Modeldb links

_data/citations.yaml

@@ -1,5 +1,17 @@
 # DO NOT EDIT, GENERATED AUTOMATICALLY
 
+- id: doi:10.1101/2025.10.28.685063
+  title: Stochastic choice drives variability in patch foraging decisions across species
+  authors:
+  - Emma V. Scholey
+  - Matthew A.J. Apps
+  - Mark D. Humphries
+  publisher: openRxiv
+  date: '2025-10-29'
+  link: https://doi.org/g98xgz
+  orcid: 0000-0002-1906-2581
+  plugin: orcid.py
+  file: orcid.yaml
 - id: doi:10.1523/ENEURO.0431-23.2024
   title: The Computational Bottleneck of Basal Ganglia Output (and What to Do About
     it)
@@ -166,7 +178,7 @@
   - Mathew H. Evans
   - Rasmus S. Petersen
   - Mark D. Humphries
-  publisher: Cold Spring Harbor Laboratory
+  publisher: openRxiv
   date: '2019-12-11'
   link: https://doi.org/gkt7xc
   orcid: 0000-0002-1906-2581

_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

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 %}