Latest news for the Scientific Computing Research Unit
Dr Rizqah Kamies joined the Scientific Computing Research Unit in 2017 as a postdoctoral fellow. Rizqah manged the Cancer Translation Laboratory and worked on testing computational designs of key cancer targets inhibitors.
Dr Chris Barnett attended the Galaxy Community Conference 2019 in Freiburg, Germany. He presented on "Galaxy Computational Chemistry" and overviewed his collaborative research on creating computational tools, the BRIDGE platform (see the publication) and the Galaxy computational chemistry community. Applications for the tools include investigation of molecular conformation, protein dynamics and bio-orthogonal sugars. Tools for analysis of bio-orthogonal sugars and post analysis of ab initio MD simulations are in further development. Many of the tools are currently available at https://cheminformatics.usegalaxy.eu in collaboration with Björn Grüning, Simon Bray and the University of Freiburg.
Congratulations to Ananya Gangopadhyay, who graduated in April with a Masters Degree in Computational Science, with distinction, her thesis titled Accelerator-based Look-up Table for Coarse-grained simulations.
Matthew Coulson is a Master student in the informatics group of the Scientific Computing Research Unit. His research has dealt mainly with unsupervised learning techniques, creating software to aid in the separation of samples into clusters. This research formed the subject for his Masters in Computational Science. One of the key research themes in the SCR Unit is a molecular understanding of cancer. The software Matthew developed uses gene-expression data to provide a visualization which assists in differentiation between different types of cancer cells, as well as cancer vs. non-cancer cells.
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) has been published in Bioinformatics. The paper presents the foundations of BRIDGE developed on the Galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor. We illustrate the basic BRIDGE simulation and analytics capabilities on a previously reported CBH1 protein simulation.
Congratulations to Mr Ju-Young Kim, who graduated in December 2018! His MSc. focused on a bioinformatics analysis of breast cancer genes, his thesis title is "Transcriptional Regulation of Glycosyltransferase Genes In Mcf-7 Human Breast Cancer Cell Line Following Drug Treatment".
Coming from a background in biochemistry, Ju-Young relied on the interdisciplinary approach that SCRU takes in its projects to learn the necessary coding skills to complete his project . His time at SCRU allowed him to supplement his skill set with the growing field of computational science, saying that “having a scientific domain knowledge, backed up by good computational/programming skills was something that was truly valuable” and he recognised that these computing skills would afford him new opportunities in the future.
When asked to comment on his time at SCRU, he said that “Today I can without any doubt say that the skills and knowledge I developed at SCRU are truly valuable skills that have prepared me for my job”.
Mr Ju-Young Kim is now employed as a Machine Learning Engineer at Praelexis (Pty) Ltd. Click here to read more about his experience in the Scientific Computing Research Unit.
The CHPC conference concluded on Thursday 6th December, which also saw the BRIDGE (Biomolecular Reaction & Interaction Dynamics Global Environment) workshop take place. This workshop outlined molecular dynamics and analysis which can be a source of confusion for newcomers and researchers from neighbouring disciplines. BRIDGE is a web application that aims to address this and enable users to simulate and analyse molecular systems using curated workflows. Professor Naidoo introduced the workshop, while the workshop itself was run by Dr Chris Barnett and PhD student Tharindu Senapathi. The workshop was well attended, playing host to 31 researchers. We were thankful to receive computing support from the CHPC, the ilifu cloud and SANBI.
Researchers from across South Africa gathered in Century City for the Centre for High Performance Computing (CHPC) Conference. The conference was held from the 2-6 of December 2018 and attracted researchers from South Africa’s top research institutions, including Wits University, University of Kwazulu Natal and Stellenbosch University.
Professor Kevin Naidoo was an invited speaker and presented - “Advancing Computational Science in South African Academia through Social and Cyber Networks” on 4th December. Emre Kaya, Tharindu Senapathi, Tomás Bruce-Chwatt, Ananya Gangopadhyay, Matthew Coulson, Daniel Flowers, Jess Nel, Edgar Abuto and Lenard Carroll all presented posters at the conference. Lenard Carroll supervised by Dr Gerhard Venter won 2nd place for his poster entitle “A Combined Computational and Experimental Investigation of the Dissolution of Chitin in Organic Electrolyte Solutions”.
Prof Kevin Naidoo one of twenty of the country’s leading scholars and scientists was inaugurated as a Member of the Academy of Science of South Africa (ASSAf) at the annual Awards Ceremony on 10 October 2018. He is one of the four UCT scientists honoured by ASSAf.
The Nobel Prize in Medicine 2018 was awarded jointly to cancer researchers James P. Allison and Tasuku Honjo who discovered a cancer therapy that works by inhibition of negative immune regulation. Both researchers independently discovered methods of "removing the brakes" or stimulating the immune system to fight cancer - now called immune checkpoint therapy.
One of the proteins responsible, Programmed Death-1 (PD-1) protein, binds sialic acid confirming the critical role of carbohydrates in the fight against cancer (read more about this sialic acid binding immunoglobulin (Ig)-like lectin).
The 2018 Scientific Computing International Lecture Series (SCILS) visiting scholar will be Dr Niclas Karlsson (PI of Glyco Inflammatory Group at the University of Gothenburg, Sweden)
Dr Karlsson a Glycobioinformatician will present a departmental lecture titled "Osteoarthritis - A life science glycoproblem".
Dr Karlsson is the PI on the UniCarb-DB database that stores, integrates and processes data from manually annotated ms spectra glyco fragments.
The Scientific Computing Research Unit will be a hosting a workshop – “Molecular Dynamics using BRIDGE” at the 2018 CHPC National Conference. This will take place on the 6th December at the Century City Convention Centre. For more info see http://bit.ly/2C4ybCW. Please register online and on the CHPC registration page:
Hope to see you there! Tweet to us at @scicompute with the #bridge #galaxy #chpc2018 hashtags.