    ([ 7, 3]  0.045009) 
    ([ 8, 3]  0.043753) 
    |              | 
  }
  From:  (7, 4)  {
    ([ 5, 4]  0.049234) 
    ([ 6, 4]  0.047900) 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 5)  {
    |              | 
    ([ 6, 5]  0.042828) 
    |              | 
    ([ 8, 5]  0.037682) 
    |              | 
  }
  From:  (7, 6)  {
    |              | 
    ([ 6, 6]  0.037030) 
    ([ 7, 6]  0.044259) 
    ([ 8, 6]  0.041799) 
    |              | 
  }
  From:  (7, 7)  {
    ([ 5, 7]  0.035986) 
    |              | 
    |              | 
    ([ 8, 7]  0.033227) 
    |              | 
  }
  From:  (7, 8)  {
    |              | 
    ([ 6, 8]  0.030956) 
    ([ 7, 8]  0.045726) 
    |              | 
    |              | 
  }
  From:  (7, 9)  {
    ([ 5, 9]  0.036202) 
    |              | 
    |              | 
    ([ 8, 9]  0.037945) 
    ([ 9, 9]  0.045150) 
  }
  From:  (8, 1)  {
    |              | 
    |              | 
    ([ 8, 1]  0.034692) 
    ([ 9, 1]  0.040816) 
    |              | 
  }
  From:  (8, 2)  {
    ([ 6, 2]  0.036789) 
    |              | 
    |              | 
    |              | 
    ([ 1, 2]  0.044633) 
  }
  From:  (8, 3)  {
    |              | 
    |              | 
    ([ 8, 3]  0.047830) 
    ([ 9, 3]  0.031146) 
    ([ 1, 3]  0.045243) 
  }
  From:  (8, 4)  {
    |              | 
    |              | 
    ([ 8, 4]  0.039735) 
    |              | 
    ([ 1, 4]  0.035982) 
  }
  From:  (8, 5)  {
    ([ 6, 5]  0.044561) 
    |              | 
    |              | 
    ([ 9, 5]  0.047103) 
    ([ 1, 5]  0.035856) 
  }
  From:  (8, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 6]  0.040426) 
  }
  From:  (8, 7)  {
    |              | 
    |              | 
    ([ 8, 7]  0.046374) 
    |              | 
    |              | 
  }
  From:  (8, 8)  {
    |              | 
    ([ 7, 8]  0.046173) 
    |              | 
    |              | 
    |              | 
  }
  From:  (8, 9)  {
    |              | 
    ([ 7, 9]  0.041112) 
    |              | 
    ([ 9, 9]  0.042006) 
    ([ 1, 9]  0.034436) 
  }
  From:  (9, 1)  {
    |              | 
    ([ 8, 1]  0.033503) 
    ([ 9, 1]  0.049338) 
    ([ 1, 1]  0.043869) 
    ([ 2, 1]  0.040728) 
  }
  From:  (9, 2)  {
    ([ 7, 2]  0.048993) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 3)  {
    |              | 
    ([ 8, 3]  0.049047) 
    |              | 
    ([ 1, 3]  0.034832) 
    |              | 
  }
  From:  (9, 4)  {
    ([ 7, 4]  0.048428) 
    ([ 8, 4]  0.044247) 
    |              | 
    ([ 1, 4]  0.037240) 
    |              | 
  }
  From:  (9, 5)  {
    |              | 
    ([ 8, 5]  0.042382) 
    |              | 
    |              | 
    ([ 2, 5]  0.048872) 
  }
  From:  (9, 6)  {
    ([ 7, 6]  0.041662) 
    |              | 
    |              | 
    |              | 
    ([ 2, 6]  0.041992) 
  }
  From:  (9, 7)  {
    |              | 
    ([ 8, 7]  0.036223) 
    |              | 
    ([ 1, 7]  0.032784) 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    ([ 8, 8]  0.037608) 
    ([ 9, 8]  0.032858) 
    |              | 
    ([ 2, 8]  0.048182) 
  }
  From:  (9, 9)  {
    ([ 7, 9]  0.034927) 
    ([ 8, 9]  0.031032) 
    |              | 
    |              | 
    |              | 
  }
}

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