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Abstract
Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This webinar will present a collection of FAIR notebooks built using the BioExcel Building Blocks library and covering various areas of the biomolecular simulation field, such as Molecular Dynamics (MD), protein-ligand docking, molecular checking/modeling, molecular interactions and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system, and the current collection is available here: https://mmb.irbbarcelona.org/biobb/workflows.
Presenter
Adam Hospital is a Postdoctoral fellow at the Molecular Modeling and Bioinformatics Unit (MMB) – Institute for Research in Biomedicine in Barcelona (IRB-Barcelona) and research software engineer for the Spanish National Institute of Bioinformatics (INB, ELIXIR-ES). From a computer science background, he jumped to the bioinformatics world and got trapped by the fascinating field of structural bioinformatics. He has been involved in scientific projects at IRB and 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”. He has developed and coordinated a set of public web servers and databases related to macromolecular structure flexibility, included in the INB integrated platform for macromolecular flexibility.
