Code and simulation data for model of ideal chemotactic agent combining spatial and temporal gradient-sensing
Authors/Creators
- 1. TU Dresden
- 2. University of Zagreb
Description
This repository contains python code and simulation data files for a preprint entitled “Chemotactic agents combining spatial and temporal gradient-sensing boost spatial comparison if they are large, slow, and less persistent” 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-0.1.zip’ is a snapshot (tag 0.1) of the git repository used for all simulations and data analysis in the preprint, available also here:
https://github.com/rodjul42/pyegotaxis
The file ‘readme.MD’ in ‘pyegotaxis-0.1.zip’ includes instructions for installation and a minimal example.
The jupyter notebooks contained in notebooks.zip recreate figures 2, 3, 4, 5 of the preprint, as well as the Supplementary Movies S1, S2, S3, S4, S5, using the data files.
Data files needed to recreate figures:
| 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 |
| expdata.hdf |
Needed for Fig 5 SC vs TC data from experiments |
| expdata_trajectories.npz |
Needed for Fig 5 Trajectories from experiments |
| infoD0_sum.fea |
Needed for Fig 2 and S1 Infotaxis no motility noise |
| infoDrot_sum.fea |
Needed for Fig 3 and S2 Infotaxis motility noise |
| infoINFO_small_sum.fea |
Needed for Fig 4 Infotaxis SC vs TC |
| infoRoblam_small_sum.fea |
Needed for Fig S6 Infotaxis robustness sensing noise |
| maxLD0_sum.fea |
Needed for Fig 2 and S1 Maximum likelihood no motility noise |
| maxLDrot_sum.fea |
Needed for Fig 3 and S2 Maximum likelihood motility noise |
| maxLINFO_small_sum.fea |
Needed for Fig 4 Maximum likelihood SC vs TC |
| maxLRoblam_small_sum.fea |
Needed for Fig S6 Maximum likelihood robustness sensing noise |
| mDrotinfo_sum.fea |
Needed for Fig S7 infotaxis robustness motility noise |
| mDrotmaxL_sum.fea |
Needed for Fig S7 Maximum likelihood robustness motility noise |
| 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 |
Files
notebooks.zip
Files
(9.4 GB)
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