update

Author: salvadord

README.md

@@ -4,17 +4,7 @@ Multiscale model of mouse primary motor cortex (M1) developed using NetPyNE (www
 
 The model is described in the following paper: 
 
-- Dura-Bernal S, Neymotin SA, Suter BA, Dacre J, Joao VS Moreira, Eugenio Urdapilleta, Schiemann J, Duguid I, Shepherd GMG, Lytton WW. **Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics.** BioRxiv 2022.02.03.479040; doi: https://doi.org/10.1101/2022.02.03.479040. (Under review in Cell Reports) 
-
-A previous version of the model was also described in the following papers:
-
-- Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal R, Hines M, Shepherd GMG, Lytton WW. **NetPyNE: a tool for data-driven multiscale modeling of brain circuits.** eLife 2019;8:e44494 
-
-- Sivagnanam S, Gorman W, Doherty D, Neymotin SA, Fang S, Hovhannisyan H, Lytton WW, Dura-Bernal S. **Simulating large-scale models of brain neuronal circuits using Google Cloud Platform.** Practice and Experience in Advanced Research Computing, PEARC2020. 10.1145/3311790.3399621
-
-A modified version of the model was used to benchmark CoreNEURON in the following paper:
-
-- Awile O, Kumbhar P, Cornu N, Dura-Bernal S, Gonzalo JK, Lupton O, Magkanaris I, McDougal R, Newton AJH, Pereira A, Savulescu A, Carnevale NT, Hines M, Lytton WW, Schurmann F. **Modernizing the NEURON Simulator for Sustainability, Portability, and Performance**. Frontiers in Neuroinformatics (Under Revision). Research Topic: "Neuroscience, Computing, Performance, and Benchmarks: Why It Matters to Neuroscience How Fast We Can Compute." 
+- Dura-Bernal S, Neymotin SA, Suter BA, Dacre J, Moreira JVS, Urdapilleta E, Schiemann J, Duguid I, Shepherd GMG, Lytton WW. **Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics.** BioRxiv 2022.02.03.479040; doi: https://doi.org/10.1101/2022.02.03.479040. (Under review in Cell Reports) 
 
 
 ## Setup and execution

analysis/README.md

@@ -0,0 +1,17 @@
+# Primary motor cortex (M1) circuits model
+## Description
+Multiscale model of mouse primary motor cortex (M1) developed using NetPyNE (www.netpyne.org).
+
+The model is described in the following paper: 
+
+- Dura-Bernal S, Neymotin SA, Suter BA, Dacre J, Moreira JVS, Urdapilleta E, Schiemann J, Duguid I, Shepherd GMG, Lytton WW. **Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics.** BioRxiv 2022.02.03.479040; doi: https://doi.org/10.1101/2022.02.03.479040. (Under review in Cell Reports) 
+
+
+## Setup and execution
+
+This code can be used to reproduce the analysis and figures in the paper. It requires having access to the experimental data and data generated by the model -- see /data/README.md for instructions on how to download. 
+
+Some analysis functions requires NetPyNE; see installations instructions here: http://netpyne.org/install.html#
+
+
+For further information please contact: salvador.dura-bernal@downstate.edu.

data/README.md

@@ -0,0 +1,16 @@
+# Primary motor cortex (M1) circuits model
+## Description
+Multiscale model of mouse primary motor cortex (M1) developed using NetPyNE (www.netpyne.org).
+
+The model is described in the following paper: 
+
+- Dura-Bernal S, Neymotin SA, Suter BA, Dacre J, Moreira JVS, Urdapilleta E, Schiemann J, Duguid I, Shepherd GMG, Lytton WW. **Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics.** BioRxiv 2022.02.03.479040; doi: https://doi.org/10.1101/2022.02.03.479040. (Under review in Cell Reports) 
+
+
+## Downloading the data
+All the experimental data and data generated by the model has been made publicly available online at: (Gdrive link)
+
+
+
+For further information please contact: salvador.dura-bernal@downstate.edu.
+

sim/init.py

@@ -71,6 +71,7 @@ def modifyMechsFunc(simTime):
 # Simulation option 1: standard
 # sim.runSim()                              # run parallel Neuron simulation (calling func to modify mechs)
 
+print(cfg.modifyMechs)
 # Simulation option 2: interval function to modify mechanism params
 sim.runSimWithIntervalFunc(1000.0, modifyMechsFunc)       # run parallel Neuron simulation (calling func to modify mechs)