TUTORIAL: Introduction to Python programming for bioscientists

Tutorial to be presented online in the Intelligent Systems for Molecular Biology (ISMB) 2022 edition, including hands-on activities and exercises.

Speakers

• Pedro de Carvalho Braga Ilidio Silva (master student) @pedroilidio
• Hemanoel Passarelli Araujo (PhD candidate) @Passarelli-bio
• Vinícius Henrique Franceschini dos Santos (undergraduate student) @vhfsantos
• Renato Augusto Corrêa dos Santos, PhD @SantosRAC

Expected audience

Researchers at different education levels with interest in learning programming skills for bioinformatics.

Level of programming skills: beginners.

Learning Objectives

• Introduce Google Colab digital notebooks
• Present the basic logic and data structures in Python
• Provide hands-on experience in analyzing biological sequences using Biopython

Material available in this repository

• Folder "Digital_Notebooks"
  • Tutorial_JupyterNotebook_Colab.ipynb: basic introduction to Colab and overview of its main functionalities.
  • ISMB_2022_Python.ipynb: complete notebook with the hands-on activity proposed to our ISMB 22 tutorial: Introduction to Python programming for bioscientists.
• Folder "Data"
  • Wuhan-Hu-1_19A.fasta: FASTA file containing a spike protein sequence of the reference strain.
  • spike_proteins.fasta: contains additional FASTA sequences, that correspond to other virus variants.
  • clustal_spike_msa.txt: a multiple sequence alignment (MSA) of the spike proteins to explore mutations.
  • envelope_protein.fasta: FASTA file containing a sequence of envelope protein.
  • surface_glycoprotein.fasta: FASTA file containing a sequence of surface glycoprotein.
  • nucleocapsid_phosphoprotein.fasta: FASTA file containing a sequence of nucleocapsid phosphoprotein.
• Folder "Initial_Proposal"
  • ISMB 2022 - Tutorial Proposal.pdf: PDF with the proposal submitted to ISMB organization.

Release history

• v1.0.0 - initial version (sent to Steven Learn on June 29)