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_12
output.36trials
output.RestingState
output.test
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weightslist.txt *
                            
% Sun Sep 27 13:28:07 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)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 3, 1]  0.000654) 
  }
  From:  (1, 2)  {
    ([ 8, 2]  0.000808) 
    ([ 9, 2]  0.000591) 
    ([ 1, 2]  0.001082) 
    ([ 2, 2]  0.000069) 
    ([ 3, 2]  0.000101) 
  }
  From:  (1, 3)  {
    ([ 8, 3]  0.001590) 
    ([ 9, 3]  0.000938) 
    ([ 1, 3]  0.001593) 
    |              | 
    ([ 3, 3]  0.001464) 
  }
  From:  (1, 4)  {
    ([ 8, 4]  0.000499) 
    ([ 9, 4]  0.000943) 
    ([ 1, 4]  0.001776) 
    |              | 
    |              | 
  }
  From:  (1, 5)  {
    ([ 8, 5]  0.000328) 
    ([ 9, 5]  0.001020) 
    |              | 
    ([ 2, 5]  0.000438) 
    ([ 3, 5]  0.000799) 
  }
  From:  (1, 6)  {
    ([ 8, 6]  0.000757) 
    ([ 9, 6]  0.001223) 
    |              | 
    ([ 2, 6]  0.001696) 
    |              | 
  }
  From:  (1, 7)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 3, 7]  0.001665) 
  }
  From:  (1, 8)  {
    ([ 8, 8]  0.000322) 
    |              | 
    ([ 1, 8]  0.000021) 
    |              | 
    ([ 3, 8]  0.000478) 
  }
  From:  (1, 9)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 9]  0.001412) 
    ([ 3, 9]  0.001689) 
  }
  From:  (2, 1)  {
    |              | 
    ([ 1, 1]  0.000535) 
    ([ 2, 1]  0.000210) 
    |              | 
    ([ 4, 1]  0.001658) 
  }
  From:  (2, 2)  {
    ([ 9, 2]  0.001802) 
    |              | 
    |              | 
    |              | 
    ([ 4, 2]  0.000235) 
  }
  From:  (2, 3)  {
    ([ 9, 3]  0.000421) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (2, 4)  {
    |              | 
    ([ 1, 4]  0.001517) 
    |              | 
    |              | 
    ([ 4, 4]  0.001467) 
  }
  From:  (2, 5)  {
    ([ 9, 5]  0.000184) 
    ([ 1, 5]  0.000246) 
    |              | 
    |              | 
    ([ 4, 5]  0.001876) 
  }
  From:  (2, 6)  {
    ([ 9, 6]  0.000522) 
    |              | 
    |              | 
    |              | 
    ([ 4, 6]  0.001182) 
  }
  From:  (2, 7)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 4, 7]  0.000450) 
  }
  From:  (2, 8)  {
    |              | 
    |              | 
    |              | 
    ([ 3, 8]  0.000567) 
    ([ 4, 8]  0.001491) 
  }
  From:  (2, 9)  {
    |              | 
    ([ 1, 9]  0.000192) 
    |              | 
    |              | 
    ([ 4, 9]  0.001522) 
  }
  From:  (3, 1)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000073)   }
  From:  (3, 2)  {
    ([ 1, 2]  0.001403) 
    ([ 2, 2]  0.000948) 
    |              | 
    |              | 
    ([ 5, 2]  0.001080) 
  }
  From:  (3, 3)  {
    ([ 1, 3]  0.001497) 
    |              | 
    ([ 3, 3]  0.000358) 
    |              | 
    ([ 5, 3]  0.000613) 
  }
  From:  (3, 4)  {
    |              | 
    ([ 2, 4]  0.000693) 
    |              | 
    |              | 
    ([ 5, 4]  0.000969) 
  }
  From:  (3, 5)  {
    |              | 
    ([ 2, 5]  0.000234) 
    ([ 3, 5]  0.000400) 
    ([ 4, 5]  0.000216) 
    ([ 5, 5]  0.001027) 
  }
  From:  (3, 6)  {
    ([ 1, 6]  0.000628) 
    ([ 2, 6]  0.001245) 
    ([ 3, 6]  0.001515) 
    ([ 4, 6]  0.000203) 
    ([ 5, 6]  0.000171) 
  }
  From:  (3, 7)  {
    ([ 1, 7]  0.001067) 
    |              | 
    |              | 
    ([ 4, 7]  0.000604) 
    |              | 
  }
  From:  (3, 8)  {
    |              | 
    |              | 
    ([ 3, 8]  0.000734) 
    ([ 4, 8]  0.000722) 
    ([ 5, 8]  0.000855) 
  }
  From:  (3, 9)  {
    ([ 1, 9]  0.000498) 
    ([ 2, 9]  0.001526) 
    |              | 
    ([ 4, 9]  0.001833) 
    |              | 
  }
  From:  (4, 1)  {
    |              | 
    ([ 3, 1]  0.001175) 
    ([ 4, 1]  0.001670) 
    ([ 5, 1]  0.000400) 
    |              | 
  }
  From:  (4, 2)  {
    ([ 2, 2]  0.000783) 
    ([ 3, 2]  0.000135) 
    |              | 
    ([ 5, 2]  0.001132) 
    |              | 
  }
  From:  (4, 3)  {
    ([ 2, 3]  0.001260) 
    |              | 
    ([ 4, 3]  0.000343) 
    ([ 5, 3]  0.001066) 
    |              | 
  }
  From:  (4, 4)  {
    ([ 2, 4]  0.000674) 
    ([ 3, 4]  0.001052) 
    ([ 4, 4]  0.001672) 
    ([ 5, 4]  0.001315) 
    |              | 
  }
  From:  (4, 5)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 6, 5]  0.000145) 
  }
  From:  (4, 6)  {
    ([ 2, 6]  0.000879) 
    ([ 3, 6]  0.000611) 
    |              | 
    ([ 5, 6]  0.001652) 
    |              | 
  }
  From:  (4, 7)  {
    |              | 
    ([ 3, 7]  0.000308) 
    ([ 4, 7]  0.000108) 
    |              | 
    |              | 
  }
  From:  (4, 8)  {
    |              | 
    ([ 3, 8]  0.000123) 
    |              | 
    |              | 
    ([ 6, 8]  0.001512) 
  }
  From:  (4, 9)  {
    ([ 2, 9]  0.001539) 
    |              | 
    |              | 
    ([ 5, 9]  0.001821) 
    ([ 6, 9]  0.000485) 
  }
  From:  (5, 1)  {
    ([ 3, 1]  0.001394) 
    ([ 4, 1]  0.001883) 
    |              | 
    ([ 6, 1]  0.001910) 
    ([ 7, 1]  0.000647) 
  }
  From:  (5, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 6, 2]  0.001855) 
    ([ 7, 2]  0.001150) 
  }
  From:  (5, 3)  {
    |              | 
    ([ 4, 3]  0.000516) 
    ([ 5, 3]  0.000399) 
    |              | 
    |              | 
  }
  From:  (5, 4)  {
    ([ 3, 4]  0.000158) 
    |              | 
    ([ 5, 4]  0.001743) 
    ([ 6, 4]  0.000331) 
    |              | 
  }
  From:  (5, 5)  {
    |              | 
    |              | 
    ([ 5, 5]  0.000378) 
    ([ 6, 5]  0.000357) 
    |              | 
  }
  From:  (5, 6)  {
    ([ 3, 6]  0.001836) 
    ([ 4, 6]  0.000397) 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.000221) 
    |              | 
    ([ 5, 7]  0.000713) 
    |              | 
    |              | 
  }
  From:  (5, 8)  {
    ([ 3, 8]  0.000106) 
    |              | 
    |              | 
    ([ 6, 8]  0.000379) 
    ([ 7, 8]  0.000766) 
  }
  From:  (5, 9)  {
    ([ 3, 9]  0.001332) 
    ([ 4, 9]  0.001664) 
    ([ 5, 9]  0.001540) 
    ([ 6, 9]  0.000417) 
    |              | 
  }
  From:  (6, 1)  {
    ([ 4, 1]  0.000282) 
    ([ 5, 1]  0.001230) 
    ([ 6, 1]  0.000827) 
    |              | 
    ([ 8, 1]  0.001493) 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.000128) 
    ([ 5, 2]  0.001671) 
    |              | 
    ([ 7, 2]  0.001307) 
    ([ 8, 2]  0.001020) 
  }
  From:  (6, 3)  {
    |              | 
    |              | 
    ([ 6, 3]  0.000199) 
    ([ 7, 3]  0.000512) 
    |              | 
  }
  From:  (6, 4)  {
    ([ 4, 4]  0.001471) 
    |              | 
    ([ 6, 4]  0.001595) 
    ([ 7, 4]  0.001892) 
    |              | 
  }
  From:  (6, 5)  {
    ([ 4, 5]  0.001225) 
    |              | 
    |              | 
    ([ 7, 5]  0.000163) 
    ([ 8, 5]  0.001192) 
  }
  From:  (6, 6)  {
    ([ 4, 6]  0.000049) 
    ([ 5, 6]  0.001923) 
    ([ 6, 6]  0.000181) 
    ([ 7, 6]  0.001578) 
    |              | 
  }
  From:  (6, 7)  {
    |              | 
    ([ 5, 7]  0.001434) 
    |              | 
    ([ 7, 7]  0.001875) 
    |              | 
  }
  From:  (6, 8)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.001928)   }
  From:  (6, 9)  {
    |              | 
    |              | 
    ([ 6, 9]  0.001223) 
    ([ 7, 9]  0.000502) 
    |              | 
  }
  From:  (7, 1)  {
    |              | 
    ([ 6, 1]  0.000050) 
    |              | 
    ([ 8, 1]  0.001627) 
    |              | 
  }
  From:  (7, 2)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.000989)   }
  From:  (7, 3)  {
    |              | 
    ([ 6, 3]  0.000898) 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 4)  {
    ([ 5, 4]  0.000033) 
    ([ 6, 4]  0.001905) 
    |              | 
    ([ 8, 4]  0.000160) 
    ([ 9, 4]  0.000874) 
  }
  From:  (7, 5)  {
    |              | 
    ([ 6, 5]  0.000295) 
    |              | 
    |              | 
    |              | 
  }
  From:  (7, 6)  {
    |              | 
    |              | 
    ([ 7, 6]  0.001448) 
    ([ 8, 6]  0.001116) 
    ([ 9, 6]  0.000390) 
  }
  From:  (7, 7)  {
    |              | 
    ([ 6, 7]  0.000392) 
    ([ 7, 7]  0.000927) 
    ([ 8, 7]  0.001919) 
    ([ 9, 7]  0.000848) 
  }
  From:  (7, 8)  {
    |              | 
    ([ 6, 8]  0.000542) 
    |              | 
    ([ 8, 8]  0.000360) 
    ([ 9, 8]  0.000463) 
  }
  From:  (7, 9)  {
    |              | 
    |              | 
    ([ 7, 9]  0.000473) 
    ([ 8, 9]  0.000024) 
    ([ 9, 9]  0.000348) 
  }
  From:  (8, 1)  {
    ([ 6, 1]  0.001189) 
    |              | 
    |              | 
    ([ 9, 1]  0.001765) 
    |              | 
  }
  From:  (8, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 9, 2]  0.000809) 
    |              | 
  }
  From:  (8, 3)  {
    |              | 
    ([ 7, 3]  0.000054) 
    ([ 8, 3]  0.001388) 
    ([ 9, 3]  0.000957) 
    ([ 1, 3]  0.001819) 
  }
  From:  (8, 4)  {
    ([ 6, 4]  0.000660) 
    |              | 
    |              | 
    |              | 
    ([ 1, 4]  0.000897) 
  }
  From:  (8, 5)  {
    ([ 6, 5]  0.001481) 
    ([ 7, 5]  0.000826) 
    ([ 8, 5]  0.000073) 
    |              | 
    |              | 
  }
  From:  (8, 6)  {
    ([ 6, 6]  0.000446) 
    ([ 7, 6]  0.001014) 
    ([ 8, 6]  0.001570) 
    ([ 9, 6]  0.000186) 
    ([ 1, 6]  0.000301) 
  }
  From:  (8, 7)  {
    |              | 
    |              | 
    |              | 
    ([ 9, 7]  0.001294) 
    ([ 1, 7]  0.001485) 
  }
  From:  (8, 8)  {
    ([ 6, 8]  0.000827) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (8, 9)  {
    ([ 6, 9]  0.000054) 
    ([ 7, 9]  0.001717) 
    ([ 8, 9]  0.000149) 
    |              | 
    ([ 1, 9]  0.000246) 
  }
  From:  (9, 1)  {
    ([ 7, 1]  0.001870) 
    ([ 8, 1]  0.001727) 
    |              | 
    ([ 1, 1]  0.001484) 
    |              | 
  }
  From:  (9, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 1, 2]  0.000535) 
    |              | 
  }
  From:  (9, 3)  {
    ([ 7, 3]  0.000197) 
    |              | 
    ([ 9, 3]  0.001314) 
    ([ 1, 3]  0.001026) 
    ([ 2, 3]  0.000285) 
  }
  From:  (9, 4)  {
    |              | 
    ([ 8, 4]  0.001121) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 5)  {
    |              | 
    ([ 8, 5]  0.001284) 
    ([ 9, 5]  0.001455) 
    ([ 1, 5]  0.001341) 
    ([ 2, 5]  0.001536) 
  }
  From:  (9, 6)  {
    |              | 
    |              | 
    |              | 
    ([ 1, 6]  0.000205) 
    ([ 2, 6]  0.000189) 
  }
  From:  (9, 7)  {
    ([ 7, 7]  0.001045) 
    |              | 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    ([ 8, 8]  0.001355) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 9)  {
    |              | 
    |              | 
    ([ 9, 9]  0.001256) 
    ([ 1, 9]  0.001934) 
    ([ 2, 9]  0.000507) 
  }
}

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