Are you interested in computational biomolecular simulation methods such as molecular dynamics, docking, and free energy calculations, but hesitant to take the first step? What if you could start smoothly using an interactive, graphical user interface like a Jupyter Notebook? What if you could easily build pipelines that chain together different programs using a single, interoperable library and a single syntax?
Join this webinar session, where we will introduce the BioExcel Building Blocks (BioBB), a fully interoperable software library comprising a collection of Python wrappers on top of biomolecular simulation tools such as GROMACS, AmberTools, Open Babel and ACPYPE. The philosophy behind its design follows best practices and FAIR principles for software development, making BioBB easy to find, install, and use and facilitating reproducibility and reusability. The webinar will introduce demonstration workflows implemented in Jupyter notebooks using the BioBB library (e.g. protein MD simulation setup with GROMACS), and briefly present the first steps involved in building and running complex workflows using the command line, with examples of workflows tackling real scientific problems.
Adam Hospital is postdoctoral fellow in the Molecular Modelling and Bioinformatics Unit (MMB) hosted by the Institute for Research in Biomedicine in Barcelona (IRB-Barcelona) and research software engineer for the Spanish National Institute of Bioinformatics (INB).
From a computer science background, Adam jumped to the bioinformatics world and got trapped by the fascinating field of structural bioinformatics. After 2 years, he joined INB, where he has been working for more than 10 years. INB has recently become the Spanish node of ELIXIR, which is building a sustainable European infrastructure for biological information. He has been involved in scientific projects developed at IRB and also at the Barcelona Supercomputing Center (BSC), and he is currently leading the workflows team in the BioExcel CoE. While working as a bioinformatician, he obtained his PhD in Biotechnology from the University of Barcelona with his thesis “High Throughput Computational Studies of Macromolecular Structure Flexibility”. At INB he has developed a set of public web servers and databases related to macromolecular structure flexibility, including MDWeb, NAFlex and BigNASim.
Register for webinar
Title: Computational biomolecular simulation workflows with BioExcel building blocks
Date: 10th September, 2020 Time: 15:00 CEST / 14:00 BST