UFS HPC Training 2022
As a part of the UFS HPC’s commitment to providing support to our users we are offering training sessions during June and July.
This page will provide all information regarding the training.
Location
All training sessions will be held in Lab E in the Computer Labs opposite the library.
Participants
All current users and perspective users of the HPC may attend the training sessions. This includes staff and post-graduate students.
Registration
Registration for the training sessions are handled by the University’s Indico event management system (events.ufs.ac.za). This system offers two methods of logging in: The first is using your University account credentials (the “Login with LDAP” button) and the second is via an Indico account that can be created separately (The “Indico” button).
Please note that only Staff can login using their University account credentials. All students (Postdocs included) will need to create Indico accounts to be able to register for the training sessions.
Please note that registration needs to be performed for each session you wish to attend. I.e. registering for one session DOES NOT register you automatically for the other sessions.
Session Capacity
Due to COVID-19 restrictions, each session will be limited to 25 participants only. However, if the need arises, additional training sessions will be scheduled later on in 2022 for perspective participants who were unable to secure a place for the first round of training.
Please note that all training material, and audio/video recordings of the training sessions, will be made availible after the training sessions.
Training Schedule
| Date | Session | Registration Link | Time |
|---|---|---|---|
| 10/06/2022 | UFS HPC Introductory Training | https://events.ufs.ac.za/event/1555/ | 9:00 AM - 17 :00 PM |
| 14/06/2022 | UFS HPC Introductory Training | https://events.ufs.ac.za/event/1526/ | 9:00 AM - 17 :00 PM |
| 21/06/2022 | OMICS Introductory Training - Biological Databases and Sequences | https://events.ufs.ac.za/event/1539/ | 9:00 AM - 17 :00 PM |
| 28/06/2022 | OMICS Introductory Training - Introduction to Genomics | https://events.ufs.ac.za/event/1540/ | 9:00 AM - 17 :00 PM |
| 05/07/2022 | OMICS Introductory Training - Introduction to Transcriptomics | https://events.ufs.ac.za/event/1541/ | 9:00 AM - 17 :00 PM |
| 12/07/2022 | OMICS Introductory Training - Introduction to Proteomics | https://events.ufs.ac.za/event/1542/ | 9:00 AM - 17 :00 PM |
Training in other research fields
The OMICS training is primarily intended for researchers in the life-sciences (which covers multiple departments) and will be used as a test-run for future user-training programs. We intend to expand similar training to other research fields as well, thus covering our entire research community. However, this would likely require expertise outside of the UFS HPC unit to achieve this. We would thus love to engage with supervisors in these fields on ideas for training. Please get in touch with us at hpc@ufs.ac.za.
Session Specific Information
UFS HPC Introductory Training
Prerequisites
Only basic computer skills are required.
Description
A general introductory training session on concepts in High-Performance computing and how to use the UFS HPC. This includes a follow-along, practical demonstration/tutorial for using the Linux Terminal. This training session is meant for all new users of the UFS HPC and is not research area specific.
OMICS Introductory Training
Prerequisites
- Linux Terminal skills on a comparable level as skills taught in UFS HPC Introductory Training
- Undergraduate/basic knowledge of biochemistry (Nucleic Acids / Proteins)
Description
Recently, we have seen growth in the HPC user community, particularly in users from the life-sciences domain on campus. Given that we have in-house expertise in this research area, we will be offering introductory training sessions in Bioinformatics and the OMICS sciences.
According to the central dogma of molecular biology biological information flows from DNA to RNA and finally to Proteins. In the past it was only possible to investigate single molecules or a small subsets of molecules in each of the previously mentioned domains. However, as technology advanced, it became increasingly possible to capture information on the entire complement (or close to it) of DNA, RNA and proteins.
This birthed the modern research domains of the OMICS sciences. Consequently, as the amount of biological information increased, there was a concurrent development of a new informatics field, known as bioinformatics, which was (and still is) primarily responsible for providing the analysis tools required to deal with the massive amounts of data generated by the OMICS fields.
In this training series the participant will be introduced to fields of bioinformatics, genomics, transcriptomics and proteomics. The main aim is to arm the participant with the starting knowledge to dive deeper into any of the primary OMICS sciences.
Biological Databases and Sequences
Biological sequences are often the starting point (bioinformatics-wise) for many analysis pipelines used in the OMICS sciences. Thus, knowledge of how sequences are stored and processed is an essential starting point for training in the OMICS sciences.
Please
Introduction to Genomics
Genomics are mainly concerned with the entire complement of DNA in a cell or organism. Obtaining the genome of organisms are often the starting point in any investigation about the molecular composition of organism of interest. For example, one of the first responses to the COVID-19 pandemic was the sequencing (retrieval) the SARS-CoV2's genome.
Introduction to Transcriptomics
The field of Transcriptomics focuses on the entire complement of RNA in cell or organism. While many non-coding RNA molecules exist and is studied using transcriptomic analyses, the main application of transcriptomics is to investigate the differences in the expression and repression of genes and clusters of genes as the organism is exposed to different environmental conditions. For instance, under normal conditions, a bacteria will not produce (express) heat-shock proteins to protect it against sudden increases in temperature. However when it is exposed to a sudden increase in temperature the organism will start producing these proteins, and the first step in this process (before we get the proteins) is the production of more transcripts (mRNA) for the gene than encodes for the protein. Using transcriptomic analysis one may demonstrate and interrogate this response more closely, and even identify additional potential gene products that play a role in the process due to changes in its expression.
Introduction to Proteomics
While Transcriptomics gives us a hint of which proteins will likely be expressed, proteomics gives us precise information on the full complement of proteins ultimately present in the organism. Also, proteins can often be modified after translation (translation is the process of the cell machinery reading the mRNA transcript and producing the protein from that information), and this is often a way that is used to change the properties of the protein. Post-translational modifications will not be resolved by transcriptomics, however using proteomics techniques and analyses will reveal these post-translational modifications.