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];
/
lsnm_in_python-master
visual_model
subject_netgettest
output.36trials
attsefd2.w
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ev1hev1h.w
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ifd1efd1.w
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infrexfr.w
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iv1hev1h.w
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iv4hev4h.w
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lgnsev1h.bak
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lgnsev1v.bak
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netgen1 *
weightslist.txt
                            
% Tue May 24 15:52:21 2016

% Input Layer: (9, 9)
% Output Layer: (9, 9)
% Fanout Size: (1, 5)

Connect(ev1h, ev4h)  {
  From:  (1, 1)  {
    |              |     ([ 1, 9]  0.032205)     ([ 1, 1]  0.033707)     |              |     ([ 1, 3]  0.033029) 
  }
  From:  (1, 2)  {
    |              |     ([ 1, 1]  0.049226)     ([ 1, 2]  0.040016)     |              |     ([ 1, 4]  0.030044) 
  }
  From:  (1, 3)  {
    |              |     |              |     ([ 1, 3]  0.045437)     ([ 1, 4]  0.035086)     |              | 
  }
  From:  (1, 4)  {
    ([ 1, 2]  0.047882)     |              |     ([ 1, 4]  0.044675)     ([ 1, 5]  0.047890)     ([ 1, 6]  0.031172) 
  }
  From:  (1, 5)  {
    ([ 1, 3]  0.033159)     |              |     ([ 1, 5]  0.031543)     |              |     |              | 
  }
  From:  (1, 6)  {
    |              |     ([ 1, 5]  0.032184)     ([ 1, 6]  0.045530)     ([ 1, 7]  0.043267)     ([ 1, 8]  0.049439) 
  }
  From:  (1, 7)  {
    |              |     ([ 1, 6]  0.041670)     ([ 1, 7]  0.047810)     |              |     ([ 1, 9]  0.047294) 
  }
  From:  (1, 8)  {
    |              |     |              |     |              |     ([ 1, 9]  0.038116)     |              | 
  }
  From:  (1, 9)  {
    ([ 1, 7]  0.037019)     |              |     |              |     |              |     ([ 1, 2]  0.049003) 
  }
  From:  (2, 1)  {
    |              |     |              |     ([ 2, 1]  0.032823)     ([ 2, 2]  0.045378)     ([ 2, 3]  0.045668) 
  }
  From:  (2, 2)  {
    ([ 2, 9]  0.048402)     |              |     ([ 2, 2]  0.044451)     |              |     ([ 2, 4]  0.042510) 
  }
  From:  (2, 3)  {
    ([ 2, 1]  0.033381)     ([ 2, 2]  0.048035)     |              |     ([ 2, 4]  0.036022)     |              | 
  }
  From:  (2, 4)  {
    ([ 2, 2]  0.039763)     ([ 2, 3]  0.032801)     |              |     |              |     ([ 2, 6]  0.036446) 
  }
  From:  (2, 5)  {
    ([ 2, 3]  0.045802)     |              |     |              |     ([ 2, 6]  0.043638)     |              | 
  }
  From:  (2, 6)  {
    ([ 2, 4]  0.047729)     |              |     |              |     ([ 2, 7]  0.049903)     ([ 2, 8]  0.041743) 
  }
  From:  (2, 7)  {
    |              |     ([ 2, 6]  0.031772)     ([ 2, 7]  0.030774)     |              |     |              | 
  }
  From:  (2, 8)  {
    |              |     |              |     ([ 2, 8]  0.044081)     |              |     ([ 2, 1]  0.039190) 
  }
  From:  (2, 9)  {
    ([ 2, 7]  0.047258)     |              |     ([ 2, 9]  0.049498)     ([ 2, 1]  0.039416)     ([ 2, 2]  0.038211) 
  }
  From:  (3, 1)  {
    |              |     ([ 3, 9]  0.037380)     |              |     |              |     |              | 
  }
  From:  (3, 2)  {
    |              |     ([ 3, 1]  0.033648)     ([ 3, 2]  0.046716)     |              |     ([ 3, 4]  0.032547) 
  }
  From:  (3, 3)  {
    ([ 3, 1]  0.039612)     |              |     ([ 3, 3]  0.030202)     |              |     |              | 
  }
  From:  (3, 4)  {
    ([ 3, 2]  0.031809)     |              |     ([ 3, 4]  0.043425)     ([ 3, 5]  0.042562)     |              | 
  }
  From:  (3, 5)  {
    ([ 3, 3]  0.033615)     ([ 3, 4]  0.045377)     |              |     ([ 3, 6]  0.045461)     ([ 3, 7]  0.031448) 
  }
  From:  (3, 6)  {
    |              |     ([ 3, 5]  0.041567)     ([ 3, 6]  0.031588)     |              |     ([ 3, 8]  0.034416) 
  }
  From:  (3, 7)  {
    ([ 3, 5]  0.032656)     |              |     ([ 3, 7]  0.041502)     |              |     ([ 3, 9]  0.047891) 
  }
  From:  (3, 8)  {
    |              |     |              |     ([ 3, 8]  0.044183)     ([ 3, 9]  0.044344)     |              | 
  }
  From:  (3, 9)  {
    ([ 3, 7]  0.036866)     |              |     |              |     ([ 3, 1]  0.049082)     ([ 3, 2]  0.043296) 
  }
  From:  (4, 1)  {
    |              |     |              |     ([ 4, 1]  0.032864)     |              |     |              | 
  }
  From:  (4, 2)  {
    ([ 4, 9]  0.044703)     ([ 4, 1]  0.043304)     ([ 4, 2]  0.044104)     ([ 4, 3]  0.048274)     ([ 4, 4]  0.043648) 
  }
  From:  (4, 3)  {
    |              |     ([ 4, 2]  0.035863)     |              |     ([ 4, 4]  0.043645)     |              | 
  }
  From:  (4, 4)  {
    |              |     |              |     |              |     ([ 4, 5]  0.031099)     |              | 
  }
  From:  (4, 5)  {
    ([ 4, 3]  0.041351)     ([ 4, 4]  0.044685)     |              |     |              |     ([ 4, 7]  0.049852) 
  }
  From:  (4, 6)  {
    |              |     ([ 4, 5]  0.033975)     |              |     |              |     |              | 
  }
  From:  (4, 7)  {
    |              |     ([ 4, 6]  0.039625)     ([ 4, 7]  0.034758)     |              |     |              | 
  }
  From:  (4, 8)  {
    ([ 4, 6]  0.049977)     ([ 4, 7]  0.041757)     ([ 4, 8]  0.044873)     |              |     ([ 4, 1]  0.040812) 
  }
  From:  (4, 9)  {
    ([ 4, 7]  0.045592)     ([ 4, 8]  0.041649)     ([ 4, 9]  0.048587)     ([ 4, 1]  0.045435)     |              | 
  }
  From:  (5, 1)  {
    |              |     ([ 5, 9]  0.034928)     ([ 5, 1]  0.034061)     ([ 5, 2]  0.033462)     |              | 
  }
  From:  (5, 2)  {
    |              |     ([ 5, 1]  0.044166)     ([ 5, 2]  0.035677)     ([ 5, 3]  0.048749)     ([ 5, 4]  0.038039) 
  }
  From:  (5, 3)  {
    ([ 5, 1]  0.032921)     ([ 5, 2]  0.047787)     |              |     ([ 5, 4]  0.038919)     |              | 
  }
  From:  (5, 4)  {
    ([ 5, 2]  0.040267)     |              |     |              |     ([ 5, 5]  0.033284)     ([ 5, 6]  0.039149) 
  }
  From:  (5, 5)  {
    |              |     ([ 5, 4]  0.042686)     |              |     |              |     ([ 5, 7]  0.032397) 
  }
  From:  (5, 6)  {
    ([ 5, 4]  0.046953)     ([ 5, 5]  0.037284)     ([ 5, 6]  0.035100)     ([ 5, 7]  0.039703)     ([ 5, 8]  0.033687) 
  }
  From:  (5, 7)  {
    ([ 5, 5]  0.049882)     ([ 5, 6]  0.041542)     ([ 5, 7]  0.041679)     |              |     |              | 
  }
  From:  (5, 8)  {
    |              |     ([ 5, 7]  0.041412)     ([ 5, 8]  0.034571)     ([ 5, 9]  0.039201)     ([ 5, 1]  0.043526) 
  }
  From:  (5, 9)  {
    |              |     |              |     ([ 5, 9]  0.031613)     ([ 5, 1]  0.035476)     |              | 
  }
  From:  (6, 1)  {
    ([ 6, 8]  0.044143)     |              |     ([ 6, 1]  0.036705)     ([ 6, 2]  0.044796)     |              | 
  }
  From:  (6, 2)  {
    |              |     |              |     |              |     ([ 6, 3]  0.037916)     |              | 
  }
  From:  (6, 3)  {
    |              |     ([ 6, 2]  0.040932)     ([ 6, 3]  0.032873)     |              |     ([ 6, 5]  0.030353) 
  }
  From:  (6, 4)  {
    |              |     |              |     |              |     |              |     |              | 
    ([ 1, 1]  0.042288)   }
  From:  (6, 5)  {
    ([ 6, 3]  0.045589)     |              |     |              |     |              |     ([ 6, 7]  0.041566) 
  }
  From:  (6, 6)  {
    |              |     |              |     |              |     |              |     |              | 
    ([ 1, 1]  0.043607)   }
  From:  (6, 7)  {
    |              |     |              |     ([ 6, 7]  0.042719)     |              |     ([ 6, 9]  0.043728) 
  }
  From:  (6, 8)  {
    |              |     |              |     ([ 6, 8]  0.032120)     ([ 6, 9]  0.033284)     ([ 6, 1]  0.039956) 
  }
  From:  (6, 9)  {
    ([ 6, 7]  0.036687)     |              |     |              |     |              |     ([ 6, 2]  0.044541) 
  }
  From:  (7, 1)  {
    |              |     |              |     |              |     |              |     ([ 7, 3]  0.043742) 
  }
  From:  (7, 2)  {
    |              |     ([ 7, 1]  0.044169)     ([ 7, 2]  0.031129)     ([ 7, 3]  0.044798)     ([ 7, 4]  0.031143) 
  }
  From:  (7, 3)  {
    ([ 7, 1]  0.032300)     |              |     ([ 7, 3]  0.047485)     |              |     |              | 
  }
  From:  (7, 4)  {
    |              |     ([ 7, 3]  0.048067)     |              |     ([ 7, 5]  0.048847)     ([ 7, 6]  0.042480) 
  }
  From:  (7, 5)  {
    ([ 7, 3]  0.036576)     |              |     |              |     |              |     |              | 
  }
  From:  (7, 6)  {
    |              |     |              |     |              |     ([ 7, 7]  0.031823)     ([ 7, 8]  0.031725) 
  }
  From:  (7, 7)  {
    ([ 7, 5]  0.049851)     |              |     |              |     ([ 7, 8]  0.036116)     ([ 7, 9]  0.042990) 
  }
  From:  (7, 8)  {
    ([ 7, 6]  0.032605)     |              |     ([ 7, 8]  0.037466)     |              |     ([ 7, 1]  0.035434) 
  }
  From:  (7, 9)  {
    |              |     ([ 7, 8]  0.044901)     |              |     |              |     ([ 7, 2]  0.049725) 
  }
  From:  (8, 1)  {
    |              |     ([ 8, 9]  0.033286)     |              |     |              |     ([ 8, 3]  0.043686) 
  }
  From:  (8, 2)  {
    ([ 8, 9]  0.032795)     |              |     ([ 8, 2]  0.032973)     ([ 8, 3]  0.037181)     |              | 
  }
  From:  (8, 3)  {
    |              |     ([ 8, 2]  0.048986)     ([ 8, 3]  0.031407)     |              |     |              | 
  }
  From:  (8, 4)  {
    ([ 8, 2]  0.042195)     ([ 8, 3]  0.032382)     ([ 8, 4]  0.043922)     ([ 8, 5]  0.049320)     ([ 8, 6]  0.030156) 
  }
  From:  (8, 5)  {
    ([ 8, 3]  0.040692)     ([ 8, 4]  0.044093)     ([ 8, 5]  0.037892)     |              |     |              | 
  }
  From:  (8, 6)  {
    ([ 8, 4]  0.039377)     |              |     ([ 8, 6]  0.038894)     |              |     |              | 
  }
  From:  (8, 7)  {
    |              |     ([ 8, 6]  0.035027)     ([ 8, 7]  0.035786)     |              |     ([ 8, 9]  0.043079) 
  }
  From:  (8, 8)  {
    ([ 8, 6]  0.040419)     ([ 8, 7]  0.033836)     ([ 8, 8]  0.042968)     |              |     |              | 
  }
  From:  (8, 9)  {
    |              |     |              |     |              |     |              |     |              | 
    ([ 1, 1]  0.043883)   }
  From:  (9, 1)  {
    ([ 9, 8]  0.032492)     ([ 9, 9]  0.038356)     ([ 9, 1]  0.040667)     ([ 9, 2]  0.031805)     |              | 
  }
  From:  (9, 2)  {
    ([ 9, 9]  0.032808)     |              |     |              |     |              |     |              | 
  }
  From:  (9, 3)  {
    ([ 9, 1]  0.045685)     |              |     ([ 9, 3]  0.046239)     |              |     |              | 
  }
  From:  (9, 4)  {
    |              |     ([ 9, 3]  0.042398)     |              |     ([ 9, 5]  0.033185)     |              | 
  }
  From:  (9, 5)  {
    |              |     |              |     ([ 9, 5]  0.041094)     |              |     ([ 9, 7]  0.044040) 
  }
  From:  (9, 6)  {
    |              |     |              |     ([ 9, 6]  0.046560)     |              |     ([ 9, 8]  0.039376) 
  }
  From:  (9, 7)  {
    |              |     ([ 9, 6]  0.046934)     |              |     ([ 9, 8]  0.035343)     ([ 9, 9]  0.044102) 
  }
  From:  (9, 8)  {
    ([ 9, 6]  0.040342)     |              |     ([ 9, 8]  0.037538)     ([ 9, 9]  0.048944)     ([ 9, 1]  0.037546) 
  }
  From:  (9, 9)  {
    ([ 9, 7]  0.034493)     ([ 9, 8]  0.033260)     |              |     ([ 9, 1]  0.038922)     ([ 9, 2]  0.040312) 
  }
}

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