News
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.
Available at https://github.com/scientificomputing/BRIDGE & https://cheminformatics.usegalaxy.eu