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  • Building pharmacological workflow blocks for virtual screening (BioExcel and OpenPHACTS)

    17 July 2017

    Building pharmacological workflow blocks for virtual screening (BioExcel and OpenPHACTS) https://tess.elixir-europe.org/events/building-pharmacological-workflow-blocks-for-virtual-screening BioExcel’s webinar series continues with Nick Lynch, who will introduce Open PHACTS, an integrated pharmacological data platform and [BioExcel strategic partner](http://bioexcel.eu/partnership-between-bioexcel-and-open-phacts-foundation/). 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](http://www.openphacts.org/) 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](http://bioexcel.eu/) 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](http://bioexcel.eu/research/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](http://bioexcel.eu/category/webinar/) include an audience Q&A session during which attendees can ask questions and make suggestions. Please [**register** at https://attendee.gotowebinar.com/register/295609582301212161](https://attendee.gotowebinar.com/register/295609582301212161) - 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 []
  • BioSimSpace – filling the gaps between molecular simulation codes

    27 June 2018

    BioSimSpace – filling the gaps between molecular simulation codes https://tess.elixir-europe.org/events/biosimspace-filling-the-gaps-between-molecular-simulation-codes [BioSimSpace](https://biosimspace.org) is a flagship software project from the [CCP-BioSim](https://ccpbiosim.ac.uk) and [HEC-BioSim](https://hecbiosim.ac.uk) 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
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