5.3. Runtime kernel description provided by the platform¶
After opening the Jupyter Lab interface, you can see the runtime kernel provided by the platform Fig. 5.18 .
Fig. 5.18 Running kernel provided by the platform¶
Currently, the platform provides the following three kernels for running and using. Later, the common kernel and default class libraries in the kernel will be added according to needs.
Python 3.11 [System]
Python 3.12 [Conda]
R 4.4 [Conda]
Note
Currently, you have little understanding of Python bioinformatics related technologies. If you need to install relevant class libraries, please contact the Information Center.
If you have special needs for running the kernel, you can contact the information center to customize it for users.
5.3.1. Kernel description: Python 3.11 [System]¶
The Python used is Python 3.11 that comes with the server operating system. Relevant modules are packaged by the Debian development team and run stably, but the versions are relatively old; generally speaking, software packages entering the Debian repository means that they are relatively mature and will have better development support. If you have no special requirements for the version you are running, this kernel is recommended. Installed modules include:
General Scientific Computing Module:
python3-pandas
python3-numpy
python3-scipy
Common modules for geographical information:
python3-gdal
python3-pyproj
python3-shapely
python3-fiona
python3-mapnik
python3-geopandas
python3-mapscript
python3-cairosvg
python3-cartopy
python3-folium
python3-fiona
python3-rasterio
Bioinformatics module:
python3-skbio
python3-biotools
python3-biopython
5.3.2. Kernel description: Python 3.12 [Conda]¶
Geographic information kernel installed based on Conda environment, Python version 3.12.
The installed geographical information modules include:
gdal
geopandas
shapely
folium
The installed bioinformatics modules include:
neurokit2
5.3.3. Kernel description: R 4.4 [Conda]¶
R language kernel installed based on Conda environment, version R 4.4.1. Installed modules include:
r-devtools
r-ggplot2
r-reshape2
r-corrplot