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
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weightslist.txt
                            
% Tue May 24 15:52:21 2016

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

Connect(ev4v, ev1v)  {
  From:  (1, 1)  {
    ([ 8, 1]  0.000679) 
    ([ 9, 1]  0.000086) 
    |              | 
    |              | 
    |              | 
  }
  From:  (1, 2)  {
    |              | 
    ([ 9, 2]  0.001558) 
    ([ 1, 2]  0.001019) 
    ([ 2, 2]  0.000024) 
    ([ 3, 2]  0.001779) 
  }
  From:  (1, 3)  {
    ([ 8, 3]  0.000631) 
    |              | 
    ([ 1, 3]  0.001183) 
    ([ 2, 3]  0.000085) 
    |              | 
  }
  From:  (1, 4)  {
    ([ 8, 4]  0.000927) 
    ([ 9, 4]  0.000564) 
    ([ 1, 4]  0.000799) 
    ([ 2, 4]  0.000876) 
    |              | 
  }
  From:  (1, 5)  {
    ([ 8, 5]  0.000364) 
    ([ 9, 5]  0.000740) 
    |              | 
    ([ 2, 5]  0.000696) 
    ([ 3, 5]  0.001539) 
  }
  From:  (1, 6)  {
    |              | 
    |              | 
    ([ 1, 6]  0.001320) 
    ([ 2, 6]  0.001980) 
    |              | 
  }
  From:  (1, 7)  {
    ([ 8, 7]  0.000557) 
    ([ 9, 7]  0.001404) 
    ([ 1, 7]  0.001377) 
    ([ 2, 7]  0.000239) 
    |              | 
  }
  From:  (1, 8)  {
    ([ 8, 8]  0.001224) 
    |              | 
    |              | 
    |              | 
    ([ 3, 8]  0.001567) 
  }
  From:  (1, 9)  {
    ([ 8, 9]  0.000901) 
    ([ 9, 9]  0.001017) 
    |              | 
    ([ 2, 9]  0.000164) 
    ([ 3, 9]  0.000640) 
  }
  From:  (2, 1)  {
    ([ 9, 1]  0.000737) 
    |              | 
    |              | 
    |              | 
    ([ 4, 1]  0.001232) 
  }
  From:  (2, 2)  {
    ([ 9, 2]  0.000439) 
    |              | 
    |              | 
    ([ 3, 2]  0.000470) 
    |              | 
  }
  From:  (2, 3)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.001363)   }
  From:  (2, 4)  {
    ([ 9, 4]  0.000107) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (2, 5)  {
    |              | 
    ([ 1, 5]  0.001628) 
    |              | 
    ([ 3, 5]  0.000109) 
    |              | 
  }
  From:  (2, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 4, 6]  0.000531) 
  }
  From:  (2, 7)  {
    ([ 9, 7]  0.000322) 
    |              | 
    |              | 
    |              | 
    ([ 4, 7]  0.000773) 
  }
  From:  (2, 8)  {
    ([ 9, 8]  0.001805) 
    |              | 
    ([ 2, 8]  0.001677) 
    |              | 
    ([ 4, 8]  0.000191) 
  }
  From:  (2, 9)  {
    |              | 
    ([ 1, 9]  0.000108) 
    |              | 
    ([ 3, 9]  0.001817) 
    ([ 4, 9]  0.001536) 
  }
  From:  (3, 1)  {
    ([ 1, 1]  0.000845) 
    |              | 
    |              | 
    ([ 4, 1]  0.001323) 
    ([ 5, 1]  0.001007) 
  }
  From:  (3, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 4, 2]  0.000254) 
    ([ 5, 2]  0.000663) 
  }
  From:  (3, 3)  {
    ([ 1, 3]  0.001975) 
    ([ 2, 3]  0.001344) 
    ([ 3, 3]  0.001286) 
    ([ 4, 3]  0.001582) 
    ([ 5, 3]  0.001761) 
  }
  From:  (3, 4)  {
    |              | 
    ([ 2, 4]  0.001788) 
    |              | 
    |              | 
    |              | 
  }
  From:  (3, 5)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 5, 5]  0.001731) 
  }
  From:  (3, 6)  {
    ([ 1, 6]  0.000785) 
    |              | 
    |              | 
    ([ 4, 6]  0.000986) 
    ([ 5, 6]  0.001247) 
  }
  From:  (3, 7)  {
    ([ 1, 7]  0.001092) 
    ([ 2, 7]  0.001469) 
    |              | 
    ([ 4, 7]  0.000232) 
    ([ 5, 7]  0.001921) 
  }
  From:  (3, 8)  {
    |              | 
    ([ 2, 8]  0.001427) 
    |              | 
    ([ 4, 8]  0.001164) 
    ([ 5, 8]  0.001753) 
  }
  From:  (3, 9)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.001806)   }
  From:  (4, 1)  {
    |              | 
    |              | 
    ([ 4, 1]  0.000507) 
    |              | 
    ([ 6, 1]  0.001311) 
  }
  From:  (4, 2)  {
    ([ 2, 2]  0.001142) 
    |              | 
    |              | 
    ([ 5, 2]  0.000136) 
    |              | 
  }
  From:  (4, 3)  {
    |              | 
    ([ 3, 3]  0.001724) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 4)  {
    ([ 2, 4]  0.001344) 
    |              | 
    |              | 
    ([ 5, 4]  0.001162) 
    ([ 6, 4]  0.000838) 
  }
  From:  (4, 5)  {
    ([ 2, 5]  0.000851) 
    ([ 3, 5]  0.000680) 
    ([ 4, 5]  0.000342) 
    |              | 
    |              | 
  }
  From:  (4, 6)  {
    |              | 
    ([ 3, 6]  0.001707) 
    |              | 
    ([ 5, 6]  0.000533) 
    |              | 
  }
  From:  (4, 7)  {
    |              | 
    ([ 3, 7]  0.000669) 
    ([ 4, 7]  0.000014) 
    |              | 
    |              | 
  }
  From:  (4, 8)  {
    ([ 2, 8]  0.001668) 
    |              | 
    |              | 
    |              | 
    ([ 6, 8]  0.000813) 
  }
  From:  (4, 9)  {
    |              | 
    ([ 3, 9]  0.000084) 
    ([ 4, 9]  0.000570) 
    ([ 5, 9]  0.001568) 
    |              | 
  }
  From:  (5, 1)  {
    ([ 3, 1]  0.000288) 
    ([ 4, 1]  0.000606) 
    |              | 
    ([ 6, 1]  0.001818) 
    |              | 
  }
  From:  (5, 2)  {
    ([ 3, 2]  0.000828) 
    ([ 4, 2]  0.001970) 
    ([ 5, 2]  0.000493) 
    ([ 6, 2]  0.001728) 
    ([ 7, 2]  0.000861) 
  }
  From:  (5, 3)  {
    |              | 
    |              | 
    ([ 5, 3]  0.000799) 
    ([ 6, 3]  0.001615) 
    ([ 7, 3]  0.000349) 
  }
  From:  (5, 4)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 4]  0.000651) 
    |              | 
  }
  From:  (5, 5)  {
    ([ 3, 5]  0.001930) 
    ([ 4, 5]  0.001641) 
    |              | 
    ([ 6, 5]  0.000428) 
    ([ 7, 5]  0.000157) 
  }
  From:  (5, 6)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 6]  0.000011) 
    |              | 
  }
  From:  (5, 7)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 7]  0.000160) 
    |              | 
  }
  From:  (5, 8)  {
    ([ 3, 8]  0.001395) 
    ([ 4, 8]  0.000163) 
    |              | 
    ([ 6, 8]  0.000372) 
    ([ 7, 8]  0.001206) 
  }
  From:  (5, 9)  {
    ([ 3, 9]  0.001143) 
    |              | 
    |              | 
    ([ 6, 9]  0.001613) 
    ([ 7, 9]  0.000311) 
  }
  From:  (6, 1)  {
    ([ 4, 1]  0.000966) 
    ([ 5, 1]  0.001880) 
    |              | 
    |              | 
    ([ 8, 1]  0.000986) 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.000347) 
    |              | 
    |              | 
    |              | 
    ([ 8, 2]  0.000107) 
  }
  From:  (6, 3)  {
    |              | 
    ([ 5, 3]  0.000604) 
    |              | 
    |              | 
    |              | 
  }
  From:  (6, 4)  {
    |              | 
    ([ 5, 4]  0.000089) 
    |              | 
    ([ 7, 4]  0.000425) 
    |              | 
  }
  From:  (6, 5)  {
    |              | 
    ([ 5, 5]  0.000959) 
    ([ 6, 5]  0.000640) 
    |              | 
    ([ 8, 5]  0.001009) 
  }
  From:  (6, 6)  {
    ([ 4, 6]  0.001880) 
    ([ 5, 6]  0.000541) 
    |              | 
    |              | 
    |              | 
  }
  From:  (6, 7)  {
    ([ 4, 7]  0.000627) 
    |              | 
    |              | 
    ([ 7, 7]  0.000158) 
    |              | 
  }
  From:  (6, 8)  {
    ([ 4, 8]  0.000162) 
    |              | 
    |              | 
    |              | 
    ([ 8, 8]  0.001551) 
  }
  From:  (6, 9)  {
    ([ 4, 9]  0.000740) 
    ([ 5, 9]  0.000012) 
    |              | 
    ([ 7, 9]  0.001388) 
    ([ 8, 9]  0.001389) 
  }
  From:  (7, 1)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000534)   }
  From:  (7, 2)  {
    ([ 5, 2]  0.000121) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 3)  {
    |              | 
    ([ 6, 3]  0.000467) 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 4)  {
    ([ 5, 4]  0.000187) 
    ([ 6, 4]  0.000089) 
    |              | 
    |              | 
    ([ 9, 4]  0.000175) 
  }
  From:  (7, 5)  {
    ([ 5, 5]  0.000119) 
    |              | 
    ([ 7, 5]  0.001073) 
    ([ 8, 5]  0.001067) 
    |              | 
  }
  From:  (7, 6)  {
    ([ 5, 6]  0.000682) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 7)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 9, 7]  0.000197) 
  }
  From:  (7, 8)  {
    |              | 
    |              | 
    ([ 7, 8]  0.000701) 
    ([ 8, 8]  0.000018) 
    ([ 9, 8]  0.001374) 
  }
  From:  (7, 9)  {
    |              | 
    |              | 
    ([ 7, 9]  0.000689) 
    ([ 8, 9]  0.000703) 
    |              | 
  }
  From:  (8, 1)  {
    ([ 6, 1]  0.000212) 
    ([ 7, 1]  0.001751) 
    |              | 
    |              | 
    |              | 
  }
  From:  (8, 2)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 2]  0.000997) 
  }
  From:  (8, 3)  {
    |              | 
    |              | 
    ([ 8, 3]  0.000905) 
    |              | 
    ([ 1, 3]  0.000897) 
  }
  From:  (8, 4)  {
    |              | 
    |              | 
    ([ 8, 4]  0.000365) 
    |              | 
    |              | 
  }
  From:  (8, 5)  {
    ([ 6, 5]  0.001370) 
    ([ 7, 5]  0.000080) 
    ([ 8, 5]  0.000557) 
    ([ 9, 5]  0.001628) 
    ([ 1, 5]  0.001554) 
  }
  From:  (8, 6)  {
    ([ 6, 6]  0.000123) 
    |              | 
    |              | 
    |              | 
    ([ 1, 6]  0.001138) 
  }
  From:  (8, 7)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000569)   }
  From:  (8, 8)  {
    ([ 6, 8]  0.001189) 
    |              | 
    ([ 8, 8]  0.001904) 
    ([ 9, 8]  0.001709) 
    ([ 1, 8]  0.000136) 
  }
  From:  (8, 9)  {
    ([ 6, 9]  0.001270) 
    ([ 7, 9]  0.001858) 
    |              | 
    ([ 9, 9]  0.001698) 
    ([ 1, 9]  0.000526) 
  }
  From:  (9, 1)  {
    ([ 7, 1]  0.001398) 
    ([ 8, 1]  0.001978) 
    ([ 9, 1]  0.000138) 
    ([ 1, 1]  0.001076) 
    |              | 
  }
  From:  (9, 2)  {
    ([ 7, 2]  0.000486) 
    |              | 
    ([ 9, 2]  0.001151) 
    |              | 
    |              | 
  }
  From:  (9, 3)  {
    |              | 
    |              | 
    ([ 9, 3]  0.001141) 
    |              | 
    |              | 
  }
  From:  (9, 4)  {
    |              | 
    |              | 
    |              | 
    ([ 1, 4]  0.000595) 
    |              | 
  }
  From:  (9, 5)  {
    ([ 7, 5]  0.001393) 
    |              | 
    |              | 
    ([ 1, 5]  0.001827) 
    ([ 2, 5]  0.001064) 
  }
  From:  (9, 6)  {
    ([ 7, 6]  0.001907) 
    |              | 
    ([ 9, 6]  0.001802) 
    ([ 1, 6]  0.000139) 
    |              | 
  }
  From:  (9, 7)  {
    |              | 
    ([ 8, 7]  0.001182) 
    |              | 
    ([ 1, 7]  0.000416) 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    |              | 
    ([ 9, 8]  0.001798) 
    ([ 1, 8]  0.001196) 
    |              | 
  }
  From:  (9, 9)  {
    |              | 
    ([ 8, 9]  0.001250) 
    |              | 
    |              | 
    |              | 
  }
}

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