Domain A: Knowledge and intellectual abilities

The knowledge and intellectual abilities needed to be able to carry out excellent research.

Information management

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

DateTimeVenue
To be confirmedTo be confirmedTo be confirmed

This workshop is an introduction to EndNote Desktop, the networked version of EndNote, the electronic reference manager which is available on campus to all members of the University. During this workshop, amongst other things, you will have the opportunity to:

  • create an Endnote library of references
  • import references from bibliographic databases relevant to your research
  • insert those references into a Word document
  • use Word to create citations and a bibliography in the style of your choice using EndNote
  • save attachments to references in your EndNote library.

Audience

People who:

  • would like to manage their references and related files in a private reference library
  • would like to easily insert their references into Word in the citation style of their choice
  • would like to share references with colleagues.

Content

The session will include a demonstration of the main features of EndNote and information on where to go for further help and assistance with the database at Cardiff University.

For the most part the session will involve attendees undertaking exercises in the main uses of the database in storing references and using it in conjunction with Word. These exercises include:

  • EndNote Library - adding references manually and changing the output style
  • EndNote and Word
    • Inserting citations and references into a Microsoft Word document
    • Changing the output style of a Word document and the layout of a bibliography
    • Modifying citations
    • How to remove EndNote citations and references from a Word document
  • How to import references from databases into EndNote
  • Creating EndNote library groups and group sets
  • Adding and annotating files (including PDFs) to an EndNote library
  • How to take a word count of a Word document which does not count citations, footnotes and bibliography references

Learning outcomes

  • Store references and files in your own EndNote Library.
  • Import references and files from other databases into EndNote.
  • Use Endnote with Word to create citations, footnotes and bibliography references in the style of your choice.

Course dates

DateTimeVenue
To be confirmedTo be confirmedTo be confirmed

Technical and research skills: Advanced Research Computing

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

DateTimeDelivery method
8 February 202111:00-12:00Further details to be released post booking

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

DateTimeDelivery method
22 February 2021 (Part 1)11:00-12:00Further details to be released post booking
23 February 2021 (Part 2)11:00-12:00Further details to be released post booking
24 February 2021 (Part 3)11:00-12:00Further details to be released post booking
25 February 2021 (Part 4)11:00-12:00Further details to be released post booking

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

DateTimeDelivery method
15 February 2021 (Part 1)11:00-12:00Further details to be released post booking
16 February 2021 (Part 2)11:00-12:00Further details to be released post booking
17 February 2021 (Part 3)11:00-12:00Further details to be released post booking
18 February 2021 (Part 4)11:00-12:00Further details to be released post booking

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

DateTimeDelivery method
26 April 2021 (Part 1)11:00-12:00Further details to be released post booking
27 April 2021 (Part 2)11:00-12:00Further details to be released post booking
28 April 2021 (Part 3)11:00-12:00Further details to be released post booking
29 April 2021 (Part 4)11:00-12:00Further details to be released post booking

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

DateTimeDelivery method
19 April 2021 (Part 1)11:00-12:00Further details to be released post booking
20 April 2021 (Part 2)11:00-12:00Further details to be released post booking
21 April 2021 (Part 3)11:00-12:00Further details to be released post booking
22 April 2021 (Part 4)11:00-12:00Further details to be released post booking

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

DateTimeDelivery method
22 March 2021 (Part 1)11:00-12:00Further details to be released post booking
23 March 2021 (Part 2)11:00-12:00Further details to be released post booking
24 Mach 2021 (Part 3)11:00-12:00Further details to be released post booking
25 March 2021 (Part 4)11:00-12:00Further details to be released post booking

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

DateTimeDelivery method
15 March 2021 (Part 1)11:00-12:00Further details to be released post booking
16 March 2021 (Part 2)11:00-12:00Further details to be released post booking
17 March 2021 (Part 3)11:00-12:00Further details to be released post booking
18 March 2021 (Part 4)11:00-12:00Further details to be released post booking

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

Session 1

DateTimeDelivery method
9 February 2021 (Part 1)11:00-12:00Further details to be released post booking
10 February 2021 (Part 2)11:00-12:00Further details to be released post booking
11 February 2021 (Part 3)11:00-12:00Further details to be released post booking
12 February 2021 (Part 4)11:00-12:00Further details to be released post booking

Session 2

DateTimeDelivery method
10 May 202111:00-12:00Further details to be released post booking
11 May 202111:00-12:00Further details to be released post booking
12 May 202111:00-12:00Further details to be released post booking
13 May 202111:00-12:00Further details to be released post booking

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

DateTimeDelivery method
8 March 2021 (Part 1)11:00-12:00Further details to be released post booking
9 March 2021 (Part 2)11:00-12:00Further details to be released post booking
10 March 2021 (Part 3)11:00-12:00Further details to be released post booking
11 March 2021 (Part 4)11:00-12:00Further details to be released post booking

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

DateTimeDelivery method
1 March 2021 (Part 1)11:00-12:00Further details to be released post booking
2 March 2021 (Part 2)11:00-12:00Further details to be released post booking
3 March 2021 (Part 3)11:00-12:00Further details to be released post booking
4 March 2021 (Part 4)11:00-12:00Further details to be released post booking

Length

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

Technical and research skills: IT skills

This full-day course will provide an introduction to the Java programming language and its usage. After attending this course you will have acquired the basic skills in programming in Java and an understanding of the ideas of object oriented programming. Topics covered in this course for beginners include:

  • an introduction to classes and objects
  • discussion of the basic elements of a class (i.e. constructors, methods and instance variables)
  • arithmetic operators and mathematical methods
  • comparison operators and the use of conditional statements
  • iterative control using for, while and do statements
  • formatting of output.

The course will be run with a mixture of both taught and practical work. Prior programming experience is not necessary but would be advantageous. You should have some knowledge of UNIX/LINUX before attending, or have attended the UNIX/LINUX: An Introduction course.

Course dates

DateTimeVenue
To be confirmedTo be confirmedTo be confirmed

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

DateTimeVenue
To be confirmedTo be confirmedTo be confirmed

Technical and research skills: Packages

This course is designed for the complete beginner as well as those who have used previous versions of the software. Participants will learn how to use NVivo for literature review; build a practice project using sample data files provided; and build the ‘scaffolding’ or the structure of own project.

Audience

This course would be of particular interest to those who:

  • are currently working on their literature review
  • are about to carry out  qualitative data collection
  • have already collected their data and are ready to use NVivo to transcribe, code and analyse.

Content

Morning:

  • explore how NVivo works through a sample project
  • create a practice project
  • import into the practice project, different types of data sources
  • learn to transcribe an audio file in NVivo
  • learn to code a transcript into both “open codes” and “thematic coding framework”
  • create memos for field notes, reflective notes, supervision meeting notes, annotations, hyperlinks and See Also Links
  • generate “word cloud” for poster presentation.

Afternoon:

  • organise your open codes into thematic coding structure using colour
  • classify your data by their demographic attributes and values
  • examine your coding using Coding Stripes and highlights
  • briefly test your coding for relational coding
  • learn how to use Coding and Matrix Queries
  • learn how to use Mind map, Concept map and explore diagram will be provided

Learning outcomes

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

  • use NVivo for their literature review
  • 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.

Course dates

DateTimeVenue
To be confirmedTo be confirmedTo be confirmed

Technical and research skills: Techniques

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

DateTimeVenue
To be confirmedTo be confirmedTo be confirmed