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SUMMARY:Webinar: Pathfinders - Catalysis
DESCRIPTION:This webinar continues our look at our pathfinder activities in the current phase. The subject of this webinar is experimental data capture in catalysis research. This is the focus of Pathfinder 1 which is led by Abraham Nieva de la Hidalga. \nThe recording of this webinar is now available on Youtube. \nExperimental Data Capture: producing publish ready data from processing and analysis processes\, example with XAS data processing.\nAbstract: In this seminar we will demonstrate two techniques for processing and analysing data that generate the required metadata to create FAIR digital objects. These objects can then be published as supporting information for the results obtained. This approach requires minimum intervention from the researcher performing the processing and analysis tasks. Consequently\, these methods are ideal for improving the practices of publishing data\, facilitate reproducibility of results\, and support greater reuse of published data. \nThe two proposed techniques are based on the use of the X-Ray Larch Python Library. The first technique uses Jupyter notebooks and MLProvLab. This approach is suitable for small scale spectra analysis\, this is processing and analysis of a small number of XAS readings being studied. The second technique leverages Galaxy tools and workflows. This approach is suitable for large scale spectra analysis\, which encompasses processing and analysis of large numbers of XAS readings\, such as those resulting from in situ and operando experiments. \nBoth techniques produce the metadata required for reproducing the results\, including data used\, parameters set at each stage\, sequence of operations and mapping between inputs and outputs. We will discuss the benefits of these type of tools such as\, less work in documenting supporting data by producing publishing ready data objects\, comparison of results when varying parameters and exploratory testing of different parameter combinations. \nAt the end of this seminar\, you will be able to practice with your actual data using the resources presented (Jupyter notebooks). Additionally\, we invite the community to provide ideas for improvements of the tools and for supplying ideas for further development. \n			\n			\n				\n				\n				\n				\n			\n				\n				\n				\n				\n				\n				\n				\n				\n				\n				\n				Watch the recording\nYou can watch the recording of this webinar via our youtube channel. \n\n			\n				\n				\n				\n				\n				The pathfinders aim to focus development in strategic areas with the aim to explore and establish exemplar systems that can be brought under the PSDI umbrella and act as templates for future phases of the project. For those that wish to get some more information about the pathfinders before the webinar please go to: https://www.psdi.ac.uk/current-work/wp4-pathfinders/ \nThe PSDI team looks forward to seeing you at the webinar\, if you have any questions you can always get in contact with us.
URL:https://www.psdi.ac.uk/event/webinar-psdi-pf1/
LOCATION:Online\, Virtual Event\, Online
CATEGORIES:Webinar
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DTSTART;TZID=Europe/London:20231018T140000
DTEND;TZID=Europe/London:20231018T150000
DTSTAMP:20260430T144939
CREATED:20230824T170822Z
LAST-MODIFIED:20240108T142255Z
UID:34686-1697637600-1697641200@www.psdi.ac.uk
SUMMARY:Webinar: Pathfinders - Biomolecular Simulation
DESCRIPTION:This webinar continues our look at our pathfinder activities in the current phase. The subject of this webinar is pathfinder 4 which focuses on process orchestration in Biomolecular Simulation. This webinar will be presented by James Gebbie and Jas Kalayan. \nThe recording of this webinar is now available on Youtube. \nFAIR Data for the Biomolecular Simulation Community\nAbstract: \nThe biomolecular simulation community produces vast amounts of data to study complex biological systems at atomic scales. Yet\, how we store\, share\, and reuse our data is not well defined. One problem is that our simulation pipelines are difficult to replicate without detailed descriptions of each step. Another problem is the data files we produce can often be too large to store on the national compute facilities\, which most of this data is produced on. In this webinar we present possible solutions to address these two problems; firstly\, a software tool to record data provenance towards FAIR [1] compliant formats\, and the other an online data repository to store and share this data. \nFor reproducible data\, we utilise the powerful AiiDA Python infrastructure [2\,3] to develop our aiida-gromacs plugin [4]\, for tracking all inputs and outputs from simulation protocols performed with the GROMACS MD engine [5]. We show how aiida-gromacs can be used with minimal changes to how researchers already work\, to allow for easy adoption of provenance tools within our community. \nTo address the findable and accessible components of FAIR compliancy\, we also briefly present our prototype data infrastructure. Our aim is to allow researchers to directly upload data produced via aiida-gromacs onto our database for easy access\, querying and visualisation of simulation data/metadata online. \nWe encourage the biomolecular simulation community to try aiida-gromacs\, we have installation guides and tutorials available online. Please have a go\, contribute\, and provide us with feedback for improving aiida-gromacs! \n[1] Wilkinson\, Mark D. et al. (2016). Scientific Data\, 3(1)\, 160018. \n[2] https://www.aiida.net/sections/about.html \n[3] Huber\, Sebastiaan P. et al. (2020). Scientific Data\, 7(1)\, 300. \n[4] https://aiida-gromacs.readthedocs.io/en/latest/index.html \n[5] https://www.gromacs.org/ \n			\n			\n				\n				\n				\n				\n			\n				\n				\n				\n				\n				\n				\n				\n				\n				\n				\n				Watch the recording\nYou can watch the recording of this webinar via our youtube channel. \n\n			\n				\n				\n				\n				\n				The pathfinders aim to focus development in strategic areas with the aim to explore and establish exemplar systems that can be brought under the PSDI umbrella and act as templates for future phases of the project. For those that wish to get some more information about the pathfinders before the webinar please go to: https://www.psdi.ac.uk/current-work/wp4-pathfinders/ \nThe PSDI team looks forward to seeing you at the webinar\, if you have any questions you can always get in contact with us.
URL:https://www.psdi.ac.uk/event/webinar-psdi-pf4/
LOCATION:Online\, Virtual Event\, Online
CATEGORIES:Webinar
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