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event-046: QGameTheory: An R package for teaching quantum computing and quantum game theory to students
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2021-03-16T14:30:00+00:00
2021-03-16T14:40:00+00:00
QGameTheory: An R package for teaching quantum computing and quantum game theory to students
This is a package that has been written in the R programming language. As we know, R is an open-source software that is being widely used by statisticians and scientists all over the world. The purpose of this package is to build a very simple open-source project that will teach the basics of quantum computing and quantum game theory to interested students starting in this field. Available in the CRAN repository, this package can be used to learn the basics to simulate the results of simple quantum circuits and also learn basics of quantum game theory models. Some of the models included in this package are quantum penny flip, quantum prisoner’s dilemma, and more.
https://sorse.github.io//programme/posters/event-046/
SORSE.enquiries@gmail.com
SORSE
2021-03-09
event-048: A new distributed data analysis framework for better scientific collaborations
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2021-03-03T10:30:00+00:00
2021-03-03T10:45:00+00:00
A new distributed data analysis framework for better scientific collaborations
A common challenge for projects with multiple involved research institutes is a well-defined and productive collaboration. All parties measure and analyze different aspects, depend on each other, share common methods, and exchange the latest results, findings, and data. Today this exchange is often impeded by a lack of ready access to shared computing and storage resources. In our talk, we present a new and innovative remote procedure call (RPC) framework. We focus on a distributed setup, where project partners do not necessarily work at the same institute, and do not have access to each others resources.
We present an application programming interface (API) developed in Python that enables scientists to collaboratively explore and analyze sets of distributed data. It offers the functionality to request remote data through a comfortable interface, and to share and invoke single computational methods or even entire analytical workflows and their results. The prototype enables researchers to make their methods accessible as a backend module running on their own infrastructure. Hence researchers from other institutes may apply the available methods through a lightweight python or Javascript API. In the end, the overhead for both, the backend developer and the remote user, is very low. The effort of implementing the necessary workflow and API usage equalizes the writing of code in a non-distributed setup. Besides that, data do not have to be downloaded locally, the analysis can be executed “close to the data” while using the institutional infrastructure where the eligible data set is stored.
With our prototype, we demonstrate distributed data access and analysis workflows across institutional borders to enable effective scientific collaboration.
This framework has been developed in a joint effort of the DataHub and Digitial Earth initiatives within the Research Centers of the Helmholtz Association of German Research Centres, HGF.
https://sorse.github.io//programme/talks/event-048/
SORSE.enquiries@gmail.com
SORSE
2021-03-03
event-042: Wikidata as a research tool for data modelling and integration in the humanities - Examples from the German Wikimedia Fellow Program Free Knowledge
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2021-03-03T10:00:00+00:00
2021-03-03T10:30:00+00:00
Wikidata as a research tool for data modelling and integration in the humanities - Examples from the German Wikimedia Fellow Program Free Knowledge
Research Software Engineers and their work is becoming increasingly important in digital humanities research just as digital humanities gain traction. Not just developing and extending software are important for this process, data creation, data publication and data management are equally critical; as the idiom goes, “data matures like wine, applications like fish”. Therefore, RSEs need to store their ‘wine’ FAIRly to make it accessible in the future. In this talk we present Wikidata as a data integration hub for FAIR Linked Open Data (LOD), that can be used with many research software tools, e.g. SPARQLing Unicorn, QGIS plugin and Scholia. Wikidata is the information storage system in the Wikimedia Universe. In particular, Wikidata is ideal for data modeling and immediate publishing as any user can create their own (semantic) data model and map it to Wikidata. A number of tools and APIs already exist for applying Wikidata to open research [1]. As an example use case we will present two projects from the German Wikimedia Fellow-Programme Free Knowledge. The first, Irish Ogham Stones in the Wikimedia Universe [2], focuses on linking different data sets on Ogham Stones within the Wikimedia Universe and the second, Smashed Dishes – Archaeological Sources in Wikidata [3], aims to create possibilities for amateur archaeologists to collect and publish their data. As a conclusion, we will discuss the advantages we found in using Wikidata. These include enhanced data re-usability and availability, FAIRly published data and data and possibilities for data integration between diverse data sources and research software. Data and software integration may lead to Linked Open Data and, the resulting interoperability opens up new possibilities for RSEs.
https://sorse.github.io//programme/talks/event-042/
SORSE.enquiries@gmail.com
SORSE
2021-03-03
event-043: Little Minions in Archaeology - an open space for RSE software and small scripts in digital archaeology
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2021-03-03T10:45:00+00:00
2021-03-03T10:55:00+00:00
Little Minions in Archaeology - an open space for RSE software and small scripts in digital archaeology
In our daily work, small self-made scripts, home-grown small applications and small hardware devices significantly help us to get work done. These little helpers - “little minions” - often reduce our workload or optimise our workflows, although they are not often presented to the outside world and the research community. Instead, we generally focus on presenting the results of our research and silently use our small tools to generate these, without not even pointing to them, especially to the source code or building instructions. In archaeology, research software is underrepresented in conference talks as well as in research publications. We have to promote these little minions in the RSE community and make them visible. That is why we created a Working Group for Little Minions at the CAA (https://caa-international.org) conference for digital archaeological research and created a session that focus on these “little minions” and invite researchers to share their little helpers, so that the scientific community may benefit and - perhaps - create spontaneously special minion interest groups. In such a minion session we are focussing on lightning talks - aka “minion talks” - where a wide range of tools are shared. Each “minion talk” explains the innovative character and mode of operation of the digital tool. Open Science is the aim of the little minions. Therefore, our aim is that all minions are non-proprietary, open and freely available (e.g. GitHub, GitLab, etc.). The last are not obligatory and tools that are not (yet) available can also be accepted.A constantly expanding list of little minions can be found at https://github.com/caa-minions/minions. In this poster we will present our concept to promote research software at scientific conferences and share our experience on the idea.
https://sorse.github.io//programme/posters/event-043/
SORSE.enquiries@gmail.com
SORSE
2021-03-03
event-044: How FAIR is your research software?
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2021-03-09T17:00:00+00:00
2021-03-09T17:30:00+00:00
How FAIR is your research software?
FAIR software is a topic of growing importance in the research software landscape. There have been efforts to describe the how the FAIR principles apply to research software and work in this direction is still ongoing.
https://sorse.github.io//programme/software-demos/event-044/
SORSE.enquiries@gmail.com
SORSE
2021-03-01
event-040: Four pillars of a reproducible PhD
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2021-03-16T14:40:00+00:00
2021-03-16T14:50:00+00:00
Four pillars of a reproducible PhD
Reproducibility and sustainability of research and associated software are increasingly viewed as priorities by publishers, funders and the academic community. The process of writing a thesis can be a playground where modern PhD students can explore new tools and techniques for improving the reproducibility and sustainability of their research, however the number of possible tools is vast and potentially overwhelming. This talk and associated blog post present the author’s personal opinion on the four underpinning elements of a reproducible PhD: version control, automation, open publishing and sustainable software; and describes specific tools and principles used in the production of the author’s thesis. This description may offer a template for future students wishing to perform reproducible research.
https://sorse.github.io//programme/posters/event-040/
SORSE.enquiries@gmail.com
SORSE
2021-02-22
event-045: Why do we need an EuSSI?
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2021-03-10T13:00:00+00:00
2021-03-10T14:30:00+00:00
Why do we need an EuSSI?
Software sustainability is an important aspect of research software engineering. Good practices in software sustainability are still evolving and are not yet universally standardized. Different practices have emerged within domain specific communities, and expertise is additionally shared in local communities. This leads to different sets of rules being practiced by different communities, despite all of them sharing similar objectives. Knowledge transfer and sharing expertise between communities will benefit all involved communities by avoiding duplication of efforts and identifying common grounds for good practices. This is the goal of the European Software Sustainability Infrastructure (EuSSI).
https://sorse.github.io//programme/discussions/event-045/
SORSE.enquiries@gmail.com
SORSE
2021-02-19
event-039: On the evaluation of research software: the CDUR procedure
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2021-03-16T14:00:00+00:00
2021-03-16T14:30:00+00:00
On the evaluation of research software: the CDUR procedure
The goal of the proposed talk is to present the publication
https://sorse.github.io//programme/talks/event-039/
SORSE.enquiries@gmail.com
SORSE
2021-02-19
event-035: Research On The Go
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2021-02-18T14:00:00+00:00
2021-02-18T15:00:00+00:00
Research On The Go
Software for research comes in many different forms and technologies. This includes software that runs on mobile devices. The demand for this is growing, whether it is for “citizen-science” projects or in clinical and educational research. In this SORSE (online) roundtable event, we discuss
examples of mobile apps for research
what are the challenges for mobile apps in and for research. In particular:
logistic of deploying and delivering mobile apps
maintenance costs
distribution of apps - what are the options
how to build the right team for mobile apps development
what technology stacks are used in mobile app development. And what determines the choice?
Note: this event will be recorded for a podcast.
https://sorse.github.io//programme/panels/event-035/
SORSE.enquiries@gmail.com
SORSE
2021-01-27
event-031: Building Research Software Communities: How to increase engagement in your community
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2021-03-17T09:00:00+00:00
2021-03-17T11:00:00+00:00
Building Research Software Communities: How to increase engagement in your community
Communities are a very important aspect of the development and sustainability of research software engineering. It was as the result of a community meeting back in 2012 that the Research Software Engineering (RSE) movement came about. This goes to show the potential power of a group of individuals coming together from a range of different research backgrounds with common challenges, important ideas and a desire to drive change. Research software communities provide a place for RSEs and researchers to build knowledge, develop networks and find collaborators. They also provide a space to develop policies and advocate for the importance of RSE and the best practices it promotes.
https://sorse.github.io//programme/workshops/event-031/
SORSE.enquiries@gmail.com
SORSE
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2021-03-18T09:00:00+00:00
2021-03-18T11:00:00+00:00
Building Research Software Communities: How to increase engagement in your community
Communities are a very important aspect of the development and sustainability of research software engineering. It was as the result of a community meeting back in 2012 that the Research Software Engineering (RSE) movement came about. This goes to show the potential power of a group of individuals coming together from a range of different research backgrounds with common challenges, important ideas and a desire to drive change. Research software communities provide a place for RSEs and researchers to build knowledge, develop networks and find collaborators. They also provide a space to develop policies and advocate for the importance of RSE and the best practices it promotes.
https://sorse.github.io//programme/workshops/event-031/
SORSE.enquiries@gmail.com
SORSE
2021-01-22
event-041: Embedding a Jupyter Notebook
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2021-01-20T15:00:00+00:00
2021-01-20T16:00:00+00:00
Embedding a Jupyter Notebook
Many RSEs and researchers are familiar with using Jupyter Notebooks to analyse data and output results, but how can this functionality be included within a larger platform or application? Creating a new analysis tool would take a lot of developer hours, and so a more cost-effective solution could be to embed Jupyter within your application.
https://sorse.github.io//programme/posters/event-041/
SORSE.enquiries@gmail.com
SORSE
2021-01-14
event-025: Development of an Automated High-Throughput Animal Training Platform
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2021-01-20T15:00:00+00:00
2021-01-20T16:00:00+00:00
Development of an Automated High-Throughput Animal Training Platform
In traditional neuroscience laboratory research, training animals to execute sensorimotor tasks is time consuming, labor and resource intensive, and prone to human bias and error. The Research Software Engineering team at Harvard University’s Faculty of Arts and Science Research Computing (FASRC) has developed an automated training system pipeline that standardizes and automates animal training. The pipeline consists of Teensy microcontrollers that monitor animal training events, RaspberryPis that orchestrate and log training instructions, PiCameras that record subjects, and open-source software, including a Vue web interface, a Flask server, and a PostGreSQL database.
https://sorse.github.io//programme/talks/event-025/
SORSE.enquiries@gmail.com
SORSE
2021-01-14
event-037: RSE careers in France: the French National Centre for Scientific Research (CNRS) option
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2021-02-23T14:00:00+00:00
2021-02-23T15:00:00+00:00
RSE careers in France: the French National Centre for Scientific Research (CNRS) option
In this talk, I will introduce the French National Centre for Scientific Research (CNRS). The CNRS is an interdisciplinary public research organisation under the administrative supervision of the French Ministry of Higher Education and Research. Its main role is to advance knowledge for the benefit of society. It is the only French organisation for multidisciplinary research and a key player in international research, as well as a recognised innovator. It is a unique provider of researchers for universities but more importantly it offers a sustainable career path for engineers and technicians. The engineers and technicians from the CNRS contribute to and support research over 200 occupations from numerous professional fields, including sciences of the living world, chemical sciences, the humanities and social sciences, computer science, information, administration, and management. In this talk, I will focus in particular on the career of Research Software Engineer (RSE) via the CNRS and how RSEs contribute to the excellence of the French research in High Performance Computing.
https://sorse.github.io//programme/talks/event-037/
SORSE.enquiries@gmail.com
SORSE
2021-01-10
event-036: Code Review Community
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2021-01-20T15:00:00+00:00
2021-01-20T16:00:00+00:00
Code Review Community
Code review for research software is the process by which peers evaluate each other’s source code. This involves checking that the code does what it claims and is written in a way that can easily be read, maintained, and built upon. Code review is an important tool for ensuring that software is high-quality and reusable, and should be a widely-adopted “best practice”.
https://sorse.github.io//programme/posters/event-036/
SORSE.enquiries@gmail.com
SORSE
2021-01-10
event-007: Particle image velocimetry to study cell migration
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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
2021-01-10
event-033: Applying Scrum to Research Software Projects
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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
2021-01-10
event-032: Research Software and the Modelling of COVID-19 in the UK
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2021-01-13T15:00:00+00:00
2021-01-13T16:30:00+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
2021-01-10
event-030: Research Squirrel Engineers - An independent squirrel network for RSEs in DH and archaeology
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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
2021-01-10
event-029: My project expired and my team left, so let’s rewrite all the software from scratch
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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
2021-01-10
event-028: European Environment for Scientific Software Installations (EESSI)
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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
2021-01-10
event-026: The Continual Road to an Inclusive Definition and Use of Terms for the US Research Software Engineer Community
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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
2021-01-10
event-022: Learnings from developing and maintaining a research software that has been used more than 3 million times in the last 3 years
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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
2021-01-10
event-023: Optimal time frequency analysis for biological data - pyBOAT
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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
2021-01-10
event-027: Digital Humanities RSE: King’s Digital Lab as experiment and lifecycle
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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
2021-01-10
event-002: Switching off the label ‘women in tech’
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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
2021-01-10
event-001: I wanna dance with somebody
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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
2021-01-10
event-017: What do we (not) know about RSE?
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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
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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
2021-01-10
event-016: FAIR 4 Research Software
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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
2021-01-10
event-020: Improving FAIRness with containers
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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
2021-01-10
event-018: How to understand and improve the performance of your parallel applications using the POP Methodology
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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
2021-01-10
event-015: Bringing Imaging-Based Artificial Intelligence into Clinical Practice in NHS Radiology
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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
2021-01-10
event-014: Becoming a self-employed RSE web developer.
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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
2021-01-10
event-019: Executable Research Article (ERA): Enrich a research paper with code and data
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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
2021-01-10
event-013: Research Software Directories: What, Why and How?
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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
2021-01-10
event-034: Web apps with the power of Python
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2021-02-03T16:00:00+00:00
2021-02-03T17:00:00+00:00
Web apps with the power of Python
Learn how to speak Python for the web!
https://sorse.github.io//programme/software-demos/event-034/
SORSE.enquiries@gmail.com
SORSE
2020-12-14
event-011: Configuring Sphinx from scratch: making your own documentation and making your documentation your own
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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-009: From experimental software to research infrastructure maturity
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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-021: Goodbot, Badbot? Engineering trust into conversational interfaces
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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-006: Towards an NLP Pipeline for Conflict Narrative Detection
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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
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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-005: Help! I’m a Research Software Manager!
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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-012: UXF - Framework for creating Virtual Reality human behavior experiments in Unity
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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
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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-038: When Spreadsheets Attack! (and other maths disasters.)
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2020-12-17T14:45:00+00:00
2020-12-17T16:45:00+00:00
When Spreadsheets Attack! (and other maths disasters.)
In October 2020 the UK government lost thousands of COVID test results because
they hit the limit of the maximum number of rows in an Excel file. This is but
one of many, many mistakes made all around the world because of spreadsheet
abuse. In 2012 the State Office of Education in Utah miscalculated its budget to
the tune of $25 million because of what State Superintendent Larry Shumway
called ‘a faulty reference’ in a spreadsheet. In 2011 the village of West
Baraboo in Wisconsin miscalculated how much their borrowing would cost by
$400,000 because a range being summed missed one important cell.
https://sorse.github.io//programme/talks/event-038/
SORSE.enquiries@gmail.com
SORSE