What do I use?

Last updated: 2023/07/12

There used to a Q and A series on Biostars (the link I had no longer works and I can't find it anymore) that asked well-known bioinformaticians what tools they use for their work. They were well-known because they were the developers behind popular bioinformatics tools. I'm not sure why it's gone as I'm always interested in finding out how other people work. Perhaps it got too many people arguing with each other? Or maybe people didn't find it interesting.

Anyway, the questions asked were:

  1. What hardware do you use?
  2. What is your text editor?
  3. What software do you use for your work?
  4. What do you use to create plots and charts?
  5. What do you consider the best language to do bioinformatics with?
  6. What bioinformatics tools/software do not get enough recognition?

Below are my updated answers.

What hardware do I use?

I use an ordinary Dell laptop for work and it isn't even worth mentioning the model because there's nothing special about it. I use it simply to SSH to the High Performance Computing server, which does all the work, and I use it for web browsing.

What is your text editor?

I use Vim. I have used it for many years relying on just the basic features. Recently I have been looking for ways to work with Vim more efficiently, which typically means reducing the number of keystrokes. Besides learning about other Vim features and I'm also exploring and using more plugins. I use vim-plug to install plugins and here are the ones I am currently using.

Plug 'tpope/vim-sensible'
Plug 'junegunn/seoul256.vim'
Plug 'gabrielelana/vim-markdown'
Plug 'godlygeek/tabular'
Plug 'vim-scripts/groovy.vim'
Plug 'LukeGoodsell/nextflow-vim'
Plug 'bronson/vim-trailing-whitespace'
Plug 'altercation/vim-colors-solarized'
Plug 'airblade/vim-gitgutter'
Plug 'tpope/vim-fugitive'
Plug 'junegunn/vim-easy-align'

What software do you use for your work?

I use Vim and RStudio Server (with Vim key bindings) to write all my code (mostly in R, Bash, Python). I use Git (and GitHub) to keep track of my code. I write all my documentation in Markdown and use MkDocs to render the code into a nice web page. I use Docker for installing and running software and to create analysis environments. I also use Conda for installing various tools. I use WDL and Cromwell as my workflow management system but I am currently learning about Nextflow and will be migrating my workflows to Nextflow. Finally, I use a lot of genomics tools that are too many to list.

What do you use to create plots and charts?

I plot everything using ggplot2. I used to use base R graphics but ggplot2 makes some annoying things (like adding a legend) very easy.

What do you consider the best language to do bioinformatics with?

(I wonder if this is the question that got this series removed.) There is no best language because each language has its strength and weaknesses. That said, if you do not know any programming languages, learn Python. It's multi-purpose, easy to read and write, and a lot of bioinformatics is done using Python.

What bioinformatics tools/software do not get enough recognition?

While not a tool or software, blogs don't get enough recognition!

Print Friendly, PDF & Email



Creative Commons License
This work is licensed under a Creative Commons
Attribution 4.0 International License
.

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.