Domain A: Knowledge and intellectual abilities

The aim of this course is to introduce you to the techniques that will help researchers to develop a more systematic search strategy for literature and systematic reviews. This workshop will be most useful to those undertaking research in biomedical and health sciences or the social sciences.

Audience

This course should prove to be of particular interest to:

• staff employed on healthcare research projects
• staff involved in applying for grant applications
• staff supervising doctoral candidates.

Content

The course content is as follows:

• formulating a focused question
• identifying important concepts within the question
• identifying search terms to describe those concepts
• sensitivity' and 'specificity'
• Preparation of the search strategy using Boolean operators, truncation, and other key features of strategy development
• literature search methodology
• approaches to verifying the performance of the strategy.

The learners will be encouraged to relate the techniques explored directly to their research topic and there will be opportunities to discuss specific issues encountered.

Learning outcomes

On completion of this course, it is expected that learners will be able to:

• understand the difference between background versus foreground questions
• convert the need for information into an answerable question
• identify important concepts within a research question and capture search terms to describe those concepts
• identify appropriate information resources to search
• search effectively applying advance search techniques
• document the search process.

Entry requirements

It would be helpful for the delegates to have some experience of searching bibliographic databases.

Course dates

This workshop is for those who already possess expertise and a working knowledge of the desktop version of EndNote, the version of EndNote which is available on the University network (therefore, this workshop is not for students who have not used EndNote before or who have little experience with EndNote). The workshop will focus primarily on the desktop version of EndNote as opposed to the web-based version, EndNote Online. It is also tailored for users of the Windows EndNote program rather than the Mac program. The workshop will also offer troubleshooting advice to answer your specific queries. To ensure the trainer is appropriately prepared, you will be contacted before the session to supply any questions that you may have, in advance of the workshop.

Audience

This workshop is for those who already possess expertise and a working knowledge of the desktop version of EndNote and would like to expand their knowledge of the software.

Content

For the most part attendees will work through EndNote Desktop exercises of relevance and interest to their teaching and research. The workshop will also offer troubleshooting advice to answer specific queries that attendees have regarding EndNote Desktop.

Learning outcomes

On completion of this course, it is expected that learners will possess a greater knowledge of the EndNote Desktop software and its functionality.

Course date

Advanced Research Computing is a hugely powerful technique which is already enabling and transforming research in more than half of the schools across the University. These techniques use leading-edge IT resources and tools to pursue research, including computer simulation and modelling, manipulating and storing large amounts of data, and many other methods to solve research problems that would otherwise be extremely difficult, if not impossible.

If your research has the potential to use these techniques, or even if you are curious to just find out more, attending the 1 hour online session will give a quick insight into what research computing means and how you can use it.

It will also explain how Advanced Research Computing @ Cardiff (ARCCA) could help you to do your computer-processing based research much more effectively.

Prerequisites

None.

Course dates

The Linux command line interface is used to copy files, run programs, and perform many interactive functions, but it also supplies many of the features of more sophisticated general-purpose programming languages, such as flow control, variables, and subroutines. Making use of this expanded functionality allows the user to automate repetitive tasks, chain operations together in job submission scripts, and interact with a variety of command line tools.

This online course will show how to create and run a script, detail the syntax and structure, and demonstrate how to use common text processing tools such as ‘sed’ and ‘awk’ to expand text processing functionality, with the overall goal of increasing productivity in a research environment by reducing the amount of time taken on regular housekeeping operations.

Prerequisites

Attended ARC: An Introduction to Linux with Command Line (& Windows).

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

Linux, and in particular the use of the command-line, has always been a training need when users have come from a Windows background in order to use Cardiff University’s Supercomputer (Hawk). This practical course will concentrate on the use of techniques to improve researchers’ understanding of the command line, use of common editing tools, and will answer any queries users may have in using the Linux interface.

This course will also include how to interact with the Supercomputer from a Windows environment. This will include getting the best out of PuTTy, how to use WinSCP to copy files to and from Hawk and how to bring graphical interfaces back from the supercomputer using Xming. Whilst this course is tailored to help users quickly and easily run jobs on the supercomputer, many of these Linux commands are useful for general Linux systems.

Prerequisites

None.

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

Using container technology (such as Docker or Singularity) is one technique used to reproduce research outputs and to simplify software environments with complex dependencies across many systems.  Docker is not suited for a HPC environment due to its requirements to access the system with special permissions, one solution is to use another technology called Singularity that simplifies the containerisation to just the filesystem and make it compatible with the host system (to access specialised hardware such as Infiniband and GPUs).  MPI can also work with containers if the MPI inside the container is compatible with the MPI library on the host system.

This course will cover the setting up the environment, downloading and running existing containers, building your own container and how to make it work with important HPC technologies such as GPUs and MPI.

Prerequisites

Attended ARC: Supercomputing for Beginners or actively be using the Hawk supercomputer prior to this workshop.

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

Artificial Intelligence, Machine Learning and Deep Learning techniques are becoming more relevant on several research fields for which scientists rely on deep learning frameworks such as TensorFlow, PyTorch etc. These are commonly already GPU-accelerated, so researchers can get productive within a relatively small amount of time without any GPU programming. However, obtaining a basic insight of how CUDA is used to exploit specific hardware traits and how this impacts Machine Learning performance can aid in the optimization of research workflows.

This course will introduce the main core concepts behind the CUDA programming model and Machine Learning and the impact of hardware on Machine Learning based programs.

Prerequisites

Experience of a programming language is required; knowledge of Python, C or C++ and a working knowledge of Linux is essential

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

A modern supercomputer can be considered, at its simplest, to be a collection of individual computers (known as ‘nodes’), each with their own pool of memory, connected to each other via a very fast and sophisticated network. Conventional programs are limited by the fact they can only scale up to the size of a single node, whereas there may be hundreds or even thousands of nodes available. Taking full advantage of the power of modern supercomputers requires the ability to efficiently distribute work across multiple nodes via a communications protocol known as the Message Passing Interface (MPI).

This course describes the fundamentals of MPI programming, demonstrates how to break up a single piece of work into node-sized blocks, and allows the user to create and run simple MPI programs using a common set of communication functions.

Prerequisites

Experience of a programming language is required; knowledge of Fortran, Python or C, and a working knowledge of Linux is essential.

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

This course introduces programmers to the basics of parallel programming. OpenMP is a standard method of sharing work amongst threads within the same computer; this has become common recently due to its ease of use and support amongst the most common compilers. OpenMP uses shared memory within the computer to communicate between threads and there are many methods available to distribute the work. OpenMP is written using compiler directives/pragmas to tell the compiler how to distribute pieces of code across the multiple threads.

Prerequisites

Experience of a programming language is required; knowledge of Fortran, Python or C, and a working knowledge of Linux is essential.

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

NextFlow is becoming a popular method to design workflows when many steps are required to generate your research outputs.  NextFlow is written in Python and compatible with job schedulers (SLURM) and is written in a file format to express dependencies.  Sharing and porting your NextFlow workflows is a key design principle and it should be possible to write once and run anywhere.

This course will cover installing NextFlow, configuring it to use SLURM, running some simple workflows and how to write your own configuration for your own workflows.

Prerequisites

Attended ARC: Supercomputing for Beginners or actively be using the Hawk supercomputer prior to this workshop.

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

The Hawk supercomputer can be used in lots of different ways – this course aims to review some of the techniques that should help users get the best out of the cluster for their own research.

This will cover a number of features of the system that should help improve the performance of jobs submitted to the cluster, including:

• using advanced features in the Slurm Job scheduler (including array jobs)
• learn how to profile and debug your job in Slurm, and set the correct resource requirements to enable faster turnaround on the supercomputer
• develop more efficient job scripts to run your software
• provide an overview of the high performance Lustre filesystem to get better performance in Slurm jobs and associated best practices when using this filesystem; use of the GPU partition
• and, if requested, management of Slurm scripts with an overview of revision control software such as Git and importance of documentation and comments in code development.

Prerequisites

Attended ARC: Supercomputing for Beginners or actively be using the Hawk supercomputer prior to this workshop.

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

Hawk is Cardiff University’s supercomputer - hosted, maintained and developed by ARCCA/Supercomputing Wales. This  online course provides an overview of the cluster and explains how to use the system. It is a mix of presentation material and worked examples, which give users the chance to ask questions and run jobs in a controlled, friendly environment. By the end of the course, you should be able to access Hawk from a Windows PC, have a better understanding of the software environment (compilers, profilers and debugging tools available on the cluster), understand how to use the module environment (to load software) and be able to submit jobs to the system (through the Slurm job scheduler). This course will also provide an overview of some of the other courses and services provided which will enable users to improve their usage of advanced research computing facilities (both ARCCA facilities but also applicable to Linux clusters in general).

This course is open to all Cardiff University staff and students with an interest in using the University’s supercomputer system.

Prerequisites

Attended ARC: An Introduction to Linux with Command Line (& Windows) or equivalent experience.

Course dates

Length

4-hour online course, divided across 4 days, each with a 1-hour session.

Java programming for beginners, no programming experience needed. Suitable for someone who wants to start programming or has already done programming in another language. Practical course with most of it spent trying to solve programming puzzles to build people’s confidence, for future self-learning of programming material.

Audience

This course should prove to be of particular interest to those who:

• want to learn programming but are unsure how to start
• have some experience in another language and want to switch to Java.

Content

Java primer covering the basics from data types, looping and a brief introduction to object orientated programming.

Learning outcomes

On completion of this course, it is expected that learners will be able to:

• Install Java platform on their own machine.
• Write, compile and run a simple Java program.
• Simple debugging of a Java program.
• Have confidence to self-learn other topics in Java.

Course dates

This session will introduce the UNIX/LINUX operating system. Topics covered include:

• file hierarchy
• UNIX commands
• file and directory protection
• redirection of input and output
• modifying environment variables
• setting terminal characteristics
• the bash shell
• phases of shell interpretation
• using grep and sed and writing basic scripts.

Students with no prior UNIX/LINUX knowledge should attend this course prior to attending ‘Java: An Introduction’.

Course dates

This one-day hands-on workshop is designed for the complete beginner as well as those who are self-taught and want to start again. You will learn how to use NVivo to manage your research data, set up a project from scratch, bring in data, code and develop your thematic coding framework, query your data and explore with maps, charts and diagrams.

Audience

This course would be of particular interest to those who:

• are currently about to collect interview/qualitative data.
• have already collected qualitative data and are ready to use NVivo to organise, code, explore, analyse and report.
• PhD researchers; Early, Mid and Expert Researchers.

Content

• The course will start with a quick introduction of NVivo, using a sample project that comes with the software.
• You will build a learning project from scratch, using sample transcripts provided.
• You will build the ‘scaffolding’ of your own project – create data storage folders, import transcripts/files, explore, code, annotate, memo and analyse.

Learning outcomes

On completion of this course, participants will be able to:

• Create an NVivo project to manage the flow of all their research data – including interviews, supervision meeting notes, researcher’s own reflections, field notes, memos, annotations, etc.
• Organise the thematic coding framework and carry out some coding.
• Explore the query functions for analysis
• Generate maps, charts and diagrams.

Further support

Following attendance of this workshop delegates will also be given the opportunity to access a webinar based support drop-in clinic session with the facilitator. Details of this clinic will be circulated to attendees who complete the full day's training.

Course date

The purpose of this workshop is to assist new users of the programming language “R,” particularly those who intend to use it for applied statistical analysis for substantive research projects.

The primary beneficiaries of this workshop are those who have either no or very rudimentary training in R but are willing to invest the effort into learning a new skill. Completion of this workshop provides users with a foundation from which to build their knowledge of this programming language and attain fluency in R for future use on research projects.

Audience

This workshop should prove to be of particular interest to those who:

• Research staff who have difficulty working with other statistical programs
• Postgraduate researchers working on their theses
• Students and staff who would like to learn a new skill
• Professional services staff who engage in database management and analysis

Content

Participants will, at the completion of this workshop, be able to create, read in, manipulate, analyse, visualize, and save data using R. They will be given an overview of R packages, scripting, how objects are stored and read by R, which nouns and verbs are useable in R, and advanced packages such as dplyr or tidyverse.

Learning outcomes

On completion of this course, it is expected that learners will be able to:

• Reading in or creating their own datasets
• Manipulate that dataset by creating new variables and merging datasets together
• Analyse their data using a variety of statistical techniques
• Visualize their analysis with tables and graphics
• Output their analysis and visualizations for use in writing academic research papers, white papers, or office memos
• Continue learning R on their own

Course date

This course is delivered over three half-day sessions.

The aim is examine the myths and misconceptions behind systematic reviews and teach participants how to plan, conduct and communicate the results of a systematic review.

Audience

This course should prove to be of particular interest to researchers who:

• work on health and social care research
• are involved in applying for grant applications
• supervise doctoral candidates.

Content

The course content is as follows:

• background to systematic reviews and other evidence reviews
• examine myths and misconceptions regarding systematic reviews
• advantages and disadvantages of conducting systematic reviews
• the steps of conducting a systematic review.

Learning outcomes

On completion of this course, it is expected that learners will be able to:

• understand the role of systematic review and its significance
• understand the stages of a systematic review
• comprehend the importance of a protocol a systematic review in understanding how to develop a research question; search strategy; inclusion and exclusion criteria; critical appraisal, data extraction; and dissemination.

Course dates