Interactive Bioinformatics Tutorials
Neat web-based sandbox of bioinformatics tutorials, providing a sandbox for some of the common tools.
Public
Get to Know Benchling Validated Cloud
Webinar covering information about Benchling's "Validated Cloud" offering.
Genomics Boot Camp
The Genomics Boot Camp is a resource that helps you to start your journey in practical analysis of genomic data, with a focus on SNP data. The chapters follow the same structure all the time: provide background information and practical insight to the topic, and when appropriate exercises to reinforce the obtained knowledge. The Genomics Boot Camp as a whole was designed to cater to various learning preferences with written text, video demonstrations, and the possibility of hands-on exercises. There is a certain overlap between the book and the YouTube channel contents, but each has unique pieces of information as well. So for the full experience, I suggest checking out both.
Solving the Sequence Alignment problem in Python
Sequence alignment code, in Python, with a good explanation of the problem and the solution.
Using rapid prototyping to choose a bioinformatics workflow management system
Paper about how a group selected a workflow management system. I'm not sure it's that worthy of a writeup, at least not as seen via the lens of a software developer, but it's a useful perspective to read it to get some insight into how others approach this.
Researchers generate complete human X chromosome sequence
Some good comments in here that explain some of the issues, and solutions, of acquiring a full sequence of a chromosome.
Free online bioinformatics course
Many biomedical research graduate programs have been compelled to “go online” with little or no notice due to the COVID-19 pandemic. Since many professors are distinctly uncomfortable in front of a camera, students may not get exposure to some of the topics that they might have expected. Since my move to South Africa in 2015, I have tried to deposit video on YouTube (and PDFs of the slides to Google Drive) every time I have delivered a lecture for students. Since I teach a fairly broad range of coursework, the catalog of topics may be useful for students working from home or for departments that are trying to ensure their students get the training they need. This page indexes the series of lectures I have made available. I hope you enjoy watching them as much as I have enjoyed creating them!
Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, co - Nucleotide - NCBI
Genbank data for SARS-CoV-2.
On the performance and design of BioSequences compared to the Seq language | BioJulia
Interesting article that compares Seq to Julia, and in doing so results in speed improvements in a bioinformatics library for Julia.
How did the 5 bases get their names
Neat little twitter thread that outlines how the five bases (4 DNA and U for RNA) got their names.
Seq language
A high-performance, Pythonic language for bioinformatics
Seq: A high-performance language for bioinformatics
Paper about a language, that is pretty much a twist on Python that's aimed at getting higher performance for bioinformatics applications.
ST.25 - Standard for the presentation of nucleotide and amino acid sequence listings in patent applications
BED File Format
Article that outlines the format of BED files.
Rate Limiting
The API rate limits for Benchling.
Palindromic Sequence
Description of palindromic sequences in DNA.
Benchling API
Documentation for the Benchling API.
Uberon
An anatomical ontology that represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates
Sarah Carey on Twitter: "Today I keep trying to type "fasta" and end up typing "pasta". So, I made a pasta.fasta… "
Rather silly but enjoyable twitter thread where someone makes fasta files of pasta.
Home · BioSequences.jl
Collection of bioinformatics tools for Julia.
Pairwise Sequence Alignment using Biopython – Towards Data Science
Short introduction to pairwise alignment using BioPython.
Starting off in Bioinformatics — Turning DNA sequences into Protein sequences
Article that describes how DNA is turned into protein sequences.
Starting off in Bioinformatics — DNA Nucleotides and Strands
Introduction to DNA nucleotides,strands, etc.
DNA Sequence Data Analysis — Starting off in Bioinformatics
Handy background about DNA Sequencing and sequence assembly.
Starting off in Bioinformatics — RNA Transcription and Translation
Useful introduction to transcription and translation.
Lab41/squiggle: 📈 DNA Sequence Visualization for Humans
Interesting DNA sequence visualisation library.
Nucleotide ambiguity codes
Handy list of IUPAC nucleotide code along with the complements.
IUPAC Codes
Handy list of IUPAC nucleotide codes.
2bit file format
Details of the format of 2bit files
the Synthetic Biology Open Language (SBOL) | a language for genetic design