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intro_python_ismb2022

https://github.com/santosrac/intro_python_ismb2022

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    Found .zenodo.json file
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    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (7.3%) to scientific vocabulary

Keywords

bioinformatics biology education python sars-cov-2 tutorial
Last synced: 4 months ago · JSON representation ·

Repository

Basic Info
Statistics
  • Stars: 9
  • Watchers: 3
  • Forks: 3
  • Open Issues: 0
  • Releases: 1
Topics
bioinformatics biology education python sars-cov-2 tutorial
Created almost 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

DOI

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"
  • 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.
    • clustalspikemsa.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)

Owner

  • Name: Renato Augusto Corrêa dos Santos
  • Login: SantosRAC
  • Kind: user
  • Location: Piracicaba
  • Company: University of São Paulo

Ph.D. in Genetics and Molecular Biology | Bioinformatician. Post-doc researcher in the Laboratory of Computational, Evolutionary and Systems Biology - LabBCES

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Correa dos Santos"
  given-names: "Renato Augusto"
  orcid: "https://orcid.org/0000-0003-0826-5479"
- family-names: "Ilídio Silva"
  given-names: "Pedro de Carvalho Braga"
  orcid: "https://orcid.org/0000-0002-5750-0204"
- family-names: "Passarelli Araujo"
  given-names: "Hemanoel"
- family-names: "Franceschini dos Santos"
  given-names: "Vinícius Henrique"
title: "intro_python_ismb2022"
version: 1.0.0
doi: 10.5281/zenodo.6779795
date-released: 2022-06-29
url: "https://github.com/SantosRAC/intro_python_ismb2022"

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