Code and simulation data for model of ideal chemotactic agent combining spatial and temporal gradient-sensing
收藏NIAID Data Ecosystem2026-05-02 收录
下载链接：
https://zenodo.org/record/8421581
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资源简介：
This repository contains python code and simulation data files for the paper “Information theory of chemotactic agents using both spatial and temporal gradient-sensing” by Julian Rode, Maja Novak, Benjamin M. Friedrich.
The code in this repository was developed by Julian Rode based on an earlier version by Andrea Auconi in the research group of Benjamin M. Friedrich at TU Dresden, Dresden, Germany.
The python package ‘pyegotaxis’ contained in ’pyegotaxis-0.2.zip’ is a snapshot (tag 0.2) of the git repository used for all simulations and data analysis in the paper, available also here:https://github.com/rodjul42/pyegotaxis
The file ‘readme.MD’ in ‘pyegotaxis-0.2.zip’ includes instructions for installation and a minimal example.
The jupyter notebooks contained in notebooks.zip recreate the figures 2-5 of the paper, as well as the supplementary figures S1-S10 and movies, using the data files.
Data files needed to recreate figures:
maxLD0_sum.fea
Needed for Fig 2 and S1
Maximum likelihood no motility noise
infoD0_sum.fea
Needed for Fig 2 and S1
Infotaxis no motility noise
maxLDrot_sum.fea
Needed for Fig 3 and S2
Maximum likelihood motility noise
infoDrot_sum.fea
Needed for Fig 3 and S2
Infotaxis motility noise
infoINFO_small_sum.fea
Needed for Fig 4 and Fig 5
Infotaxis SC vs TC
maxLINFO_small_sum.fea
Needed for Fig 4 and Fig 5
Maximum likelihood SC vs TC
expdata.hdf
Needed for Fig 5
SC vs TC data from experiments
expdata_trajectories.npz
Needed for Fig 5
Trajectories from experiments
expdata.hdf
Needed for Fig 5
SC vs TC data from experiments
10008_0.0.npz
Needed for Fig S3
example for SC vs TC infotaxis
2222_0.0.npz
Needed for Fig S3
example for SC vs TC maximum likelihood
Drotlam_kernel_large_sum2.fea
Needed for Fig S4
Infotaxis motility noise larger domain
spaceD_lT_sum.fea
Needed for Fig S5
infotaxis smaller space discretization and normal target size
spaceD_O_sum.fea
Needed for Fig S5
infotaxis normal space discretization and normal target size
spaceD_sum.fea
Needed for Fig S5
infotaxis smaller space discretization and smaller target size
infomaxlEXP_sum.fea
Needed for Fig S6
Maximum likelihood SC vs TC for exponentialconcentration field
infoInfoEXP_20_sum.fea
Needed for Fig S6
Infotaxis SC vs TC for exponentialconcentration field
infoRoblam_small_sum.fea
Needed for Fig S7
Infotaxis robustness sensing noise
maxLRoblam_small_sum.fea
Needed for Fig S7
Maximum likelihood robustness sensing noise
mDrotinfo_sum.fea
Needed for Fig S8
infotaxis robustness motility noise
mDrotmaxL_sum.fea
Needed for Fig S8
Maximum likelihood robustness motility noise
gamma.fea
Needed for Fig S9
infotaxis robustness non-radial concentration field, x(t0)=(-R0,0)
gamma2.fea
Needed for Fig S9
infotaxis robustness non-radial concentration field, x(t0)=(0,-R0)
vdrift.fea
Needed for Fig S10
infotaxis robustness concentration field distorted by drift, x(t0)=(0,-R0)
vdrift2.fea
Needed for Fig S10
infotaxis robustness concentration field distorted by drift, x(t0)=(-R0,0)
vdrift3.fea
Needed for Fig S10
infotaxis robustness concentration field distorted by drift, x(t0)=(R0,0)
创建时间：
2024-06-10
