NAISS Training Newsletter

# NAISS Training Newsletter This document: https://hackmd.io/@UPPMAX/NAISS-training-news Note: If the event involves teachers outside of UPPMAX and NAISS, please add *Collaboration with $institution* under the workshop title. ## week 02 Re-runs: NAISS events: - Online: Awk Workshop, 15-16 January, 2026 - Online training workshop: Basic Singularity/Apptainer workshop, 19 February 2026 University events: - Online course: Introduction to Linux and UPPMAX, 19 - 21 January 2026 New events: - Introduction to Python for HPC - CodeRefinery tools workshop ============================================================================================= Online workshop: Intro to Python for HPC, 3 March, 2026 This 1-day course lets you write and run Python code on an HPC cluster. The goal of the first half of the course, is to run Python on an HPC cluster, with little focus on the Python language itself. The goal of the second half of the course, is to learn the basics of Python and can be done from your local computer as well. The pace of this highly interactive course is set by the majority of learners, ensuring that any complete beginner has enough time for exercises. At the end of the day, you should feel comfortable with writing and running Python code on either HPC or your local computer. When: Tuesday, March 3rd, 2026, 9:00 - 16:00 Where: Online via Zoom Course information and registration: https://docs.uppmax.uu.se/courses_workshops/intro_to_python/ ============================================================================================= Save the date Online workshop: CodeRefinery workshop on tools and techniques for reproducible research, 17-19 and 24-26 of March 2026 Are you writing code for your research? Do you struggle to reproduce results of your own or others computations? Join the online CodeRefinery workshop during 6 days: Intro to git and collaborative git: 17 - 19 of March 2026. Reproducible research and other topics: 24 - 26 of March 2026. The CodeRefinery (https://coderefinery.org) workshop aims to support researchers of all domains, levels and preferred programming languages to write more reproducible research code. The workshop is held online (streamed on Twitch) with hands-on sessions. The registration will open very soon and will be announced in the future edition of the NAISS training newsletter. ============================================================================================= ## week 48 NAISS events: ============================================================================================= **Online: "Awk Workshop", 15-16 January, 2026** *Collaboration with NBIS* AWK is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool. This two-day workshop aims to promote and demonstrate the flexibility of the tool, where the overhead of more sophisticated approaches and programming languages is not worth the bother. Learn how to - use Awk as an advanced grep command, capable of arithmetic selection rules with control over the content of the matched lines - perform simple conversions, analysis or filter you data on the fly making it easy to plot or read in your favorite research tool - handle and take advantage of data split over multiple file data sets - use Awk as simple function or data generator - perform simple sanity checks on your results The workshop aims to promote the awk tool for use in everyday research work and urges you to find solutions yourself rather than expecting ready-made ones. The material given during the seminar will not be a complete guide or a manual but rather an overview of the capabilities, particular strengths, and common disadvantages. **When:** Thursday-Friday, 15-16, January, 2026 **Where:** Online on Zoom **Registration form:** https://forms.gle/AM5YpGRPJDjbVkLa9 For more information, please visit: https://docs.uppmax.uu.se/courses_workshops/awk/ ============================================================================================= **Online training workshop: Basic Singularity/Apptainer workshop** 9:15-12:00, 13:15-16:00 - 19 February 2026. The online workshop is an introduction to the basic concepts of containerized software environment solutions within the Singularity framework https://sylabs.io/singularity/. During the workshop you will have the opportunity to follow the interactive guide on - how to run Singularity containers - how to build your own - good (and bad) practices on designing and building Singularity recipes - build and/or host container remotely and what are the limitations To fully benefit from the workshop, basic Linux system administration experience is highly desirable i.e. knowledge of package management and common tools for building and/or managing software: git, pip, conda, wget, curl … When: 19 February, 2026 Where: Online via Zoom Web page: https://docs.uppmax.uu.se/courses_workshops/singularity/ Registration: https://forms.gle/3XJ5xstF3rbuZyaz6 ============================================================================================= University events: ============================================================================================= Online course: Introduction to Linux and UPPMAX, 19-21 January, 2026 This 3-day course provides an introduction to the high-performance computing (HPC) environment offered at UPPMAX. It offers an overview on how the systems work and covers skills from basic Linux usage to more advanced tips and tricks. The lectures covering Linux and bash scripting are cluster-agnostic and may be attended by non-UPPMAX users as well. When: January 19-21, 2026 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/uppmax_intro_course/. ============================================================================================= ## week 42 New: **Online workshop: Log in and Transfer Files to/from HPC Clusters, 14 November, 2025** In this 3-hour workshop you learn to transfer files to and from Swedish academic HPC clusters. We will cover graphical as well as terminal tools and you will work highly interactively. A log in session will be included as well. At the end of the day, you should be comfortable in transferring files between your local computer and a cluster and cross-clusters, and choosing the right tools for your use cases. The workshop is intended for beginner users but with some Linux experience. You do not need to be a member of a NAISS project in order to join the workshop. A course project on one of the NAISS clusters will be available to those. When: Friday, November 14, 2025 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/naiss_transfer/. --- **Online hackathon: Bianca In-Depth: Improve Your Handling of Sensitive Research Data, 18 November, 2025** Are you already working with sensitive data in your research and feel that your workflows can be improved? If yes, welcome to 1-day hackathon where you'll learn smarter ways of working on the Bianca cluster. We will tell you how to do file transfer from a terminal, advanced Slurm, and installing custom software and packages. To attend this event, we expect you to be able to login to Bianca, submit a simple Slurm batch job, and know the basics of file transfer. A NAISS-SENS course project will be available to all participants. When: Tuesday, November 18, 9.00-16.00 Where: online via Zoom For more information and registration please visit: https://docs.uppmax.uu.se/courses_workshops/bianca_intermediate/. --- **Online course: Python for Scientific Computing, 25-27 November** *Organized by Aalto University, CodeRefinery, and partners* This is a medium-advanced course in Python tools such as NumPy, SciPy, Matplotlib, and Pandas. It is suitable for people who have a basic understanding of basic Python and want to know some internals and important libraries for science. Read the learner personas to see if the course is right for you. Prerequisites include basic programming in Python. The course streamed via Twitch (the CodeRefinery channel) so that anyone may follow along without registration. There is a "Notes" link (collaborative edited notes) which is used for asking questions during the course. The course is organized by Aalto Scientific Computing in collaboration with CodeRefinery, and multiple Nordic partners. For more information, please visit: https://scicomp.aalto.fi/training/scip/python-for-scicomp-2025/. --- ## week 40 Re-runs: NAISS training Online course: Introduction to running R, Matlab, and Julia in HPC, 6-8+10 October 2025 Online training workshop: Basic Singularity/Apptainer workshop, 13 October, 2025 Online workshop: Intro to Python for HPC, 14 October, 2025 Online workshop series: Large Language Model Workshop, 19-21 Nov 2025 CodeRefinery event CodeRefinery workshop on tools and techniques for reproducible research (online), multiple dates September and October University events Introduction to Linux and UPPMAX, Uppsala, 15-17 October, 2025 ============================================================================================= **Online course: Programming Formalisms, 23-24, 27-29 October 2025** *Collaboration between UPPMAX and NBIS* The goal of this highly-interactive 5-day course is to be able to develop academic software that you can trust to be 'good enough'. We assume you have written code 'that (sometimes) just works'. The course follows a formal development process from start to finish, with a selection of topics and best practices we think are most important, with the goal of developing academic software that is actually good enough. When: October 23–24 and 27–29 at 9:00-16:00 each day. Where: online via Zoom More info and registration, please visit https://docs.uppmax.uu.se/courses_workshops/programming_formalisms/. ============================================================================================= ## week 37? Re-runs: NAISS training: Online training workshop: Basic Singularity/Apptainer workshop, 13 October, 2025 Online workshop series: LLM Workshop, 19-21 Nov 2025 CodeRefinery event: CodeRefinery tools workshop (online) University events Online course: Introduction to Linux and UPPMAX, 15-17 October, 2025 New: UPPMAX Drop-in, weekly on Tuesdays Online workshop: Intro to Python for HPC, 14 October, 2025 ============================================================================================= UPPMAX Drop-in Join to the UPPMAX staff for any questions you may have regarding our clusters or services. When: every Tuesday at 14:00 - 15:00 Where: https://uu-se.zoom.us/j/63765794350 ============================================================================================= Online workshop: Intro to Python for HPC, 14 October, 2025 This 1-day course helps you get started with Python, by working ourselves through an online and free book. Although the focus is on learning Python, we do work in an HPC environment and you will be taught the bare minimum to run Python on an UPPMAX HPC cluster. The pace of this highly interactive course is set by the majority of learners, ensuring that any complete beginner has enough time for exercises. At the end of the day, you should feel comfortable with the basics of Python and feel familiar to a book on Python to help you on your next steps. When: Tuesday October 14th 2025, 9:00 - 16:00 Where: Online via Zoom Course information and registration: https://docs.uppmax.uu.se/courses_workshops/intro_to_python/ ============================================================================================= ## week 35 The date for the UPPMAX intro course was wrong in the summary of the previous newletter. I am including the advertisement text for it to this email as well. Also, the CodeRefinery workshop is updated to reflect the local KTH Library room open to everyone (up to a certain number due to room size limits). There are some new co-events, those have been / will be shared by Birgitte and Weine. Re-runs: NAISS training: Online workshop: Log in and Transfer Files to/from HPC Clusters, 5 September, 2025 Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 15 September, 2025 Online training workshop: Basic Singularity/Apptainer workshop, 13 October, 2025 CodeRefinery event: CodeRefinery tools workshop (online) University events Online course: Introduction to Linux and UPPMAX, Uppsala, 15-17 October, 2025 ============================================================================================= Online course: Introduction to Linux and UPPMAX, 15-17 October, 2025 This 3-day course provides an introduction to the high-performance computing (HPC) environment offered at UPPMAX. It offers an overview on how the systems work and covers skills from basic Linux usage to more advanced tips and tricks. The lectures covering Linux and bash scripting are cluster-agnostic and may be attended by non-UPPMAX users as well. When: October 15-17, 2025 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/uppmax_intro_course/. ============================================================================================= CodeRefinery workshop on tools and techniques for reproducible research (online), multiple dates in September and October Are you writing code for your research? Do you struggle to reproduce results of your own or others computations? Join the online CodeRefinery workshop during nine half days: Intro to git and collaborative git: September 9-11, at 11:00-13:00 and 14:00-15:30. Reproducible research and other topics spread over 6 following weeks Wednesdays with exercises: September 17, 24, October 1, 8, 15, and 22 at 12:30-14:00. The CodeRefinery workshop aims to support researchers of all domains, levels and preferred programming languages to write more reproducible research code. The workshop is held online (streamed on Twitch) with hands-on sessions. Interaction with the participants and live help is guaranteed by a variety of means. The KTH Library offers local helpers during Sep 9-11 (please check the event page, separate registration required, limited spaces available). More info and registration on the CodeRefinery workshop website: https://coderefinery.github.io/2025-09-09-workshop/ ============================================================================================= ## week 34 Re-runs: NAISS training On-site workshop: "Awk Workshop", Uppsala, 28-29 August, 2025 Online training seminar: Cluster architecture and job submission, 2 September 2025 at 13:30 Online workshop: Log in and Transfer Files to/from HPC Clusters, 5 September, 2025 Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 15 September, 2025 Online training workshop: Basic Singularity/Apptainer workshop, 13 October, 2025 CodeRefinery event CodeRefinery tools workshop (online) University events Online course: Introduction to Linux and UPPMAX, Uppsala, 15-17 October, 2025 ============================================================================================= CodeRefinery workshop on tools and techniques for reproducible research (online) Are you writing code for your research? Do you struggle to reproduce results of your own or others computations? Join the online CodeRefinery workshop during nine half days: Intro to git and collaborative git: September 9-11, at 11:00-13:00 and 14:00-15:30. Reproducible research and other topics spread over 6 following weeks Wednesdays with exercises: September 17, 24, October 1, 8, 15, and 22 at 12:30-14:00. The CodeRefinery workshop aims to support researchers of all domains, levels and preferred programming languages to write more reproducible research code. The workshop is held online and is free of charge. More info and registration on the CodeRefinery workshop website: https://coderefinery.github.io/2025-09-09-workshop/ ============================================================================================= Online course: Introduction to Linux and UPPMAX, 15-17 October, 2025 This 3-day course provides an introduction to the high-performance computing (HPC) environment offered at UPPMAX. It offers an overview on how the systems work and covers skills from basic Linux usage to more advanced tips and tricks. The lectures covering Linux and bash scripting are cluster-agnostic and may be attended by non-UPPMAX users as well. When: October 15-17, 2025 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/uppmax_intro_course/. ============================================================================================= ## week 25 NAISS training events **On-site workshop: "Awk Workshop", Uppsala, 28-29 August, 2025** AWK is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool. This two-day workshop aims to promote and demonstrate the flexibility of the tool, where the overhead of more sophisticated approaches and programming languages is not worth the bother. Learn how to - use Awk as an advanced grep command, capable of arithmetic selection rules with control over the content of the matched lines - perform simple conversions, analysis or filter you data on the fly making it easy to plot or read in your favorite research tool - handle and take advantage of data split over multiple file data sets - use Awk as simple function or data generator - perform simple sanity checks on your results The workshop aims to promote the awk tool for use in everyday research work and urges you to find solutions yourself rather than expecting ready-made ones. The material given during the seminar will not be a complete guide or a manual but rather an overview of the capabilities, particular strengths, and common disadvantages. **When:** Thursday-Friday, 28-29, August, 2025 **Where:** Uppsala, EBC, House 7, room 1003, MazeMap https://link.mazemap.com/0jgt9Zan **Registration form:** https://forms.gle/UMYGX9VVwfaCUrPv9 For more information, please visit: https://docs.uppmax.uu.se/courses_workshops/awk/ --- **Online workshop: Log in and Transfer Files to/from HPC Clusters, 5 September, 2025** In this 3-hour workshop you learn to transfer files to and from Swedish academic HPC clusters. We will cover graphical as well as terminal tools and you will work highly interactively. A log in session will be included as well. At the end of the day, you should be comfortable in transferring files between your local computer and a cluster and cross-clusters, and choosing the right tools for your use cases. The workshop is intended for beginner users but with some Linux experience. You do not need to be a member of a NAISS project in order to join the workshop. A course project on one of the NAISS clusters will be available to those. When: September 5, 2025 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/naiss_transfer/. --- **Online workshop: Introduction to Bianca: Handling Sensitive Research Data, September 15, 2025** Are you just beginning to work with sensitive data in your research? If yes, welcome to a 1-day introduction to handling sensitive data on the UPPMAX cluster, Bianca. We will tell you about NAISS-SENS, how to login to Bianca, transfer files via wharf, basics of the SLURM workload manager and the module system. The workshop is intended for beginner users of the Bianca cluster. You do not need to be a member of a NAISS-SENS project in order to join the workshop. A SUPR course project will be available to all participants. The workshop will consist of both lectures and exercise sessions. When: September 15, 2025 Where: online via Zoom For more information and registration please visit: https://docs.uppmax.uu.se/courses_workshops/bianca_intro/. --- **Online training workshop: Basic Singularity/Apptainer workshop** 9:15-12:00, 13:15-16:00 - 13 October 2025. The online workshop is an introduction to the basic concepts of containerized software environment solutions within the Singularity framework https://sylabs.io/singularity/. During the workshop you will have the opportunity to follow the interactive guide on - how to run Singularity containers - how to build your own - good (and bad) practices on designing and building Singularity recipes - build and/or host container remotely and what are the limitations To fully benefit from the workshop, basic Linux system administration experience is highly desirable i.e. knowledge of package management and common tools for building and/or managing software: git, pip, conda, wget, curl … When: 13 October, 2025 Where: online via Zoom Web page: https://docs.uppmax.uu.se/courses_workshops/singularity/ Registration: https://forms.gle/6oA4AKBaF6JmVQ2L6 --- CodeRefinery events Save the date: CodeRefinery tools workshop (online) When: September 9-11 2025 + 6 following Wednesdays New format: September 9-11 - focus on Git, while the following 6 Wednesdays will cover: reproducible research, documentation, testing, and more. Registration opening soon https://coderefinery.org/workshops/upcoming/. --- University events **On-site course: Introduction to Linux and UPPMAX, Uppsala, 25-27 August, 2025** This 3-day course provides an introduction to the high-performance computing (HPC) environment offered at UPPMAX. It offers an overview on how the systems work and covers skills from basic Linux usage to more advanced tips and tricks. The lectures covering Linux and bash scripting are cluster-agnostic and may be attended by non-UPPMAX users as well. When: August 25-27, 2025 Where: EBC, Uppsala For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/uppmax_intro_course/. --- ## week 15, 2025 Whisper update: New event: **Online workshop: Transferring Files to/from HPC Clusters, May 16, 2025** In this 3-hour workshop you learn to transfer files to and from Swedish academic HPC clusters. We will cover graphical as well as terminal tools and you will work highly interactively. A log in session will be included as well. At the end of the day, you should be comfortable in transferring files between your local computer and a cluster and cross-clusters, and choosing the right tools for your use cases. The workshop is intended for beginner users but with some Linux experience. You do not need to be a member of a NAISS project in order to join the workshop. A course project on one of the NAISS clusters will be available to those. When: Tuesday, May 16 2025, 09:00-12:00 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/naiss_transfer/. ## week 13, 2025 New event: Online hackathon: Bianca In-Depth: Improve Your Handling of Sensitive Research Data, 23 May Are you already working with sensitive data in your research and feel that your workflows can be improved? If yes, welcome to 1-day hackathon where you'll learn smarter ways of working on the Bianca cluster. We will tell you how to do file transfer from a terminal, advanced Slurm, using IDEs (e.g. RStudio), and installing custom software and packages. To attend this event, we expect you to be able to login to Bianca, submit a simple Slurm batch job, and know the basics of file transfer. A NAISS-SENS course project will be available to all participants. When: Friday, May 23, 9.00-16.00 Where: online via Zoom For more information and registration please visit: https://docs.uppmax.uu.se/courses_workshops/bianca_intermediate/. ## week 07, 2025 (sent) Dear Joachim, **Re-runs:** **NAISS training** Online course: Introduction to Python, March 4, 2025 Online workshop: Transferring Files to/from HPC Clusters, 7 March 2025 Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 19 March 2025 Online course: Introduction to running R, Matlab, and Julia in HPC, 24-26 March 2025 **CodeRefinery** Online workshop: CodeRefinery workshop, March 25-27, and April 1-3, 2025 **University events** Monthly Workshop Series: Whisper Transcription demonstration note: the Feb 4 instance is past; March 4, April 4, May 5 left **New NAISS events:** Online training course: Using Python in an HPC environment, 24-25 and 28-29 April 2025 input sent by Birgitte Online course: Programming Formalisms, 5-9 May 2025 ad further below, registration to open during the day Best regards, Diana ============================================================================================= **Online course: Programming Formalisms, 5-9 May 2025** *Collaboration between UPPMAX and NBIS* The goal of this highly-interactive 5-day course is to be able to develop academic software that you can trust to be 'good enough'. We assume you have written code 'that (sometimes) just works'. The course follows a formal development process from start to finish, with a selection of topics and best practices we think are most important, with the goal of developing academic software that is actually good enough. When: May 5-9 from 9:00-16:00 each day Where: online via Zoom More info and registration, please visit https://docs.uppmax.uu.se/courses_workshops/programming_formalisms/. ============================================================================================= ## week 02, 2025 (sent) Dear Joachim, **Re-runs:** - [x] Awk workshop - [x] Basic Singularity Running and Building Singularity Containers **R/Julia/Matlab** I understood that Birgitte has sent you text for this workshop. Please add the UPPMAX link https://docs.uppmax.uu.se/courses_workshops/R_matlab_julia/ to it. **New events:** - [x] Introduction to Linux and UPPMAX - [x] Introduction to Python - [x] Transferring Files to/from HPC Clusters - [x] Introduction to Bianca: Handling Sensitive Research Data Please find the advertisement text to the new events further below. Best regards, Diana --- **Online course: Introduction to Linux and UPPMAX, February 10-12, 2025** This 3-day course provides an introduction to the high-performance computing (HPC) environment offered at UPPMAX. It offers an overview on how the systems work and covers skills from basic Linux usage to more advanced tips and tricks. The lectures covering Linux and bash scripting are cluster-agnostic and may be attended by non-UPPMAX users as well. When: February 10-12, 2025 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/uppmax_intro_course/. --- **Online course: Introduction to Python, March 4, 2025** This 1-day course helps you get started with Python, by working through an online and free book. We make use of the UPPMAX HPC cluster to write and run Python code, but you may use a different machine if you prefer. The pace of this highly interactive course is set by the majority of learners, ensuring that any complete beginner has enough time for exercises. At the end of the day, you should feel comfortable with the basics of Python and feel familiar to a book on Python to help you on your next steps. When: Tuesday, March 4, 2025, 09:00-16:00 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/intro_to_python/. --- **Online workshop: Transferring Files to/from HPC Clusters, March 7, 2025** In this 3-hour workshop you learn to transfer files to and from Swedish academic HPC clusters. We will cover graphical as well as terminal tools and you will work highly interactively. At the end of the day, you should be comfortable in transferring files between your local computer and a cluster and cross-clusters, and choosing the right tools for your use cases. The workshop is intended for beginner users but with some Linux experience, see the course link below. You do not need to be a member of a NAISS project in order to join the workshop. A course project on one of the NAISS clusters will be available to those. When: Tuesday, March 7 2025, 09:00-12:00 Where: online via Zoom For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/naiss_transfer/. --- **Online workshop: Introduction to Bianca: Handling Sensitive Research Data, March 19, 2025** Are you just beginning to work with sensitive data in your research? If yes, welcome to a 1-day introduction to handling sensitive data on the UPPMAX cluster, Bianca. We will tell you about NAISS-SENS, how to login to Bianca, transfer files via wharf, basics of the SLURM workload manager and the module system. The workshop is intended for beginner users of the Bianca cluster. You do not need to be a member of a NAISS-SENS project in order to join the workshop. A SUPR course project will be available to all participants. The workshop will consist of both lectures and exercise sessions. When: March 19, 2025 Where: online via Zoom For more information and registration please visit: https://docs.uppmax.uu.se/courses_workshops/bianca_intro/. --- ## week 38 Re-run: Basic Singularity: Running and Building Singularity Containers (UPPMAX + HPC2N) Re-run: R/Python/Julia/Matlab (UPPMAX + HPC2N + LUNARC) and the 3 new events below --- **Online hackathon: Bianca In-Depth: Improve Your Handling of Sensitive Research Data, 11 November** Are you already working with sensitive data in your research and feel that your workflows can be improved? If yes, welcome to 1-day hackathon where you'll learn smarter ways of working on the Bianca cluster. We will tell you how to do file transfer from a terminal, advanced SLURM, using IDEs (e.g. RStudio), and installing custom software and packages. To attend this event, we expect you to be able to login to Bianca, submit a simple Slurm batch job, and know the basics of file transfer. A NAISS-SENS course project will be available to all participants. When: Monday, November 11, 9.00-16.00 Where: online via Zoom For more information and registration please visit: https://www.uu.se/en/centre/uppmax/study/courses-and-workshops/bianca-hackathon ============================================================================================= **Online course: Python for Scientific Computing, 5-7 November** *Organized by Aalto University, CodeRefinery, and partners* This is a medium-advanced course in Python tools such as NumPy, SciPy, Matplotlib, and Pandas. It is suitable for people who have a basic understanding of basic Python and want to know some internals and important libraries for science. Read the learner personas to see if the course is right for you. The course streamed via Twitch (the CodeRefinery channel) so that anyone may follow along without registration. There is a "Notes" link (collaborative edited notes) which is used for asking questions during the course. The course is organized by Aalto Scientific Computing in collaboration with CodeRefinery, and multiple Nordic partners. For more information and registration, please visit: https://scicomp.aalto.fi/training/scip/python-for-scicomp-2024/. ============================================================================================= **Online course: Programming Formalisms, 18-22 November** *Collaboration between UPPMAX and NBIS* This full 5-day course aims to give scientists, bioinformaticians and other research engineers with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The course aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance. We will cover a formal development process form start to finish. We use Test-Driven Development as a good example of a development process, requirements modeling, risk assessment and structured design. Some of the topics covered are modular development and (code) reusability, testing and optimization. We will cover theory with bridging practical examples and applications to enhance the theoretical understanding of the principles. When: November 18-22, onboarding: November 15 For more information and registration, please visit: https://www.uu.se/en/centre/uppmax/study/courses-and-workshops/programming-formalisms. ============================================================================================= ## Week 35 Re-run: Online CodeRefinery workshop, 10-12 and 17-19 September 2024 --- **Rackham2Dardel Drop-in** UPPMAX and PDC staff welcome you to the Rackham2Dardel Drop-in When: every Tuesday at 11:15 Where: via Zoom: https://uu-se.zoom.us/j/64896912764 Please join us if you need assistance logging in to Dardel or migrating your data. --- **Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 25 September 2024** Are you just beginning to work with sensitive data in your research? If yes, welcome to a 1-day introduction to handling sensitive data on the UPPMAX cluster, Bianca. We will tell you about NAISS-SENS, how to login to Bianca, transfer files via wharf, basics of the SLURM workload manager and the module system. The workshop is intended for beginner users of Bianca. You do not need to be a member of a NAISS-SENS project in order to join the workshop. A SUPR course project will be available to all participants. The workshop will consist of both lectures and exercise sessions. When: Wednesday, September 25 Where: online via Zoom For more information and registration please visit: https://www.uu.se/en/centre/uppmax/study/courses-and-workshops/bianca-intro. --- **Online workshop: Basic Singularity: Running and Building Singularity Containers, 16 October, 2024** *Collaboration between UPPMAX and HPC2N* The online workshop is an introduction to the basic concepts of containerised software environment solutions within the Singularity framework https://sylabs.io/singularity/. During the workshop you will have the opportunity to follow the interactive guide on * how to run Singularity containers * how to build your own * good (and bad) practices on designing and building Singularity recipes * build and/or host container remotely and what are the limitations To fully benefit from the workshop, basic Linux system administration experience is highly desirable i.e. knowledge of package management and common tools for building and managing software: git, pip, conda, wget, curl, etc. Please follow the instructions at https://pmitev.github.io/UPPMAX-Singularity-workshop/installation/ to install Singularity on your computer before the workshop. When: Wednesday, October 16, 2024 Where: online via Zoom For more information and registration, please visit: https://www.uu.se/en/centre/uppmax/study/courses-and-workshops/basic-singularity. --- ## Older Advertisements --- **Online workshop: "Awk Workshop", August 22-23, 2024** Awk is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool. This two-day workshop aims to promote and demonstrate the flexibility of the tool, where the overhead of more sophisticated approaches and programming languages is not worth the bother. Learn how to use Awk as an advanced grep command, capable of arithmetic selection rules with control over the content of the matched lines perform simple conversions, analysis or filter you data on the fly making it easy to plot or read in your favorite research tool handle and take advantage of data split over multiple file data sets use Awk as simple function or data generator perform simple sanity checks on your results. The workshop aims to promote the awk tool for use in everyday research work and urges you to find solutions yourself rather than expecting ready-made ones. The material given during the seminar will not be a complete guide or a manual but rather an overview of the capabilities, particular strengths, and common disadvantages. When: August 22-23, 2024 Where: online For more information and registration, please visit: https://www.uu.se/en/centre/uppmax/study/courses-and-workshops/awk-workshop. --- **CodeRefinery Train the Trainer workshop, 4 sessions, every Tuesday between August 13 and September 3, 2024** *Organised by CodeRefinery and partners, among which are NAISS, UPPMAX, PDC, and ENCCS* Do you teach the use of computers and computational tools? Are you curious about scaling your training and learn about tested and proven practices from CodeRefinery workshops and other trainers? Join us for the CodeRefinery train the trainer workshop: four self-contained sessions on tools and techniques for computational training offer a great chance to enhance your teaching skills and learn about new tools and practices. You may join only for the episodes that are useful for you. When: August 13, 20, 27, and September 3 Where: online via Zoom For more information and registration, please visit: https://coderefinery.github.io/train-the-trainer. --- **Online workshop: CodeRefinery workshop, September 10-12, and 17-19, 2024** *Organised by CodeRefinery and partners* Are you writing code and managing data for your research? Do you feel like wasting too much time on manual work? Do you struggle to understand and reuse older code? Join the CodeRefinery workshop 12-14 and 19-21 March 2024, for free and online. The workshop covers good coding practices, reproducible research principles, and using Git for collaboration. It consists of streamed lectures and breakout room exercises with team leaders. You may register individually or as a team. In-person exercise sessions are available in some locations. For registration and more information, please visit https://coderefinery.github.io/2024-09-10-workshop. --- **Online training: Programming Formalisms course, April 22 - 26, 2024** *Collaboration between UPPMAX and NBIS* This course aims to give life scientists, bioinformaticians, and other scientists with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The course aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance. We will cover an introduction to Algorithms and Data structures, Programming Paradigms especially structured and object oriented programming and to give a overview of other paradigms like functional programming. Modular development and (code) reusability, testing and optimisation. We will cover theory with bridging practical examples and applications to enhance the theoretical understanding of the principles. For registration and more information, please visit https://www.uppmax.uu.se/support/courses-and-workshops/programming-formalisms. --- **Online workshop: CodeRefinery workshop, March 12-14 and 19-21, 2024** *Organised by CodeRefinery and partners, among which are NAISS, UPPMAX, PDC, and ENCCS* Are you writing code and managing data for your research? Do you feel like wasting too much time on manual work? Do you struggle to understand and reuse older code? Join the CodeRefinery workshop March 12-14 and 19-21, 2024. Online and free of charge. The workshop covers good coding practices, reproducible research principles, and using Git for collaboration. It offers breakout room exercises with team leaders, and you can register as a team or volunteer as a team leader. But you can also follow on your own if you prefer. In-person exercise sessions are available in some locations. You can also help us by letting your colleagues or friends know. Optional: Bring your own code sessions on March 26 and April 2. For registration and more information, please visit https://coderefinery.github.io/2024-03-12-workshop.