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_6
attsefd2.w
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weightslist.txt
                            
% Fri Aug 21 04:52:55 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)  {
    ([ 8, 1]  0.037247) 
    ([ 9, 1]  0.037695) 
    |              | 
    ([ 2, 1]  0.030086) 
    ([ 3, 1]  0.042530) 
  }
  From:  (1, 2)  {
    ([ 8, 2]  0.041263) 
    |              | 
    |              | 
    ([ 2, 2]  0.043492) 
    ([ 3, 2]  0.035167) 
  }
  From:  (1, 3)  {
    |              | 
    ([ 9, 3]  0.049118) 
    ([ 1, 3]  0.036023) 
    ([ 2, 3]  0.041346) 
    |              | 
  }
  From:  (1, 4)  {
    |              | 
    ([ 9, 4]  0.049704) 
    |              | 
    ([ 2, 4]  0.042308) 
    ([ 3, 4]  0.032362) 
  }
  From:  (1, 5)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 5]  0.030215) 
    |              | 
  }
  From:  (1, 6)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 6]  0.045263) 
    ([ 3, 6]  0.041270) 
  }
  From:  (1, 7)  {
    |              | 
    ([ 9, 7]  0.044294) 
    |              | 
    |              | 
    |              | 
  }
  From:  (1, 8)  {
    |              | 
    ([ 9, 8]  0.042005) 
    ([ 1, 8]  0.042345) 
    |              | 
    |              | 
  }
  From:  (1, 9)  {
    ([ 8, 9]  0.036362) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (2, 1)  {
    |              | 
    ([ 1, 1]  0.038846) 
    |              | 
    ([ 3, 1]  0.037333) 
    ([ 4, 1]  0.034280) 
  }
  From:  (2, 2)  {
    ([ 9, 2]  0.046523) 
    |              | 
    ([ 2, 2]  0.048287) 
    |              | 
    ([ 4, 2]  0.037149) 
  }
  From:  (2, 3)  {
    |              | 
    |              | 
    ([ 2, 3]  0.040850) 
    |              | 
    |              | 
  }
  From:  (2, 4)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.032576)   }
  From:  (2, 5)  {
    ([ 9, 5]  0.040860) 
    ([ 1, 5]  0.048032) 
    ([ 2, 5]  0.033816) 
    |              | 
    ([ 4, 5]  0.044437) 
  }
  From:  (2, 6)  {
    ([ 9, 6]  0.039280) 
    |              | 
    |              | 
    ([ 3, 6]  0.043275) 
    |              | 
  }
  From:  (2, 7)  {
    |              | 
    |              | 
    |              | 
    ([ 3, 7]  0.039198) 
    |              | 
  }
  From:  (2, 8)  {
    ([ 9, 8]  0.037989) 
    |              | 
    |              | 
    ([ 3, 8]  0.038151) 
    |              | 
  }
  From:  (2, 9)  {
    |              | 
    ([ 1, 9]  0.049991) 
    |              | 
    ([ 3, 9]  0.046272) 
    ([ 4, 9]  0.044816) 
  }
  From:  (3, 1)  {
    |              | 
    |              | 
    ([ 3, 1]  0.031367) 
    ([ 4, 1]  0.041060) 
    ([ 5, 1]  0.046896) 
  }
  From:  (3, 2)  {
    |              | 
    ([ 2, 2]  0.031622) 
    ([ 3, 2]  0.031030) 
    ([ 4, 2]  0.038533) 
    |              | 
  }
  From:  (3, 3)  {
    |              | 
    |              | 
    ([ 3, 3]  0.044794) 
    ([ 4, 3]  0.039911) 
    ([ 5, 3]  0.049210) 
  }
  From:  (3, 4)  {
    ([ 1, 4]  0.044919) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (3, 5)  {
    |              | 
    |              | 
    ([ 3, 5]  0.039168) 
    ([ 4, 5]  0.039341) 
    |              | 
  }
  From:  (3, 6)  {
    ([ 1, 6]  0.031641) 
    |              | 
    ([ 3, 6]  0.036715) 
    ([ 4, 6]  0.043906) 
    |              | 
  }
  From:  (3, 7)  {
    |              | 
    ([ 2, 7]  0.030579) 
    ([ 3, 7]  0.035889) 
    |              | 
    |              | 
  }
  From:  (3, 8)  {
    |              | 
    ([ 2, 8]  0.044062) 
    ([ 3, 8]  0.032879) 
    ([ 4, 8]  0.030843) 
    |              | 
  }
  From:  (3, 9)  {
    |              | 
    ([ 2, 9]  0.040881) 
    ([ 3, 9]  0.039239) 
    |              | 
    |              | 
  }
  From:  (4, 1)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 6, 1]  0.033623) 
  }
  From:  (4, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 5, 2]  0.036550) 
    ([ 6, 2]  0.038861) 
  }
  From:  (4, 3)  {
    |              | 
    ([ 3, 3]  0.041956) 
    |              | 
    ([ 5, 3]  0.043538) 
    |              | 
  }
  From:  (4, 4)  {
    ([ 2, 4]  0.049032) 
    ([ 3, 4]  0.033870) 
    |              | 
    |              | 
    ([ 6, 4]  0.049574) 
  }
  From:  (4, 5)  {
    ([ 2, 5]  0.042570) 
    ([ 3, 5]  0.039813) 
    |              | 
    ([ 5, 5]  0.036684) 
    ([ 6, 5]  0.035080) 
  }
  From:  (4, 6)  {
    ([ 2, 6]  0.034136) 
    |              | 
    ([ 4, 6]  0.035321) 
    ([ 5, 6]  0.034209) 
    |              | 
  }
  From:  (4, 7)  {
    ([ 2, 7]  0.030393) 
    |              | 
    ([ 4, 7]  0.045554) 
    |              | 
    |              | 
  }
  From:  (4, 8)  {
    ([ 2, 8]  0.038153) 
    ([ 3, 8]  0.037173) 
    |              | 
    ([ 5, 8]  0.037557) 
    ([ 6, 8]  0.039399) 
  }
  From:  (4, 9)  {
    ([ 2, 9]  0.030162) 
    |              | 
    ([ 4, 9]  0.033035) 
    ([ 5, 9]  0.033979) 
    |              | 
  }
  From:  (5, 1)  {
    ([ 3, 1]  0.030681) 
    |              | 
    |              | 
    ([ 6, 1]  0.048427) 
    ([ 7, 1]  0.042761) 
  }
  From:  (5, 2)  {
    ([ 3, 2]  0.039091) 
    ([ 4, 2]  0.042680) 
    |              | 
    ([ 6, 2]  0.035435) 
    ([ 7, 2]  0.044421) 
  }
  From:  (5, 3)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 3]  0.048980) 
    ([ 7, 3]  0.045251) 
  }
  From:  (5, 4)  {
    ([ 3, 4]  0.039247) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 5)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 5]  0.035543) 
    ([ 7, 5]  0.035525) 
  }
  From:  (5, 6)  {
    ([ 3, 6]  0.041172) 
    ([ 4, 6]  0.033937) 
    |              | 
    ([ 6, 6]  0.031936) 
    |              | 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.042689) 
    |              | 
    ([ 5, 7]  0.046796) 
    |              | 
    |              | 
  }
  From:  (5, 8)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.039717)   }
  From:  (5, 9)  {
    |              | 
    |              | 
    ([ 5, 9]  0.030093) 
    ([ 6, 9]  0.049462) 
    |              | 
  }
  From:  (6, 1)  {
    |              | 
    |              | 
    |              | 
    ([ 7, 1]  0.042377) 
    |              | 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.030416) 
    ([ 5, 2]  0.040265) 
    |              | 
    ([ 7, 2]  0.046701) 
    |              | 
  }
  From:  (6, 3)  {
    ([ 4, 3]  0.047645) 
    ([ 5, 3]  0.047881) 
    |              | 
    ([ 7, 3]  0.033020) 
    |              | 
  }
  From:  (6, 4)  {
    ([ 4, 4]  0.038412) 
    |              | 
    ([ 6, 4]  0.042573) 
    ([ 7, 4]  0.039163) 
    ([ 8, 4]  0.037756) 
  }
  From:  (6, 5)  {
    ([ 4, 5]  0.042700) 
    |              | 
    |              | 
    ([ 7, 5]  0.047735) 
    ([ 8, 5]  0.032605) 
  }
  From:  (6, 6)  {
    ([ 4, 6]  0.034596) 
    |              | 
    ([ 6, 6]  0.041945) 
    |              | 
    ([ 8, 6]  0.047768) 
  }
  From:  (6, 7)  {
    ([ 4, 7]  0.034190) 
    |              | 
    |              | 
    ([ 7, 7]  0.038088) 
    |              | 
  }
  From:  (6, 8)  {
    |              | 
    ([ 5, 8]  0.038737) 
    |              | 
    |              | 
    |              | 
  }
  From:  (6, 9)  {
    ([ 4, 9]  0.040230) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 1)  {
    ([ 5, 1]  0.044241) 
    ([ 6, 1]  0.036038) 
    ([ 7, 1]  0.041709) 
    ([ 8, 1]  0.030668) 
    ([ 9, 1]  0.031489) 
  }
  From:  (7, 2)  {
    ([ 5, 2]  0.044269) 
    |              | 
    |              | 
    ([ 8, 2]  0.045076) 
    ([ 9, 2]  0.032788) 
  }
  From:  (7, 3)  {
    ([ 5, 3]  0.030547) 
    |              | 
    ([ 7, 3]  0.034236) 
    ([ 8, 3]  0.047314) 
    |              | 
  }
  From:  (7, 4)  {
    ([ 5, 4]  0.038009) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 5)  {
    |              | 
    ([ 6, 5]  0.036446) 
    ([ 7, 5]  0.041822) 
    |              | 
    ([ 9, 5]  0.047839) 
  }
  From:  (7, 6)  {
    |              | 
    |              | 
    ([ 7, 6]  0.041502) 
    |              | 
    |              | 
  }
  From:  (7, 7)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 9, 7]  0.045334) 
  }
  From:  (7, 8)  {
    ([ 5, 8]  0.040577) 
    |              | 
    ([ 7, 8]  0.033472) 
    ([ 8, 8]  0.039854) 
    |              | 
  }
  From:  (7, 9)  {
    ([ 5, 9]  0.049100) 
    ([ 6, 9]  0.030736) 
    ([ 7, 9]  0.044375) 
    |              | 
    ([ 9, 9]  0.030151) 
  }
  From:  (8, 1)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.036683)   }
  From:  (8, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 9, 2]  0.043939) 
    ([ 1, 2]  0.030044) 
  }
  From:  (8, 3)  {
    ([ 6, 3]  0.034772) 
    ([ 7, 3]  0.030728) 
    |              | 
    |              | 
    |              | 
  }
  From:  (8, 4)  {
    |              | 
    |              | 
    ([ 8, 4]  0.030955) 
    |              | 
    |              | 
  }
  From:  (8, 5)  {
    |              | 
    |              | 
    ([ 8, 5]  0.035073) 
    ([ 9, 5]  0.045356) 
    ([ 1, 5]  0.044898) 
  }
  From:  (8, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.033139)   }
  From:  (8, 7)  {
    |              | 
    ([ 7, 7]  0.042641) 
    ([ 8, 7]  0.035453) 
    ([ 9, 7]  0.045907) 
    ([ 1, 7]  0.047604) 
  }
  From:  (8, 8)  {
    |              | 
    ([ 7, 8]  0.046366) 
    ([ 8, 8]  0.047488) 
    |              | 
    ([ 1, 8]  0.043765) 
  }
  From:  (8, 9)  {
    ([ 6, 9]  0.034714) 
    |              | 
    ([ 8, 9]  0.043135) 
    ([ 9, 9]  0.044778) 
    |              | 
  }
  From:  (9, 1)  {
    |              | 
    ([ 8, 1]  0.039647) 
    ([ 9, 1]  0.040430) 
    ([ 1, 1]  0.041863) 
    ([ 2, 1]  0.042551) 
  }
  From:  (9, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 1, 2]  0.037206) 
    ([ 2, 2]  0.044154) 
  }
  From:  (9, 3)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.038240)   }
  From:  (9, 4)  {
    |              | 
    ([ 8, 4]  0.037053) 
    ([ 9, 4]  0.046102) 
    ([ 1, 4]  0.044082) 
    ([ 2, 4]  0.048203) 
  }
  From:  (9, 5)  {
    ([ 7, 5]  0.036809) 
    ([ 8, 5]  0.038053) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 6)  {
    ([ 7, 6]  0.038369) 
    |              | 
    ([ 9, 6]  0.048436) 
    ([ 1, 6]  0.032078) 
    |              | 
  }
  From:  (9, 7)  {
    |              | 
    |              | 
    ([ 9, 7]  0.031806) 
    ([ 1, 7]  0.048346) 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    |              | 
    ([ 9, 8]  0.047017) 
    ([ 1, 8]  0.038272) 
    ([ 2, 8]  0.040624) 
  }
  From:  (9, 9)  {
    |              | 
    ([ 8, 9]  0.049310) 
    |              | 
    |              | 
    |              | 
  }
}

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