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11 events found

Content provider: BioExcel 

  • BioExcel 1st Annual Meeting: “Advanced Simulations for Biomolecular Research” SIG @ ECCB 2016

    4 September 2016

    The Hague, Netherlands

    BioExcel 1st Annual Meeting: “Advanced Simulations for Biomolecular Research” SIG @ ECCB 2016 The BioExcel Annual Meeting will take place as a satellite event during ECCB 2016 on 4th September in the Hague. SIG BioExcel is a major venue for knowledge exchange and networking for the computational biomolecular research community. It brings together stakeholders of 1) core applications that are supported by the center – HADDOCK (integrative modelling), GROMACS (molecular dynamics simulations) and CPMD (hybrid QM/MM methods) and 2) worklow environments and platforms for data integration and analysis such as Galaxy, Taverna, Open PHACTS, COMPSs and Copernicus. 2016-09-04 09:00:00 UTC 2016-09-04 17:00:00 UTC BioExcel World Forum, The Hague, Netherlands World Forum The Hague Netherlands 2517 JW [] [] [] [] [] []
  • GROMACS hackathon 2016

    17 - 19 October 2016

    Barcelona, Spain

    GROMACS hackathon 2016 Get together with core GROMACS developers from around the world to hack together on code! Bring your own laptop and coding problem – new integrator, fancy free-energy method, cool analysis tool, automated parameterizer, workflow implementation, meta-dynamics driver, tricky bug to fix, API design question, etc. Be ready to ask and answer questions with the gurus, and come away with new code running, progressed or well planned! 2016-10-17 09:00:00 UTC 2016-10-19 17:00:00 UTC BioExcel Barcelona Supercomputing Center, Barcelona, Spain Barcelona Supercomputing Center Barcelona Spain [] [] [] [] [] []
  • BioExcel: workflow training for computational biomolecular research

    20 - 21 October 2016

    Barcelona, Spain

    BioExcel: workflow training for computational biomolecular research The purpose of this workshop is to (1) provide an overview of the most commonly used workflow managers in the computational biomolecular field, both in a theoretical and practical way, with hands-on practice sessions. (2) Find out about how BioExcel – Europe’s new Centre of Excellence for Computational BioMolecular Research – will help you to develop and run your own pipelines using these tools and introduce you to the BioExcel Workflows Interest Group. (3) Together with experts on the different workflow managers, identify the best approach for your particular workflow problem in a “Bring Your Own Workflow” session 2016-10-20 09:00:00 UTC 2016-10-21 17:00:00 UTC BioExcel Barcelona Supercomputing Center, Barcelona, Spain Barcelona Supercomputing Center Barcelona Spain [] [] [] [] [] []
  • Large-scale analytical workflows on the cloud using Galaxy and Globus

    16 November 2016

    Large-scale analytical workflows on the cloud using Galaxy and Globus We would like to invite you to attend the 8th webinar in BioExcel’s webinar series on computational methods and applications for biomolecular research, which will take place on 16th November 2016: Presenter: Ravi Madduri (introduction by Stian Soiland-Reyes) When: Wed 16th November 2016 16:00 CET (2016-11-16 15:00 UTC) Registration: Free In this BioExcel webinar we are delighted to have Ravi Madduri from Argonne National Laboratory and University of Chicago present Globus Genomics, a system developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data, combining Galaxy workflows with cloud technologies like Amazon EC2 and Globus File Transfer. This system achieves a high degree of end-to-end automation that encompasses every stage of data analysis including initial data retrieval from remote sequencing centers or storage (via the Globus file transfer system); specification, configuration, and reuse of multi-step processing pipelines (via the Galaxy workflow system); creation of custom Amazon Machine Images and on-demand resource acquisition via a specialized elastic provisioner (on Amazon EC2); and efficient scheduling of these pipelines over many processors (via the HTCondor scheduler). The system allows biomedical researchers to perform rapid analysis of large NGS datasets in a fully automated manner, without software installation or a need for any local computing infrastructure. Ravi’s work is part of the BD2K center Big Data for Discovery Science, building infrastructure for reproducible workflows using minids (minimal viable identifiers), analyzing data at scale using identified Docker containers, publish results in to Globus Publication services thus providing an end-to-end framework for reproducible research. In this BioExcel webinar, Ravi will present Globus Genomics and the technologies used to achieve large-scale analytical Galaxy workflows on the cloud. We think this will be of interest not just for the genomics community, but for any scientific workflow users who need to consider distributed deployments, data management and scalability. 2016-11-16 15:00:00 UTC 2016-11-16 16:00:00 UTC BioExcel Whole genome sequencing High-throughput sequencing Genomics Workflows University of ManchesterUniversity of ChicagoArgonne National Laboratory Please register at You will then receive an email with details of how you can connect to the webinar. [] bioinformaticianssoftware engineersGalaxy usersCloud users workshops_and_courses first_come_first_served CloudGalaxyGlobusNGSNext generation sequencing data analysis
  • BioExcel/PRACE Spring School 2017 – HPC for Life Sciences

    10 - 13 April 2017

    Stockholm, Sweden

    BioExcel/PRACE Spring School 2017 – HPC for Life Sciences BioExcel Center of Excellence is bringing together for the first time the main developers of four of the major and most popular codes for molecular modelling and simulations – GROMACS, AMBER, NAMD and VMD. This is a great opportunity for novice and experienced users to learn from the very authors of the software. The 2017 Spring School is organized jointly with PRACE, the main HPC resource provider in Europe. 2017-04-10 08:30:00 UTC 2017-04-13 17:00:00 UTC BioExcel KTH Main Campus, Stockholm, Sweden KTH Main Campus Stockholm Stockholm Sweden SE-100 44 Molecular modelling Data visualisation Simulation experiment [] Vera Matser - PRACE [] 60 workshops_and_courses first_come_first_served []
  • Foundation skills for HPC in computational biomolecular research

    3 - 7 July 2017

    Hinxton, United Kingdom

    Foundation skills for HPC in computational biomolecular research This 5-day BioExcel Summer School will use project-based learning to empower life scientists to get the most out of using computers. Using example problems and challenges that life-scientists will come across in their day-to-day work, e.g. obtaining data, installing software, cleaning data, analysing data, this course will help participants gain the foundational computational skills needed to move into the domain of high-end computing. 2017-07-03 16:33:00 UTC 2017-07-07 14:00:00 UTC BioExcel EMBL-EBI South Building and ELIXIR Hub, Hinxton, United Kingdom EMBL-EBI South Building and ELIXIR Hub Hinxton Cambridgeshire United Kingdom Computational biology EMBL-EBI Vera Matser - [] [] workshops_and_courses [] []
  • Building pharmacological workflow blocks for virtual screening (BioExcel and OpenPHACTS)

    17 July 2017

    Building pharmacological workflow blocks for virtual screening (BioExcel and OpenPHACTS) BioExcel’s webinar series continues with Nick Lynch, who will introduce Open PHACTS, an integrated pharmacological data platform and [BioExcel strategic partner]( Nick is joined by Stian Soiland-Reyes and Adam Hospital who will explain in details how BioExcel is building a Virtual Screening workflow combining Open PHACTS with the BioExcel-supported tools for biomolecular simulation and modelling. The [Open PHACTS Discovery Platform]( brings together vast amounts of linked data in a single integrated, open infrastructure providing a platform for researchers to access and query publicly-available pharmacological data. The platform integrates major open data sources (e.g. ChEMBL, UniProt, WikiPathways, SureChEMBL, DrugBank, Disgenet and their associated Chemistry) on compounds, patents, diseases, targets and pathways; linked by identifiers, semantic and structural chemistry information, re-exposed as a collection of unified web APIs, workflow components plus tool integrations. The platform is maintained by the [Open PHACTS Foundation](), which is supported by members from biopharmaceutical industry and Research Organisations with an active developer and user community. [BioExcel]( is an European Centre of Excellence that support academia and industry in the use of high-end computing in biomolecular research. Part of BioExcel’s roadmap for workflows is to develop Workflow Blocks for biomolecular simulation and modelling, which includes Open PHACTS as a data service. Such blocks, including the Open PHACTS platform, can be deployed in private or public cloud environments, and used to build portable pipelines. BioExcel is currently developing a series of [pilot use cases](, including a Virtual Screening workflow using Open PHACTS. In this webinar, **Nick Lynch** (Open PHACTS Foundation), **Stian Soiland-Reyes** (The University of Manchester) and **Adam Hospital** (IRB Barcelona) will present the Open PHACTS platform and how it will be used with BioExcel workflow blocks to build a virtual screening pipeline. [BioExcel webinars]( include an audience Q&A session during which attendees can ask questions and make suggestions. Please [**register** at]( - you will then receive an email with details of how you can connect to the webinar. 2017-07-17 15:00:00 UTC 2017-07-17 16:00:00 UTC BioExcel Molecular modelling Workflows Pharmacology University of Manchester Stian Soiland-Reyes, The University of Manchester [] [] workshops_and_courses registration_of_interest []
  • CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF

    28 February 2018

    CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF The [Common Workflow Language (CWL)]( is a community-led specification for describing analysis _workflows_ and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and _high performance computing_ (HPC) environments. [IBM Spectrum LSF]( (formerly IBM Platform LSF) is a complete workload management solution for demanding HPC environments. Featuring intelligent, policy-driven scheduling, it helps organizations accelerate research and design while controlling costs through superior resource utilization. Recognizing the popularity of CWL among LSF users, we introduce a new open source project **CWLEXEC** to support running CWL workflows on LSF. The project will feature smooth integration with LSF with high efficiency and scalability, self-healing of workflows, support user-specified submission options while keeping CWL definitions portable, and other benefits. * **Title**: CWLEXEC: A new open source tool to run CWL workflows on LSF * **Presenter:** Qingda Wang, Principal Architect, IBM Spectrum LSF Family Products and OEM * **Time**: 2018-02-28 14:00 GMT / 15:00 CET 2018-02-28 14:00:00 UTC 2018-02-28 15:00:00 UTC BioExcel Bioinformatics Genomics Workflows University of ManchesterBioExcel CoE Stian Soiland-Reyes [] bioinformaticiansHPC users workshops_and_courses registration_of_interest WorkflowsCWLHPCLSF
  • BioSimSpace – filling the gaps between molecular simulation codes

    27 June 2018

    BioSimSpace – filling the gaps between molecular simulation codes [BioSimSpace]( is a flagship software project from the [CCP-BioSim]( and [HEC-BioSim]( biomolecular modelling communities. The project aims to make it easier for researchers to develop, share and re-use biomolecular simulation workflow nodes. The software problem in our community is that we have lots of different pieces of software that are all incompatible and are not interoperable. This forces the community to hand-write small scripts for converting between different file formats, or to generate different software input files. The resulting scripts are specific for the software and task performed, leading to the community generating lots of bespoke and brittle workflows. BioSimSpace solves this problem by providing an **interoperability layer** between the major molecular simulation packages. In effect, BioSimSpace provides the shims that fill in the gaps between codes. BioSimSpace Python scripts can be run from the command line, used as workflow nodes in packages such as Knime, or run on the cloud as Jupyter notebooks. In this talk, we will show how BioSimSpace has been implemented, will talk about its capabilities and our future plans, and will demonstrate some BioSimSpace workflow nodes running on the cloud. 2018-06-27 15:00:00 UTC 2018-06-27 16:00:00 UTC BioExcel Molecular modelling Molecular dynamics Workflows University of Manchester [] IntermediateBeginners [] [] GROMACSPythonKNIMEJupyter notebook
  • Software Sustainability – Why and How to do it

    21 November 2019

    Software Sustainability – Why and How to do it This is a BioExcel webinar by Steve Crouch from [Software Sustainability Institute]( (SSI). We’ll explore the importance of **research software**, and the practices we can employ to develop it to help ensure its **sustainability** in the short, medium, and long term. We’ll also look at the different and emerging styles of _Management Plans_ for software, and how _software evaluation_ can identify areas for improvement and assist in the shaping of future development goals, and the potential for automation to allow evaluation to be conducted at scale. Software has a crucial role in the research process across many disciplines. As it continues to underpin our science and help push the boundaries of what is achievable, it becomes increasingly important that the sustainability of our software is given sufficient attention to ensure it can continue to evolve and grow to meet ever-changing research goals. 2019-11-21 14:00:00 UTC 2019-11-21 15:00:00 UTC [] Register at [] [] [] registration_of_interest Webinarsustainabilityresearch softwaresoftware development
  • BioExcel Summer School on Biomolecular Simulations

    4 - 11 June 2021

    BioExcel Summer School on Biomolecular Simulations The summer school will include lectures and hands-on sessions on the following topics: - Molecular Dynamics simulations - Biomolecular Docking - Free energy calculations - Advanced sampling methods (Metadynamics) - BioExcel Building Blocks (BioBB) - Quantum mechanics/molecular mechanics (QM/MM) During the hands-on computer practicals you will make use of the BioExcel flagship software and tools: e.g. GROMACS, HADDOCK, PMX, BioBB, and CP2K. The trainers, developers and/or experts in the use of the software, will provide guidance and support. **Audience and Prerequisites** The summer school is intended for researchers (primarily PhD and post-docs) using or planning to use biomolecular modeling and simulation in their everyday research. Familiarity with Linux and basic knowledge of molecular modelling software is a requirement. 2021-06-04 13:00:00 UTC 2021-06-11 16:10:00 UTC BioExcel Molecular modelling Molecular dynamics [] [] Early Career Researcher 30 workshops_and_courses [] biomolecular simulationsmolecular dynamicsMolecular dockingfree energyQM/MM

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