IBL Bioinformatics Wiki

Welcome to the Wiki page for all researchers doing or willing to do some bioinformatics.

This Wiki site prioritizes collaboration. We welcome your assistance in identifying typos, misinformation, faults, and any other issues. Your contributions and suggestions are highly valued; please share them by creating new “Issues” on our GitHub page. Thank you for your valuable input.

If you wish to contribute further, such as by writing a new section, kindly initiate the process by creating an issue beforehand. This ensures smooth coordination and alignment with the project’s objectives.

IBL Servers

• IBL Linux Servers
  • IBL Servers and specs
  • Private GPU node in ALICE cluster
  • Basic knowledge of using linux shell
  • Get access
  • Usage guidelines
  • How to connect
  • What is Research Network
  • Leiden University gateways
• Server configurations
  • General storage
  • Transfer data with Research Drive
  • Sharing data and software environment
  • Home directory quota explained
  • Micromamba instead of Conda
  • Jump between servers
• Execute programs
  • Prepare micromamba
  • Execute an already installed program
  • Do not analyse large dataset in your home directory
  • Plan and notify others before execute long program
  • File transfer
  • How to run long jobs
  • Run a command in an environment without activation
• Install programs
  • What is an environment
  • Install a program
  • Setting up config file
  • Premissions of shared environments on BLIS
  • Monitoring disk space
• Common questions
  • Discussion group
  • Home directory quota
  • Micromamba or Conda
  • Shared storage
  • Shared environments

SSH access

• SSH basics
  • What is SSH
  • Determine your network location
  • CLI or GUI?
  • Get help
• MobaXterm setup
  • Portable edition
  • Start MobaXterm
  • Generate SSH key pairs
  • Put public keys to servers
• Command line setup
  • Start a CLI
  • SSH through SSH gateway
  • Setup
  • Make direct SSH connection (University Desktop with PowerShell)
  • No Guarantee

ALICE

• ALICE server from Leiden University
  • How to get an account
  • IBL on ALICE
  • Transfer data
• Running GROMACS on ALICE guide
  • 1. GROMACS
  • 2. Loading the necessary modules
  • 3. Input files
  • 4. PDB2GMX
  • 5. Setting up the simulation box
  • 6. Solvating the system
  • 7. Adding ions
  • 8. Energy minimization
  • 9. Equilibration run, temperature
  • 10. Equilibration run, pressure
  • 11. Production run
• HPC ALICE BLASTP
  • Preparation before running BLAST
  • 1. Single protein vs entire nr database
  • 2. Single protein vs a specific taxonomic group
  • 3. Searching only a specific region of the protein
  • 4. Searching for divergent or remote homologs
  • 5. Region-specific search for divergent homologs
  • 6. Performance and scaling guidelines
  • Summary of key options
  • Large query searches
• AlphaFold3 on ALICE
  • 1. input
  • 3. Understanding output
  • 4. Visualising output
  • 5. Final remarks

IBL RDM Howtos

• RDM IBL Howtos
  • Direct access URL
  • Terminology
  • PI preparation
  • Application
  • IBL Research software support
• Research Data Storage
  • Direct access URL
  • Intended structure
  • Nextcloud and Research Drive
  • Application and invitation
  • Expand storage space
• Electronic Lab Notebook
  • ELN direct access URL
  • Application entries
  • Usage policy
  • Setup autosharing within group
  • Tutorial videos
  • Benchling is not recommended as a general ELN
• Using GitHub or GitLab in Research
  • What Git tracks and what it does not
  • Recommended workflow
  • Summary

Tools

• Software Environment
  • Create an environment for a set of programs
  • Multi-user Linux server
  • Install an environment manager
  • Basic commands
• Setup micromamba
  • IBL server users
  • Why choose Micromamba instead of Conda on BLIS?
  • Install micromamba from scratch
• Doing BLAST on your local computer
  • Basic sequence format - FASTA
  • How BLAST works
  • Setup command line BLAST tool set
  • Run your first BLAST job locally
• Run RStudio in web browser
  • Why you need it
  • Server configuration for RStudio
• BLAST Tabular Output Guide
  • 1. What is BLAST tabular output
  • 2. The classic 12-column BLAST table
  • 3. Custom tabular output (recommended)
  • 4. Core blastp-specific fields
  • 5. Coverage and length fields (important)
  • 6. Taxonomy-aware fields (nr database)
  • 7. Sequence-including fields (can inflate output)
  • 8. Fields mainly for nucleotide-based BLAST
  • 9. Recommended column sets
  • 10. Other BLAST programs (summary)
  • 11. How to list all available fields locally
  • 12. Final advice

Admin tools

• IBL bioinformatics servers administration tools
  • Asked to create a user or a group?
  • Want to create many users at once?
• Useful IPA commands
  • Before you start
  • User management
  • Group management
  • Password policy
• Home directory template for new users on IBL servers
  • Actual execution flow
• Maintain the system
  • Update the system from time to time
  • Reboot the system if necessary
  • Check who has running sessions

Report issue

If you find anything in this site that can be better, please create an “Issue” at Issues page.

How to do that:

1. You will need a GitHub account because this documentation repository uses GitHub Issues; a nickname is also fine 😊

2. Identify the page you find wrong, check the “Address bar” of your browser.

3. After you logged in GitHub, head to Issues page, click the green “New issue” button.

4. Write a “Title” and “description”. Include the webpage “Address” if you are referring to it. Please check “Preview” when you finished.

5. (optional) You can @snail123815 if it is urgent.

6. (optional) You can add Labels by clicking the gear icon next to “Labels” on the right side.

7. Lastly, click the green “Submit new issue” button.

We (currently only @snail123815) will review it and correct asap.

Contribute more

If you think I am too slow on responding your issues, you are more than welcome to contribute by making changes directly. It is a bit more work then you might think, but I am sure you will learn a lot from the process.

Check the front page (“Code” tab if you in the “Issues” tab) of our GitHub repository. I wrote a brief introduction on how to do this in README file.

Maintainer(s)

Chao Du @snail123815

Contributors:

• You!

• Belmin Bajramovic @B-Bajramovic

• Joost Willemse @Karivtan

• Nicole Schmidt-Hebbel @nicoleyshebbel

Previously involved:

• Edder Bustos Diaz @EdderDaniel

• Caspar Schmeits @Capspar