From 65c26755c52624bfd943e55c27bfc066fb846290 Mon Sep 17 00:00:00 2001 From: mdhumphries Date: Thu, 29 Jan 2026 11:46:50 +0000 Subject: [PATCH 1/3] Update index.md --- code-simulation/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/code-simulation/index.md b/code-simulation/index.md index 55ec03f8..cf167b66 100644 --- a/code-simulation/index.md +++ b/code-simulation/index.md @@ -19,7 +19,7 @@ nav: {% include section.html background="images/background.jpg" dark=true %} -{% include button.html icon="fa-solid fa-laptop-code" text="All our models on ModelDB" link="https://senselab.med.yale.edu/modeldb/author_matches.py?author=Humphries+MD" style="button" %} +{% include button.html icon="fa-solid fa-laptop-code" text="All our models on ModelDB" link="https://modeldb.science/modelauthor/Humphries%20MD" style="button" %} {% include section.html %} From 501035651341ec73091bf0dc889e72cd0dfe2f6a Mon Sep 17 00:00:00 2001 From: mdhumphries Date: Thu, 29 Jan 2026 11:49:47 +0000 Subject: [PATCH 2/3] Update simulations.yaml --- _data/simulations.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_data/simulations.yaml b/_data/simulations.yaml index 1bb73517..3b2772b0 100644 --- a/_data/simulations.yaml +++ b/_data/simulations.yaml @@ -2,7 +2,7 @@ subtitle: Dynamics of the three-dimensional striatum group: featured image: images/blue_wiring.png - link: http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=137502 + link: https://modeldb.science/137502 description: A model of the 3D anatomical network of the striatum's GABAergic microcircuit between the SPNs and FSIs. Neurons are Izhikevich models tuned to reproduce key dynamic properties. Includes dopaminergic modulation of ion channels and synaptic connections. Scalable to any volume of striatal tissue. The code here is from [Humphries et al 2010 PLoS Computational Biology](https://doi.org/10.1371/journal.pcbi.1001011). An updated version of the model is in [Tomkins et al 2014 Front Comput Neurosci](https://doi.org/10.3389/fncom.2013.00192). tags: - striatum @@ -12,7 +12,7 @@ - title: Spiking neuron model of the basal ganglia subtitle: Action selection and spiking neurons image: images/Paper_Figures/SpikingModel.png - link: http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=83559 + link: https://modeldb.science/83559 description: The model in [Humphries et al (2006) J Neurosci](https://doi.org/10.1523/JNEUROSCI.3486-06.2006). tags: - basal ganglia @@ -23,7 +23,7 @@ - title: Control of behaviour by the brainstem reticular formation subtitle: Action selection in the brainstem image: images/scheibel_dendrites_edit.png - link: http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=128816 + link: https://modeldb.science/128816 description: Anatomy and dynamics of the medial reticular formation, and theories for its role in action selection. See review in [Humphries et al (2007) Phil Trans Roy Soc B](https://doi.org/10.1098/rstb.2007.2057). tags: - reticular formation From 5e7317804ebccc1e054d5b696384b77361a8022c Mon Sep 17 00:00:00 2001 From: mdhumphries <9415988+mdhumphries@users.noreply.github.com> Date: Thu, 29 Jan 2026 11:51:58 +0000 Subject: [PATCH 3/3] Update citations --- _cite/.cache/cache.db | Bin 57344 -> 53248 bytes _data/citations.yaml | 14 +++++++++++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 2ec0cb3d7adf895064684964f8fb446a1eeb922a..ff13e3ed229786636f76dac37ac19610e1d5992b 100644 GIT binary patch delta 4772 zcmZvfdt6iJ8OQUIgxnJp0zpKBBI1QyfPh#PXsh+oR=nV4)xaSHh(dxSSar@=u(kEW zhZ!H#&iS#l_U^2(V_U7$&06a$t=-c5#ai3X+Rn9`Zu@j~cI}?$JtoJl`-41ubAIP} z-}B~op7(h-|4zBNU%5R;ovBbLOfh>U%N(qK#{$#Ril8P42vDbmc3Xv}{z zKO!3KyUZ57S!q><0~`E`kKP>C+X#b>!rBJqXl+Djt_uVk{p&E94*&4eq|9QzP-igW z=BzOF3d%ffI3h#>;Yh$2w)M6uJ*+VhUR~E7@U3q3*R^+qA|YR>Rc-5C4G!ms>{Uv) 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