This talk provides an overview of persistent memory and memory virtualization software working together. Dr. Sun explains how Big Memory Computing accelerates bioinformatic pipelines by eliminating IO to storage and by enabling parallelism. The talk references results from deployments at Analytical Biosciences and The Translational Genomics Research Institute (TGen).
Phyre2 is a web server to predict protein structure from sequence ( http://www.sbg.bio.ic.ac.uk/phyre2/ ) with ~ 100,000 unique IP hits per year. Missense3D ( http://missense3d.bc.ic.ac.uk/ ) is a web server to analyse the structural impact of a missense variants with precomputed results for ~4M human variants available in Missense3d-DB.
An update on the tools, methods and datasets available from the CATH protein structure classification database, including the latest developments on clustering functional families (FunFams) within hugely populated evolutionary superfamilies, FunVar webpages and novel data visualization tools
Here we present a novel, accessible and user-friendly platform for protein design. DeepChain helps life science researchers design and optimize protein-protein interactions, and is directly applicable to drug discovery.
Due to the Covid-19 pandemic, ‘German Network for Bioinformatics Infrastructure – de.NBI’ training activities transitioned from in-person to virtual formats. Building on de.NBI cloud infrastructure, an accessible and reusable platform, hereby presented, was developed to deliver computational online courses, and a set of online training best practices were identified.
The EMBL-EBI provides free access to a powerful full-featured text search engine as well as to core bioinformatics sequence analysis applications via web and programmatic interfaces. In this Technology Track talk, I would like to describe the latest improvements to the services and highlight their importance during the current pandemic.
In order to understand COVID-19 and develop treatments and vaccines to fight it, EMBL-EBI and partners operate the COVID-19 Data Portal (https://www.covid19dataportal.org). This Technical Track demonstrates how the portal is organised and the functionality it offers to enable users to find and navigate the many data resources it integrates.
The PerMedCoE project will provide an efficient and sustainable roadmap to scale up a collection of relevant computational biology tools to leverage the next generation of HPC exascale platforms. In this presentation, we will summarize the main strategies we are following to achieve such a challenging goal.
This talk will demonstrate how the GenePattern Notebook environment, notebook.genepattern.org, extends the analytical and reproducible research capabilities of Jupyter Notebook and GenePattern for scientists at all levels of computational sophistication. We will also discuss recent additions to the environment, including new tools and featured notebooks, project spaces, and JupyterLab compatibility.
Pathway Tools provides an extensive array of capabilities covering genome informatics, pathway informatics, regulatory informatics, and analysis of transcriptomics and metabolomics data. The BioCyc database (DB) collection now includes 18,000 organism-specific Pathway/Genome Databases (PGDBs). BioCyc PGDBs have been curated from 130,000 publications.