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_8
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weightslist.txt
                            
% Fri Aug 21 22:55:21 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)  {
    |              | 
    ([ 9, 1]  0.001940) 
    |              | 
    ([ 2, 1]  0.000351) 
    ([ 3, 1]  0.001182) 
  }
  From:  (1, 2)  {
    ([ 8, 2]  0.001860) 
    |              | 
    ([ 1, 2]  0.000069) 
    ([ 2, 2]  0.000035) 
    |              | 
  }
  From:  (1, 3)  {
    |              | 
    ([ 9, 3]  0.001091) 
    |              | 
    ([ 2, 3]  0.000675) 
    |              | 
  }
  From:  (1, 4)  {
    |              | 
    ([ 9, 4]  0.001016) 
    |              | 
    |              | 
    |              | 
  }
  From:  (1, 5)  {
    ([ 8, 5]  0.000897) 
    ([ 9, 5]  0.001355) 
    |              | 
    ([ 2, 5]  0.000022) 
    |              | 
  }
  From:  (1, 6)  {
    |              | 
    ([ 9, 6]  0.001218) 
    ([ 1, 6]  0.001584) 
    ([ 2, 6]  0.001004) 
    ([ 3, 6]  0.001445) 
  }
  From:  (1, 7)  {
    ([ 8, 7]  0.001696) 
    ([ 9, 7]  0.001717) 
    |              | 
    |              | 
    ([ 3, 7]  0.001194) 
  }
  From:  (1, 8)  {
    ([ 8, 8]  0.000364) 
    |              | 
    ([ 1, 8]  0.001333) 
    |              | 
    |              | 
  }
  From:  (1, 9)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 3, 9]  0.001065) 
  }
  From:  (2, 1)  {
    |              | 
    ([ 1, 1]  0.001351) 
    |              | 
    ([ 3, 1]  0.001294) 
    |              | 
  }
  From:  (2, 2)  {
    ([ 9, 2]  0.000593) 
    |              | 
    ([ 2, 2]  0.001578) 
    ([ 3, 2]  0.000003) 
    ([ 4, 2]  0.001221) 
  }
  From:  (2, 3)  {
    |              | 
    |              | 
    |              | 
    ([ 3, 3]  0.001699) 
    ([ 4, 3]  0.001108) 
  }
  From:  (2, 4)  {
    |              | 
    ([ 1, 4]  0.001073) 
    ([ 2, 4]  0.000677) 
    ([ 3, 4]  0.000497) 
    ([ 4, 4]  0.000689) 
  }
  From:  (2, 5)  {
    |              | 
    |              | 
    ([ 2, 5]  0.001116) 
    ([ 3, 5]  0.001851) 
    |              | 
  }
  From:  (2, 6)  {
    ([ 9, 6]  0.001540) 
    ([ 1, 6]  0.000149) 
    |              | 
    |              | 
    ([ 4, 6]  0.000952) 
  }
  From:  (2, 7)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 4, 7]  0.000768) 
  }
  From:  (2, 8)  {
    |              | 
    |              | 
    ([ 2, 8]  0.001108) 
    |              | 
    |              | 
  }
  From:  (2, 9)  {
    ([ 9, 9]  0.001519) 
    ([ 1, 9]  0.000754) 
    ([ 2, 9]  0.001970) 
    ([ 3, 9]  0.001541) 
    ([ 4, 9]  0.001589) 
  }
  From:  (3, 1)  {
    ([ 1, 1]  0.001317) 
    ([ 2, 1]  0.000185) 
    ([ 3, 1]  0.000647) 
    |              | 
    |              | 
  }
  From:  (3, 2)  {
    ([ 1, 2]  0.000511) 
    |              | 
    |              | 
    |              | 
    ([ 5, 2]  0.001850) 
  }
  From:  (3, 3)  {
    |              | 
    ([ 2, 3]  0.001219) 
    ([ 3, 3]  0.001991) 
    |              | 
    ([ 5, 3]  0.000130) 
  }
  From:  (3, 4)  {
    |              | 
    ([ 2, 4]  0.001223) 
    |              | 
    |              | 
    ([ 5, 4]  0.001102) 
  }
  From:  (3, 5)  {
    |              | 
    |              | 
    ([ 3, 5]  0.000426) 
    |              | 
    |              | 
  }
  From:  (3, 6)  {
    |              | 
    ([ 2, 6]  0.001975) 
    ([ 3, 6]  0.001330) 
    |              | 
    ([ 5, 6]  0.001462) 
  }
  From:  (3, 7)  {
    |              | 
    |              | 
    ([ 3, 7]  0.001225) 
    |              | 
    ([ 5, 7]  0.000244) 
  }
  From:  (3, 8)  {
    ([ 1, 8]  0.001241) 
    ([ 2, 8]  0.000809) 
    ([ 3, 8]  0.001668) 
    ([ 4, 8]  0.001701) 
    ([ 5, 8]  0.000385) 
  }
  From:  (3, 9)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000805)   }
  From:  (4, 1)  {
    ([ 2, 1]  0.000588) 
    ([ 3, 1]  0.001796) 
    ([ 4, 1]  0.000227) 
    |              | 
    |              | 
  }
  From:  (4, 2)  {
    |              | 
    ([ 3, 2]  0.000256) 
    |              | 
    ([ 5, 2]  0.000641) 
    |              | 
  }
  From:  (4, 3)  {
    ([ 2, 3]  0.000944) 
    ([ 3, 3]  0.000760) 
    ([ 4, 3]  0.001639) 
    ([ 5, 3]  0.000442) 
    ([ 6, 3]  0.000154) 
  }
  From:  (4, 4)  {
    |              | 
    |              | 
    |              | 
    ([ 5, 4]  0.000177) 
    |              | 
  }
  From:  (4, 5)  {
    ([ 2, 5]  0.000842) 
    ([ 3, 5]  0.000388) 
    ([ 4, 5]  0.000272) 
    |              | 
    |              | 
  }
  From:  (4, 6)  {
    |              | 
    ([ 3, 6]  0.000340) 
    |              | 
    ([ 5, 6]  0.000096) 
    ([ 6, 6]  0.000881) 
  }
  From:  (4, 7)  {
    |              | 
    |              | 
    ([ 4, 7]  0.000071) 
    ([ 5, 7]  0.001315) 
    ([ 6, 7]  0.001886) 
  }
  From:  (4, 8)  {
    |              | 
    ([ 3, 8]  0.001725) 
    |              | 
    |              | 
    ([ 6, 8]  0.001712) 
  }
  From:  (4, 9)  {
    ([ 2, 9]  0.001170) 
    ([ 3, 9]  0.000078) 
    ([ 4, 9]  0.000349) 
    ([ 5, 9]  0.001347) 
    ([ 6, 9]  0.001257) 
  }
  From:  (5, 1)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 1]  0.001163) 
    |              | 
  }
  From:  (5, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 2]  0.000025) 
    ([ 7, 2]  0.000776) 
  }
  From:  (5, 3)  {
    |              | 
    ([ 4, 3]  0.000545) 
    ([ 5, 3]  0.000995) 
    ([ 6, 3]  0.001198) 
    ([ 7, 3]  0.000374) 
  }
  From:  (5, 4)  {
    |              | 
    ([ 4, 4]  0.001801) 
    ([ 5, 4]  0.000440) 
    ([ 6, 4]  0.001826) 
    |              | 
  }
  From:  (5, 5)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 5]  0.000210) 
    |              | 
  }
  From:  (5, 6)  {
    ([ 3, 6]  0.001395) 
    |              | 
    |              | 
    ([ 6, 6]  0.000467) 
    ([ 7, 6]  0.000355) 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.001504) 
    |              | 
    ([ 5, 7]  0.001983) 
    ([ 6, 7]  0.000588) 
    ([ 7, 7]  0.001305) 
  }
  From:  (5, 8)  {
    |              | 
    ([ 4, 8]  0.000931) 
    |              | 
    |              | 
    ([ 7, 8]  0.001537) 
  }
  From:  (5, 9)  {
    ([ 3, 9]  0.000791) 
    |              | 
    ([ 5, 9]  0.001344) 
    |              | 
    ([ 7, 9]  0.000886) 
  }
  From:  (6, 1)  {
    ([ 4, 1]  0.001627) 
    ([ 5, 1]  0.000665) 
    |              | 
    ([ 7, 1]  0.001894) 
    |              | 
  }
  From:  (6, 2)  {
    |              | 
    ([ 5, 2]  0.000080) 
    |              | 
    ([ 7, 2]  0.000856) 
    |              | 
  }
  From:  (6, 3)  {
    |              | 
    ([ 5, 3]  0.001590) 
    ([ 6, 3]  0.000441) 
    ([ 7, 3]  0.001369) 
    |              | 
  }
  From:  (6, 4)  {
    ([ 4, 4]  0.000979) 
    |              | 
    ([ 6, 4]  0.000703) 
    ([ 7, 4]  0.001583) 
    |              | 
  }
  From:  (6, 5)  {
    |              | 
    |              | 
    ([ 6, 5]  0.000807) 
    |              | 
    ([ 8, 5]  0.001422) 
  }
  From:  (6, 6)  {
    |              | 
    ([ 5, 6]  0.000936) 
    ([ 6, 6]  0.001278) 
    ([ 7, 6]  0.001547) 
    ([ 8, 6]  0.001971) 
  }
  From:  (6, 7)  {
    ([ 4, 7]  0.000858) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (6, 8)  {
    |              | 
    |              | 
    ([ 6, 8]  0.001185) 
    ([ 7, 8]  0.000987) 
    ([ 8, 8]  0.001526) 
  }
  From:  (6, 9)  {
    ([ 4, 9]  0.000559) 
    |              | 
    ([ 6, 9]  0.000359) 
    ([ 7, 9]  0.000605) 
    |              | 
  }
  From:  (7, 1)  {
    |              | 
    |              | 
    ([ 7, 1]  0.000344) 
    |              | 
    ([ 9, 1]  0.000640) 
  }
  From:  (7, 2)  {
    |              | 
    ([ 6, 2]  0.001273) 
    ([ 7, 2]  0.000438) 
    ([ 8, 2]  0.000342) 
    |              | 
  }
  From:  (7, 3)  {
    ([ 5, 3]  0.000257) 
    |              | 
    |              | 
    |              | 
    ([ 9, 3]  0.000758) 
  }
  From:  (7, 4)  {
    ([ 5, 4]  0.000072) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 5)  {
    |              | 
    |              | 
    ([ 7, 5]  0.001895) 
    |              | 
    ([ 9, 5]  0.001963) 
  }
  From:  (7, 6)  {
    ([ 5, 6]  0.000724) 
    |              | 
    ([ 7, 6]  0.001317) 
    ([ 8, 6]  0.001482) 
    ([ 9, 6]  0.000157) 
  }
  From:  (7, 7)  {
    ([ 5, 7]  0.000742) 
    |              | 
    ([ 7, 7]  0.001108) 
    |              | 
    ([ 9, 7]  0.000514) 
  }
  From:  (7, 8)  {
    ([ 5, 8]  0.001864) 
    ([ 6, 8]  0.001062) 
    ([ 7, 8]  0.000854) 
    ([ 8, 8]  0.000792) 
    ([ 9, 8]  0.001780) 
  }
  From:  (7, 9)  {
    |              | 
    ([ 6, 9]  0.001010) 
    |              | 
    ([ 8, 9]  0.001856) 
    ([ 9, 9]  0.001584) 
  }
  From:  (8, 1)  {
    ([ 6, 1]  0.001221) 
    |              | 
    ([ 8, 1]  0.000502) 
    ([ 9, 1]  0.001862) 
    ([ 1, 1]  0.001254) 
  }
  From:  (8, 2)  {
    |              | 
    |              | 
    ([ 8, 2]  0.001176) 
    ([ 9, 2]  0.001578) 
    ([ 1, 2]  0.001658) 
  }
  From:  (8, 3)  {
    |              | 
    ([ 7, 3]  0.000700) 
    |              | 
    ([ 9, 3]  0.000968) 
    ([ 1, 3]  0.000579) 
  }
  From:  (8, 4)  {
    ([ 6, 4]  0.000611) 
    |              | 
    |              | 
    |              | 
    ([ 1, 4]  0.001152) 
  }
  From:  (8, 5)  {
    |              | 
    ([ 7, 5]  0.000631) 
    |              | 
    |              | 
    ([ 1, 5]  0.001557) 
  }
  From:  (8, 6)  {
    |              | 
    |              | 
    ([ 8, 6]  0.001803) 
    ([ 9, 6]  0.000734) 
    ([ 1, 6]  0.000301) 
  }
  From:  (8, 7)  {
    ([ 6, 7]  0.001006) 
    ([ 7, 7]  0.000736) 
    |              | 
    ([ 9, 7]  0.001836) 
    |              | 
  }
  From:  (8, 8)  {
    ([ 6, 8]  0.001685) 
    |              | 
    |              | 
    |              | 
    ([ 1, 8]  0.001809) 
  }
  From:  (8, 9)  {
    ([ 6, 9]  0.000213) 
    ([ 7, 9]  0.000008) 
    |              | 
    ([ 9, 9]  0.001830) 
    |              | 
  }
  From:  (9, 1)  {
    ([ 7, 1]  0.001830) 
    ([ 8, 1]  0.001758) 
    ([ 9, 1]  0.000772) 
    ([ 1, 1]  0.001431) 
    ([ 2, 1]  0.001784) 
  }
  From:  (9, 2)  {
    |              | 
    |              | 
    ([ 9, 2]  0.001817) 
    ([ 1, 2]  0.000033) 
    ([ 2, 2]  0.001538) 
  }
  From:  (9, 3)  {
    ([ 7, 3]  0.001387) 
    ([ 8, 3]  0.000904) 
    |              | 
    ([ 1, 3]  0.000883) 
    |              | 
  }
  From:  (9, 4)  {
    ([ 7, 4]  0.001047) 
    ([ 8, 4]  0.001641) 
    ([ 9, 4]  0.000215) 
    |              | 
    ([ 2, 4]  0.001073) 
  }
  From:  (9, 5)  {
    ([ 7, 5]  0.000802) 
    ([ 8, 5]  0.001201) 
    ([ 9, 5]  0.000315) 
    ([ 1, 5]  0.000085) 
    ([ 2, 5]  0.000893) 
  }
  From:  (9, 6)  {
    ([ 7, 6]  0.000665) 
    ([ 8, 6]  0.000218) 
    ([ 9, 6]  0.001886) 
    ([ 1, 6]  0.001428) 
    |              | 
  }
  From:  (9, 7)  {
    ([ 7, 7]  0.000714) 
    ([ 8, 7]  0.001808) 
    ([ 9, 7]  0.000203) 
    ([ 1, 7]  0.000422) 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    ([ 8, 8]  0.000260) 
    ([ 9, 8]  0.001360) 
    ([ 1, 8]  0.001393) 
    ([ 2, 8]  0.001653) 
  }
  From:  (9, 9)  {
    |              | 
    ([ 8, 9]  0.001928) 
    ([ 9, 9]  0.000434) 
    ([ 1, 9]  0.000903) 
    |              | 
  }
}

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