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event-033: Applying Scrum to Research Software Projects

 
2021-01-26T14:30:00+00:00 2021-01-26T15:00:00+00:00 Applying Scrum to Research Software Projects Background Scrum is a modern, agile and widely used software development methodology. Rather than trying to set requirements in stone at the beginning of a project, Scrum embraces the idea that requirements will change during all software projects. It takes an iterative, incremental approach and focuses on regular delivery of working software to customers. Can it be applied to research software projects and if so what are the best approaches? https://sorse.github.io//programme/talks/event-033/ SORSE.enquiries@gmail.com SORSE
2020-11-30

event-032: Research Software and the Modelling of COVID-19 in the UK

 
2021-01-11T15:00:00+00:00 2021-01-11T16:30:00+00:00 Research Software and the Modelling of COVID-19 in the UK The onset of the COVID-19 pandemic in early 2020 created an urgent need for epidemiological and infectious disease modelling. In the UK, a surge of local and national initiatives quickly emerged to support existing research groups with the increased demands of this crisis, and Research Software Engineers (RSEs) played a pivotal role in these responses. Many questions abound. For new collaborations, what were the difficulties and solutions in quickly setting up networks across varied institutions and between collaborators with disparate expertise? For existing institutions, how were established codes and frameworks adapted to tackle the dynamic situation? How did researchers perceive RSEs and the impact of their involvement? Which general, non-domain-specific software skills and practices were required for success? In situations where research software is extended beyond its initial purpose for broader consumption, how do RSEs in conjunction with researchers help promote trust in the outputs? How will software created during this crisis be maintained to ensure sustainability and preparedness for future use? https://sorse.github.io//programme/panels/event-032/ SORSE.enquiries@gmail.com SORSE
2020-11-30

event-030: Research Squirrel Engineers - An independent squirrel network for RSEs in DH and archaeology

 
2021-02-11T16:00:00+00:00 2021-02-11T16:15:00+00:00 Research Squirrel Engineers - An independent squirrel network for RSEs in DH and archaeology People who write code for research are few and far between in the archaeological sciences. Quite often they are regarded as technicians and their function in research projects reduced to those of “helpers”, diminishing their contribution to the success of the undertaking. Nowadays some students of the humanities are trained in digital technologies to bridge the information gap between the different fields (Digital Humanities, DH). A similar situation can be found in Digital and Computational Archaeology, though the two disciplines only marginally influenced each other (Hugget 10.12759/hsr.37.2012.3.86-105). Some centers of Digital Archaeology work closely with DH departments and some DH specialists moved from archaeology to the broader field of DH, which shows that the job market in Digital Archaeology does not offer enough possibilities. The temporary nature of research related projects is another reason for an unstable job market in the field. To mitigate the effects of this instability, increased workload, surveillance and underappreciation, Hugget calls for a resilient scholarship in a digital age (Hugget 10.5334/jcaa.25). One important aspect he names on the individual level is forming a community for networking and support. We will present the “Research Squirrel Engineers”, an open, diverse and international network, which aims at RSEs connecting and developing their own ideas for side projects independent from institutions (and funding). Within the Research Squirrel community, currently two members have an engineering background (computer science, geoinformatics) whereas the other two studied a humanities subject (archaeology). By focusing on their own research interests they help RSEs to retain joy in their job, diversify and showcase their skill sets. So far Squirrels focus on (Linked) Open Data projects, but are happy to receive suggestions and new research squirrels joining at SORSE. https://sorse.github.io//programme/talks/event-030/ SORSE.enquiries@gmail.com SORSE
2020-11-30

event-029: My project expired and my team left, so let’s rewrite all the software from scratch

 
2021-01-26T14:00:00+00:00 2021-01-26T14:30:00+00:00 My project expired and my team left, so let's rewrite all the software from scratch Peano is a framework for large-scale simulations using dynamically adaptive Cartesian grids. It is used today for Earthquake and Black Hole simulations, for example. The fourth generation of the software is currently under development. https://sorse.github.io//programme/talks/event-029/ SORSE.enquiries@gmail.com SORSE
2020-11-30

event-011: Configuring Sphinx from scratch: making your own documentation and making your documentation your own

 
2020-11-03T15:00:00+00:00 2020-11-03T16:00:00+00:00 Configuring Sphinx from scratch: making your own documentation and making your documentation your own In this demonstration we will build a mature documentation system from scratch for a dummy project using the Sphinx documentation generator, the infrastructure of choice for the documentation of a huge number of modern software projects, including of Python itself. https://sorse.github.io//programme/software-demos/event-011/ SORSE.enquiries@gmail.com SORSE
2020-11-10

event-015: Bringing Imaging-Based Artificial Intelligence into Clinical Practice in NHS Radiology

 
2020-12-07T14:00:00+00:00 2020-12-07T14:30:00+00:00 Bringing Imaging-Based Artificial Intelligence into Clinical Practice in NHS Radiology Whilst there are over 200 Imaging/Radiology AI Companies world wide there are currently only about 50 FDA approved algorithms. There are also significant barriers to overcome in bringing AI to the NHS landscape. In Bolton NHS Foundation Trust we are the first NHS Organisation to deploy the Qure.AI solution into clinical practice. https://sorse.github.io//programme/talks/event-015/ SORSE.enquiries@gmail.com SORSE
2020-11-03

event-009: From experimental software to research infrastructure maturity

 
2020-12-07T14:30:00+00:00 2020-12-07T15:00:00+00:00 From experimental software to research infrastructure maturity The challenges facing research software development are manifold and have long been a major topic at RSE conferences. https://sorse.github.io//programme/talks/event-009/ SORSE.enquiries@gmail.com SORSE
2020-11-03

event-016: FAIR 4 Research Software

 
2020-11-17T07:00:00+00:00 2020-11-17T10:00:00+00:00 FAIR 4 Research Software The software has become essential for research. To improve the Findability, Accessibility, Interoperability, and Reuse of research software, it is desirable to develop and apply a set of FAIR Guiding Principles for software. Application of the FAIR principles to software will continue to advance the aims of the open science movement. The FAIR 4 Research Software Working Group (FAIR4RS WG) aims to enable coordination of existing community-led discussions on how to define and apply FAIR principles to research software, and achieve adoption of these principles. The FAIR4RS WG is jointly convened as an RDA Working Group, FORCE11 Working Group, and Research Software Alliance (ReSA) Taskforce, in recognition of the importance of this work. Since July 2020, the group has been analysing existing work in this area and has started drafting community-agreed-upon FAIR principles for research software. This workshop will provide the following opportunities: https://sorse.github.io//programme/workshops/event-016/ SORSE.enquiries@gmail.com SORSE
 
2020-11-19T16:00:00+00:00 2020-11-19T19:00:00+00:00 FAIR 4 Research Software The software has become essential for research. To improve the Findability, Accessibility, Interoperability, and Reuse of research software, it is desirable to develop and apply a set of FAIR Guiding Principles for software. Application of the FAIR principles to software will continue to advance the aims of the open science movement. The FAIR 4 Research Software Working Group (FAIR4RS WG) aims to enable coordination of existing community-led discussions on how to define and apply FAIR principles to research software, and achieve adoption of these principles. The FAIR4RS WG is jointly convened as an RDA Working Group, FORCE11 Working Group, and Research Software Alliance (ReSA) Taskforce, in recognition of the importance of this work. Since July 2020, the group has been analysing existing work in this area and has started drafting community-agreed-upon FAIR principles for research software. This workshop will provide the following opportunities: https://sorse.github.io//programme/workshops/event-016/ SORSE.enquiries@gmail.com SORSE
2020-10-19

event-026: The Continual Road to an Inclusive Definition and Use of Terms for the US Research Software Engineer Community

 
2020-10-22T14:30:00+00:00 2020-10-22T14:45:00+00:00 The Continual Road to an Inclusive Definition and Use of Terms for the US Research Software Engineer Community An important part of building a strong and resilient community is fostering collaboration between individuals with varying backgrounds, expertise, and viewpoints and building a diverse and inclusive community. While the term Research Software Engineering was initially suggested in 2010, there are many different definitions of Research Software Engineers (RSEs) and their community. The US-RSE Association uses “We like an inclusive definition of Research Software Engineers to encompass those who regularly use expertise in programming to advance research.” One of the first community events of the US-RSE Association was a Birds-of-Feather session at PEARC19, where the discussion revealed that participants wanted to learn if the RSE community could include them, and questions arose who would be interested in such an association and community beyond RSEs themselves. These discussions have continued since then and we realized that any definition of RSE will probably change over time. https://sorse.github.io//programme/talks/event-026/ SORSE.enquiries@gmail.com SORSE
2020-09-15

event-022: Learnings from developing and maintaining a research software that has been used more than 3 million times in the last 3 years

 
2020-11-10T10:30:00+00:00 2020-11-10T11:00:00+00:00 Learnings from developing and maintaining a research software that has been used more than 3 million times in the last 3 years Manually annotated images and videos are a fundamental part of many research projects and industrial applications. However, manual image annotation tools are often designed to address one specific use case and lack the flexibility to be reused across different projects. Furthermore, these tools often have complex installation and setup procedure which presents a barrier to non-technical users. To address these limitations, we created the VGG Image Annotator VIA, which is a light weight, standalone and offline software package that does not require any installation or setup and runs solely in a web browser. The VIA software allows human annotators to define and describe spatial regions in images or video frames, and temporal segments in audio or video. These manual annotations can be exported to plain text data formats such as JSON and CSV and therefore are amenable to further processing by other software tools. VIA also supports collaborative annotation of a large dataset by a group of human annotators. The BSD open source license of this software allows it to be used in any academic project or commercial application. https://sorse.github.io//programme/talks/event-022/ SORSE.enquiries@gmail.com SORSE
2020-09-15

event-021: Goodbot, Badbot? Engineering trust into conversational interfaces

 
2020-11-10T10:00:00+00:00 2020-11-10T10:30:00+00:00 Goodbot, Badbot? Engineering trust into conversational interfaces As more people interact with bots driven by Artificial Intelligence, it is important to understand how to create relationships based on trust. The FinTrust Project at Newcastle University is looking at the role of machine learning in banking, particularly in the context of automated chatbots and how the presence of socio-emotional features impacts the intention to use. Researchers from social sciences and computing are examining how trust can be measured, how trust is gained and lost, and what implications this might have on design considerations. https://sorse.github.io//programme/talks/event-021/ SORSE.enquiries@gmail.com SORSE
2020-09-15

event-023: Optimal time frequency analysis for biological data - pyBOAT

 
2020-12-04T14:00:00+00:00 2020-12-04T15:00:00+00:00 Optimal time frequency analysis for biological data - pyBOAT Methods for the quantification of rhythmic biological signals have been essential for the discovery of function and design of biological oscillators. Advances in live measurements have allowed recordings of unprecedented resolution revealing a new world of complex heterogeneous oscillations with multiple noisy non-stationary features. However, our understand- ing of the underlying mechanisms regulating these oscillations has been lagging behind, partially due to the lack of simple tools to reliably quantify these complex non-stationary features. With this challenge in mind, we have developed pyBOAT, a Python-based fully automatic stand-alone software that integrates multiple steps of non-stationary oscillatory time series analysis into an easy-to-use graphical user interface. pyBOAT implements continuous wavelet analysis which is specifically designed to reveal time-dependent features. In this work we illustrate the advantages of our tool by analyzing complex non-stationary time-series profiles. Our approach integrates data-visualization, optimized sinc-filter detrending, amplitude envelope removal and a subsequent continuous-wavelet based time- frequency analysis. Finally, using analytical considerations and numerical simulations we discuss unexpected pitfalls in commonly used smoothing and detrending operations. https://sorse.github.io//programme/software-demos/event-023/ SORSE.enquiries@gmail.com SORSE
2020-09-15

event-006: Towards an NLP Pipeline for Conflict Narrative Detection

 
2020-10-22T14:00:00+00:00 2020-10-22T14:30:00+00:00 Towards an NLP Pipeline for Conflict Narrative Detection This talk is about PhD research into developing an NLP pipeline for Conflict Narrative Detection. In response to increased incidences of online abuse, a new industry of hate speech detection using NLP has emerged. Accordingly, we tested NLP technologies used by this industry to discover how quantitatively analysing language distorts meaning. We compiled a dataset comprising “Mein Kampf” from Hitler, “War on Terror” texts from George Bush and Osama bin Laden, and in how he advocated for non-violence, speeches from Martin Luther King provide control data. We tested both general-purpose and state-of-the-art sentiment analysis technologies from TextBlob, Google and IBM. Where distinctive results would be expected from a dataset of extremes, our tests show that regardless of technical sophistication, these technologies are unable to distinguish abusive from non-abusive texts. We address this problem with quantitatively analysing language by offering Conflict Narrative Detection as a new approach. Using a series of experiments published on GitHub, participants will learn about developing a sociotechnical pipeline to detect conflict narratives using the spaCy NLP python library. “Conflict narrative” means a narrative produced by an orator who intends to legitimise violence against their outgroup. Accordingly, guiding technical design is the theory of “cultural violence” from Peace Research, which explores processes of violence legitimisation. Detecting a conflict narrative means inferring what cultural violence calls the “Self-Other Gradient”. What follows is a hypothesis whereby the steeper the Self-Other Gradient in favour of an orator’s ingroup, the more legitimate acts of violence against their outgroup become. To infer this gradient, we move beyond quantitatively analysing language by employing qualitative methods, such as hypernymy. Accordingly, qualitative data produced by the pipeline represent the language patterns used to legitimise violence. Participants will learn how the Self-Other Gradient and these language patterns provide new data for tackling online abuse. https://sorse.github.io//programme/talks/event-006/ SORSE.enquiries@gmail.com SORSE
2020-09-15

event-024: Partner Event - HPC Champions Workshop

 
2020-09-17T12:00:00+00:00 2020-09-17T16:00:00+00:00 Partner Event - HPC Champions Workshop The next HPC Champions workshop will be held virtually over 2 afternoons on the 17th/18th September, and will involve talks, discussion sessions and working group sessions. Topics covered will include updates from the national and regional supercomputing sites, training, and plans for knowledge and skills repositories. https://sorse.github.io//programme/workshops/event-024/ SORSE.enquiries@gmail.com SORSE
 
2020-09-18T12:00:00+00:00 2020-09-18T16:00:00+00:00 Partner Event - HPC Champions Workshop The next HPC Champions workshop will be held virtually over 2 afternoons on the 17th/18th September, and will involve talks, discussion sessions and working group sessions. Topics covered will include updates from the national and regional supercomputing sites, training, and plans for knowledge and skills repositories. https://sorse.github.io//programme/workshops/event-024/ SORSE.enquiries@gmail.com SORSE
2020-09-14

event-027: Digital Humanities RSE: King’s Digital Lab as experiment and lifecycle

 
2020-09-29T15:00:00+00:00 2020-09-29T16:30:00+00:00 Digital Humanities RSE: King's Digital Lab as experiment and lifecycle This SORSE event describes King’s Digital Lab (KDL), a Research Software Engineering lab operating within the Faculty of Arts and Humanities at King’s College London (UK). The KDL team of 18 project managers, analysts, designers, engineers, and systems managers specialise in arts & humanities, cultural heritage, and creative industries research and development. The talk will provide a current state overview of the lab, and describe our RSE HR roles (see https://zenodo.org/record/2564790) and a relatively recent trial initiative that defines the different ways the team can contribute to research. A more technically-oriented overview of our ongoing work in refining the fundamental components of KDL Software Development Lifecycle (see https://github.com/kingsdigitallab/sdlc-for-rse/) will also be provided, including descriptions of our modelling workflows, processes, and efforts to increase sustainability, reproducibility, and research data management best practice (https://zenodo.org/record/3361580#.X09x6mdKhhE). https://sorse.github.io//programme/talks/event-027/ SORSE.enquiries@gmail.com SORSE
2020-09-08

event-017: What do we (not) know about RSE?

 
2020-10-28T08:00:00+00:00 2020-10-28T11:00:00+00:00 What do we (not) know about RSE? Research Software Engineering (RSE) is increasingly being established as a field and profession in its own right. Since the term was coined about a decade ago, RSE has also been the subject of empirical research to gain knowledge and evidence about the various aspects involved. For example, the 2017 “State of the Nation Report” by Alys Brett et al. (https://doi.org/10.5281/zenodo.495360) presents survey data about the demographics of UK-based RSEs, and Rotem Botvinik-Nezer et al. (https://doi.org/10.1038/s41586-020-2314-9) report on the extreme variability of results they found when they let many teams develop analysis programs for the same dataset. Such findings are the basis for the international RSE community to provide support and develop solutions for open problems. https://sorse.github.io//programme/workshops/event-017/ SORSE.enquiries@gmail.com SORSE
 
2020-10-30T15:00:00+00:00 2020-10-30T18:00:00+00:00 What do we (not) know about RSE? Research Software Engineering (RSE) is increasingly being established as a field and profession in its own right. Since the term was coined about a decade ago, RSE has also been the subject of empirical research to gain knowledge and evidence about the various aspects involved. For example, the 2017 “State of the Nation Report” by Alys Brett et al. (https://doi.org/10.5281/zenodo.495360) presents survey data about the demographics of UK-based RSEs, and Rotem Botvinik-Nezer et al. (https://doi.org/10.1038/s41586-020-2314-9) report on the extreme variability of results they found when they let many teams develop analysis programs for the same dataset. Such findings are the basis for the international RSE community to provide support and develop solutions for open problems. https://sorse.github.io//programme/workshops/event-017/ SORSE.enquiries@gmail.com SORSE
2020-09-08

event-002: Switching off the label ‘women in tech’

 
2020-09-02T13:50:00+00:00 2020-09-02T14:30:00+00:00 Switching off the label 'women in tech' The focus of the talk is on the ways in which women are discursively constructed in the context of professional spaces in tech clusters. This is to give time to consider how the label “women in tech” (WiT) is dominated by the masculine perspective of tech work and characterised by how individuals perform “identity work”. It has become apparent that the WiT label was already being used as shorthand for a problem very much with a name and her name is “woman”. https://sorse.github.io//programme/talks/event-002/ SORSE.enquiries@gmail.com SORSE
2020-09-04

event-001: I wanna dance with somebody

 
2020-09-02T13:10:00+00:00 2020-09-02T13:50:00+00:00 I wanna dance with somebody The Carpentries vision is to be the leading inclusive community teaching data and coding skills. Our first lesson program, Software Carpentry, was founded on several core values, including feedback, gratitude, and collaboration. The role research and data plays in your personal and professional life may contribute to your personal values and confidence in working with data. Have you ever considered your journey to data, your personal values, and whether they align? During this talk we will explore your personal journey to data and research, all while contemplating the following: How do your personal values align with your work as a Research Software Engineer? This talk is a pulse check. Be prepared to take notes, dig deep, and wrestle with issues of equity, inclusion, and accessibility. https://sorse.github.io//programme/talks/event-001/ SORSE.enquiries@gmail.com SORSE
2020-09-04

event-005: Help! I’m a Research Software Manager!

 
2020-10-07T16:30:00+00:00 2020-10-07T16:50:00+00:00 Help! I'm a Research Software Manager! Research software development teams are too important to be managed poorly. But no one teaches us to be good managers — especially in academia. https://sorse.github.io//programme/talks/event-005/ SORSE.enquiries@gmail.com SORSE
2020-09-01

event-019: Executable Research Article (ERA): Enrich a research paper with code and data

 
2020-09-09T14:00:00+00:00 2020-09-09T15:00:00+00:00 Executable Research Article (ERA): Enrich a research paper with code and data Code and data are important research output and integral to a full understanding of research findings and experimental approaches in a paper. However, traditional research articles seldom have these embedded in the manuscript’s narrative, but instead, leave them as “supplementary materials”, if they are openly available. https://sorse.github.io//programme/software-demos/event-019/ SORSE.enquiries@gmail.com SORSE
2020-08-31

event-020: Improving FAIRness with containers

 
2020-10-07T16:00:00+00:00 2020-10-07T16:30:00+00:00 Improving FAIRness with containers The FAIR guiding principles state that published research objects should be made Findable, Accessible, Interoperable, and Reusable for other researchers. Data repositories provide research dissemination following FAIR principles while also developing standards and tools to facilitate them. However, increased use of advanced research methods, such as virtual containers, supercomputers and GPUs, is introducing new challenges for research sharing. There is no standardized way of describing and disseminating such research outputs in data repositories. Furthermore, dissemination of data within virtual containers like Docker may hinder some of the commonly supported principles, such as findability and accessibility. https://sorse.github.io//programme/talks/event-020/ SORSE.enquiries@gmail.com SORSE
2020-08-26

event-018: How to understand and improve the performance of your parallel applications using the POP Methodology

 
2020-10-16T09:00:00+00:00 2020-10-16T09:30:00+00:00 How to understand and improve the performance of your parallel applications using the POP Methodology HPC applications are often very complex and their behavior depends on a wide range of factors from algorithms, to programming models, library and language implementations and hardware. The task of understanding performance bottlenecks of a parallel code and making improvements often ends up being a daunting trial and error process. To make the problem even more complicated, many HPC applications inherit different layers of legacy code, written and optimized for a different computing era. To optimize the performance of a parallel application, the first step is to understand the behavior of the application. However, there is often a lack of quantitative understanding of the actual behavior of HPC applications. The Performance Optimisation and Productivity (POP) Centre of Excellence, funded by the EU under the Horizon 2020 Research and Innovation Programme, attempts to establish a quantitative methodology for the assessment of parallel codes. This methodology uses a set of hierarchical metrics, where each metric represents relative impact of one cause of inefficiency in parallel codes. These metrics provide a standard, objective way to characterise different aspects of the performance of parallel codes. In this talk, I will review the development of these metrics and give examples of how use of these metrics allowed us to quickly identify the performance bottlenecks of applications from different domains of science and engineering. In addition, the POP methodology facilitates training HPC experts and performance analysts by defining a common and systematic approach to assessing and improving parallel codes. https://sorse.github.io//programme/talks/event-018/ SORSE.enquiries@gmail.com SORSE
2020-08-26

event-014: Becoming a self-employed RSE web developer.

 
2020-10-16T09:30:00+00:00 2020-10-16T10:00:00+00:00 Becoming a self-employed RSE web developer. This is a two part talk, initially focussing on how I changed career and established a sole trader business, the second part on the latest web development techniques I use. https://sorse.github.io//programme/talks/event-014/ SORSE.enquiries@gmail.com SORSE
2020-08-26

event-013: Research Software Directories: What, Why and How?

 
2020-09-16T18:00:00+00:00 2020-09-16T19:30:00+00:00 Research Software Directories: What, Why and How? This discussion session will focus on Research Software Directories: catalogues to showcase the software outputs of an institution or community. We will introduce the topic before demonstrating three independently-developed open source directories, explaining their respective benefits and ease of use, deployment and maintenance. Then we intend to form breakout groups to discuss some of the challenges associated with maintaining and curating such directories. https://sorse.github.io//programme/discussions/event-013/ SORSE.enquiries@gmail.com SORSE
2020-08-26

event-012: UXF - Framework for creating Virtual Reality human behavior experiments in Unity

 
2020-09-22T19:00:00+00:00 2020-09-22T19:30:00+00:00 UXF - Framework for creating Virtual Reality human behavior experiments in Unity Recent advances in technology has meant that Virtual Reality (VR) is now a feasible tool for performing human behaviour experiments. Scientists dream of being able to have full control over human sensory inputs, as well as complete measurement of responses. VR is coming closer to fulfilling this wish, but researchers must grapple with complex commercial tools (e.g. Unity) in order to create content. We present the Unity Experiment Framework (UXF), an open source toolkit for developing virtual reality experiments in Unity. UXF contains a suite of programming patterns, data collection features, and user interfaces which can be used by researchers to speed up development. This talk discusses the general uses of VR in human behaviour research, the conceptual design of UXF, and how UXF features are used in real experiments in psychology & neuroscience. https://sorse.github.io//programme/talks/event-012/ SORSE.enquiries@gmail.com SORSE
2020-08-26

event-010: Towards Knowledge Graphs of Research Software metadata

 
2020-09-22T19:30:00+00:00 2020-09-22T20:00:00+00:00 Towards Knowledge Graphs of Research Software metadata Research software is a key asset for understanding, reusing and reproducing results in computational sciences. An increasing amount of software is stored in code repositories, which usually contain human readable instructions indicating how to use it and set it up. However, developers and researchers often need to spend a significant amount of time to understand how to invoke a software component, prepare data in the required format, and use it in combination with other software. In addition, this time investment makes it challenging to discover and compare software with similar functionality. In this talk I will describe our efforts to address these issues by creating and using Open Knowledge Graphs that describe research software in a machine readable manner. Our work includes: 1) an ontology that extends schema.org and codemeta, designed to describe software and the specific data formats it uses; 2) an approach to publish software metadata as an open knowledge graph, linked to other Web of Data objects; and 3) a framework for automatically extracting metadata from software repositories; and 4) a framework to curate, query, explore and compare research software metadata in a collaborative manner. The talk will illustrate our approach with real-world examples, including a domain application for inspecting and discovering hydrology, agriculture, and economic software models; and the results of our framework when enriching the research software entries in Zenodo.org. https://sorse.github.io//programme/talks/event-010/ SORSE.enquiries@gmail.com SORSE
2020-08-26

event-007: Particle image velocimetry to study cell migration

 
2021-02-11T16:15:00+00:00 2021-02-11T16:45:00+00:00 Particle image velocimetry to study cell migration Particle image velocimetry (PIV) is a widely used optical method originally developed to understand fluid dynamics by tracking seeded particles moving through a fluid. In the context of biological disciplines, image-based pseudo-PIV is now a common tool to examine flows in tissues and cells, by exploiting the ability of tracking movement in time-lapse bioimages where features of interest are fluorescently tagged. A feature within a field of view at a specific time frame is searched for in subsequent frames by means of image cross-correlation. This allows for particle tracking and for the definition of a vector velocity field. We applied this technique to study cell migration, with a specific focus on retrograde flows of the actin cytoskeleton and their correlation to cell motion (Yolland et al., 2019). The aim of this software demonstration is to briefly introduce how the algorithm works, show the best strategies for parameter setting and demonstrate how to run it. Some application examples will be presented within the cell migration remit. The software can be found at https://github.com/stemarcotti/PIV; it is written in MATLAB and was tested with version R2018b (Curve Fitting Toolbox required). https://sorse.github.io//programme/software-demos/event-007/ SORSE.enquiries@gmail.com SORSE

event-028: European Environment for Scientific Software Installations (EESSI)

 
2020-11-25T15:00:00+00:00 2020-11-25T16:00:00+00:00 European Environment for Scientific Software Installations (EESSI) What if there was a way to avoid having to install a broad range of scientific software from scratch on every workstation, HPC cluster, or cloud instance you use or maintain, without compromising on performance? https://sorse.github.io//programme/software-demos/event-028/ SORSE.enquiries@gmail.com SORSE