Init

How to get started in the Korf Lab

Discord

We communicate mostly by Discord. See the #announcements and #rules channels.

KorLab/init

This repository has a number of files in the root directory which are considered the onboarding documents for the lab. Please read them completely in the following order:

• README.md this document
• 01_MENTORING.md Ian's mentoring philosphy
• 02_EXPECTATIONS.md what to expect when joining the lab
• 03_RULES.md best practices that are important enough to be called rules
• 04_COMPUTER.md set up your computer for bioinformatics science
• 05_WALKTHROUGH.md experience some bioinformatics applications
• 06_CLASSICS.md learn bioinformatics programming by studying the classics
• 07_EXAM.md take the official KorfLab Bioinformatics Exam
• 08_HALL_OF_FAME.md honor roll of people who have passed the exam

There are also some directories with various files you may find useful.

• bin Python-based programs
  • benchmark a simple benchmark to measure performance of your computer
  • data-faker creates synthetic exons and introns for testing
  • data-shrinker genomic dataset minimizer
  • fasta-demo increasingly sophisticated ways to read FASTA files
  • fastgff draft example of using sqlite3 to manage FASTA and GFF3
  • fq-faker sample fake reads from a sequence
  • kmer-gizmo count and compare kmer frequencies in DNA
  • model-tester creates and evaluates sequence models
  • mysbatch mock sbatch for dev purposes
  • seq-stats report statistics about sequences in a FASTA file
  • space-waste look for duplicate and uncommpressed files
• lib some libraries
  • korflab.py common bioinformatics functions in Python
  • FAlite.pm ancient FASTA iterator in Perl
• data "Rule #1" data
• etc config files (shell customizations and conda environments)