Webinar: Introduction to PSDI

Online Virtual Event, Online

Welcome to the Physical Sciences Data Infrastructure (PSDI) webinar series. In the first of the new series a broad introduction to PSDI will be provided. This will include the aims of the project, the team and an overview of the work packages.

Free

Webinar: Pathfinders – Process Recording

Online Virtual Event, Online

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. The recording of this webinar is now available on Youtube. Abstract: 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. This 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 […]

Free

Webinar: Pathfinders – Catalysis

Online Virtual Event, Online

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. The recording of this webinar is now available on Youtube. Experimental Data Capture: producing publish ready data from processing and analysis processes, example with XAS data processing. Abstract: 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. The 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 […]

Free

Webinar: Pathfinders – Biomolecular Simulation

Online Virtual Event, Online

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. The recording of this webinar is now available on Youtube. FAIR Data for the Biomolecular Simulation Community Abstract: The 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 compliant formats, and the other an online data repository to store and share this data. For reproducible data, we utilise the powerful AiiDA Python infrastructure to develop our aiida-gromacs plugin , for tracking all inputs and outputs from simulation protocols performed with the GROMACS MD […]

Free

Webinar: Data Revival

Online Virtual Event, Online

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. The recording of this webinar is now available on YoutubeMaking the intangible tangible: The journey from lab notebook to digital insight The 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 […]

Free

Webinar: Pathfinder – Data to Knowledge

Online Virtual Event, Online

Register here: https://us06web.zoom.us/webinar/register/WN_jk6RwUt7SbuHz4toJm31zQ 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).This webinar will be presented by Alin Elena and Federica Zanca from Science and Technology Facilities Council Daresbury Laboratory. Abstract  AI 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 […]

Free

Webinar: Sample Tracking with Ampletracks

Online Virtual Event, Online

Register here: https://us06web.zoom.us/webinar/register/WN_7t0s4FqJSYiL8e0UoHqeYA This webinar continues the PSDI webinar series, in this webinar representatives from PSDI Partner the Henry Royce Institute present their Ampletracks sample tracking system.This webinar will be presented by Stavrina Dimosthenous (Henry Royce Institute) and Ben Jefferson. Abstract  Ampletracks is a configurable web-app built, originally, for sample tracking in and out of laboratory environments. In this talk, we will discuss Ampletracks in brief, and why and how we built Ampletracks. We will demonstrate Ampletracks implemented for a materials science audience. We will demonstrate the ‘User’ workflow, and Ampletracks features across the multiple ways to register a sample record, and intrinsic (like record type) and extrinsic (unlike record type) relationships between records. We will then demonstrate how to set different permission profiles for users, and ‘superuser’ permissions. To finish, we will briefly discuss other domains to apply Ampletracks, and how we use Ampletracks to track the development of Ampletracks.Stavrina Dimosthenous is a Data Curator at the Henry Royce Institute for advanced materials (Royce) in the UK, based at the Royce Hub Building at The University of Manchester. She holds a PhD in Materials Science, and has conducted research in materials science and computational materials science across the UK […]

Free

Webinar: Using the Galaxy Platform in Large Scale Experiments

Online Virtual Event, Online

This webinar continues our look at our pathfinder activities in the current phase. The subject of this webinar is pathfinder 7 and will discuss how their software helps in workflows containing large data sets generated by simulations and experiments at national facilities. This webinar will be presented by Leandro Liborio from STFC, Harwell

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