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_4
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weightslist.txt
                            
% Wed Aug 19 21:41:29 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)  {
    |              | 
    ([ 9, 1]  0.045720) 
    ([ 1, 1]  0.044907) 
    ([ 2, 1]  0.030811) 
    |              | 
  }
  From:  (1, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 2]  0.032054) 
    |              | 
  }
  From:  (1, 3)  {
    ([ 8, 3]  0.039800) 
    ([ 9, 3]  0.036917) 
    ([ 1, 3]  0.030439) 
    ([ 2, 3]  0.039656) 
    |              | 
  }
  From:  (1, 4)  {
    ([ 8, 4]  0.036823) 
    |              | 
    ([ 1, 4]  0.036180) 
    |              | 
    |              | 
  }
  From:  (1, 5)  {
    |              | 
    ([ 9, 5]  0.046208) 
    ([ 1, 5]  0.049926) 
    ([ 2, 5]  0.035414) 
    ([ 3, 5]  0.043410) 
  }
  From:  (1, 6)  {
    |              | 
    |              | 
    ([ 1, 6]  0.043744) 
    ([ 2, 6]  0.034645) 
    |              | 
  }
  From:  (1, 7)  {
    ([ 8, 7]  0.036900) 
    ([ 9, 7]  0.031384) 
    ([ 1, 7]  0.041637) 
    ([ 2, 7]  0.043643) 
    |              | 
  }
  From:  (1, 8)  {
    ([ 8, 8]  0.041013) 
    ([ 9, 8]  0.036506) 
    |              | 
    |              | 
    |              | 
  }
  From:  (1, 9)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 9]  0.039300) 
    |              | 
  }
  From:  (2, 1)  {
    ([ 9, 1]  0.041456) 
    |              | 
    ([ 2, 1]  0.045897) 
    ([ 3, 1]  0.035553) 
    |              | 
  }
  From:  (2, 2)  {
    |              | 
    ([ 1, 2]  0.030339) 
    ([ 2, 2]  0.047741) 
    |              | 
    ([ 4, 2]  0.047190) 
  }
  From:  (2, 3)  {
    |              | 
    ([ 1, 3]  0.031949) 
    |              | 
    ([ 3, 3]  0.032331) 
    ([ 4, 3]  0.031444) 
  }
  From:  (2, 4)  {
    |              | 
    ([ 1, 4]  0.030875) 
    |              | 
    |              | 
    ([ 4, 4]  0.040831) 
  }
  From:  (2, 5)  {
    ([ 9, 5]  0.048993) 
    |              | 
    |              | 
    |              | 
    ([ 4, 5]  0.047810) 
  }
  From:  (2, 6)  {
    |              | 
    ([ 1, 6]  0.048561) 
    ([ 2, 6]  0.035570) 
    |              | 
    |              | 
  }
  From:  (2, 7)  {
    |              | 
    ([ 1, 7]  0.031554) 
    ([ 2, 7]  0.035265) 
    ([ 3, 7]  0.034069) 
    ([ 4, 7]  0.043563) 
  }
  From:  (2, 8)  {
    ([ 9, 8]  0.038659) 
    ([ 1, 8]  0.035040) 
    ([ 2, 8]  0.037691) 
    |              | 
    |              | 
  }
  From:  (2, 9)  {
    |              | 
    |              | 
    ([ 2, 9]  0.041489) 
    |              | 
    ([ 4, 9]  0.036437) 
  }
  From:  (3, 1)  {
    ([ 1, 1]  0.049553) 
    ([ 2, 1]  0.031762) 
    ([ 3, 1]  0.041770) 
    ([ 4, 1]  0.042969) 
    ([ 5, 1]  0.037695) 
  }
  From:  (3, 2)  {
    ([ 1, 2]  0.037413) 
    ([ 2, 2]  0.037455) 
    |              | 
    ([ 4, 2]  0.033207) 
    ([ 5, 2]  0.044662) 
  }
  From:  (3, 3)  {
    ([ 1, 3]  0.033155) 
    ([ 2, 3]  0.049492) 
    ([ 3, 3]  0.036972) 
    ([ 4, 3]  0.031936) 
    ([ 5, 3]  0.032676) 
  }
  From:  (3, 4)  {
    ([ 1, 4]  0.045692) 
    |              | 
    ([ 3, 4]  0.032455) 
    ([ 4, 4]  0.037287) 
    ([ 5, 4]  0.035226) 
  }
  From:  (3, 5)  {
    ([ 1, 5]  0.043728) 
    |              | 
    ([ 3, 5]  0.033183) 
    ([ 4, 5]  0.047630) 
    ([ 5, 5]  0.035407) 
  }
  From:  (3, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 5, 6]  0.045604) 
  }
  From:  (3, 7)  {
    |              | 
    ([ 2, 7]  0.041677) 
    |              | 
    ([ 4, 7]  0.031787) 
    |              | 
  }
  From:  (3, 8)  {
    |              | 
    |              | 
    |              | 
    ([ 4, 8]  0.047570) 
    ([ 5, 8]  0.045945) 
  }
  From:  (3, 9)  {
    ([ 1, 9]  0.045472) 
    |              | 
    ([ 3, 9]  0.045159) 
    ([ 4, 9]  0.033739) 
    ([ 5, 9]  0.048553) 
  }
  From:  (4, 1)  {
    ([ 2, 1]  0.047277) 
    ([ 3, 1]  0.046457) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 2)  {
    ([ 2, 2]  0.040593) 
    ([ 3, 2]  0.033002) 
    |              | 
    ([ 5, 2]  0.038271) 
    |              | 
  }
  From:  (4, 3)  {
    ([ 2, 3]  0.043509) 
    |              | 
    |              | 
    ([ 5, 3]  0.044882) 
    |              | 
  }
  From:  (4, 4)  {
    ([ 2, 4]  0.049158) 
    ([ 3, 4]  0.044907) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 5)  {
    |              | 
    ([ 3, 5]  0.038407) 
    ([ 4, 5]  0.036422) 
    |              | 
    ([ 6, 5]  0.048484) 
  }
  From:  (4, 6)  {
    |              | 
    ([ 3, 6]  0.031501) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 7)  {
    |              | 
    |              | 
    ([ 4, 7]  0.042240) 
    ([ 5, 7]  0.039749) 
    ([ 6, 7]  0.031221) 
  }
  From:  (4, 8)  {
    ([ 2, 8]  0.048357) 
    |              | 
    ([ 4, 8]  0.039197) 
    ([ 5, 8]  0.040555) 
    ([ 6, 8]  0.045147) 
  }
  From:  (4, 9)  {
    |              | 
    |              | 
    |              | 
    ([ 5, 9]  0.038055) 
    |              | 
  }
  From:  (5, 1)  {
    ([ 3, 1]  0.039897) 
    |              | 
    |              | 
    ([ 6, 1]  0.037868) 
    |              | 
  }
  From:  (5, 2)  {
    |              | 
    ([ 4, 2]  0.032539) 
    ([ 5, 2]  0.049214) 
    ([ 6, 2]  0.033343) 
    |              | 
  }
  From:  (5, 3)  {
    ([ 3, 3]  0.046594) 
    ([ 4, 3]  0.039270) 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 4)  {
    ([ 3, 4]  0.044093) 
    |              | 
    ([ 5, 4]  0.048458) 
    |              | 
    |              | 
  }
  From:  (5, 5)  {
    ([ 3, 5]  0.040990) 
    |              | 
    ([ 5, 5]  0.041781) 
    ([ 6, 5]  0.038029) 
    ([ 7, 5]  0.037406) 
  }
  From:  (5, 6)  {
    ([ 3, 6]  0.049726) 
    ([ 4, 6]  0.030235) 
    |              | 
    ([ 6, 6]  0.043651) 
    ([ 7, 6]  0.039390) 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.033162) 
    ([ 4, 7]  0.048762) 
    ([ 5, 7]  0.033885) 
    |              | 
    |              | 
  }
  From:  (5, 8)  {
    |              | 
    ([ 4, 8]  0.047524) 
    ([ 5, 8]  0.033156) 
    |              | 
    ([ 7, 8]  0.040494) 
  }
  From:  (5, 9)  {
    ([ 3, 9]  0.036071) 
    ([ 4, 9]  0.046290) 
    |              | 
    ([ 6, 9]  0.048090) 
    ([ 7, 9]  0.040545) 
  }
  From:  (6, 1)  {
    ([ 4, 1]  0.033484) 
    ([ 5, 1]  0.044649) 
    ([ 6, 1]  0.033705) 
    |              | 
    ([ 8, 1]  0.047413) 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.032224) 
    |              | 
    |              | 
    ([ 7, 2]  0.031293) 
    |              | 
  }
  From:  (6, 3)  {
    ([ 4, 3]  0.042641) 
    ([ 5, 3]  0.045747) 
    |              | 
    ([ 7, 3]  0.034192) 
    |              | 
  }
  From:  (6, 4)  {
    ([ 4, 4]  0.044729) 
    ([ 5, 4]  0.048642) 
    ([ 6, 4]  0.030974) 
    ([ 7, 4]  0.037783) 
    |              | 
  }
  From:  (6, 5)  {
    ([ 4, 5]  0.034596) 
    |              | 
    ([ 6, 5]  0.034712) 
    |              | 
    |              | 
  }
  From:  (6, 6)  {
    ([ 4, 6]  0.035538) 
    ([ 5, 6]  0.030672) 
    ([ 6, 6]  0.042471) 
    |              | 
    ([ 8, 6]  0.045675) 
  }
  From:  (6, 7)  {
    ([ 4, 7]  0.036688) 
    |              | 
    |              | 
    ([ 7, 7]  0.048299) 
    |              | 
  }
  From:  (6, 8)  {
    ([ 4, 8]  0.037695) 
    |              | 
    ([ 6, 8]  0.035844) 
    |              | 
    |              | 
  }
  From:  (6, 9)  {
    |              | 
    ([ 5, 9]  0.046346) 
    ([ 6, 9]  0.037657) 
    ([ 7, 9]  0.049805) 
    ([ 8, 9]  0.043794) 
  }
  From:  (7, 1)  {
    |              | 
    ([ 6, 1]  0.040792) 
    |              | 
    |              | 
    ([ 9, 1]  0.045622) 
  }
  From:  (7, 2)  {
    ([ 5, 2]  0.031306) 
    |              | 
    ([ 7, 2]  0.034501) 
    |              | 
    ([ 9, 2]  0.032905) 
  }
  From:  (7, 3)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.044379)   }
  From:  (7, 4)  {
    ([ 5, 4]  0.036569) 
    ([ 6, 4]  0.039895) 
    |              | 
    ([ 8, 4]  0.042735) 
    |              | 
  }
  From:  (7, 5)  {
    |              | 
    ([ 6, 5]  0.032983) 
    ([ 7, 5]  0.030711) 
    ([ 8, 5]  0.032755) 
    |              | 
  }
  From:  (7, 6)  {
    ([ 5, 6]  0.045274) 
    |              | 
    |              | 
    ([ 8, 6]  0.042507) 
    ([ 9, 6]  0.036070) 
  }
  From:  (7, 7)  {
    ([ 5, 7]  0.041074) 
    ([ 6, 7]  0.034914) 
    |              | 
    ([ 8, 7]  0.045100) 
    |              | 
  }
  From:  (7, 8)  {
    ([ 5, 8]  0.043661) 
    ([ 6, 8]  0.041448) 
    ([ 7, 8]  0.044618) 
    ([ 8, 8]  0.039052) 
    ([ 9, 8]  0.044619) 
  }
  From:  (7, 9)  {
    |              | 
    ([ 6, 9]  0.041942) 
    |              | 
    ([ 8, 9]  0.035621) 
    ([ 9, 9]  0.045523) 
  }
  From:  (8, 1)  {
    |              | 
    |              | 
    ([ 8, 1]  0.049356) 
    |              | 
    ([ 1, 1]  0.048852) 
  }
  From:  (8, 2)  {
    ([ 6, 2]  0.037579) 
    ([ 7, 2]  0.038077) 
    ([ 8, 2]  0.040195) 
    |              | 
    ([ 1, 2]  0.035691) 
  }
  From:  (8, 3)  {
    |              | 
    |              | 
    |              | 
    ([ 9, 3]  0.037958) 
    ([ 1, 3]  0.040908) 
  }
  From:  (8, 4)  {
    |              | 
    ([ 7, 4]  0.035772) 
    ([ 8, 4]  0.045223) 
    ([ 9, 4]  0.037578) 
    |              | 
  }
  From:  (8, 5)  {
    ([ 6, 5]  0.035450) 
    |              | 
    ([ 8, 5]  0.039558) 
    |              | 
    ([ 1, 5]  0.032775) 
  }
  From:  (8, 6)  {
    |              | 
    ([ 7, 6]  0.038199) 
    ([ 8, 6]  0.035047) 
    ([ 9, 6]  0.035312) 
    |              | 
  }
  From:  (8, 7)  {
    |              | 
    ([ 7, 7]  0.041048) 
    ([ 8, 7]  0.042665) 
    ([ 9, 7]  0.040432) 
    ([ 1, 7]  0.034994) 
  }
  From:  (8, 8)  {
    ([ 6, 8]  0.044117) 
    ([ 7, 8]  0.046856) 
    |              | 
    |              | 
    ([ 1, 8]  0.038938) 
  }
  From:  (8, 9)  {
    |              | 
    ([ 7, 9]  0.045778) 
    |              | 
    ([ 9, 9]  0.046453) 
    ([ 1, 9]  0.030725) 
  }
  From:  (9, 1)  {
    |              | 
    |              | 
    ([ 9, 1]  0.048105) 
    ([ 1, 1]  0.045075) 
    ([ 2, 1]  0.038726) 
  }
  From:  (9, 2)  {
    |              | 
    ([ 8, 2]  0.042810) 
    |              | 
    ([ 1, 2]  0.044651) 
    ([ 2, 2]  0.036961) 
  }
  From:  (9, 3)  {
    ([ 7, 3]  0.032056) 
    ([ 8, 3]  0.034514) 
    |              | 
    |              | 
    ([ 2, 3]  0.036510) 
  }
  From:  (9, 4)  {
    |              | 
    ([ 8, 4]  0.040837) 
    ([ 9, 4]  0.031269) 
    |              | 
    |              | 
  }
  From:  (9, 5)  {
    ([ 7, 5]  0.042724) 
    ([ 8, 5]  0.042410) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 6)  {
    |              | 
    |              | 
    ([ 9, 6]  0.035055) 
    ([ 1, 6]  0.042108) 
    |              | 
  }
  From:  (9, 7)  {
    ([ 7, 7]  0.040436) 
    ([ 8, 7]  0.049243) 
    ([ 9, 7]  0.034821) 
    ([ 1, 7]  0.035141) 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    ([ 8, 8]  0.034958) 
    ([ 9, 8]  0.038644) 
    ([ 1, 8]  0.034550) 
    ([ 2, 8]  0.040858) 
  }
  From:  (9, 9)  {
    |              | 
    |              | 
    |              | 
    ([ 1, 9]  0.044364) 
    ([ 2, 9]  0.030523) 
  }
}

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