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_3
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weightslist.txt
                            
% Wed Aug 19 14:47:03 2015

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

Connect(ev4v, ev1v)  {
  From:  (1, 1)  {
    ([ 8, 1]  0.000742) 
    ([ 9, 1]  0.000551) 
    ([ 1, 1]  0.001089) 
    ([ 2, 1]  0.001540) 
    |              | 
  }
  From:  (1, 2)  {
    ([ 8, 2]  0.001243) 
    ([ 9, 2]  0.001685) 
    |              | 
    |              | 
    ([ 3, 2]  0.001375) 
  }
  From:  (1, 3)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000984)   }
  From:  (1, 4)  {
    ([ 8, 4]  0.000317) 
    ([ 9, 4]  0.001698) 
    ([ 1, 4]  0.000729) 
    ([ 2, 4]  0.000439) 
    ([ 3, 4]  0.000060) 
  }
  From:  (1, 5)  {
    |              | 
    |              | 
    ([ 1, 5]  0.001930) 
    ([ 2, 5]  0.000937) 
    |              | 
  }
  From:  (1, 6)  {
    |              | 
    ([ 9, 6]  0.001988) 
    |              | 
    ([ 2, 6]  0.001258) 
    ([ 3, 6]  0.000790) 
  }
  From:  (1, 7)  {
    |              | 
    |              | 
    ([ 1, 7]  0.000199) 
    |              | 
    |              | 
  }
  From:  (1, 8)  {
    ([ 8, 8]  0.000997) 
    |              | 
    |              | 
    ([ 2, 8]  0.000777) 
    ([ 3, 8]  0.001462) 
  }
  From:  (1, 9)  {
    ([ 8, 9]  0.001734) 
    ([ 9, 9]  0.000485) 
    ([ 1, 9]  0.000210) 
    ([ 2, 9]  0.001558) 
    |              | 
  }
  From:  (2, 1)  {
    ([ 9, 1]  0.001514) 
    ([ 1, 1]  0.001120) 
    |              | 
    |              | 
    ([ 4, 1]  0.001813) 
  }
  From:  (2, 2)  {
    ([ 9, 2]  0.001628) 
    ([ 1, 2]  0.000675) 
    |              | 
    ([ 3, 2]  0.000516) 
    ([ 4, 2]  0.001416) 
  }
  From:  (2, 3)  {
    ([ 9, 3]  0.000596) 
    ([ 1, 3]  0.001482) 
    ([ 2, 3]  0.000803) 
    |              | 
    ([ 4, 3]  0.001274) 
  }
  From:  (2, 4)  {
    |              | 
    ([ 1, 4]  0.000585) 
    |              | 
    ([ 3, 4]  0.000867) 
    ([ 4, 4]  0.001640) 
  }
  From:  (2, 5)  {
    |              | 
    |              | 
    |              | 
    ([ 3, 5]  0.000316) 
    ([ 4, 5]  0.000409) 
  }
  From:  (2, 6)  {
    ([ 9, 6]  0.000559) 
    ([ 1, 6]  0.000773) 
    |              | 
    |              | 
    ([ 4, 6]  0.000187) 
  }
  From:  (2, 7)  {
    |              | 
    |              | 
    ([ 2, 7]  0.001700) 
    |              | 
    ([ 4, 7]  0.000517) 
  }
  From:  (2, 8)  {
    ([ 9, 8]  0.001005) 
    ([ 1, 8]  0.000921) 
    ([ 2, 8]  0.001797) 
    ([ 3, 8]  0.000270) 
    ([ 4, 8]  0.000230) 
  }
  From:  (2, 9)  {
    |              | 
    ([ 1, 9]  0.000569) 
    |              | 
    ([ 3, 9]  0.000360) 
    ([ 4, 9]  0.001128) 
  }
  From:  (3, 1)  {
    |              | 
    ([ 2, 1]  0.001236) 
    ([ 3, 1]  0.000744) 
    ([ 4, 1]  0.001204) 
    ([ 5, 1]  0.001116) 
  }
  From:  (3, 2)  {
    ([ 1, 2]  0.001041) 
    ([ 2, 2]  0.000844) 
    ([ 3, 2]  0.000602) 
    ([ 4, 2]  0.000449) 
    ([ 5, 2]  0.000547) 
  }
  From:  (3, 3)  {
    ([ 1, 3]  0.000068) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (3, 4)  {
    |              | 
    |              | 
    |              | 
    ([ 4, 4]  0.001482) 
    |              | 
  }
  From:  (3, 5)  {
    ([ 1, 5]  0.001433) 
    ([ 2, 5]  0.000200) 
    |              | 
    |              | 
    |              | 
  }
  From:  (3, 6)  {
    ([ 1, 6]  0.000162) 
    |              | 
    |              | 
    ([ 4, 6]  0.000088) 
    |              | 
  }
  From:  (3, 7)  {
    |              | 
    ([ 2, 7]  0.001933) 
    |              | 
    |              | 
    ([ 5, 7]  0.001789) 
  }
  From:  (3, 8)  {
    ([ 1, 8]  0.000805) 
    |              | 
    ([ 3, 8]  0.000887) 
    |              | 
    ([ 5, 8]  0.001189) 
  }
  From:  (3, 9)  {
    |              | 
    ([ 2, 9]  0.001464) 
    |              | 
    ([ 4, 9]  0.000764) 
    |              | 
  }
  From:  (4, 1)  {
    |              | 
    ([ 3, 1]  0.001234) 
    ([ 4, 1]  0.001311) 
    |              | 
    ([ 6, 1]  0.000610) 
  }
  From:  (4, 2)  {
    |              | 
    ([ 3, 2]  0.001163) 
    ([ 4, 2]  0.001018) 
    |              | 
    ([ 6, 2]  0.000628) 
  }
  From:  (4, 3)  {
    |              | 
    |              | 
    ([ 4, 3]  0.000005) 
    |              | 
    |              | 
  }
  From:  (4, 4)  {
    |              | 
    |              | 
    |              | 
    ([ 5, 4]  0.001276) 
    |              | 
  }
  From:  (4, 5)  {
    ([ 2, 5]  0.001474) 
    |              | 
    ([ 4, 5]  0.000310) 
    |              | 
    |              | 
  }
  From:  (4, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.001691)   }
  From:  (4, 7)  {
    |              | 
    ([ 3, 7]  0.000447) 
    ([ 4, 7]  0.001287) 
    ([ 5, 7]  0.000236) 
    ([ 6, 7]  0.000234) 
  }
  From:  (4, 8)  {
    |              | 
    ([ 3, 8]  0.001650) 
    |              | 
    ([ 5, 8]  0.001791) 
    |              | 
  }
  From:  (4, 9)  {
    ([ 2, 9]  0.000589) 
    |              | 
    |              | 
    ([ 5, 9]  0.001378) 
    ([ 6, 9]  0.000403) 
  }
  From:  (5, 1)  {
    |              | 
    ([ 4, 1]  0.001461) 
    ([ 5, 1]  0.000618) 
    |              | 
    |              | 
  }
  From:  (5, 2)  {
    ([ 3, 2]  0.001157) 
    |              | 
    |              | 
    ([ 6, 2]  0.001156) 
    ([ 7, 2]  0.000030) 
  }
  From:  (5, 3)  {
    |              | 
    ([ 4, 3]  0.001407) 
    |              | 
    |              | 
    ([ 7, 3]  0.000302) 
  }
  From:  (5, 4)  {
    ([ 3, 4]  0.001237) 
    ([ 4, 4]  0.001297) 
    ([ 5, 4]  0.001419) 
    ([ 6, 4]  0.000066) 
    |              | 
  }
  From:  (5, 5)  {
    |              | 
    ([ 4, 5]  0.001595) 
    ([ 5, 5]  0.001027) 
    ([ 6, 5]  0.000015) 
    ([ 7, 5]  0.001012) 
  }
  From:  (5, 6)  {
    |              | 
    ([ 4, 6]  0.001300) 
    ([ 5, 6]  0.001088) 
    ([ 6, 6]  0.001244) 
    ([ 7, 6]  0.001796) 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.000319) 
    ([ 4, 7]  0.000272) 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 8)  {
    ([ 3, 8]  0.000474) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 9)  {
    |              | 
    |              | 
    ([ 5, 9]  0.001542) 
    |              | 
    ([ 7, 9]  0.000529) 
  }
  From:  (6, 1)  {
    ([ 4, 1]  0.001473) 
    ([ 5, 1]  0.000611) 
    |              | 
    ([ 7, 1]  0.001308) 
    |              | 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.000848) 
    ([ 5, 2]  0.000412) 
    ([ 6, 2]  0.001921) 
    ([ 7, 2]  0.001876) 
    ([ 8, 2]  0.000406) 
  }
  From:  (6, 3)  {
    ([ 4, 3]  0.000605) 
    |              | 
    ([ 6, 3]  0.001631) 
    ([ 7, 3]  0.000213) 
    |              | 
  }
  From:  (6, 4)  {
    |              | 
    ([ 5, 4]  0.000775) 
    ([ 6, 4]  0.000595) 
    |              | 
    |              | 
  }
  From:  (6, 5)  {
    |              | 
    |              | 
    ([ 6, 5]  0.001696) 
    ([ 7, 5]  0.001527) 
    |              | 
  }
  From:  (6, 6)  {
    |              | 
    |              | 
    ([ 6, 6]  0.000006) 
    |              | 
    ([ 8, 6]  0.000357) 
  }
  From:  (6, 7)  {
    ([ 4, 7]  0.000089) 
    |              | 
    ([ 6, 7]  0.001401) 
    ([ 7, 7]  0.000866) 
    ([ 8, 7]  0.001252) 
  }
  From:  (6, 8)  {
    ([ 4, 8]  0.000936) 
    |              | 
    ([ 6, 8]  0.000880) 
    ([ 7, 8]  0.001438) 
    |              | 
  }
  From:  (6, 9)  {
    ([ 4, 9]  0.001005) 
    ([ 5, 9]  0.001068) 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 1)  {
    ([ 5, 1]  0.000233) 
    ([ 6, 1]  0.000840) 
    ([ 7, 1]  0.001190) 
    |              | 
    ([ 9, 1]  0.000268) 
  }
  From:  (7, 2)  {
    |              | 
    |              | 
    ([ 7, 2]  0.000352) 
    ([ 8, 2]  0.000102) 
    ([ 9, 2]  0.000236) 
  }
  From:  (7, 3)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000005)   }
  From:  (7, 4)  {
    ([ 5, 4]  0.000308) 
    |              | 
    ([ 7, 4]  0.000262) 
    |              | 
    ([ 9, 4]  0.000314) 
  }
  From:  (7, 5)  {
    |              | 
    |              | 
    |              | 
    ([ 8, 5]  0.001902) 
    |              | 
  }
  From:  (7, 6)  {
    ([ 5, 6]  0.001064) 
    ([ 6, 6]  0.000008) 
    ([ 7, 6]  0.000657) 
    |              | 
    ([ 9, 6]  0.000113) 
  }
  From:  (7, 7)  {
    |              | 
    |              | 
    ([ 7, 7]  0.001735) 
    ([ 8, 7]  0.001339) 
    ([ 9, 7]  0.000701) 
  }
  From:  (7, 8)  {
    ([ 5, 8]  0.001013) 
    ([ 6, 8]  0.000932) 
    ([ 7, 8]  0.000087) 
    ([ 8, 8]  0.000192) 
    |              | 
  }
  From:  (7, 9)  {
    ([ 5, 9]  0.001956) 
    |              | 
    |              | 
    ([ 8, 9]  0.001883) 
    |              | 
  }
  From:  (8, 1)  {
    |              | 
    ([ 7, 1]  0.000445) 
    |              | 
    |              | 
    |              | 
  }
  From:  (8, 2)  {
    |              | 
    |              | 
    ([ 8, 2]  0.000561) 
    |              | 
    ([ 1, 2]  0.001915) 
  }
  From:  (8, 3)  {
    ([ 6, 3]  0.000028) 
    |              | 
    ([ 8, 3]  0.000260) 
    |              | 
    ([ 1, 3]  0.001828) 
  }
  From:  (8, 4)  {
    ([ 6, 4]  0.001982) 
    ([ 7, 4]  0.000224) 
    ([ 8, 4]  0.000615) 
    |              | 
    ([ 1, 4]  0.001439) 
  }
  From:  (8, 5)  {
    |              | 
    ([ 7, 5]  0.000323) 
    |              | 
    |              | 
    ([ 1, 5]  0.001491) 
  }
  From:  (8, 6)  {
    ([ 6, 6]  0.000826) 
    ([ 7, 6]  0.001484) 
    ([ 8, 6]  0.000660) 
    ([ 9, 6]  0.000202) 
    ([ 1, 6]  0.000591) 
  }
  From:  (8, 7)  {
    |              | 
    |              | 
    ([ 8, 7]  0.001138) 
    |              | 
    ([ 1, 7]  0.000992) 
  }
  From:  (8, 8)  {
    ([ 6, 8]  0.001250) 
    |              | 
    ([ 8, 8]  0.000128) 
    |              | 
    ([ 1, 8]  0.000610) 
  }
  From:  (8, 9)  {
    |              | 
    ([ 7, 9]  0.001472) 
    ([ 8, 9]  0.000354) 
    ([ 9, 9]  0.001883) 
    ([ 1, 9]  0.000646) 
  }
  From:  (9, 1)  {
    ([ 7, 1]  0.001219) 
    ([ 8, 1]  0.000757) 
    |              | 
    |              | 
    ([ 2, 1]  0.000681) 
  }
  From:  (9, 2)  {
    ([ 7, 2]  0.000639) 
    |              | 
    ([ 9, 2]  0.001267) 
    ([ 1, 2]  0.001731) 
    |              | 
  }
  From:  (9, 3)  {
    |              | 
    |              | 
    ([ 9, 3]  0.000692) 
    |              | 
    |              | 
  }
  From:  (9, 4)  {
    ([ 7, 4]  0.000098) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 5)  {
    ([ 7, 5]  0.001459) 
    ([ 8, 5]  0.001097) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 6)  {
    ([ 7, 6]  0.001007) 
    ([ 8, 6]  0.000842) 
    ([ 9, 6]  0.000453) 
    ([ 1, 6]  0.001524) 
    |              | 
  }
  From:  (9, 7)  {
    |              | 
    ([ 8, 7]  0.001778) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    ([ 8, 8]  0.000148) 
    |              | 
    |              | 
    ([ 2, 8]  0.001893) 
  }
  From:  (9, 9)  {
    ([ 7, 9]  0.001329) 
    ([ 8, 9]  0.000875) 
    ([ 9, 9]  0.001060) 
    |              | 
    ([ 2, 9]  0.001056) 
  }
}

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