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Slides for workshop "How do software management plans advance open science and contribute to research quality?" during the Open Science Conference 2023

Research software is widely used by researchers from all fields. Research software represents the set of operations and instructions to shape raw data to analytical and computational purposes. In this blog post, we describe how the FAIR principles apply to research software and point to useful resources.

Research software plays a crucial role in academic research and has become a key output of many research projects. A software management plan helps to implement best practices during software development and ensures that software is accessible and reusable in the short and longer term. It also contributes to the reproducibility of results and stimulates collaborative work on open-source software for research. TheNetherlands eScience CenterandNWO, the Dutch Research Council, tookthe initiative to form a working group anddevelop ed (national) guidelines for software management plans. This working group was composed of five experts in research software, representing different research organizations in the Netherlands, and roles within those organizations. The working group was active between December 2021 and September 2022.

Pitch of the Netherlands eScience Center Digital Skills Programme

As recognition of the vital importance of software for contemporary research is increasing, Research Software Engineering (RSE) is emerging as a discipline in its own right. We present an inventory of relevant research questions about RSE as a basis for future research and initiatives to advance the field, highlighting selected literature and initiatives. This work is the outcome of a RSE community workshop held as part of the 2020 International Series of Online Research Software Events (SORSE) which identified and prioritized key questions across three overlapping themes: people, policy and infrastructure. Almost half of the questions focus on the people theme, which addresses issues related to career paths, recognition and motivation; recruitment and retention; skills; and diversity, equity and inclusion. However, the people and policy themes have the same number of prioritized questions. We recommend that different types of stakeholders, such as RSE employers and policy makers, take responsibility for supporting or encouraging answering of these questions by organizations that have an interest. Initiatives such as the International Council of RSE Associations should also be engaged in this work.&nbsp

Funding organisations and those that support research software came together to explore how to effectively support both new and existing research software during the International Funders Workshop: The Future of Research Software. The crucial role of software in research is becoming increasingly apparent, as is the urgent need to sustain it and to invest in the people who develop and maintain it. Increased focus on research software will accelerate innovation, reduce information-sharing gaps, encourage innovation, and promote reproducibility, amongst other benefits. Read the report below or the short blog post from the Research Software Alliance.

The Research Software Alliance (ReSA) and the Netherlands eScience Center hosted a two-day international workshop in Amsterdam (the Netherlands) on 8-9 November 2023 to set the future agenda for national and international funders to support sustainable research software. As the importance of software in research has become increasingly apparent, so has the urgent need to sustain it. Funders can play a crucial role in this respect by ensuring structural support. Over the past few years, a variety of methods for sustaining research software have been explored, including improving and extending funding policies and instruments. During the workshop, funding organizations joined forces to explore how they can effectively contribute to making research software sustainable. In preparation of the workshop, a draft of a future international declaration, titled "Amsterdam Declaration on Funding Research Software Sustainability" was created by the Research Software Alliance, the Netherlands eScience Center and with input from stakeholders in the field.

In September 2021, the FAIR4RS WG formed subgroups to address milestones for the adoption of the FAIR4RS principles. This document is the output of subgroup 6, focused on adoption support.

Software is essential in modern research; it plays vital roles at multiple stages of the research lifecycle. The term Research Software is widely used in the academic community but, what do we mean when we use these terms? Software and research? When you think of software, you may think of a digital object that is executed on a machine. Yet software is more than just this, it is a complex and evolving artifact. It may be a concept or a project designed to solve a puzzle by a team or a community that develops its functionalities and algorithms, which might not be digital objects. Furthermore, the software artifacts are digital objects, e.g., executables and source code files for different environments. These digital artifacts, which are used in a scholarly setting, might be important in the research process, but should all these be considered Research Software? This report is the result of a discussion examining the scope of the community definition of the FAIR principles for Research Software as part of the work in the FAIR for Research Software working group (FAIR4RS). We aim to clarify the scope of the FAIR principles by identifying which software artifacts the FAIR principles should apply to. This discussion portrayed a complex landscape of software uses in research and existing definitions that can help to better understand the complexity of different types of software in academia. Finally we determine the scope of the FAIR4RS with a short and concise definition of Research Software as a separate metaphor of software in research.

The FAIR Software Route project is a joint inititiative of DANS & NLeSC which aims at establishing an online guide supporting researchers to publish and preserve their research software for the long term in an appropriate repository following the FAIR principles: Findable, Accessible, Interoperable and Reusable. The FAIR Software Route online guide will be also part of a more comprehensive resource (research-software.nl) providing information on coding best practices, software reuse, and training. A crucial step in building the FAIR Software Route online guide is to canvas the landscape of infrastructure providers in the field of software development, publication, storage and long term preservation. This exercise will capture information about existing projects, the role they play, and how they fit into a FAIR Software Route. The landscaping is also an aid to identify gaps in current practices and provide recommendations for the FAIR Software Route.

The FAIR Principles have two aspects: They were written specifically for research data and they also claim to be general for all research objects. In practice, this means that while the high-level concepts (findable, accessible, interoperable, and reusable) are generally applicable, the details of the wording, their context, and how they are applied is not. Different groups have been studying how the FAIR principles could be applied to other types of research objects, such as research software, machine learning models, and workflows, and this session will include talks on these three efforts and their status, followed by questions from the audience to the speakers and moderator.

Slides from the EuSSI SORSE session:https://sorse.github.io/programme/discussions/event-045/

Slides forTools, Practices & Systems (TPS) FebruarySeminar atThe Alan Turing Institute.

In this talk, I discussed the importance of the FAIR principles for the software tools we use to process data. Ranging from small analysis scripts to full fledged data processing pipelines, software needs to be FAIR to enable other researchers to reproduce our own experiments and reuse our software. However software and data are fundamentally different – software is executable in nature and may have intricate dependencies. FAIR principles apply differently to software than they do to data and we must be aware of these differences. Existing initiatives such as the RDA FAIR for Research Software (FAIR4RS) working group (https://www.rd-alliance.org/groups/fair-4-research-software-fair4rs-wg) and http://fair-software.eu/ are already focused on addressing these differences and raising awareness of the importance of FAIR for software.

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). The main objectives of EuSSI are to (1) produce standard guidelines and policies for good practices, (2) provide tools for software quality assessment, (3)conduct training and different community engagement, and (4) provide consultancy support on different aspects of software sustainability. However there may be other areas which should be considered. The idea of a EuSSI has been discussed in the past but has not yet materialised. Within this workshop, we will discuss the goal of EuSSI and would like to hear what a EuSSI could do for RSEs: what support do RSEs need which they cannot find in their local institutions? How should a EuSSI work with national RSE associations? We would appreciate input from early career RSEs (what obstacles you face starting as an RSE) as well as from established RSEs (what trends you see that should be considered). The European focus of EuSSI makes it easier for coordination, but excludes other geographical areas. Within the workshop, we encourage participants from outside Europe to share their views and suggestions. Since EuSSI is not a fully implemented infrastructure, the output of this session will help guide our efforts towards its creation and implementation.

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. Even though the definition of the FAIR software principles is still in flux, recommendations are available to improve software in accordance to the spirit of the FAIR principles. In this session we would like to introduce howfairis: a Python package to analyse software's compliance with the FAIR software recommendations. We will describe how howfairis analyses your code to measure its level of compliance with the FAIR software recommendations. We will show how our Github Action can test your software automatically. We will also show how to add a badge to your GitHub repository showing to the world how FAIR your software is! Given that the FAIR principles for software are still evolving, howfairis will also evolve to match new developments in the area. We would like new users to give us feedback and to contribute to the development of this tool!

Resumen Encuentro de Bioinformática en México 2021 Los principios FAIR del inglés (findable, accesible, interoperable y reusable) se traducen a localizable, accesible, interoperable y reutilizable. Estos principios son una guía para facilitar el descubrimiento de conocimientos ayudando a personas y máquinas a descubrir, acceder, integrar y analizar datos científicos apropiados para la tarea y sus algoritmos así como flujos de trabajo asociados. El término FAIR se originó en un taller de Lorentz en 2014, los principios FAIR resultantes se publicaron en 2016. El objetivo inicial de estos principios es que sean aplicables a todo tipo de objetos digitales, pero hasta ahora se les ha dado un enfoque particular en los datos de investigación. Dado que el software difiere de los datos por su naturaleza ejecutable, aplicar estos principios al software presenta desafíos particulares. En los últimos años, han surgido comunidades que trabajan en la adaptación y adopción de los principios FAIR para objetos de investigación distintos a los datos, por ejemplo FAIR para materiales de formación o FAIR para software de investigación. Nuestro grupo de trabajo FAIR4RS está estudiando y discutiendo diferentes aspectos en torno a FAIR para el software de investigación, por ejemplo, cómo se podrían adaptar los principios originales para el caso del software, cómo promover y medir la adopción, cómo apoyar la implementación, entre otros.En esta charla nos centraremos en qué es FAIR y cómo se puede aplicar al software de investigación. Luego hablaremos de una serie de desafíos de implementación e integraremos respuestas de la audiencia. Terminaremos explicando cómo los miembros de la comunidad científica e investigadores pueden involucrarse más en el proceso de aprender, contribuir o defender FAIR software.Palabras clave: FAIR, software de investigación, ciencia abierta, reproducciónreproducibilidadVideo: https://www.youtube.com/watch?v=Vy_hcWbjj7A

Presentación por invitación para el Encuentro de Bioinformática en México 2021 CDSB Los principios FAIR del inglés (findable, accesible, interoperable y reusable) se traducen a localizable, accesible, interoperable y reutilizable. Estos principios son una guía para facilitar el descubrimiento de conocimientos ayudando a personas y máquinas a descubrir, acceder, integrar y analizar datos científicos apropiados para la tarea y sus algoritmos así como flujos de trabajo asociados. El término FAIR se originó en un taller de Lorentz en 2014, los principios FAIR resultantes se publicaron en 2016. El objetivo inicial de estos principios es que sean aplicables a todo tipo de objetos digitales, pero hasta ahora se les ha dado un enfoque particular en los datos de investigación. Dado que el software difiere de los datos por su naturaleza ejecutable, aplicar estos principios al software presenta desafíos particulares. En los últimos años, han surgido comunidades que trabajan en la adaptación y adopción de los principios FAIR para objetos de investigación distintos a los datos, por ejemplo FAIR para materiales de formación o FAIR para software de investigación (FAIR4RS). Nuestro grupo de trabajo FAIR4RS está estudiando y discutiendo diferentes aspectos en torno a FAIR para el software de investigación, por ejemplo, cómo se podrían adaptar los principios originales para el caso del software, cómo promover y medir la adopción, cómo apoyar la implementación, entre otros.En esta charla nos centraremos en qué es FAIR y cómo se puede aplicar al software de investigación. Dremos algunas pautas de cómo los miembros de la comunidad científica e investigadores pueden involucrarse más en el proceso de aprender, contribuir o defender FAIR software.Palabras clave: FAIR, software de investigación, ciencia abierta, reproducciónreproducibilidadVideo: https://www.youtube.com/watch?v=Bh_wdHrjYBY

This is a guide to software development and projects at the Netherlands eScience Center. It both serves as a source of information for exactly how we work at the eScience Center, and as a basis for discussions and reaching consensus on this topic.

Research software is fundamental to today’s research, yet it does not receive the recognition it deserves. For example, research software is not yet adequately recognised in the scholarly record through citation. This situation contrasts starkly with the fact that open science and reproducible research is given ample attention at the policy level. We argue that if at the policy and institute level, everyone is convinced that open science leads towards better, more transparent and reproducible research, then visible and practical steps forward should be made that ensure that research software is treated on equal footing with publications and research data. In this paper, we present a concrete follow-up to the Declaration of Research Assessment (DORA) in the form of recommendations for raising the profile of research software. These recommendations provide steps for achieving recognition for research software as a fundamental and vital component of research. This paper focuses on the Netherlands, but the issues and recommendations could be adapted and adopted elsewhere. We divide our recommendations into four categories: Software availability and quality, Software sustainability, Training, and Human capital.

Brief overview of "Towards FAIR Principles for Research Software" paper (DOI: 10.3233/DS-190026). We discuss what makes software different from data with regard to the application of the FAIR principles, and which desired characteristics of research software go beyond FAIR. This presentation was given at the Earth Science Information Partners (ESIP) Winter Meeting held in Bethesda, MD in January 2020.

Aquest TFM té per objectiu ampliar el material didàctic existent per a l'estudi de la transmissió i transformació de moviment per a 3r d'ESO. El material existent del contingut curricular "Mecanismes per a la transmissió i transformació del moviment i la seva funció en diferents màquines" és força variat i n'hi ha moltíssim. Ara bé, no hi ha gaire informació específica sobre la transmissió de moviment rotatiu a rotatiu oscil·lant. Al llarg del desenvolupament del treball, he dissenyat dos prototips sobre aquest tipus de transmissió per ampliar el material existent. Els prototips són semblants perquè l'entrada és rotativa i la sortida és alternativa oscil·lant però en un s'aconsegueix mitjançant una palanca de primer grau i l'altre mitjançant una palanca de segon grau (vegeu les figures 3 i 4 i els vídeos [14] i [15]). Amb aquest TFM es pretén proporcionar suficient material per tal que es pugui estudiar a l'aula una bona part dels continguts del bloc curricular "Màquines i mecanismes" mitjançant la creació d'un prototip. En aquest TFM s'utilitzen dos prototips com a eina. L'alumnat tindrà la possibilitat de dissenyar i fabricar el mecanisme que se'ls ajusti millor i l'escolliran ells tot i que en aquest TFM es treballa amb els dos mecanismes esmentats. This TFM aims to expand the existing teaching material for the study of the transmission and transformation of movement for 3rd ESO. The existing material of the curricular content "Mechanisms for the transmission and transformation of movement and its function in different machines" is quite varied and there is a lot. However, there is not much specific information on the transmission of rotary motion to oscillating rotary motion. Throughout the development of the work, I have designed two prototypes on this type of transmission to expand the existing material. The prototypes are similar because the input is rotary and the output is alternately oscillating but one is achieved by a first degree lever and the other by a second degree lever (see the figures 3 and 4 and the videos [14] and [15]). The aim of this TFM is to provide enough material so that a good part of the contents of the "Machines and mechanisms" curriculum block can be studied in the classroom by creating a prototype. In this TFM two prototypes are used as a tool. Students will have the opportunity to design and manufacture the mechanism that best suits them and will choose it, however in this TFM we work with the two mentioned mechanisms Este TFM tiene por objetivo ampliar el material didáctico ya existente para el estudio de la transmisión y transformación de movimiento para 3º de ESO. El material existente del contenido curricular "Mecanismos para la transmisión y transformación del movimiento y su función en diferentes máquinas" es bastante variado y hay muchísimo. Sin embargo, no hay mucha información específica sobre la transmisión de movimiento rotativo a rotativo oscilante. A lo largo del desarrollo del trabajo, he diseñado dos prototipos sobre este tipo de transmisión para ampliar el material existente. Los prototipos son similares porque la entrada es rotativa y la salida es alternativa oscilante pero uno lo consigue mediante una palanca de primer grado y el otro mediante una palanca de segundo grado, (véanse las figuras 3 y 4 y los vídeos [14] y [15]). Con este TFM se pretende proporcionar suficiente material para que se pueda estudiar en el aula una buena parte de los contenidos del bloque curricular "Máquinas y mecanismos" mediante la creación de un prototipo. En este TFM se utilizan dos prototipos como herramienta. El alumnado tendrá la posibilidad de diseñar y fabricar el mecanismo que se le ajuste mejor y lo escogerán ellos, sin embargo, en este TFM se trabaja con los dos mecanismos mencionados

Research software is fundamental to contemporary research, yet it does not receive the recognition it rightfully deserves. This needs to change, particularly in the context of the discussions around open science and reproducibility. We argue that if open science is to truly lead towards better, more transparent, and reproducible research, then research software needs to be treated in equal footing to research data and publications at the policy level. In this paper, we present a concrete followup to the DORA declaration in the form of recommendations for raising the profile of research software. We divide our recommendations into four categories: Software availability and quality, Software sustainability, Training, and Human capital. These recommendations provide steps for achieving recognition for research software as a fundamental and vital component of research.

The authors are listed alphabeticallyby order of last name. This presentation was collaboratively prepared for and givenat a meeting withNWO (The Netherlands Organisation for Scientific Research; the national research council of the Netherlands) on 28 March 2019. Our aim wasto highlight the importance of research software in contemporary research and its relationship to research data, open science, and reproducibility in research. Our key messages to NWO: If open science is to lead towards better, more transparent, and reproducible research, then research software, research data and publications need all to be treated on equal footing at the policy level. NWO should make more explicit policies for supporting and evaluating research software. There are some differences when it comes to research software preservation (Software Sustainability) as compared to data preservation, but it shouldn’t be more difficult.

Life science research increasingly depends on computational skills that enable efficient work with large complex datasets. Unfortunately, formal curricula often lack training in this area. There is a need for specialised training that includes topics like shell scripting, basic programming skills in R or Python, data handling, reproducible computational research and open science.

Responsible data management is part of good research, and an important prerequisite for Open Science. To promote the practice of Open Science, and the principles of FAIR data and software, the Netherlands eScience Center actively participates in the National Platform Open Science. In line with this initiative, the eScience Center strives to make the research data collected or generated in the projects it participates in to become freely and sustainably available, as much as possible, for reuse by other researchers. Furthermore, the Netherlands eScience Center aims to raise awareness among researchers that responsible data management is an essential requirement for reproducibility of scientific results, and for enhancement of the correctness and transparency thereof.

Presentations given by Maria J. Cruz, Marc Galland, Carlos Martinez Ortiz, and YaseminTurkyilmaz-van der Veldenon 2 October 2018 as part of an interactive session on software reproducibility held in Utrecht, in the Netherlands, as part of the event DTL Communities@Work 2018.