BioMedical and Bioinformatics Resources

Welcome to a resources page for Bioinformatics research. Here you will find a list of links for data, tools, tutorials and related resources that may be very helpful to your work.

• Software

  • Installations

    • RStudio
    • R Programming Language
    • Python Programming Language
    • Git for Mac
    • Git for Windows
    • Git for all platforms
    • Python Programming Language
    • Python for Biologists
    • BioPython

  • Online Tools

    • sentiment viz Tweet Sentiment Visualization
    • Online R programming
    • Snippets – Run any R code you line online
    • JDoodle

• Python Programming Resources

  • Play with code from W3’s super Python Tutorial
  • Write code locally using Jupyter Interactive Python.
  • Think Python, a textbook, by Allen B. Downey Publisher Website
  • The Python Programming Language

• Online

  • Online R programming

• Articles

  • Getting started with Markdown

• Tutorials

  • Statmethods R programming Tutorial by Datacamp
  • Dealing with GenBank files in Biopython
  • Allegheny College Department of Computer Science tutorials
  • Coding Train’s Git and GitHub for Poets
  • Setting Up Git on Linux
  • Setting up Git
  • Getting Started with Python in VS Code
  • 11 Best VS Code extensions for Python (2022)
  • ssh keys
  • Luman’s ssh keys video tutorial

• Tools

  • COVID-19 Forecasts
  • Virus Explorer
  • TCoffee: http://tcoffee.crg.cat/apps/tcoffee/tutorial.html
  • Hidden Markov Models (Youtube): https://www.youtube.com/watch?v=TPRoLreU9lA
  • The Double Helix (Documentary about DNA discovery, 17 mins): https://media.hhmi.org/biointeractive/films/Double_Helix.html
  • The Chemical Structure of DNA: https://www.biointeractive.org/classroom-resources/chemical-structure-dna
  • The Structure of DNA: https://www.youtube.com/watch?v=o_-6JXLYS-k
  • The definition to 5’ end and 3’ end of a DNA strand - Simple animated HD: https://www.youtube.com/watch?v=qWZYpHSXvJo
  • What happens when your DNA is damaged?: https://www.youtube.com/watch?v=vP8-5Bhd2ag
  • Mutations and Natural Selection: https://www.youtube.com/watch?v=BBI7GoIyoog
  • Protein synthesis animation: https://www.youtube.com/watch?v=NDIJexTT9j0
  • The Lung Endothelial Cell Atlas http://www.lungendothelialcellatlas.com
  • The COPD Cell Atlas http://www.copdcellatlas.com
  • The COVID Cell Atlas: http://www.covidcellatlas.com
  • Idiopathic Pulmonary Fibrosis Cell Atlas: http://www.ipfcellatlas.com/
  • Codon Usage Database: https://www.kazusa.or.jp/codon/
  • The Comprehensive Antibiotic Resistance Database: https://card.mcmaster.ca/
  • ermB anti resistance gene: https://card.mcmaster.ca/ontology/36514]
  • SIM: Alignment tool for protein sequences: https://web.expasy.org/sim/
  • Blast analysis: https://card.mcmaster.ca/analyze
  • Diamond; a Blast alternative: http://www.diamondsearch.org/index.php
  • HMMER: biosequence analysis using profile hidden Markov models: http://hmmer.org/
  • Gene Ontology Resource: http://geneontology.org/
  • Panther Classification System: http://www.pantherdb.org/
  • Blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi
  • EGassembler: https://www.genome.jp/tools/egassembler/
  • ELM tool kit: http://elm.eu.org/
  • Protein Data Bank: http://www.rcsb.org/
  • Predict protein: https://open.predictprotein.org/
  • String: a protein database: https://string-db.org/
  • Database of protein domains, families and functional sites: https://prosite.expasy.org/
  • Needleman-Wunsch algorithm Interactive demo: http://experiments.mostafa.io/public/needleman-wunsch/
  • UGENE is free open-source cross-platform bioinformatics software: http://ugene.net/
  • The Cell Map: http://thecellmap.org/?q=pex6
  • The String Database For Analysis: http://string-db.org/
  • AmiGo: Gene products and gene annotations: http://amigo.geneontology.org/amigo/landing
  • Genetics Home Reference: https://ghr.nlm.nih.gov/
  • Northeast Structural Genomics Consortium: http://nesg.org/galleries.html
  • ModEval: An evaluation tool for protein structure models: https://modbase.compbio.ucsf.edu/modeval/
  • PyMol – A user-sponcored molecular visualization system on an open-source foundation, maintained and distributed by Schrodinger: https://pymol.org/2/
  • Qiime2 – is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed: https://qiime2.org/
  • DrugBank – a pharmaceutical knowledge base that is enabling major advances across the data-driven medicine industry: https://go.drugbank.com/
  • Augustus [gene prediction] – a software to predict genes in eukaryotic genomic sequences: http://bioinf.uni-greifswald.de/augustus/

Research and Data Resources

• An interactive visualization of the exponential spread of COVID-19: https://91-divoc.com/pages/covid-visualization/
• Project Tycho: https://www.tycho.pitt.edu/
• Cataracts and Genetics: https://knowyourdna.com/cataracts-and-genetics/
• National Human Genome Research Institute: https://www.genome.gov/
• Max Planck Institute For Molecular Genetics: https://www.molgen.mpg.de/2168/en

Resources for Cerebral Palsy

• Cerebral Palsy Guidance: https://www.cerebralpalsyguidance.com/
• Cerebral Palsy Associated Disorders: https://www.cerebralpalsyguidance.com/cerebral-palsy/associated-disorders/
• Cerebral Palsy Guide: https://www.cerebralpalsyguide.com/cerebral-palsy/coexisting-conditions/cancer/
• The Cerebral Palsy Toolkit: https://www.levinperconti.com/birth-injury/cerebral-palsy/guide-toolkit/
• Causes: https://www.cerebralpalsyguidance.com/cerebral-palsy/causes/

Note

If you find a good link for Bioinformatics research that you believe would fit nicely here, please let me know!

obonhamcarter at allegheny dot edu