This repository contains all the code to reproduce the analysis and figures of the following paper and letter, which analyses and models the ORN-LN circuit in the antennal lobe of the Drosophila larva:

Normative and mechanistic model of an adaptive circuit for efficient encoding and feature extraction

Nikolai M. Chapochnikov, Cengiz Pehlevan, Dmitri B. Chklovskii

https://doi.org/10.1073/pnas.2117484120

Please cite this paper if you use the code.

Code author: Nikolai M. Chapochnikov

Steps to reproduce the analysis and figures of the paper

Install Python 3 and the required packages (e.g., via Anaconda) in the file "required_packages.txt"

Put the folder root folder "ORN-LN_circuit" (or a link to it) in your home directory.

Running the following files "ORN-LN_circuit/bin" folder will compute data in the 'results' folder, necessary to generate the plots (below). These simulations have been prerun, so this step can be skipped.

• act_preprocess.py
• con_preprocess.py
• con_analysis_MvsW.py (only prints a significance used for plotting)
• olf_circ_offline_sims_ORN-data.py
• olf_circ_offline_sims.py
• olf_circ_online_sims_real-syn-counts.py
• olf_circ_noM_offline_sims.py
• act_odors_ORN_vs_con_ORN-LN.py
• act_odors_ORN_vs_con_ORN-LN_recon.py
• act_odors_ORN_vs_con_ORN-LN_cdf-simulations.py (only gives plots)
• act_odors_ORN_vs_con_NNC.py
• act_ORN_vs_con_ORN-LN.py

The following files with generate all the plots present in the paper, they are saved in plots/plots/folder_name/ (parameter in plots_import.py):

• plots_activity.py
• plots_activity-conn-cdf.py
• plots_connectivity.py
• plots_models-theory.py
• plots_models-theory-noM.py
• plots_models-ORN-act.py (needs to be run twice, with SCAL_W=2 and with SCAL_W=10 inside the file)
• plots_model-real-syn-counts.py plots in the paper in the folder "plots/plots_paper".

NOTE: because some simulations are non-deterministic, the generated plots might slightly differ from the plots in the paper.

Reply to Castro et al.: Do connectomes possess markers of activity-dependent synaptic plasticity?

Nikolai M. Chapochnikov, Cengiz Pehlevan, Dmitri B. Chklovskii

Code for this letter is in bin/Barnes_data

https://www.pnas.org/doi/10.1073/pnas.2317056120

Please cite this paper if you use the code.

Code author: Nikolai M. Chapochnikov