BEGIN:VCALENDAR VERSION:2.0 PRODID:-//Physical Sciences Data Infrastructure - ECPv6.15.20//NONSGML v1.0//EN CALSCALE:GREGORIAN METHOD:PUBLISH X-WR-CALNAME:Physical Sciences Data Infrastructure X-ORIGINAL-URL:https://www.psdi.ac.uk X-WR-CALDESC:Events for Physical Sciences Data Infrastructure REFRESH-INTERVAL;VALUE=DURATION:PT1H X-Robots-Tag:noindex X-PUBLISHED-TTL:PT1H BEGIN:VTIMEZONE TZID:Europe/London BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20220327T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20221030T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20230326T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20231029T010000 END:STANDARD BEGIN:DAYLIGHT TZOFFSETFROM:+0000 TZOFFSETTO:+0100 TZNAME:BST DTSTART:20240331T010000 END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:+0100 TZOFFSETTO:+0000 TZNAME:GMT DTSTART:20241027T010000 END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTART;TZID=Europe/London:20231214T140000 DTEND;TZID=Europe/London:20231214T150000 DTSTAMP:20260424T090407 CREATED:20231114T105945Z LAST-MODIFIED:20250117T134050Z UID:34729-1702562400-1702566000@www.psdi.ac.uk SUMMARY:Webinar: Pathfinder - Data to Knowledge DESCRIPTION:This webinar continues our look at our pathfinder activities in the current phase. The subject of this webinar is pathfinder 5 which focuses on transforming data to knowledge through the construction of workflows. In particular this looks machine learning for interatomic potentials (MLIP). \nThe recording of this webinar is now available on Youtube \n \n \n \n \n \n This webinar will be presented by Alin Elena and Federica Zanca from Science and Technology Facilities Council Daresbury Laboratory. \nAbstract  \nAI is ubiquitous in all walks of life and research. In the last 5 years active research in the field of understanding how atoms and molecules interact using AI has revolutionised the field. The outcome of these efforts\, machine learning interatomic potentials\, MLIP\, has produced the breakthrough that recommends them as the next paradigm change in atomistic molecular simulations\, with applications ranging from battery design to catalytic chemical reaction modelling for hydrogen storage or CO2 capture. All these advances need expensive calculations to be produced and used for training machine learning models. In addition\, the models resulting from these models are non-trivial in terms of storage and distribution compared with previous generation interatomic potentials which tended to be analytical. Current models use millions of structures for training\, and this raises new challenges around reproducibility and exploitation of these models. Physical Sciences Data Infrastructure\, PSDI\, aims to enable researchers in the field to deal with the challenges coming from generating\, using and enhancing this data. The first part of the talk will concentrate on recent advances in the field and PSDI contribution\, second part more technical will concentrate on presenting databases and workflows challenges for having reproducible and reusable data. We will present opensearch\, abcd database and aiida workflows.  \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\nThe 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-pf5/ LOCATION:Online\, Virtual Event\, Online CATEGORIES:Webinar ATTACH;FMTTYPE=image/png:https://www.psdi.ac.uk/wp-content/uploads/2023/06/PSDI_Logo_RGB_small.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20231116T140000 DTEND;TZID=Europe/London:20231116T150000 DTSTAMP:20260424T090407 CREATED:20231101T140705Z LAST-MODIFIED:20240312T111508Z UID:34711-1700143200-1700146800@www.psdi.ac.uk SUMMARY:Webinar: Data Revival DESCRIPTION:This webinar continues our look at our pathfinder activities in the current phase. The subject of this webinar is extraction of knowledge from lab books\, which is being undertaken as part of our Pathfinder 2 & 3 activities in conjunction with spin out company Data Revival. This webinar will be presented by Samuel Munday from Data Revival. \nThe recording of this webinar is now available on Youtube \n \n \n \n \n \n Making the intangible tangible: The journey from lab notebook to digital insight\nThe University of Southampton’s chemistry department has accumulated a wealth of chemical knowledge over the years\, some of which has been captured in over 2000 lab books. The vast majority of these have been sat gathering dust in a cupboard for a long time\, unable to be destroyed due to both the value of knowledge they hold and their importance for Health and Safety reporting. However\, this knowledge is intangible and difficult to access\, offering no value to the department whilst taking up space and presenting a fire risk. We present our work on turning this unstructured resource into a structured accessible database that holds FAIR data open to analytics and intelligent search. Our system utilises AI-driven natural language processing techniques\, as well as chemical structure recognition\, to extract all the types of chemical information required to create a useful\, searchable database. This database unlocks 3000 chemist years of knowledge and enables more efficient and accurate future research. In this webinar we discuss the process of digitising such an archive effectively\, the AI tools we have created to work with such unstructured knowledge at scale\, the utility of the digital database created for the chemistry department\, and the feedback received from the department on the system’s potential for further development. \nBiography\nSamuel Munday is a senior research assistant at the University of Southampton as well as being the co-director of the fledgling spin out Data Revival. He first became interested in scientific data management whilst building a predictive analytics platform for polymeric materials and realising that a lot of key data resided in a form incomprehensible to computers. This has led to the development of a series of tools for unstructured chemical data extraction and structuring\, mainly used for turning hand written lab notebooks into structured searchable databases at scale. He is currently leading the development of this platform which is beginning to show signs of success with both academic researchers and commercial partners. \n \n \n \n \n \n Watch the recording\nYou can watch the recording of this webinar via our Youtube channel. Slides are available on zenodo. \n\n\n\n\n\n\n\nThe 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-data-revival/ LOCATION:Online\, Virtual Event\, Online CATEGORIES:Webinar ATTACH;FMTTYPE=image/png:https://www.psdi.ac.uk/wp-content/uploads/2023/06/PSDI_Logo_RGB_small.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20231018T140000 DTEND;TZID=Europe/London:20231018T150000 DTSTAMP:20260424T090407 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 END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20231003T140000 DTEND;TZID=Europe/London:20231003T150000 DTSTAMP:20260424T090407 CREATED:20230824T171050Z LAST-MODIFIED:20231212T102430Z UID:34679-1696341600-1696345200@www.psdi.ac.uk 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 ATTACH;FMTTYPE=image/svg+xml:https://www.psdi.ac.uk/wp-content/uploads/2022/01/PSDI_Logo_CMYK-01.svg END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20230918T120000 DTEND;TZID=Europe/London:20230920T140000 DTSTAMP:20260424T090407 CREATED:20230420T145709Z LAST-MODIFIED:20230919T080703Z UID:34451-1695038400-1695218400@www.psdi.ac.uk SUMMARY:Machine Learning for Atomistic Modelling Autumn School 2023 DESCRIPTION:All places for the school have now been finalised\, for those attending please ensure your payment is made by 1st September. \n \n \n \n \n \n \nDate of Event: 18th 12:00 – 20th September 14:00\nLocation: Daresbury Laboratory\, in person event\nFee: £100 (covers 2 nights accommodation and catering)\nPre-requisites: Students will be expected to bring their own laptop\, to have a decent level of coding experience (see pre-requisites below) and provide a letter of support from their supervisor\n\n \n \n \n \n \n Description\nThis machine learning for materials training course is being run by the Physical Sciences Data Infrastructure (PSDI) initiative in collaboration with PSDS\, AI4SD\, STFC-SCD and CCP5.This training is targeted towards PhD students\, in particular those in the Materials and Molecular Simulations field. The aim of this training is to introduce attendees to the latest methods of machine learning applied to atomistic simulation of materials. \nThis training will encompass a number of talks and practical sessions\, focusing on the basics of machine learning\, machine learning interatomic potentials and graph neural networks. There will also be the opportunity for attendees to present a poster on their work. \n \n \n \n \n \n Learning outcomes\n\nAwareness of the state-of-the-art methods for machine learning for atomic and molecular simulations\nHands on experience of using machine learning for atomic and molecular simulations\n\nOutline Agenda – Draft\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Day 1 – 18th\n\n12:00 – 13:00: Registration & Lunch\n13:00 – 13:30: Introduction\n13:30 – 15:00: Lecture Session: Basic introduction to ML topics – Reinhard Maurer\n15:00 – 15:30: Coffee Break\n15:30 – 17:15: Practical session: Basic ML worked example – Reinhard Maurer\n17:30 – 18:30: Research Seminar – Aron Walsh\n19:00: BBQ\n\n \n \n \n \n \n \n \n \n \n \n \n Day 2 – 19th\n\n09:00 – 10:30: Lectures (1h30) Machine Learning Interatomic Potentials – Ioan Magdau\n10:30 – 11:00: Coffee\n11:00 – 12:30: Practical Session MLIP (1h30) – Ioan Magdau + Alin-Marin Elena\n12:30 – 14:00: Lunch\n14:00 – 15:30: Practical Session MLIP (1h30) – Ioan Magdau + Alin-Marin Elena\n15:30 – 16:00: Coffee\n16:00 – 18:00: Lectures: GNN talks – Keith Butler + Alex Ganose\nPoster session evening + buffet / pizza\n\n \n \n \n \n \n \n \n \n \n \n \n Day 3 – 20th\n\n09:00 – 10:30: Practical Session: Building and training GNN – Keith Butler & Alex Ganose\n10:30 – 11:00: Coffee\n11:00 – 12:30: Practical Session: Using pre trained networks – Keith Butler & Alex Ganose\n12:30 – 14:00: Lunch & Departure\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Pre-requisites\nStudents attending this course must already have a foundational level of Python experience and hands on experience of using Python in their research. You will be expected to provide your own laptop for the training course\, although software installation will not be required. A letter of support will be required from your supervisor alongside your application. This letter of support is to show the backing of your supervisor to attend the training and must be completed on headed paper\, but does not need to be detailed. A template of the minimum required content is available in this word document. \nTimelines\nThe application deadline is 30th June 2023 (including letter of support from your supervisor). Applications are now closed. You will be informed of the outcome of your application on 1st August\, you will have to accept your place within 1 week and payment is required by 1st September. These timelines have been amended due to the exceptionally high number of applications we received.  \nFood and 2 nights accommodation is included in the £100 fee paid for this event\, travel to Daresbury is not included and will need to be covered by the attendee. Please note: places on this course are limited and in the event of oversubscription to the training course we will favour a diverse group of attendees.   \n \n \n \n \n \n All places for the school have now been finalised\, for those attending please ensure your payment is made by 1st September. \n \n \n \n \n \n Organising Committee \n\nAlin-Marin Elena\, Scientific Computing Department STFC \nKeith Butler\, Queen Mary University London \nReinhard Maurer\, University of Warwick \nKim Jelfs\, Imperial College London \nAlex Ganose\, Imperial College London\nSimon Coles\, University of Southampton \nSamantha Kanza\, University of Southampton \nNicola Knight\, University of Southampton  URL:https://www.psdi.ac.uk/event/machine-learning-autumn-school-2023/ LOCATION:Daresbury Laboratory\, Keckwick Lane\, Daresbury\, WA4 4AD\, United Kingdom CATEGORIES:Training ATTACH;FMTTYPE=image/png:https://www.psdi.ac.uk/wp-content/uploads/2023/04/MLAutumnSchool-flyer.png END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20230727T140000 DTEND;TZID=Europe/London:20230727T150000 DTSTAMP:20260424T090407 CREATED:20230531T223631Z LAST-MODIFIED:20230731T153839Z UID:34495-1690466400-1690470000@www.psdi.ac.uk SUMMARY:Webinar: Pathfinders - Process Recording DESCRIPTION:In the first webinar of the series (a recording of this now available on the PSDI YouTube page) we took a look at PSDI as a whole. In this second webinar we focus down into work package 4 of the current phase\, which contains our 5 pathfinders\, in this webinar we looked at the work in Pathfinder 2: Process Recording\, which is led by Dr Samantha Kanza. \nThe recording of this webinar is now available on Youtube. \nAbstract: Process recording is fundamental to ensuring the preservation of the scientific record and enabling reproducibility. The Electronic Lab Notebook (ELN) was originally created to serve as a direct replacement for the paper lab notebook\, to ensure the digital capture and retention of the scientific record. What seemed like an obvious simple software-based solution has been anything but\, and there are now over 80 active ELNs on the market and a wide range of different approaches have been taken to digitizing scientific research across academia and industry. \nThis talk will discuss the shift in software offerings and attitudes to process recording software and report on the results of a recent survey on ELN and Notebook Usage in our physical sciences community. We will also discuss the current work that is being undertaken in this pathfinder to produce a comprehensive resource on process recording tools to aid researchers in identifying the best solution(s) for them. It will also cover research being undertaken around the different aspects of process recording\, and community recommendations for making improvements in these areas\, such as metadata\, semantics\, data standards and the use of hybrid/voice technologies. \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Bio: Dr Samantha Kanza is a Senior Enterprise Fellow at the University of Southampton. She is a Pathfinder Lead and researcher in the Physical Sciences Data Infrastructure initiative. She also coordinates the Future Blood Testing Network (www.futurebloodtesting.org) run out of Reading as well as previously co-ordinating the AI 4 Scientific Discovery Network (AI4SD – www.ai4science.network). Samantha works in the interdisciplinary research area of applying computer science techniques to the scientific domain\, specifically through the use of semantic web technologies and artificial intelligence. Her research includes looking at electronic lab notebooks and smart laboratories\, to improve the digitization and knowledge management of the scientific record using semantic web technologies; and using IoT devices in the laboratory. She has also worked on a number of interdisciplinary Semantic Web projects in different domains\, including agriculture\, chemistry and the social sciences. \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. An overview of the pathfinder will be presented as well as their goals over the course 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-pf2/ LOCATION:Online\, Virtual Event\, Online CATEGORIES:Webinar ATTACH;FMTTYPE=image/svg+xml:https://www.psdi.ac.uk/wp-content/uploads/2022/01/PSDI_Logo_CMYK-01.svg END:VEVENT BEGIN:VEVENT DTSTART;TZID=Europe/London:20230629T140000 DTEND;TZID=Europe/London:20230629T150000 DTSTAMP:20260424T090407 CREATED:20230529T155505Z LAST-MODIFIED:20230714T152132Z UID:34494-1688047200-1688050800@www.psdi.ac.uk SUMMARY:Webinar: Introduction to PSDI DESCRIPTION:Welcome to the Physical Sciences Data Infrastructure (PSDI) webinar series. This webinar series is designed to communicate the PSDI work to a wider audience! \nIn the first webinar of the series we will be presenting a broad introduction to PSDI. If you are wondering what PSDI is working on\, then this webinar will be an excellent introduction for you. In this webinar we will cover the vision of the project\, an overview of the work we have undertaken in the PSDI pilot\, the work we are currently undertaking and where we are focusing in the shorter term. Future webinars will focus in more depth on specific elements of the project. Our second webinar running in July will focus more on work undertaken in work package 4 through our pathfinders. \nThis webinar will be a presentation from the PSDI team with a chance for those attending to ask questions at the end\, the webinar will be recorded and a copy of the recording is now available on the PSDI Youtube Channel – you can subscribe to the channel to find out when future videos go live. \nThe PSDI team looks forward to seeing you at the webinar\, if you have any questions you can always get in contact with us. \n \n \n \n \n \n Watch the recording\nYou can watch the recording of this webinar via our Youtube Channel. URL:https://www.psdi.ac.uk/event/webinar-introduction-to-psdi/ LOCATION:Online\, Virtual Event\, Online CATEGORIES:Webinar ATTACH;FMTTYPE=image/svg+xml:https://www.psdi.ac.uk/wp-content/uploads/2022/01/PSDI_Logo_CMYK-01.svg END:VEVENT END:VCALENDAR