francoissabot/trainingontvm repository overview

⁠App TrainingONT: Biosphere BASE environment for ONT analysis using Jupyter

⁠Description

The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.

This IFB cloud appliance provides both the Jupyter Notebook and Lab environment (see explanations⁠). Biosphere's users can switch these environments simply by changing the relative URL of the service from '/tree' to '/lab'.

This Jupyter app is based on the Jupyter Docker Stacks (see details⁠). By default, this Biosphere app uses the stack jupyter/datascience-notebook but users can choose any other existing stack with an Advanced deployment in Biosphere portal.

Main jupyter stacks are:

• jupyter/minimal-notebook: Minimally-functional Jupyter Notebook server, Miniconda Python 3.x, Pandoc and TeX Live for notebook document conversion
• jupyter/r-notebook: Everything in jupyter/minimal-notebook and popular packages from the R ecosystem.
• jupyter/scipy-notebook: Everything in jupyter/minimal-notebook and popular packages from the scientific Python ecosystem.
• jupyter/datascience-notebook: Everything in the jupyter/scipy-notebook and jupyter/r-notebook images, plus libraries for data analysis from the Julia, Python, and R communities.
• jupyter/tensorflow-notebook: Everything in jupyter/scipy-notebook and popular Python deep learning libraries.

See a detailed list of available Jupyter stacks there⁠.

⁠Tools

• Jupyter notebook/lab⁠
• seqtk⁠
• NanoPlot⁠
• NanoComp⁠
• Minimap2⁠
• Sniffles⁠
• SURVIVOR⁠
• Raven⁠
• Flye⁠
• RagTag⁠
• Racon⁠
• Assemblytics⁠
• Bandage⁠
• Mummer⁠
• Assembly-Stats⁠

⁠Contact

• Support Cloud IFB⁠

⁠Developpers

• Francois Sabot SouthGreen Platform⁠
• Julie Orjuela-Bouniol SouthGreen Platform⁠
• Gauthier Sarah SouthGreen Platform⁠

⁠App data

• Version : 20.04
• OS : Ubuntu
• OS version : 20.04

⁠Licence

Licensed under GPLv3