BioExcel Centre of Excellence: Recent Activities

This autumn the BioExcel team at PDC have been continuing with our initiatives that support the computational biomolecular research community. The BioExcel webinar series hosted the core developers of MDAnalysis (a library for performing interoperable analyses of biomolecular simulations in Python) and the developer of 3dRS (a web-based tool for sharing interactive representations of 3D biomolecular structures and molecular dynamics trajectories). In addition, Charlotte Deane (from the University of Oxford) gave a stimulating webinar on computationally designing therapeutic antibodies. These webinars (and many more!) can be viewed at BioExcel’s YouTube channel ( www.youtube.com/c/BioExcelCoE ) or on the BioExcel website at www.bioexcel.eu/webinars . As well as hosting webinars, BioExcel has been busy organizing the second winter BioExcel School on Biomolecular Simulations, which will be held as an online course in March 2022. If you would like to join us to learn more about a wide range of topics relating to biomolecular modelling and simulations, please register at bioexcel.eu/events/bioexcel-school-on-biomolecular-simulations .

Are you (interested in) performing molecular simulation using GROMACS? If so, the following initiative may also be of interest to you. In collaboration with the EuroCC National Competence Centre Sweden (ENCCS), BioExcel has released a GROMACS tutorials web page where the tutorials that are regularly given in training workshops about GROMACS are provided as interactive Jupyter Notebooks. You can download the notebooks to run locally, or even run them in your browser using Binder (see mybinder.org ). To try the notebooks, go to tutorials.gromacs.org .

About a year ago, BioExcel helped to change the format for GROMACS support from a mailing list to a forum. That has resulted in a very active forum with more than a thousand page views per day! So if you have any questions about GROMACS, do have a look at the GROMACS forum at gromacs.bioexcel.eu . And if you are using GROMACS at an advanced level, keep a watch on the BioExcel events page bioexcel.eu/news-and-events/events  or the PDC news page www.pdc.kth.se/about/pdc-news , as BioExcel will soon hold a workshop at the CSC – IT Center for Science in Finland.