Listed in the table below are the past, present, and future CompBioMed training materials and courses. If you would like to narrow down the courses listed, please select your preferred topic, what type of user you are, your skill level, and the format of courses and materials that you are interested in.
| Title of Training | Organisation, URL, Recurring | Training dates | Short Description | Topic | User Type | Skill Level | Course Type | Notes |
|---|---|---|---|---|---|---|---|---|
| CompBioMed-PerMedCoE: Short course on HPC-based Computational Bio-Medicine | BSC Link |
Yearly | The objective of this course is to give a panorama on the use of hpc-based computational mechanics in Biomedical Sciences. The training is delivered in collaboration with the centers of excellence CompBioMed2 and PerMedCoE. | Modelling + Simulation, Application Codes | Academia, Clinical, Industry | Novice, Semi, Expert | Online self-drive/tutorial | |
| HPC training for bone fracture modelling | USFD | Yearly | HPC component offered to year 4 UG and PGT students in Mechanical Engineering, Bioengineering and General Engineering students on the use of a local HPC system to decrease computational time as part of an exercise on mesh sensitivity analyses of femoral fracture through a patient-specific model. Around 15 students enrolled to the activty in 2022/23 and the component will be offered in the coming years too. | Modelling + Simulation, Advanced computing (HPC, GPU) | Academia | Expert, Novice | Face2Face | |
| HPC training for cardiovascular blood flow modelling | USFD | Yearly | HPC component offered to year 4 UG and PGT students in Mechanical Engineering and Bioengineering on the use of a local HPC system to decrease computational time as part of an exercise on mesh sensitivity analyses of blood flow through a patient-specific model of an cerebral artery affected by an intracranial aneurysm. Around 6 students enrolled to the activty in 2022/23 and the component will be offered in the coming years too. | Modelling + Simulation, Advanced computing (HPC, GPU) | Academia | Expert, Novice | Face2Face | |
| Message Passing with MPI | EPCC, University of Edinburgh Link |
N/A – online, self-drive | The course covers all the basic knowledge required to write parallel programs using this programming model, and is directly applicable to almost every parallel computer architecture. | Intro Computing | Academia, Clinical, Industry | Novice | Online self-drive/tutorial | |
| Shared Memory Programming with OpenMP | EPCC, University of Edinburgh Link |
N/A – online, self-drive | This course covers OpenMP, the industry standard for shared-memory programming, which enables serial programs to be parallelised easily using compiler directives | Intro Computing | Academia, Clinical, Industry | Novice | Online self-drive/tutorial | |
| QM/MM with GROMACS + CP2K | EPCC, University of Edinburgh Link |
N/A – online, self-drive | This course explains key aspects relating to the use of QM/MM for biomolecular simulation with these two codes and equips participants with the ability to start using GROMACS and CP2K | Intro Computing | Academia, Clinical, Industry | Novice | Online self-drive/tutorial | |
| QM/MM simulation with GROMACS + CP2K (Fully booked) | EPCC, University of Edinburgh Link |
22-23 April 2021 | BioExcel CoE course to equip participants to perform hybrid QM/MM
simulations using the molecular dynamics code GROMACS in combination with the quantum chemistry package CP2K through an interface developed by one of the instructors |
Application | Academia, Clinical, Industry | Semi, Expert | Webinar | |
| Efficient use of the HPE Cray EX Supercomputer ARCHER2 | EPCC, University of Edinburgh Link |
20-22 April 2021 | Understand the most optimal way to port, execute and optimize applications
for ARCHER2. The workshop is a mixture of lectures and practical hands-on sessions. Example exercises will be provided but attendees are encouraged to bring their own applications. |
Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) |
Academia, Clinical, Industry | Novice, Semi, Expert | Webinar | |
| Shared Memory Programming with OpenMP | EPCC, University of Edinburgh Link |
N/A – online, self-drive | An introduction to the fundamental concepts of the shared variables model,
followed by the syntax and semantics of OpenMP and how it can be used to parallelise real programs. |
Advanced computing (HPC, GPU) | Academia, Clinical, Industry | Novice, Semi, Expert | MOOC | |
| International School on In silico Trials | UNIBO Alma Mater Studiorum - Università di Bologna | TBD | TBD | Modelling + Simulation | Academica, Clinical | Novice, Semi | Webinar | |
| Why Biology Matters? The Genome and You | UPF Link |
By exploring genomes, we can develop a more detailed biological
understanding of ourselves. This course focuses on building your knowledge of the genome, including concepts of genetic inheritance and how traits are transmitted from one generation to the next. You will learn the type of information the genome provides and the social and philosophical implications of genomes in the future. It’s encouraged, but not required, for you to have completed Why Biology Matters: Basic Concepts before this course. |
Academia | Novice | MOOC | |||
| Why Biology Matters? Basic concepts | UPF Link |
We often read news stories based on biology that we don’t understand
well enough to form an opinion about. To be able to interpret complex biological concepts such as genetic determinism, cloning, genetic engineering, the fight against ageing, eugenics, artificial selection or intelligence inheritance we need knowledge that we may not have. That’s where this online course can help. It provides a basic introduction to the biology behind these ideas, - using lessons and interviews with experts - in order to understand the implications of them for the fields of the social sciences and humanities |
Academia | Novice | MOOC | |||
| Palabos Summer School 2021 | UNIGE Link |
7-9 June 2021 | The Palabos Summer School 2021 covers selected topics in
Lattice Boltzmann theory and a practical introduction to the open-source Palabos software library. Participants should have prior exposure to the Lattice Boltzmann Method and Computational Fluid Dynamics. Typical participants could be PhD researchers who are already 1-2 years into their PhD or PostDocs (LB beginners are instead referred to Week 5 of our Mooc) |
Application | Academia, Industry | Semi, Expert | Webinar | |
| PATC: Short course on HPC-based Computational Bio-Medicine | BSC Link |
16-19 February 2021 | CompBioMed and PerMedCoE present PRACE training for computational bio-medicine. | Application, Modelling + Simulation | Academia, Clinical, Industry | Novice, Semi | Webinar | |
| Free Energy Calculations from Molecular Simulations: Applications in Life and Medical Sciences |
CompBioMed / BioExcel Link |
30-31 May 2017 | Prediction of ligand-protein binding affinities: theory, algorithms and implementation on high performance architectures |
Modelling + Simulation | Academia, Clinical, Industry | Semi, Expert | Face2Face | |
| GPU Programming with CUDA | EPCC, University of Edinburgh Link |
26-27 November 2018 (Imperial College, London) 3-4 April 2019 (Birmingham) Link | Graphics Processing Units (GPUs) were originally developed for computer gaming and other graphical tasks, but for many years have been exploited for general purpose computing in a number of areas. They offer advantages over traditional CPUs because they have greater computational capability, and use high-bandwidth memory systems (memory bandwidth is the main bottleneck for many scientific applications). This introductory course will describe GPUs, and the advantages they offer. It will teach participants how to start to program GPUs, which cannot be used in isolation, but are usually used in conjunction with CPUs. Important issues affecting performance will be covered. The course focuses on NVIDIA GPUs, and the CUDA programming language (an extension to C/C++ or Fortran). Please note the course is aimed at application programmers; it does not consider machine learning or any of the packages available in the machine learning arena. |
Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) |
Academia, Industry | Semi, Expert | Face2Face | |
| Supercomputing (EPCC-SupComp) | EPCC, University of Edinburgh Link |
6 March 2017 for 5 weeks 28 August 2017 for 5 weeks February 2018 for 5 weeks 24 September 2018 for 5 weeks |
This free online course will introduce you to what supercomputers are, how they are used and how we can exploit their full computational potential to make scientific breakthroughs. Over five weeks, we’ll look at; Supercomputers: introducing supercomputing terminology and some of the largest machines in the world; Parallel computers: how they are built from hundreds of thousands of CPUs, each similar to those in a desktop PC; Parallel computing: using parallel processing to harness the power of all of those CPUs for a single calculation; Computer simulation: how we can perform virtual experiments to make real-life predictions; Case studies: how supercomputing is making scientific breakthroughs that were never possible before. |
Modelling + simulation Intro Computing |
Academia, Clinical, Industry | Novice | MOOC | |
| Scientific Computing (EPCC SciComp) |
EPCC, University of Edinburgh Link |
31 May, 7, 14, 21 June 2017 | This course covers the fundamental concepts of numerical simulation, and how modern parallel supercomputers are used in computational science. At the end of the course, attendees should be able to: explain the motivation for the use of parallel supercomputers in computational science; describe the main models of parallel programming and propose parallelisation methods for standard problems; understand the way real numbers are stored on a computer and the way that this affects the accuracy of results; explain why random numbers are used in many simulations. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Clinical, Industry | Novice, Semi | Face2Face | |
| Message Passing Programming with MPI (EPCC MPPwMPI) |
EPCC, University of Edinburgh Link |
24-26 April 2019 (Southampton) Link 17-19 July 2019 (Edinburgh) Link |
Video recordings of all the MPI lectures from the 2014 ARCHER Associated course materials including slides, exercises and coding examples |
Advanced computing (HPC, GPU) | Academia, Industry | Expert | Online self-drive | |
| Parallel Design Patterns | EPCC, University of Edinburgh Link |
6-8 November 2018 (University of Oxford) | If you were given a serial problem, conceptually, how would you go about splitting it up into many different parts that could run concurrently on the latest parallel computers? The good news is that you don't need to reinvent the wheel. Instead, there are many different approaches (called parallel patterns) that have been developed by the community and can be used in a variety of situations. These patterns apply equally well regardless of whether your problem is computational or data-driven. Understanding and being able to apply these patterns also helps in getting to grips with existing parallel codes and optimising poorly performing computation and data codes. Whilst the lectures take a top down approach, focusing on the patterns themselves, the practical exercises give the opportunity to explore the concepts by implementing pattern-based solutions to problems using common HPC technologies. |
Advanced computing (HPC, GPU) | Academia, Industry | Semi, Expert | Face2Face | |
| Scientific Programming with Python | EPCC, University of Edinburgh Link |
17-18 September 2018 (University of Durham) | This course is aimed at programmers with little or no Python knowledge seeking to learn how to use Python for scientific computing. We will introduce Python's fundamental scientific libraries numpy, scipy and matplotlib. We will also introduce how to interface Python with Fortran and C codes, along with parallel programming methods including MPI via mpi4py. This course is free to all academics. |
Intro Computing Modelling + Simulation |
Academia, Industry | Novice, Semi | Face2Face | |
| Software Carpentry (EPCC SC) | EPCC, University of Edinburgh Link |
9-10 May 2017 Link 16 - 17 Oct 2017 Link 11-12 Dec 2017 Link 26-27 Feb 2018 Link 18-19 June 2018 Link 10-11 June 2019 (York) Link |
Software Carpentry's goal is to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day workshop, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Industry | Novice, Semi | Face2Face | |
| Introduction to HPC (EPCC introHPC) |
EPCC, University of Edinburgh Link |
N/A – online, self-drive | This material covers topics relevant to HPC and Parallel Computing as a whole, although ARCHER is often used as a specific example. All material comes from a run of the Hands-on Introduction to HPC course, held at EPCC in summer 2016. All the example codes should be easily portable to other systems with appropriate changes to Makefiles and batch submission scripts. If you have any questions, please contact the support@archer.ac.uk. See this playlist on the ARCHER YouTube channel which is a complete recording of the course. Slides are available from the Past Course Materials Repository. Exercises are available from the Past Course Materials Repository. |
Advanced computing (HPC, GPU) | Academia, Industry | Semi | Online self-drive | |
| Introduction to ARCHER (EPCC Archer) |
EPCC, University of Edinburgh Link |
N/A | This material gives details on the ARCHER hardware and software environment, and assumes familiarity with general HPC concepts (e.g. as covered in Introduction to HPC). |
Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) |
Academia, Industry | Semi | Online self-drive | |
| Handson Introduction to High Performance Computing (EPCC h-onHPC) |
EPCC, University of Edinburgh Link |
30 November - 1 December 2016 Link 10-11 July 2017 Link 10-11 May 2018 Link 2-3 July 2018 Link 9 October 2018 Link 17-18 January 2019 (Aberdeen) Link 15-16 July 2019 (Edinburgh) Link |
High-performance computing (HPC) is a fundamental technology used in solving scientific problems. Many of the grand challenges of science depend on simulations and models run on HPC facilities to make progress, for example: protein folding, the search for the Higgs boson and developing nuclear fusion. The course runs for 2 days. The first day covers the the basic concepts underlying the drivers for HPC development, HPC hardware, software, programming models and applications. The second day will provide an opportunity for more practical experience, information on performance and the future of HPC. This foundation will give the you ability to appreciate the relevance of HPC in your field and also equip you with the tools to start making effective use of HPC facilities yourself. The course is delivered using a mixture of lectures and hands-on sessions and has a very practical focus. During the hands-on sessions you will get the chance to use ARCHER with HPC experts available to answer your questions and provide insight. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Industry | Novice, Semi | Face2Face | |
| Hands-on Introduction to HPC for Life Scientists |
EPCC, University of Edinburgh Link |
29 November - 1 December 2016 Link | High-performance computing (HPC) is a fundamental technology used to solve a wide range of scientific research problems. Many important challenges in science such as protein folding, the search for the Higgs boson, drug discovery, and the development of nuclear fusion all depend on simulations, models and analyses run on HPC facilities to make progress. This course introduces HPC to life science researchers, focusing on the aspects that are most important for those new to this technology to understand. It will help you judge how HPC can best benefit your research, and equip you to go on to successfully and efficiently make use of HPC facilities in future. The course will cover basic concepts in HPC hardware, software, user environments, filesystems, and programming models. It also provides an opportunity to gain hands-on practical experience and assistance using an HPC system (ARCHER, the UK national supercomputing service) through examples drawn from the life sciences, such as biomolecular simulation. The course is delivered using a mixture of lectures and hands-on sessions and has a very practical focus. During the hands-on sessions you will get the chance to use ARCHER with HPC experts available to answer your questions and provide insight. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Industry | Novice, Semi | Face2Face | |
| HPC Carpentry | EPCC, University of Edinburgh Link |
6-7 December 2018 | This course introduces accessing remote advanced computing facilities via the command line and High Performance Computing (HPC). After completing this course, participants will: Understand motivations for using HPC in research Understand how HPC systems are put together to achieve performance and how they differ from desktops/laptops Know how to connect to remote HPC systems and transfer data Be able to use the Bash command line on remote systems Know how to use a scheduler to work on a shared system Be able to use software modules to access different HPC software Be able to work effectively on a remote shared resource This course is being run with support from the ARCHER National Supercomputing Service and The Turing Institute. |
Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) |
Academia, Industry | Novice, Semi | Face2Face | |
| Data Carpentry (EPCC DC) | EPCC, University of Edinburgh Link |
11-12 May 2017 Link 1-2 June 2017 Link 20-21 September 2018 Link 8-9 January 2019 Link |
In many domains of research, the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analysing and sharing data. Data Carpentry aims to teach the skills that will enable researchers to be more effective and productive. The course is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools. |
Modelling + simulation Advanced computing (HPC, GPU) Data Management |
Academia, Clinical, Industry | Novice, Semi, Expert | Face2Face | Clinical users are only offered Data Management |
| Hands-on Porting and Optimisation Workshop: Making the most of ARCHER (EPCC h-on POW) |
EPCC, University of Edinburgh Link |
4 April 2017 | Instead of a typical ARCHER course consisting of alternating lectures + practicals, this workshop is designed to provide an opportunity for attendees to gain individually tailored hand-on help and advice from the ARCHER team / HPC specialists and to ask questions pertaining directly to your use of ARCHER. Each attendee will be assigned a technical advisor. This advisor will work closely with you throughout the day to help run your application and any associated essential software on ARCHER and to advise on how the system can be used most efficiently, to help evaluate the application's performance (providing guidance on the use of available tools if appropriate), and to suggest possible changes that could be made to the code to improve its performance. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Industry | Novice, Semi | Face2Face | |
| Introduction to Scientific Computing with Python (EPCC Pyth) |
EPCC, University of Edinburgh Link |
24-25 April 2017 Link 19-20 June 2017 Link |
This course is aimed at programmers with basic Python knowledge seeking to learn how to use Python for scientific computing. We will introduce Python's fundamental scientific libraries such NumPy, SciPy and Matplotlib. We will also introduce how to interface Python with Fortran and C codes, and outline how to implement message-passing in Python with mpi4py. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Industry | Novice, Semi | Face2Face | |
| Message Passing Programming with MPI (EPCC MPPwMPI) |
EPCC, University of Edinburgh Link |
15–17 February 2017 Link 19–21 April 2017 Link 12-13 July 2017 Link 31 August -1 September 2017 Link 11-12 September 2017 Link 11-13 April 2018 Link 4-6 July 2018 Link 28-30 November 2018 Link |
The world's largest supercomputers are used almost exclusively to run applications which are parallelised using Message Passing. This course covers all the basic knowledge required to write parallel programs using this programming model, and is directly applicable to almost every parallel computer architecture. Parallel programming by definition involves co-operation between processors to solve a common problem. The programmer has to define the tasks that will be executed by the processors, and also how these tasks are to synchronise and exchange data with one another. In the message-passing model the tasks are separate processes that communicate and synchronise by explicitly sending each other messages. All these parallel operations are performed via calls to some message-passing interface that is entirely responsible for interfacing with the physical communication network linking the actual processors together. This course uses the de facto standard for message passing, the Message Passing Interface (MPI). It covers point-to-point communication, non-blocking operations, derived datatypes, virtual topologies, collective communication and general design issues. The course is taught using a variety of methods including formal lectures, practical exercises, programming examples and informal tutorial discussions. This enables lecture material to be supported by the tutored practical sessions in order to reinforce the key concepts. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Industry | Semi | Face2Face | |
| OpenMP Online | EPCC, University of Edinburgh Link |
Week 1 - Wed, 24 October 2018 Week 2 - Wed, 31 October 2018 Week 3 - Wed, 7 November 2018 Week 4 - Wed, 21 February 2019 |
Almost all modern computers now have a shared-memory architecture with multiple CPUs connected to the same physical memory, for example multicore laptops or large multi-processor compute servers. This course covers OpenMP, the industry standard for shared-memory programming, which enables serial programs to be parallelised easily using compiler directives. Users of desktop machines can use OpenMP on its own to improve program performance by running on multiple cores; users of parallel supercomputers can use OpenMP in conjunction with MPI to better exploit the shared-memory capabilities of the compute nodes. This course will cover an introduction to the fundamental concepts of the shared variables model, followed by the syntax and semantics of OpenMP and how it can be used to parallelise real programs. Hands-on practical programming exercises will be included, with access to HPC provided for the duration of the course. |
Advanced computing (HPC, GPU) | Academia, Industry | Semi | Webinar | |
| Practical Introduction to Data Science - MOOC (EPCC-PiDSmooc) |
EPCC, University of Edinburgh Link |
Yearly | This online course will introduce the important ideas and concepts of data science and will allow you to gain the basic skills that would be expected of a data scientist. It has two broad themes, namely the importance of looking after data (so that it can be analysed) and data analytics techniques. It's a practical course so you will get to try out these techniques and explore these ideas using common Data Science tools and languages including R and Python. This course in an assessed course, and on completion of this course you will receive a Postgraduate Professional Development Award of Academic Credit (corresponding to 20 SCQF credits) from the University of Edinburgh. |
Data Management | Academia, Clinical, Industry | Novice | MOOC | |
| Practical Introduction to High Performance Computing - MOOC (EPCC PiHPCmooc) |
EPCC, University of Edinburgh Link |
Yearly | Modern supercomputers are parallel computers, gaining their power from many thousands of individual processors. Developing software to run on these systems requires using new parallel programming technologies. The course will cover all the fundamental concepts that underpin modern HPC. The course is practical in the sense that you will explore these topic by running parallel programs on real HPC systems such as the UK national supercomputer ARCHER (link is external). The same techniques can also be applied to smaller systems such as multi-core desktops, graphics processors and computing clusters. |
Modelling + simulation Advanced computing (HPC, GPU) |
Academia, Clinical, Industry | Novice | MOOC | |
| Introduction to Spark for Data Scientists |
EPCC, University of Edinburgh | 10-11 January 2019 (Edinburgh) Link | Apache Spark is an open-source framework for cluster computing, ideal for large-scale parallel data processing, that is designed for performance and ease-of-use. It is faster and simpler to use than Hadoop MapReduce, providing a rich set of APIs in Python, Java and Scala. This hands-on course will cover the following topics: Introduction to Spark Map, Filter and Reduce Running on a Spark Cluster Key-value pairs Correlations, logistic regression Decision trees, K-means |
Large scale data processing Data Management Big Data |
Academia, Industry | Semi | Face2Face | |
| Introduction to Unix (Intro Unix) | SURF Link |
On request | You'll learn about the structure of Unix operating systems and the basic commands. You'll practice working with the command line and giving a number of commands. Anyone who wants to have sufficient basic knowledge of Unix to be able to work with it on the national compute cluster Lisa or on the Cartesius supercomputer, for example. You are familiar with the Windows or OS X operating systems. |
Intro Computing | Academia, Clinical, Industry | Novice | Face2Face | |
| Introduction to data management | SURF Link |
On request | In this course we will give you an overview of the services available for researchers in the Netherlands. Specifically, we will focus on SURF’s archive service, a service easily reachable from SURF’s compute infrastructure. In the first part of the hands-on you will gather experience with graphical user interfaces that help you to move your data and you will learn about their limitations. In the second part of the hands-on you will become familiar with data transfer protocols and their command line tools. Furthermore, we will show you tools to organise and package your data and how you can incorporate data movement and management into your workflows and computational pipelines. Anyone who would like to get started with data management applications. You are familiar with the basics of programming and the Unix command line. |
Data Management | Academia, Clinical, Industry | Novice | Face2Face | |
| Parallel Programming with MPI/OpenMP |
SURF Link |
On request | Introduction to parallel programming with MPI and OpenMP. Target: Anyone with basic experience in high performance computing. |
Advanced Computing | Academia, Clinical, Industry | Semi | Face2Face | |
| Introduction to Visualization (Visual) | SURF Link |
On request | The concept of visualizing scientific data will be explained. Visualization gives you insights into remarkable phenomena in data and helps you check the accuracy of the results and present and communicate results in an understandable manner. You can, for example, display your research results using remote visualization, where datasets are too big and complex to be visualized locally (on your own laptop). Different types of data require different visualization methods, techniques and tools. You'll be given examples of 2D and 3D simulations, geographical data and networks. The visualizations comprise images and video materials and even interactive visualizations on the web. You'll practice with existing research data but you can also bring your own data with you. Anyone who would like to find out how visualization helps in understanding research data. You are familiar with scientific research. |
Visualization | Academia, Clinical, Industry | Semi | Face2Face | |
| Introduction to Machine Learning (Machine Learn) |
SURF Link |
On request | You will learn how to login and use the GPU nodes on the Cartesius supercomputer for training large neural networks. You will learn how to use several libraries and tools designed to facilitate experiments and research in the area of machine-learning. Anyone who would like to find out more about machine learning and is familiar with Unix command line and have experience in bash and python. |
Advanced Computing | Academia, Industry | Expert | Face2Face | |
| Getting started with HPC Cloud (HPC cloud) |
SURF Link |
On request | You'll learn to work with SURF's HPC Cloud. The course includes everything from logging in to the virtual environment via OpenNebula to running a simple MPI program and the execution of distributed processes. You'll perform practical tasks on the HPC Cloud and set up a cluster yourself. Anyone who would like to get started with HPC Cloud. You are familiar with the basics of programming and the Unix command line. |
Cloud | Academia, Clinical, Industry | Semi | Face2Face | |
| Getting started with the Hadoop cluster (Hadoop) |
SURF Link |
On request | You'll learn how to work with SURF's Hadoop cluster. And how to compute using MapReduce, Apache Spark, Hive, Pig and HBase. You'll practice on the Hadoop cluster yourself and locally on a virtual machine (VM). Anyone who would like to get started with the Hadoop cluster so that they can perform Big Data analyses. You are familiar with the basics of programming and the Unix command line. |
Big Data | Academia, Clinical, Industry | Semi | Face2Face | |
| Getting started with Grid computing (GRID) |
SURF Link |
On request | You'll learn how to work with SURF's Grid computing clusters and the associated data storage systems. You'll gain an overview of the basic concepts of Grid computing such as parallelizing on the Grid, task distribution, monitoring and data management. This course is also available online and you can complete it in your own time. Anyone who would like to get started with Grid computing. You are familiar with the basics of programming and the Unix command line. |
Advanced Computing | Academia, Clinical, Industry | Semi | Face2Face | |
| Getting started with the Cartesius/Lisa (HPC) |
SURF Link |
On request | You'll learn how to work with the Cartesius supercomputer and the national compute cluster Lisa. We explain when you need the supercomputer and what applications feature on the Lisa cluster. This hands-on course includes both an interactive part on the login nodes and a batch part on the worker nodes. You will use capability and capacity cluster computers. Anyone who would like to get started with Cartesius and Lisa. You are familiar with the basics of programming and the Unix command line. |
Intro Computing | Academia, Clinical, Industry | Semi | Face2Face | |
| Getting started with iRODS and EUDAT data management (iRODS-EUDAT) |
SURF Link |
On request | You'll learn how to set up a data management infrastructure with applications such as iRODS (Integrated Rule-Oriented Data System) and PIDs (persistent identifiers). Through use cases you'll gain an understanding of how they work. You'll also practice with the applications yourself on virtual machines. We also present EUDAT (European Data Infrastructure)'s data management services. Anyone who would like to get started with data management applications. You are familiar with the basics of programming and the Unix command line. |
Data Management | Academia, Clinical, Industry | Semi | Face2Face | |
| Introduction to Cloud Computing for the VPH |
SURF Link |
30 January 2018 | In this webinar, we show what a Cloud computing environment is and how it can help with your research. You will learn how to set up and access your virtual machine, as well as to install software and run your simulations. As an example, we show how to configure and run openBF, a computational library for 1D blood flow simulations in straight elastic arteries, and how to visualise the output produced by the code. Target group: Anyone who would like to get started with cloud computing environment to execute workflows and simple programcs. You are familiar with the basics of programming and the Unix command line. |
Data Management | Academia, Clinical, Industry | Novice, Semi | Webinar | |
| From skin to metagomics: exploring your microbiome |
UCL Link |
Yearly | Participants will isolate genomic DNA from their skin bacteria and use state of the art NGS sequencing and computational resources to analyse the metagenome data obtained |
Intro Computing Linux command line Application codes (Python) How to get access to and how to use resources Advanced computing (HPC, GPU) Subject specific: molecularly-based medicine |
Clinical | Novice | Face2Face | |
| Modeling and Simulation of Natural phenomena |
UNIGE Link |
NA | This course gives you an introduction to modeling methods and simulation tools for a wide range of natural phenomena. The different methodologies that will be presented here can be applied to very wide range of topics such as fluid motion, stellar dynamics, population evolution. This course does not intend to go deeply into any numerical method or process and does not provide any recipe for the resolution of a particular problem. It is rather a basic guideline towards different methodologies that can be applied to solve any kind of problem and help you pick the one best suited for you. The assignments of this course will be made as practical as possible in order to allow you to actually create from scratch short programs that will solve simple problems. Although programming will be used extensively in this course we do not require any advanced programming experience in order to complete it. |
Modelling + Simulation | Academia, Clinical, Industry | Novice, Semi | Face2Face | Novice only available for Academia |
| CADMOS HPC course | UNIGE Link |
Yearly | Introduction to HPC, MPI and scientific applications | Advance computing | Academia, Industry | Novice, Semi | Face2Face | |
| PALABOS Tutorials | UNIGE Link |
NA | Tutorials on how to use the open-source lattice-boltzmann solver Palabos | Application | Academia, Industry | Novice, Semi, Expert | Face2Face | Expert only available for Industry |
| Lattice Boltzmann method for CompBioMed (incl. Palabos) |
UNIGE Link |
19 March 2018 | The webinar provides a general introduction to the lattice Boltzmann method for computational fluid dynamics, and shows how this tool is used efficiently for biomedical applications. The provided examples include a vertebroplasty and a hemodynamics solver,both based on the open-source library Palabos. The former simulates a cement injection process in vertebroplasty, and the latter the dynamics of blood flow after the insertion of a flow diverter in an artery with an aneurysm. Both tools work with patient-specific data and are intended as support tools for medical decision making. No prior knowledge in computational fluid dynamics or the lattice Boltzmann method is required. This webinar is delivered by the Scientific and Parallel Computing Lab, which is part of the Computer Science Department of the University of Geneva, and is directed by Prof. Bastien Chopard. The two main axes of research are Complex Systems and Bioinformatics. |
Modelling + simulation Application codes Advanced computing (HPC, GPU) |
Academia, Industry | Novice, Semi, Expert | Webinar | Expert only available for Industry |
| Sensitivity analysis of a strongly coupled cardiac electro-mechanical model |
UOXF Link |
20 March 2019 | This webinar describes the computational implementation of a complex and physiologically-detailed cardiac electro-mechanical model for human hearts. The model was developed within the framework of Alya, Barcelona Supercomputing Center’s HPC-based multi-physics software, and making use of the computational resources obtained from the PRACE project (pr1efz00). Some examples of ventricular geometries (monoventricular and biventricular) are presented and the results of a global sensitivity analysis, which evaluate the sensitivities of clinically relevant quantities of interest, are also shown. |
Application codes | Academia, Clinical, Industry | Semi, Expert | Webinar | |
| HPC simulations of cardiac electrophysiology using patient specific models of the heart (using CHASTE and Alya) |
UOXF Link |
22 November 2017 | Webinar introducing the usage of Chaste focused on electrophysiological simulations at tissue and whole organ level |
Application codes | Academia | Novice, Semi | Webinar | |
| High-Throughput Molecular Dynamics (HTMD) workshop (UPF HTMD) |
UPF / Acellera Link |
10 – 11 November 2016 | The aim of this workshop is to learn the latest developments of high- throughput molecular dynamics simulations with practical lectures and real data and to give scientists the opportunity to exchange their experiences. Hands-on session and training is given using HTMD, a powerful programmable environment to prepare, handle, simulate and analyze molecular simulations, and efficient GPU-based MD simulations, and standard protocols to execute numerical experiments. At the end of the workshop, you will be able to apply what you have learned on your data/proteins. |
Modelling + simulation Subject specific: molecularly-based medicine Visualisation |
Academia, Industry | Novice, Semi | Face2Face, Webinar | |
| High Throughput Molecular Dynamics for Drug Discovery |
UPF Link |
25 October 2018 | Molecular dynamics (MD) simulations are used to capture dynamic processes of proteins across different timescales, with atomistic detail. The recent software and hardware innovations have decreased the computational cost of classical MD simulations, which can now be performed in a high-throughput manner. This has allowed MD simulations to play a relevant role in drug discovery. In this webinar we will talk about the advances and methodologies behind high-throughput simulations, and we will show how to easily prepare and set up a system to study protein-ligand binding and compute its binding properties. |
Modelling + simulation Subject specific: molecularly-based medicine Visualisation |
Academia, Industry | Novice, Semi | Webinar | |
| Introduction Computational Science | UvA Link |
Yearly | Introduction to the basic concepts of modelling and simulation | Intro computing Application codes (Python) |
Academia | Semi | Face2Face | |
| Stochastic Simulation | UvA Link |
Yearly | Monte Carlo methods in modelling and simulation | Modelling + Simulation | Academia | Semi | Face2Face | |
| Complex System Simulation | UvA Link |
Yearly | Modelling complex systems, network science, ABM, CA, etc. | Modelling + Simulation | Academia | Semi | Face2Face | |
| Scientific Computing | UvA Link |
Yearly | Numerically solving PDEs | Modelling + Simulation | Academia | Semi | Face2Face | |
| Computational Biology | UvA Link |
Yearly | Introduction to computational biology | Modelling + Simulation | Academia | Semi | Face2Face | |
| Minor Computational Science | UvA Link |
Yearly | introduction to programming in python, numerical math, modelling and simulation, and selected applications |
Modelling + Simulation | Academia | Semi | Face2Face | |
| Introduction to Computational Mechanics: Bioengineering Applications |
BSC Link |
14 February 2018 | Main concepts behind a simulation code. The Physical system and its Mathematical description. Discretization: algorithms and codes. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Introduction to HPC in Computational Modelling |
BSC / SURF Link |
14 February 2018 | This course explores the structure and characteristics of generic HPC systems, focusing on the aspects that are most important for scientists in order to run their simulations. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Computational Hemodynamics: From a notebook to HPC |
BSC / UvA Link |
14 February 2018 | In this lecture, we discuss the choice of techniques that on one hand allow us to model the behaviour of single cells accurately, and on the other hand can scale up to the level of macroscopic flows with millions of cells. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Parallel algorithms for Computational Mechanics |
BSC Link |
14 February 2018 | The first part of the seminar treats basic computer architecture and performance aspects. The second part deals with parallelization paradigms, at the node, chip and core levels. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Predicting the risk of fall - A computational modelling approach using CT2S |
BSC / USFD Link |
15 February 2018 | This session provides a brief overview of the state-of-the-art workflow, CT2S, or CT to Strength, developed in Sheffield, that would enable 3D quantitative assessment of long bones and their risks of fractures in the future. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Big Compute: HPC in the Cloud with Microsoft Azure |
BSC / Microsoft Link Yearly |
15 February 2018 | This workshop gives a tour of Cloud HPC - capabilities, challenges, solutions & best practices - from traditional "lift & shift" approaches to cloud native, all using Microsoft Azure. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Introduction to Computer-Aided Drug Design (CADD) and GPCR Modelling |
BSC / Evotec Link |
15 February 2018 | This session is an introduction to in-silico guided drug discovery, illustrated by examples from real drug discovery projects. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Innovations in HPC-training for medical, science and engineering students |
BSC / UCL Link |
15 February 2018 | This talk explores the way in which microbial communities (microbiomes) are characterised experimentally and how computational analyses performed using high-performance computing can provide insights into interactions between bacteria and the ecological communities in which they reside. Video |
Modelling + Simulation | Academia | Novice, Semi, Expert | Face2Face | |
| Data Visulization for Researchers Crash Course |
BSC Link |
16 February 2018 | This course gives an overview of the graphic design and information visualization principles used to create appealing and accurate data visualizations. |
Visualisation Data Management |
Academia | Novice, Semi, Expert | Face2Face | |
| High-Throughput Molecular Dynamics Simulations for Drug Discovery |
BSC / Acellera / UPF Link |
16 February 2018 | The session shows how MD simulations have become an excellent tool for drug discovery, thanks to the parallelzation of MD codes and the usage of GPU's. |
Visualisation Data Management |
Academia | Novice, Semi, Expert | Face2Face | |
| Fluid structure interaction applied to electromechanical models of the heart |
BSC Link |
16 February 2018 | This introductory talk starts with the mathematical and physical foundations of interface problems, particularly fluid structure interaction (FSI). |
Visualisation Data Management |
Academia | Novice, Semi, Expert | Face2Face | |
| HPC Multi-scale computational modelling using Alya Red |
BSC Link |
16 February 2018 | From an engineering point of view, Biological systems are amongst the most complex Physical systems in Nature. Multiscale, multiphysics, highly variable, large uncertainties, numerical issues, validation difficulties and extremely complex mathematical models are amongst the common features of computational biomechanics. Considering that all these problems usually show up altogether, the use of HPC-based simulations in biomechanics is a must. |
Modelling + simulation Application codes |
Academia | Novice, Semi, Expert | Face2Face | |
| Computational Biomechanics: trends in modelling and simulation |
BSC Link |
16 February 2018 | The aim of this lecture is to present an overview of the mechanics of soft tissues, focusing on continuum solid mechanics and computational perspectives. The essential ingredients of continuum mechanics are provided since they are the key in the modelling of soft biological tissues. |
Modelling + simulation Application codes |
Academia | Novice, Semi, Expert | Face2Face | |
| High Performance Computing for the VPH | CompBioMed Link |
04 September 2018 | The lectures target early phase researchers and aim to provide a short and concise introduction to HPC programming. All lectures are hands-on using Barcelona’s MareNostrum supercomputer. |
Modelling + simulation How to get access to and how to use resources (hands-on) Application codes |
Academia, Industry | Novice, Semi | Face2Face | |
| Introduction to Biomedical Applications on High Performance Computers |
EPCC, UvA Link |
07 June 2018 | This webinar introduces the fundamental concepts and basic tools of HPC environments, and includes an application example of flowing red blood cells in a vessel section. |
Modelling + simulation How to get access to and how to use resources (hands-on) Application codes |
Clinical, Academia, Industry | Novice | Webinar | |
| Message Passing with MPI | EPCC, UEDIN |
On request | The course covers all the basic knowledge required to write parallel programs using this programming model, and is directly applicable to almost every parallel computer architecture. | Advanced computing (HPC, GPU) | Clinical, Academia, Industry | Novice | Online self-drive | |
| Shared Memory Programming with OpenMP | EPCC, UEDIN |
On request | This course covers OpenMP, the industry standard for shared-memory programming, which enables serial programs to be parallelised easily using compiler directives | Advanced computing (HPC, GPU) | Clinical, Academia, Industry | Novice | Online self-drive | |
| QM/MM with GROMACS + CP2K | EPCC, UEDIN |
On request | This course explains key aspects relating to the use of QM/MM for biomolecular simulation with these two codes and equips participants with the ability to start using GROMACS and CP2K | Advanced computing (HPC, GPU) | Clinical, Academia, Industry | Novice | Online self-drive | |
| Hands-on Introduction to HPC | EPCC, UEDIN |
On request | This course aims to introduce the principles of high performance computing (HPC) systems, how they operate, and how we can utilise the computing power they can offer to model complex systems. This will start with a discussion of supercomputers (HPC systems), their purpose, hardware, and trends in computing. We will then cover material on the fundamentals of modern computers and how we can perform computations in parallel. This will lead into a discussion of how supercomputers derive their performance, and how distributed memory architecture is used in HPC systems. We will run through a concrete simulation example, discussing the details of the problem and how it can be modelled on a computer. We will then detail how parallel programming can be applied to problems to speed up a calculation, before discussing performance in parallel programs. Finally we will discuss how simulations are developed and used to make predictions, and some real world examples. Access to ARCHER2 is provided for participants to build and run the exercises. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing |
Clinical, Academia, Industry | Novice | Online self-drive | |
| HPC training for cardiovascular blood flow modelling | USFD | Yearly | HPC component offered to year 4 UG and PGT students in Mechanical Engineering and Bioengineering on the use of a local HPC system to decrease computational time as part of an exercise on mesh sensitivity analyses of blood flow through a patient-specific model of an cerebral artery affected by an intracranial aneurysm. Around 6 students enrolled to the activty in 2022/23 and the component will be offered in the coming years too. | Modellling + simulation | Academia | Novice, Expert | Face2Face | |
| HPC training for bone fracture modelling | USFD | Yearly | HPC component offered to year 4 UG and PGT students in Mechanical Engineering, Bioengineering and General Engineering students on the use of a local HPC system to decrease computational time as part of an exercise on mesh sensitivity analyses of femoral fracture through a patient-specific model. Around 15 students enrolled to the activty in 2022/23 and the component will be offered in the coming years too. | Modellling + simulation Advanced computing (HPC, GPU) |
Academia | Novice, Expert | Face2Face | |
| Using the DICE Services to move towards FAIR data in Computational Biomedical Research | SURF Link |
28 October 2021 | The main objective of this webinar is to show how the services of DICE is being used to achieve FAIR data within the CompBioMed community. Computational biomedical research is very data-intensive and compute-intensive and requires tools or platforms that facilitate large data storage, transfer and sharing. In this webinar, we give an overview of two workflows for data replication and data publication using existing services of DICE and EUDAT. These workflows facilitate managing active research data (i.e., data transfer, storage, and sharing) and preserving final research data (i.e., data archiving and publishing) within the community. We further demonstrate how these services operate and integrate with each other to align with international standards and approaches for FAIR data management. | Data Management | Clinical, Academia, Industry | Novice, Semi, Expert | Webinar | |
| Introduction to Supercomputing | SURF Link |
Monthly | In this course you will understand the main concepts of High-Performance Computing and get to know how to work with cluster systems. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing |
Academia, Industry | Novice, Semi | Webinar | |
| Introduction to SURF Research Cloud | SURF Link |
Monthly | In this course you will understand the main concepts of cloud computing and how to work with the Research Cloud system from SURF to run virtual machines on different platforms. | Cloud Computing How to get access to and how to use resources (hands-on) |
Academia, Industry | Novice, Semi | Webinar | |
| Introduction to Data Management, Research Drive and Yoda | SURF Link |
Quarterly | In this course you will understand the main concepts of data management and work with data-sharing facilities and metadata administration tools provided by SURF. Specific consultation of data-related problems will be provided upon request. | Data Management How to get access to and how to use resources (hands-on) |
Academia, Industry | Novice, Semi | Webinar | |
| Advanced Supercomputing | SURF Link |
Quarterly | In this course you will experience how to work in the most efficient way with cluster/supercomputing systems, from software installation to general indications on parallel programming. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing |
Academia, Industry | Semi, Expert | Webinar | |
| Basic Parallel Programming with MPI and OpenMP | SURF Link |
Yearly | In this course you will experience how to implement parallel codes on shared and distributed memory based on C/C++, Fortran or Python knowledge. This course is given with the materials kindly provided by HLRS (Dr. Rolf Rabenseifner) via the PRACE collaboration. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) |
Academia, Industry | Semi, Expert | Webinar | |
| MPI and OpenMP in Scientific Software Development | SURF Link |
Yearly | In this course you will experience how to work in the most efficient way with cluster/supercomputing systems, from software installation to general indications on parallel programming. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) |
Academia, Industry | Expert | Webinar | |
| Introduction to Deep Learning | SURF Link |
2-Yearly | In this course you will understand what to expect from machine learning tasks in general, and start working on Jupyter notebooks to implement and tune deep learning models. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) |
Academia, Industry | Novice, Semi | Webinar | |
| High-Performance Deep Learning | SURF Link |
2-Yearly | In this course you will experience how to work with large-scale deep learning models and exploit supercomputing power to the best extent on your training and testing tasks, using parallel model decomposition and cutting-edge techniques. You may bring your own questions on deep learning implementations for a short consultation round. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) |
Academia, Industry | Semi, Expert | Webinar | |
| CompBioMed-PerMedCoE: Short course on HPC-based Computational Bio-Medicine | BSC |
Yearly | The objective of this course is to give a panorama on the use of hpc-based computational mechanics in Biomedical Sciences. The training is delivered in collaboration with the centers of excellence CompBioMed2 and PerMedCoE. | Modelling + simulation, Application codes | Clinical, Academia, Industry | Novice, Semi, Expert | Online self-drive | |
| Data-Oriented C++ in Scientific Programming | UNIGE | On request | The MOOC teaches best practices for the development of efficient and maintainable code in data-intensive applications using the modern C++ language. Application areas are scientific simulation software, statistical data processing, and computer graphics. The course first presents the classical object-oriented approach to software development, with the use of class-based polymorphism, and illustrates typical performance shortcomings of this approach for large data processing. Course participants are then presented a “data-oriented” way to think about the code structure which resolves performance bottlenecks by putting the data at the center of the algorithm. These principles are extended to the efficient use of multi-threaded hardware, including multi-core CPUs and GPUs, using inherent parallel features of C++. | Advanced computing (HPC, GPU) | Academia, Industry | Semi, Expert | ||
| Advanced OpenMP | EPCC, UEDIN |
23 - 24 January 2024 | OpenMP is the industry standard for shared-memory programming, which enables serial programs to be parallelised using compiler directives.This course is aimed at programmers seeking to deepen their understanding of OpenMP and explore some of its more recent and advanced features. This course will cover topics including nested parallelism, OpenMP tasks, the OpenMP memory model, performance tuning, hybrid OpenMP + MPI, OpenMP implementations, and recently added features in OpenMP. Hands-on practical programming exercises make up a significant, and integral, part of this course. Attendees should be familiar with the basics of OpenMP, including parallel regions, data scoping, work sharing directives and synchronisation constructs. Access will be given to appropriate hardware for all the exercises, although many of them can also be performed on a standard Linux laptop. | Advanced computing (HPC, GPU) | Academia, Industry | Semi, Expert | Webinar | |
| Data Analysis and Visualisation in Python | EPCC, UEDIN |
7 - 8 February 2024 | Python is a general purpose programming language that is useful for writing scripts to work effectively and reproducibly with data. This is an introduction to Python designed for participants with no programming experience. | Visualisation Intro Computing |
Clinical, Academia, Industry | Novice | Webinar | |
| Data Carpentry | EPCC, UEDIN |
12 - 15 February 2024 | Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners’ existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. This workshop uses a tabular ecology dataset from the Portal Project Teaching Database and teaches data cleaning, management, analysis, and visualization. There are no pre-requisites, and the materials assume no prior knowledge about the tools. We use a single dataset throughout the workshop to model the data management and analysis workflow that a researcher would use. | Data Management Linux command line Visualisation Intro Computing |
Clinical, Academia, Industry | Novice | Webinar | |
| Using Blender for Scientific Visualisation | EPCC, UEDIN |
14 February 2024 | High-Performance Computing (HPC) simulations generate a lot of data, but conveying its significance outside our research communities poses challenges. This webinar shows how Blender, a general purpose, open-source, 3D rendering and animation software, can help enhances the appeal of 3D data by producing realistic and more engaging images and videos. This talk will focus primarily on Computational Fluid Dynamics (CFD) results, but the workflow and findings can be applied or transposed to any field working with 3D visualisation. This is an introduction to Python designed for participants with no programming experience. | Visualisation | Clinical, Academia, Industry | Semi, Expert | Webinar | |
| Understanding parallel I/O performance through profiling | EPCC, UEDIN |
21 February 2024 | File Input and Output ( I/O ) often become a severe bottleneck when parallel applications run on large numbers of processors. In this talk, we will show how to use I/O profiling tools , such as Recorder and Darshan, to understand and increase the I/O performance of an application. We will investigate a large portion of the I/O software stack, including Lustre, POSIX calls, MPI-IO and HDF5 libraries. As an example, we will investigate the I/O performance of a simple application writing a 3D array to the filesystem and the I/O behaviour of a real application, such as Nektar++.This is an introduction to Python designed for participants with no programming experience. | Visualisation | Academia, Industry | Semi, Expert | Webinar | |
| Introduction to Metagenomic analyses using HPC | UCL / EPCC, UEDIN ">Link |
Yearly | BIOC0002 course workshop: running metagenomics analysis on HPC using QIIME2 (3 hours) | Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Academia | Novice | Face2Face | |
| Introduction to Supercomputing | UCL / SURF ">Link |
December 2021 | BIOC0003 course workshop: Introduction to Supercomputers with hands on tutorial (3 hours) | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing |
Academia | Novice | Face2Face | |
| Specialist Research Project in Metagenomics | UCL / EPCC, UEDIN ">Link |
Yearly | BIOC0023: Data science with integrated experimental and computational metagenomics workflow | Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Academia | Novice | Face2Face | |
| Specialist Research Project in Metagenomics | UCL / EPCC, UEDIN ">Link |
On request | BIOC0023: Data science with integrated experimental and computational metagenomics workflow | Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Academia | Novice | Webinar | |
| Integrated experimental and computational metagenomics workflow | UCL / USFD / EPCC, UEDIN | December 2017 - March 2018 | BIOC3301: Integrated experimental and computational metagenomics workflow | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Academia | Novice | Face2Face | |
| From Skin to Metagenomics: Exploring Your Microbiome. | UCL / EPCC, UEDIN ">Link |
28 January 2021 | Running metagenomics analysis on HPC using QIIME2: eight sessions of 3 hours each. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Clinical | Novice | Webinar | |
| From Skin to Metagenomics: Exploring Your Microbiome | UCL / EPCC, UEDIN ">Link |
Yearly | Microbiome sampling and running metagenomics analysis on HPC using QIIME2: eight sessions of 3 hours each. This course is suitable for either 1st or 2nd year medical students. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Clinical | Novice | Face2Face | |
| PATC: Short course on HPC-based Computational Bio-Medicine | UCL / BSC |
Yearly February 2018-2022 | The objective of this course is to give a panorama on the use of hpc-based computational mechanics in Biomedical Sciences. The training is delivered in collaboration with the centers of excellence CompBioMed2 and PerMedCoE. Every February 2018-2022 | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Academia | Semi | Webinar | |
| BSC Training Course: Short course on HPC-based Computational Bio-Medicine | UCL / BSC |
Yearly | The objective of this course is to give a panorama on the use of HPC-based computational mechanics in Biomedical Sciences. The training is delivered in collaboration with the centers of excellence CompBioMed2, PerMedCoE and Dreams. | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Academia | Semi | Webinar | |
| From Skin to Metagenomics: Exploring Your Microbiome | USFD / UCL / EPCC, UEDIN |
Yearly September 2020-2023 | From Skin to Metagenomics: Exploring Your Microbiome, hybird (face2face and webinar) | Advanced computing (HPC, GPU) Linux command line How to get access to and how to use resources (hands-on) Intro Computing Large scale data processing |
Clinical | Novice | Face2Face, Webinar | |
| Data Science and Computational Models in Biomedicine (CompBioMed) | UPF | Yearly | Interdepartmental elective in computational biomedicine with hands-on guided tutorials | Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) Modelling and simulation |
Clinical, Academia | Novice | Face2Face | |
| Introduction to Supercomputing, part I | SURF |
Monthly | If you need to perform many calculations, or analyses that are too big for your own system, clusters and supercomputers will provide the computing power you need. In this course, you will learn how to work with these large computing systems! | Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) Intro Computing |
Academia, Industry | Novice, Semi | Webinar | |
| Introduction to Supercomputing, part 2 | SURF |
Bi-monthly | Using a high-performance computing system in the most effective and efficient way is not an easy task. Therefore, this course brings a follow-up to the first introductory Supercomputing course (part I), where you can take a deeper dive into the use of supercomputers with a special focus on efficiency and good practices and a very practical approach. | Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) |
Academia, Industry | Semi, Expert | Face2Face | |
| Introduction to SURF Research Cloud | SURF |
Bi-monthly | Intro Computing Cloud Computing |
Academia, Industry | Novice, Semi | Face2Face | ||
| Introduction to Data Management, Research Drive and Yoda | SURF |
Tri-monthly | This workshop will provide you with the knowledge you need to make your research data FAIR (findable, accessible, interoperable and reusable) using various services and tools. In particular, you will learn how to work with the data sharing and storage tool Research Drive, or also with Yoda, an integral support tool for the whole data life cycle. | Data Management How to get access to and how to use resources (hands-on) |
Academia, Industry | Novice, Semi | Face2Face | |
| IntroductionIntroduction to Deep Learning to Data Management, Research Drive and Yoda | SURF |
Tri-monthly | Our online course "Introduction to Deep Learning" will teach you the theoretical ánd practical basics of deep learning. In the course, you'll learn how deep neural networks work and how they are optimized. During our hands-on sessions you will have the opportunity to work on our high-performance systems and train neural networks to solve an image classification problem. We'll cover various neural network architectures: from a basic fully connected network, to a convolutional neural network and variational auto-encoders (time permitting). | Advanced computing (HPC, GPU) How to get access to and how to use resources (hands-on) |
Academia, Industry | Semi, Expert | Face2Face | |
| High-Performance Deep Learning | SURF |
Quarterly | Our online course on high-performance machine learning provides the necessary skills to train neural networks and extract the most relevant information from datasets. During our hands-on sessions you will have the opportunity to work on our high-performance systems with different types of data, and learn how to tune your model to obtain optimal results in the most efficient way. The first day will focus on basic deep learning knowledge and skills. The second day will focus on training neural networks on high-performance computing clusters. | Data Management Advanced computing (HPC, GPU) Bid Data Large scale data processing |
Academia, Industry | Semi, Expert | Face2Face | |
| Sensitive Data Management and EUDAT Services | SURF |
Annually | This course has a specific focus on how to treat sensitive data in a safe way, particularly using the available tools that will ensure to implement an efficient and secure data life cycle. | Data Management How to get access to and how to use resources (hands-on) |
Academia, Industry | Semi, Expert | Face2Face |