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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.
Available at https://github.com/scientificomputing/BRIDGE & https://cheminformatics.usegalaxy.eu
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.
To find out more about the BRIDGE platform visit https://github.com/scientificomputing/BRIDGE or contact us.