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_13
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netgen1 *
weightslist.txt *
                            
% Tue Sep 29 05:24:59 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]  0.000045) 
    ([ 9, 1]  0.001890) 
    ([ 1, 1]  0.000135) 
    |              | 
    ([ 3, 1]  0.000309) 
  }
  From:  (1, 2)  {
    |              | 
    ([ 9, 2]  0.000173) 
    ([ 1, 2]  0.001795) 
    ([ 2, 2]  0.000240) 
    |              | 
  }
  From:  (1, 3)  {
    ([ 8, 3]  0.000412) 
    |              | 
    |              | 
    |              | 
    ([ 3, 3]  0.000781) 
  }
  From:  (1, 4)  {
    ([ 8, 4]  0.001429) 
    ([ 9, 4]  0.000403) 
    |              | 
    |              | 
    |              | 
  }
  From:  (1, 5)  {
    |              | 
    ([ 9, 5]  0.000648) 
    ([ 1, 5]  0.001665) 
    |              | 
    ([ 3, 5]  0.001703) 
  }
  From:  (1, 6)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 6]  0.000638) 
    |              | 
  }
  From:  (1, 7)  {
    ([ 8, 7]  0.000487) 
    ([ 9, 7]  0.001050) 
    ([ 1, 7]  0.001225) 
    |              | 
    |              | 
  }
  From:  (1, 8)  {
    |              | 
    ([ 9, 8]  0.001395) 
    |              | 
    ([ 2, 8]  0.001770) 
    |              | 
  }
  From:  (1, 9)  {
    ([ 8, 9]  0.001377) 
    ([ 9, 9]  0.001642) 
    |              | 
    |              | 
    |              | 
  }
  From:  (2, 1)  {
    ([ 9, 1]  0.000960) 
    ([ 1, 1]  0.001054) 
    |              | 
    |              | 
    ([ 4, 1]  0.001373) 
  }
  From:  (2, 2)  {
    |              | 
    ([ 1, 2]  0.001831) 
    ([ 2, 2]  0.000967) 
    |              | 
    |              | 
  }
  From:  (2, 3)  {
    |              | 
    ([ 1, 3]  0.000673) 
    |              | 
    |              | 
    ([ 4, 3]  0.000049) 
  }
  From:  (2, 4)  {
    |              | 
    ([ 1, 4]  0.000959) 
    ([ 2, 4]  0.001439) 
    |              | 
    |              | 
  }
  From:  (2, 5)  {
    ([ 9, 5]  0.001308) 
    |              | 
    |              | 
    ([ 3, 5]  0.000640) 
    |              | 
  }
  From:  (2, 6)  {
    ([ 9, 6]  0.000423) 
    ([ 1, 6]  0.000597) 
    |              | 
    |              | 
    ([ 4, 6]  0.001762) 
  }
  From:  (2, 7)  {
    |              | 
    ([ 1, 7]  0.000625) 
    |              | 
    ([ 3, 7]  0.000271) 
    ([ 4, 7]  0.000341) 
  }
  From:  (2, 8)  {
    ([ 9, 8]  0.001157) 
    |              | 
    ([ 2, 8]  0.000191) 
    |              | 
    |              | 
  }
  From:  (2, 9)  {
    ([ 9, 9]  0.000611) 
    ([ 1, 9]  0.000573) 
    |              | 
    |              | 
    ([ 4, 9]  0.000384) 
  }
  From:  (3, 1)  {
    ([ 1, 1]  0.000855) 
    |              | 
    ([ 3, 1]  0.000301) 
    |              | 
    |              | 
  }
  From:  (3, 2)  {
    ([ 1, 2]  0.001611) 
    |              | 
    ([ 3, 2]  0.000084) 
    ([ 4, 2]  0.000012) 
    ([ 5, 2]  0.000276) 
  }
  From:  (3, 3)  {
    ([ 1, 3]  0.000626) 
    |              | 
    ([ 3, 3]  0.000817) 
    |              | 
    ([ 5, 3]  0.000241) 
  }
  From:  (3, 4)  {
    |              | 
    ([ 2, 4]  0.001583) 
    |              | 
    |              | 
    ([ 5, 4]  0.001129) 
  }
  From:  (3, 5)  {
    ([ 1, 5]  0.001584) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (3, 6)  {
    ([ 1, 6]  0.001215) 
    ([ 2, 6]  0.000442) 
    |              | 
    |              | 
    |              | 
  }
  From:  (3, 7)  {
    |              | 
    |              | 
    ([ 3, 7]  0.001446) 
    |              | 
    |              | 
  }
  From:  (3, 8)  {
    |              | 
    ([ 2, 8]  0.000791) 
    ([ 3, 8]  0.001537) 
    ([ 4, 8]  0.001773) 
    ([ 5, 8]  0.000397) 
  }
  From:  (3, 9)  {
    |              | 
    ([ 2, 9]  0.000698) 
    |              | 
    ([ 4, 9]  0.001262) 
    |              | 
  }
  From:  (4, 1)  {
    |              | 
    |              | 
    |              | 
    ([ 5, 1]  0.000437) 
    ([ 6, 1]  0.000775) 
  }
  From:  (4, 2)  {
    ([ 2, 2]  0.000422) 
    |              | 
    ([ 4, 2]  0.000502) 
    |              | 
    ([ 6, 2]  0.001736) 
  }
  From:  (4, 3)  {
    |              | 
    ([ 3, 3]  0.001216) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 4)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.001229)   }
  From:  (4, 5)  {
    |              | 
    ([ 3, 5]  0.001047) 
    |              | 
    ([ 5, 5]  0.001716) 
    ([ 6, 5]  0.001820) 
  }
  From:  (4, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000273)   }
  From:  (4, 7)  {
    |              | 
    ([ 3, 7]  0.000899) 
    |              | 
    |              | 
    ([ 6, 7]  0.000119) 
  }
  From:  (4, 8)  {
    ([ 2, 8]  0.001894) 
    |              | 
    ([ 4, 8]  0.001373) 
    |              | 
    ([ 6, 8]  0.001293) 
  }
  From:  (4, 9)  {
    |              | 
    |              | 
    ([ 4, 9]  0.001608) 
    |              | 
    |              | 
  }
  From:  (5, 1)  {
    ([ 3, 1]  0.001736) 
    ([ 4, 1]  0.001127) 
    ([ 5, 1]  0.001272) 
    |              | 
    ([ 7, 1]  0.000719) 
  }
  From:  (5, 2)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 7, 2]  0.000106) 
  }
  From:  (5, 3)  {
    |              | 
    |              | 
    ([ 5, 3]  0.000429) 
    |              | 
    |              | 
  }
  From:  (5, 4)  {
    |              | 
    ([ 4, 4]  0.001969) 
    ([ 5, 4]  0.000270) 
    ([ 6, 4]  0.001024) 
    |              | 
  }
  From:  (5, 5)  {
    |              | 
    ([ 4, 5]  0.001650) 
    |              | 
    ([ 6, 5]  0.000480) 
    ([ 7, 5]  0.000598) 
  }
  From:  (5, 6)  {
    |              | 
    ([ 4, 6]  0.000830) 
    ([ 5, 6]  0.001580) 
    |              | 
    |              | 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.001608) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 8)  {
    ([ 3, 8]  0.001371) 
    ([ 4, 8]  0.001095) 
    |              | 
    ([ 6, 8]  0.000193) 
    ([ 7, 8]  0.000865) 
  }
  From:  (5, 9)  {
    |              | 
    ([ 4, 9]  0.000121) 
    ([ 5, 9]  0.001622) 
    |              | 
    ([ 7, 9]  0.000042) 
  }
  From:  (6, 1)  {
    |              | 
    |              | 
    |              | 
    ([ 7, 1]  0.001962) 
    |              | 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.000715) 
    |              | 
    ([ 6, 2]  0.001684) 
    ([ 7, 2]  0.001405) 
    |              | 
  }
  From:  (6, 3)  {
    |              | 
    |              | 
    |              | 
    ([ 7, 3]  0.001785) 
    ([ 8, 3]  0.000139) 
  }
  From:  (6, 4)  {
    |              | 
    ([ 5, 4]  0.000960) 
    ([ 6, 4]  0.000814) 
    |              | 
    ([ 8, 4]  0.001841) 
  }
  From:  (6, 5)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 8, 5]  0.001320) 
  }
  From:  (6, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.001329)   }
  From:  (6, 7)  {
    ([ 4, 7]  0.000696) 
    |              | 
    ([ 6, 7]  0.000871) 
    |              | 
    ([ 8, 7]  0.000568) 
  }
  From:  (6, 8)  {
    |              | 
    ([ 5, 8]  0.001823) 
    |              | 
    |              | 
    ([ 8, 8]  0.001082) 
  }
  From:  (6, 9)  {
    |              | 
    ([ 5, 9]  0.000320) 
    ([ 6, 9]  0.001858) 
    ([ 7, 9]  0.001400) 
    |              | 
  }
  From:  (7, 1)  {
    |              | 
    |              | 
    ([ 7, 1]  0.001651) 
    |              | 
    |              | 
  }
  From:  (7, 2)  {
    ([ 5, 2]  0.000522) 
    |              | 
    ([ 7, 2]  0.001441) 
    |              | 
    ([ 9, 2]  0.001293) 
  }
  From:  (7, 3)  {
    ([ 5, 3]  0.001844) 
    |              | 
    ([ 7, 3]  0.001677) 
    ([ 8, 3]  0.000025) 
    ([ 9, 3]  0.001519) 
  }
  From:  (7, 4)  {
    |              | 
    |              | 
    ([ 7, 4]  0.000320) 
    ([ 8, 4]  0.000861) 
    ([ 9, 4]  0.000380) 
  }
  From:  (7, 5)  {
    ([ 5, 5]  0.000055) 
    ([ 6, 5]  0.000299) 
    ([ 7, 5]  0.000825) 
    ([ 8, 5]  0.001421) 
    |              | 
  }
  From:  (7, 6)  {
    |              | 
    ([ 6, 6]  0.000770) 
    |              | 
    |              | 
    ([ 9, 6]  0.000258) 
  }
  From:  (7, 7)  {
    |              | 
    ([ 6, 7]  0.000143) 
    ([ 7, 7]  0.000601) 
    ([ 8, 7]  0.000610) 
    ([ 9, 7]  0.000203) 
  }
  From:  (7, 8)  {
    ([ 5, 8]  0.000402) 
    ([ 6, 8]  0.001025) 
    ([ 7, 8]  0.000773) 
    |              | 
    |              | 
  }
  From:  (7, 9)  {
    ([ 5, 9]  0.001326) 
    ([ 6, 9]  0.000525) 
    |              | 
    |              | 
    |              | 
  }
  From:  (8, 1)  {
    |              | 
    ([ 7, 1]  0.001642) 
    |              | 
    |              | 
    |              | 
  }
  From:  (8, 2)  {
    ([ 6, 2]  0.001851) 
    ([ 7, 2]  0.000083) 
    ([ 8, 2]  0.000932) 
    ([ 9, 2]  0.000896) 
    |              | 
  }
  From:  (8, 3)  {
    ([ 6, 3]  0.001013) 
    |              | 
    ([ 8, 3]  0.001029) 
    |              | 
    ([ 1, 3]  0.000515) 
  }
  From:  (8, 4)  {
    |              | 
    |              | 
    |              | 
    ([ 9, 4]  0.000385) 
    |              | 
  }
  From:  (8, 5)  {
    ([ 6, 5]  0.001635) 
    ([ 7, 5]  0.000493) 
    |              | 
    ([ 9, 5]  0.001901) 
    ([ 1, 5]  0.001550) 
  }
  From:  (8, 6)  {
    |              | 
    |              | 
    ([ 8, 6]  0.000534) 
    ([ 9, 6]  0.000766) 
    |              | 
  }
  From:  (8, 7)  {
    ([ 6, 7]  0.001949) 
    ([ 7, 7]  0.001517) 
    ([ 8, 7]  0.000291) 
    ([ 9, 7]  0.000453) 
    |              | 
  }
  From:  (8, 8)  {
    |              | 
    |              | 
    |              | 
    ([ 9, 8]  0.001591) 
    ([ 1, 8]  0.001617) 
  }
  From:  (8, 9)  {
    ([ 6, 9]  0.000452) 
    ([ 7, 9]  0.001554) 
    ([ 8, 9]  0.001128) 
    |              | 
    |              | 
  }
  From:  (9, 1)  {
    ([ 7, 1]  0.000143) 
    |              | 
    ([ 9, 1]  0.001639) 
    |              | 
    ([ 2, 1]  0.000604) 
  }
  From:  (9, 2)  {
    ([ 7, 2]  0.001672) 
    ([ 8, 2]  0.000333) 
    |              | 
    |              | 
    ([ 2, 2]  0.000143) 
  }
  From:  (9, 3)  {
    ([ 7, 3]  0.001957) 
    |              | 
    |              | 
    ([ 1, 3]  0.000597) 
    ([ 2, 3]  0.001810) 
  }
  From:  (9, 4)  {
    |              | 
    ([ 8, 4]  0.000705) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 5)  {
    ([ 7, 5]  0.000190) 
    |              | 
    ([ 9, 5]  0.001355) 
    ([ 1, 5]  0.001502) 
    |              | 
  }
  From:  (9, 6)  {
    ([ 7, 6]  0.000037) 
    |              | 
    |              | 
    |              | 
    ([ 2, 6]  0.000962) 
  }
  From:  (9, 7)  {
    ([ 7, 7]  0.000592) 
    ([ 8, 7]  0.001927) 
    |              | 
    ([ 1, 7]  0.000819) 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    ([ 8, 8]  0.000320) 
    ([ 9, 8]  0.001593) 
    |              | 
    |              | 
  }
  From:  (9, 9)  {
    |              | 
    |              | 
    ([ 9, 9]  0.001655) 
    ([ 1, 9]  0.001525) 
    ([ 2, 9]  0.000657) 
  }
}

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