What are the two cultures of bioinformatics software?

What are the two cultures of bioinformatics software?

Many tools and resources in bioinformatics are available on the Internet, including major browsers and genomes major (NCBI, Ensembl, UCSC) portals.

The following are:

  • accessible (no programming expertise needed)
  • Easy to browse for depth and width exploration
  • Highly popular
  • familiar (on any web browser OR Plastic platform)
What are the two cultures of bioinformatics software?

Bioinformatics and genomics: two cultures

  • Many bioinformatics tools and resources are available on the command-line interface (sometimes abbreviated CLI).
  • These are often on the Linux platform (or other Unixlike platforms such as the Mac command line). They are essential for many bioinformatics and genomics applications.
  • Most bioinformatics software is written for the Linux platform.
  • Many bioinformatics datasets are so large (e.g. high throughput technologies generate millions to billions or even trillions of data points) requiring command-line tools to manipulate the data.
Bioinformatics and genomics: two cultures

Should you learn to use the Linux operating system? Yes, if you want to use mainstream bioinformatics tools. Should you learn Python or Perl or R or another programming language?

It’s a good idea if you want to go deeper into bioinformatics, but also, it depends on what your goals are. Many software tools can be run in Linux on the command-line without needing to program.

Think of this figure like a map. Where are you now?

Where do you want to go?

Some web-based (GUI) and command-line (CLI) software

Some web-based (GUI) and command-line (CLI) software

What are the two cultures of bioinformatics software?

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