Computing Course November 2022

Z011 (WCW Congreszalen)


WCW Congreszalen

Science Park 125 1098 XG Amsterdam

Join our two-day computing course (or parts of it) to learn about the following topics and more:

First day focus: 'You and computer resources'

Nikhef colleagues will talk about Nikhef's centralised services, give hands-on workshops, practical examples and do's and don'ts of which services (not) to use and how. This day will cover a broad range of topics, including but not limited to the following:

  • How to login; (protecting) ssh keys, proxy tunnels
  • General unix principles, basic scripting and programming
  • How to use interactive nodes, login servers and storage (dCache) and why
  • Using certificates, how to; security, how user environments work and analysis frameworks
  • Fall in love with Stoomboot, batch jobs, GPU's, system queues
  • Learn how to work with CVMFS, containers and Conda
  • Where to go for help (we don't bite, and we have cake!)

Second day focus: 'You and data'

Colleagues of Nikhef and CWI will take you through the world of Research Data Management, in a mix of theoretical and practical courses. The goal of the day is to give you the knowledge, setup and experience to intertwine RDM in your (daily) work/research. Including (but not limited to) the following topics:

  • FAIR principles, Dublin Core Metadata standard, create your own ORCID
  • How to fill in a (mock) data management plan & Code of Conduct
  • Adding licenses for data and software re-usability, and why this is crucial
  • Research information repositories (Zenodo, arXiv); how to use them
  • Importance of, and how to do (immutable) journal keeping
  • How to relate journal entries (and Jupyterhub) to corresponding data

*Note for PhD students: the second day of the course ('You and data') is mandatory to follow at least once during your PhD.

  • Tuesday, November 22
    • 8:30 AM 5:00 PM
      Computing Course: You and computer resources
      • 8:30 AM
        Walk-in & Coffee 30m
      • 9:00 AM
        Welcome & Introduction 15m
        • Introduction of the services that are going to be talked about in the Computing Course
        • Know where to ask for help with questions or problems
        • Know where to find documentation
        • For newcomers: highlight the centralised services of Nikhef
        Speaker: Jeff Templon
      • 9:15 AM
        You and others; Security & Privacy 15m
        • Understand why security is important for you and your colleagues
        • Learn basic measures to work securely
        • Understand what is meant with privacy: rights and responsibilities
        Speaker: Ronald Starink
      • 9:30 AM
        You and a laptop 30m
        • Know how to encrypt your harddrive
        • Know how to backup your laptop
        • Know how to setup EduVPN
        • Know how to mount your home dir on your laptop; do’s and don’ts
        • Know about different local storage areas; and which to use for what
        Speaker: Bart van der Wal
      • 10:00 AM
        You, your laptop, and somebody else; how to work together 1h
        • Know how to send big files: SURF Filesender
        • Know how to find and use SURFdrive and CernBox
        • Understand which services are safe to use and which are not
        • Know how to use Identity Services & Federated Login
        • Know how to use Zoom and Mattermost
        Speaker: David Groep (Nikhef)
      • 11:00 AM
        Coffee 20m
      • 11:20 AM
        You, login and Linux 1h
        • Know how to login; ssh keys, protecting ssh keys, do’s and don’t
        • Understand basic principles of security with passwords
        • Know how to setup and safely use (proxy) tunnels; do’s and don’ts
        • Know how to manage your personal home page
        • Understand and apply general unix principles
        • Know about the basics of scripting and programming
        • Know how to use the most common command line tools
        • Understand file permissions and how to change them
        • Understand how to use login servers and what they’re not intended for
        Speaker: Dennis van Dok
      • 12:20 PM
        Lunch 1h 10m
      • 1:30 PM
        You, Jupyter, submit nodes and interactive nodes 45m
        • Understand shared resource etiquette for using interactive nodes
        • Understand when to use your home directory, /project, /data, and /dcache for storage (Stoomboot)
        • Know how to login and open Jupyter Notebooks on (JupyterHub)
        • Know how to setup a user environment to run group’s analysis framework (with conda in some cases)
        • Know how to obtain a grid x509 proxy certificate and add it to a browser
        • Understand basic principles of security with certificates
        • Know how to view your Nikhef dcache storage from your browser
        Speakers: Mary Hester (Nikhef), Roel Aaij
      • 2:15 PM
        Coffee 30m
      • 2:45 PM
        You, stoomboot, and a thesis as a present 55m
        • Understand when and how to submit a (CPU) batch job
        • Understand basic principles and use of CVMFS, Containers and Conda
        • Know how batch system queues work and what resources are available
        • Know how to write a job description file for a (local? Grid?) batch job
        • Know how to write a batch script (script that runs non-interactively & what is diff with previous?)
        • Know how to write data to dcache using data transfer protocols such as xrootd, webdav, gridftp
        • Understand the pitfalls for scaling up batch jobs
        Speaker: Dennis van Dok
      • 3:40 PM
        When the stoomboot is not enough 40m
        • Understand when and how to submit a GPU job
        • Know how to add VO information to grid proxy certificate (use grid-proxy-init / voms-proxy-init)
        • Know how to write efficient code, and what not to do
        • Know how to find your experiment framework (
        Speaker: Roel Aaij
      • 4:20 PM
        When you are in need of some help 20m
        • Who are you going to call?
        • Where to go when something is wrong
        • Learn about basic troubleshooting tools
        • Helpdesk,, stbc users mailinglist
        • Office Hours
        Speaker: Bart van der Wal
  • Wednesday, November 23
    • 9:00 AM 5:00 PM
      Computing Course: You and data
      • 9:30 AM
        Walk-in & Coffee 30m
      • 10:00 AM
        You and your research data 30m
        • Know about the FAIR principles and are able to assess your own data product with respect to these principles.
        • Know the 5 Principles and know where to find the full text and the Standards for good research practices (section 3).
        • Know about the Code of Conduct for Scientific integrity (2018) and its relation to reproducibility, documentation, reporting (including FAIR meta-data), and the prevention of CoIs.
        • Know that students' reports are to be treated in confidence.
        • Know about the Dublin Core meta-data elements
        Speaker: Reinder Radersma (Data Competence Center - CWI/NWO-I)
      • 10:30 AM
        When your data becomes part of something bigger 1h 30m
        • Know common persistent identifier schemes; at least DOI, and ORCID.
        • Possess an ORCID identifier and know how to update basic information in their ORCID record.
        • Know the importance of applying licenses to data and software for re-usability.
        • Know the basic licenses for data and software, and know where to find guidance on license application and the main differences between licenses.
        • Know the basic outline of a data management plan.
        • Know how to fill in a mock data management plan in NWO format using the on-line tools.
        Speaker: David Groep (Nikhef)
      • 12:00 PM
        Lunch 1h
      • 1:00 PM
        When software enters the stage 2h
        • Learn how to structure directories to manage processes, incoming, intermediate, and final research data, and to keep (persistent) references to data elements relative to its root.
        • Learn about research information repositories, and at least get to know Zenodo and arXiv.
        • Learn how to upload mock data or slides to Zenodo (in the environment) and complete the meta-data requirements.
        • Learn about the importance of (immutable) journal keeping and how to relate journal entries (and Jupyter notebooks) to the corresponding data
        Speaker: Roel Aaij
      • 3:00 PM
        Coffee 20m
      • 3:20 PM
        When you are in need of some help 1h 40m
        • Know where to find research data management guidance at Nikhef (web pages, mail, in-person).
        • Know where to find help & guidance for research issues and integrity at Nikhef
        • Room for questions and in-depth help
        Speaker: David Groep (Nikhef)