<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="3.10.0">Jekyll</generator><link href="https://agbeltran.github.io/feed.xml" rel="self" type="application/atom+xml" /><link href="https://agbeltran.github.io/" rel="alternate" type="text/html" /><updated>2024-08-09T01:15:16-07:00</updated><id>https://agbeltran.github.io/feed.xml</id><title type="html">Alejandra Gonzalez-Beltran, PhD</title><subtitle>Computer &amp; Data Scientist working on data standards and software tools to enable data sharing and research reproducibility</subtitle><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><entry><title type="html">Best Practices for Software Registries and Repositories</title><link href="https://agbeltran.github.io/posts/2021/08/best-practices-software-repositories" rel="alternate" type="text/html" title="Best Practices for Software Registries and Repositories" /><published>2021-08-04T00:00:00-07:00</published><updated>2021-08-04T00:00:00-07:00</updated><id>https://agbeltran.github.io/posts/2021/08/best-practices-software-repositories</id><content type="html" xml:base="https://agbeltran.github.io/posts/2021/08/best-practices-software-repositories"><![CDATA[<p>(This post is cross-posted on the <a href="https://scicodes.net/best-practices-for-software-registries-and-repositories/">SciCodes website</a>,
the <a href="https://www.software.ac.uk/blog">SSI blog</a>, the <a href="http://ascl.net/wordpress/2021/08/04/best-practices-for-software-registries-and-repositories/">ASCL blog</a>,
and the <a href="https://www.force11.org/blog/best-practices-software-registries-and-repositories">FORCE11 blog</a>, <a href="https://bssw.io/blog_posts/best-practices-for-software-registries-and-repositories">Better Scientific Software (BSSW) website</a>.)</p>

<p>Software is a fundamental element of the scientific process, and cataloguing scientific software is helpful to enable
software discoverability. During the years 2019-2020, the <a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#authors">Task Force on Best Practices for Software Registries</a>
of the <a href="https://www.force11.org/group/software-citation-working-group">FORCE11 Software Citation Implementation Working Group</a>
worked to create <a href="https://arxiv.org/abs/2012.13117">Nine Best Practices for Scientific Software Registries and Repositories</a>.
In this post, we explain why scientific software registries and repositories are important, why we wanted to create a
list of best practices for such registries and repositories, the process we followed, what the best practices include,
and what the next steps for this community are.</p>

<h2 id="why-are-scientific-software-registries-and-repositories-important">Why are scientific software registries and repositories important?</h2>

<p>Scientific software registries and repositories support identifying and finding software, provide information for software
citation, foster long-term preservation and reuse of computational methods, and ultimately, improve research reproducibility
and replicability.</p>

<h2 id="why-did-we-write-these-guidelines">Why did we write these guidelines?</h2>

<p>Managers of scientific software registries and repositories have been working independently to run their services and provide
useful information and tools to users in different communities. The Best Practices for Software Registries Task Force
participants had different perspectives representing a heterogeneous set of resources, but came together for the common
goal of creating a list of best practices for scientific software registries. These shared practices help to raise awareness
of software as a research output, enable credit for software creators, and guide curators working on software catalogues
through the steps to consider when setting up their software registries. In the longer term, we hope to improve the interoperability
of the software metadata supported by different services.</p>

<p>The goals that we considered for writing the guidelines were:</p>

<ul>
  <li>to have a minimal number of best practices, easy to adopt by repository managers</li>
  <li>to be broadly applicable to most or all of our resources</li>
  <li>to be descriptive on a meta level, not prescriptive, and focused on what the best practices should do or provide, not on what a suggested policy or element should specifically say.</li>
</ul>

<h2 id="what-are-the-best-practices">What are the best practices?</h2>

<p>Our guidelines, listed below, provide an overview of the key points to take into consideration when creating a software registry. They are:</p>

<ul>
  <li>Provide a public scope statement (<a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#policy-examples-scope-statement">examples</a>)</li>
  <li>Provide guidance for users</li>
  <li>Provide guidance to software contributors (<a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#policy-examples-authorship">examples</a>)</li>
  <li>Establish an authorship policy</li>
  <li>Share your metadata schema (<a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#policy-examples-metadata-schema">examples</a>)</li>
  <li>Stipulate conditions of use (<a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#policy-examples-conditions-of-use-policy">examples</a>)</li>
  <li>State a privacy policy (<a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#policy-examples-privacy-policy">examples</a>)</li>
  <li>Provide a retention policy (<a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#policy-examples-retention-policy">examples</a>)</li>
  <li>Disclose your end-of-life policy (<a href="https://asclnet.github.io/SWRegistryWorkshop/Products/BestPractices.html#policy-examples-end-of-life-policy">examples</a>)</li>
</ul>

<p><a href="https://arxiv.org/abs/2012.13117">Our pre-print</a> offers more explanation about each guideline and a longer list of implementations
that we found when we were doing our work on these practices.</p>

<h2 id="what-process-did-we-follow-to-produce-the-guidelines">What process did we follow to produce the guidelines?</h2>

<p>Representatives from numerous software registries and repositories were involved in the FORCE11 Software Citation Implementation
Working Group (SCIWG). Alice Allen proposed that we form a task force within the SCIWG for writing up some best practices for the
registries and repositories, and with acceptance by the co-chairs of the SCIWG and interest from relevant people, the Task Force
on Best Practices for Software Registries was formed. Initially, we gathered information from members of this Task Force to learn
more about each resource and to identify some of our overlapping interests. We then identified potential best practices based on
prior issues we experienced running our services and  discussed what each potential practice might include or exclude.</p>

<p>Through iterative deliberations, we determined which of the potential practices were the most broadly applicable. With generous
funding from the <a href="https://sloan.org/">Alfred P. Sloan Foundation</a>, we hosted a <a href="https://asclnet.github.io/SWRegistryWorkshop/">workshop</a>
for scientific registries and repositories, part of which was devoted to gathering final consensus around the Best Practices.
The workshop included registries who were not part of the Task Force, resulting in a broader set of contributions to the final list.</p>

<h2 id="what-are-the-next-steps-for-the-group">What are the next steps for the group?</h2>

<p>Our goal is to continue our efforts by implementing these practices more uniformly in our own registries and repositories and
reducing the burdens of adoption. We have created SciCodes, a 
<a href="https://scicodes.net/2021/04/09/welcome-to-scicodes/">consortium of scientific software registries and repositories</a>, which is
now defining the next priorities to tackle, such as tracking the impact of good
<a href="https://www.villanovau.com/resources/bi/metadata-importance-in-data-driven-world/">metadata</a>, improving interoperability between
registries, and making our metadata more discoverable by search engines and services such as
<a href="https://scholar.google.com/">Google Scholar</a>, <a href="https://orcid.org/">ORCID</a>, and discipline indexes. We are also sharing tools and
ideas in a <a href="https://scicodes.net/presentations/">series of presentations</a> that are recorded and available for viewing on the 
<a href="https://scicodes.net/">SciCodes website</a>, so please check them out!</p>]]></content><author><name>Alejandra Gonzalez-Beltran, Alice Allen, Allen Lee, Daniel Garijo, Thomas Morrell, SciCodes Consortium</name></author><summary type="html"><![CDATA[(This post is cross-posted on the SciCodes website, the SSI blog, the ASCL blog, and the FORCE11 blog, Better Scientific Software (BSSW) website.)]]></summary></entry><entry><title type="html">Evidence for the importance of research software</title><link href="https://agbeltran.github.io/posts/2020/08/ReSA-evidence" rel="alternate" type="text/html" title="Evidence for the importance of research software" /><published>2020-06-08T00:00:00-07:00</published><updated>2020-06-08T00:00:00-07:00</updated><id>https://agbeltran.github.io/posts/2020/08/ReSA-evidence</id><content type="html" xml:base="https://agbeltran.github.io/posts/2020/08/ReSA-evidence"><![CDATA[<p>(This post is cross-posted on the <a href="http://urssi.us/blog/2020/06/08/evidence-for-the-importance-of-research-software/">URSSI blog</a>, the <a href="https://www.software.ac.uk/blog/2020-06-08-evidence-importance-research-software">SSI blog</a> and the <a href="https://blog.esciencecenter.nl/evidence-for-the-importance-of-research-software-1cb4a49077f3">Netherlands eScience Center blog</a>, and is archived in <a href="https://doi.org/10.5281/zenodo.3873832">Zenodo</a>)</p>

<p>This blog analyses work evidencing the importance of research software to research outcomes, to enable the research software community to find useful evidence to share with key influencers. This analysis considers papers relating to meta-research, policy, community, education and training, research breakthroughs and specific software.</p>

<p>The <a href="http://www.researchsoft.org/">Research Software Alliance</a> (ReSA) <a href="http://www.researchsoft.org/resa-taskforces-join-us/">Taskforce for the importance of research software</a> was formed initially to bring together existing evidence showing the importance of research software in the research process. This kind of information is critical to achieving ReSA’s vision to have research software recognised and valued as a fundamental and vital component of research worldwide.</p>

<p><strong>Methodology</strong></p>

<p>The Taskforce has utilised crowdsourcing to locate resources in line with ReSA’s mission to bring research software communities together to collaborate on the advancement of research software. The Taskforce invited <a href="https://groups.google.com/forum/?pli=1#!forum/research-software-alliance">ReSA google group members</a> in late 2019 to submit evidence about the importance of software in research to a <a href="https://www.zotero.org/groups/2400609/resa/library">Zotero group library</a>. Evidence could be from a wide range of sources including newspapers, blogs, peer-reviewed journals, policy documents and datasets.</p>

<p>The submissions to Zotero submitted to date highlight the significant role that software plays in research. We decided to tag the submissions based on analysis of the submissions and how <a href="http://urssi.us/blog/2020/03/11/the-research-software-alliance-resa-and-the-community-landscape/">some community research software organisations</a> categorise focus areas. Some of the documents were also tagged by country and/or research discipline to enable users to search from that perspective were relevant. This resulted in tagging of submissions with one or more of the following tags, which are explained in the following sections:</p>

<ul>
  <li>Meta-research</li>
  <li>Policy</li>
  <li>Community</li>
  <li>Education and training</li>
  <li>Research breakthroughs</li>
  <li>Software</li>
</ul>

<p><strong>Submission contents</strong></p>

<p>Explanation of each category, and examples of some of the resources, are highlighted below. It should be noted that some of the resources mentioned below are important in a number of the categories; however, have only been cited here in one category.</p>

<p><strong>Meta-research</strong> contains resources that include analysis of how software is developed and used in research:</p>

<ul>
  <li><a href="https://www.oecd-ilibrary.org/science-and-technology/charting-the-digital-transformation-of-science_1b06c47c-en">Charting the digital transformation of science: Findings from the 2018 OECD International Survey of Scientific Authors (ISSA2)</a> includes evidence that 25% of research produces new code.</li>
  <li><a href="https://uk.sagepub.com/en-gb/eur/technologies-for-social-science-research">The Ecosystem of Technologies for Social Science Research</a> tracks increase in the use of software tools, along with characteristics of key tools. It is noted that whilst many commercial tools are available, the more innovative ones are coming out of academia.</li>
  <li><a href="https://www.nature.com/articles/514550a">The top 100 papers</a> analyses the top 100 _Nature _papers and finds that the vast majority describe experimental methods or software that have become essential in their fields.</li>
  <li><a href="https://doi.org/10.5281/zenodo.14809">UK Research Software Survey</a> considers responses of 1,000 randomly chosen researchers to show that more than 90% of researchers acknowledged software as being important for their own research, and about 70% of researchers said that their research would not be possible without software.</li>
  <li><a href="https://arxiv.org/abs/1706.06527">Understanding Software in Research: Initial Results from Examining Nature and a Call for Collaboration</a> reveals that “32 of the 40 papers examined mention software, and the 32 papers contain 211 mentions of distinct software, for an average of 6.5 mentions per paper.”</li>
</ul>

<p><strong>Policy</strong> is used to tag resources that focus on policy related to software, including the need for increased policy focus in this area.</p>

<ul>
  <li><a href="https://f1000research.com/articles/9-295/v1">An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action</a> examines how German funding bodies are increasingly acknowledging the importance and value of sustainable research software and related infrastructures, and makes recommendations on how to further improve this.</li>
  <li><a href="https://doi.org/10.1109/MCSE.2018.2883051">Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained</a> found that the US National Science Foundation made 18,592 awards totaling $9.6 billion to projects that<a href="https://arxiv.org/pdf/1811.08473.pdf"> </a>mentioned “software” in their abstracts between 1995-2016, which suggests that government funding policy needs to recognise the critical nature of research software.</li>
  <li><a href="https://www.rd-alliance.org/group/rda-covid19-rda-covid19-omics-rda-covid19-epidemiology-rda-covid19-clinical-rda-covid19-0">RDA COVID-19 Working Group Recommendations and Guidelines</a> contains recommendations for policy makers, funders, publishers and research community members working to overcome the challenges of COVID-19.</li>
  <li><a href="https://op.europa.eu/en/publication-detail/-/publication/fd0f6775-e0dd-11e9-9c4e-01aa75ed71a1">Recognising the importance of software in research: Research Software Engineers (RSEs), a UK example - Study</a> is a case study that discusses the current challenges faced by RSEs and policy conclusions to further help support RSEs and to contribute to the progress of open science in Europe.</li>
  <li><a href="https://www.ukri.org/research/infrastructure/">UK’s research and innovation infrastructure: opportunities to grow our capability</a> highlights the importance of software by recognising software and skills as one of the six computational and e-infrastructure themes.</li>
</ul>

<p><strong>Community</strong> considers work on the importance of research software communities in ensuring best practice in software development.</p>

<ul>
  <li><a href="https://sinews.siam.org/Details-Page/computational-research-software-challenges-and-community-organizations-working-for-culture-change">Computational Research Software: Challenges and Community Organizations Working for Culture Change</a> identifies the importance of sustained community in the development of high-quality software, and introduces efforts by grassroots organisations and projects to improve software quality, productivity, and sustainability. These endeavors ensure the integrity of research results and enable more effective collaboration.</li>
  <li><a href="https://doi.org/10.1109/MCSE.2018.2883051">Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained</a> provides an overview of the grass-roots organisations and projects that have evolved to address growing technical and social challenges in research software productivity, quality, reproducibility, and sustainability. This article then discusses opportunities to leverage their synergistic activities while nurturing work toward emerging software ecosystems.</li>
</ul>

<p><strong>Education and training</strong> identifies work that considers issues round skills, training, career paths and reward structures.</p>

<ul>
  <li><a href="https://doi.org/10.1109/SANER.2018.8330263">How do scientists develop scientific software? An external replication</a> considers how scientists acquire software engineering knowledge to suggest improvements in this process.</li>
  <li><a href="http://arxiv.org/abs/1507.03989">Software Use in Astronomy: an Informal Survey</a> finds that all participants use software in their research, and identifies the ten most popular tools. 90% of participants write at least some of their own software. while only 8% of them report that they have received substantial training in software development.</li>
  <li><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005755">Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators</a> highlights the importance of skills in software development for data analysis, with 90% of respondents indicating they are currently or will soon be analyzing large data sets.</li>
</ul>

<p><strong>Research breakthroughs</strong> include papers on significant research accomplishments that acknowledge reliance on research software tools:</p>

<ul>
  <li><a href="https://numfocus.org/case-studies/first-photograph-black-hole">Case Study: First Photograph of a Black Hole, Enabled by NumFOCUS Tools</a>.</li>
  <li><a href="https://pegasus.isi.edu/2016/02/11/pegasus-powers-ligo-gravitational-waves-detection-analysis/">Pegasus powers LIGO gravitational wave de­tection analysis</a>.</li>
  <li><a href="https://phys.org/news/2018-08-software-framework-drug-discovery-ieee.html">Software framework designed to accelerate drug discovery wins IEEE International Scalable Computing Challenge</a>.</li>
</ul>

<p><strong>Software</strong> has been applied as a tag to resources that mention particular pieces of software, including when this is part of a broader focus in the resource. This category includes a sample of the tens of thousands of papers that rely on research software and that collectively build knowledge in a field, for example:</p>

<ul>
  <li><a href="https://doi.org/10.1016/j.cell.2018.02.031">Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture</a>.</li>
  <li><a href="https://doi.org/10.1186/s13059-019-1763-7">Challenges in funding and developing genomic software: roots and remedies</a>.</li>
  <li><a href="https://arstechnica.com/information-technology/2019/10/chemists-discover-cross-platform-python-scripts-not-so-cross-platform/">Researchers find bug in Python script may have affected hundreds of studies</a>.</li>
  <li><a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006958">Securing the future of research computing in the biosciences</a>.</li>
  <li><a href="https://interestingengineering.com/these-7-cern-spinoffs-show-the-project-isnt-just-theoretical">These 7 CERN Spinoffs Show The Project Isn’t Just Theoretical</a>.</li>
</ul>

<p><strong>Other useful approaches</strong></p>

<p>This analysis has been useful in elucidating some of the ways in which the value of software can be demonstrated. However, there are also other approaches that could be useful. For example, methods to evaluate economic value are providing valuable statistics for research data, but comparable examples for research software are rare. The recent European Union publication, <a href="https://op.europa.eu/en/publication-detail/-/publication/d375368c-1a0a-11e9-8d04-01aa75ed71a1">Cost-benefit analysis for FAIR research data</a><span style="text-decoration:underline;">,</span> finds that the overall cost to the European economy of not having Findable, Accessible, Interoperable and Reusable (FAIR) research data is €10.2bn per year in Europe. A 2014 Australian study by <a href="https://www.ands.org.au/__data/assets/pdf_file/0019/393022/open-research-data-report.pdf">Houghton and Gruen</a> similarly demonstrates the economic value of data, estimating the value of Australian public research data at over $1.9 billion a year. One of the few economic valuations of research software is a 2017 analysis by <a href="https://nectar.org.au/wp-content/uploads/2016/06/Estimating-the-value-and-impact-of-Nectar-Virtual-Laboratories-2017.pdf">Sweeny et al. </a>of the return on investment generated by three Australian virtual laboratories, which provide access to research software and data for researchers, was at least double the investment for every measure. This indicated that the services had a significant economic and user impact - by one measure the value of one virtual laboratory was over 100 times the cost of investment. It would be useful if more studies were undertaken to demonstrate the economic benefits of research software using different methodologies.</p>

<p><strong>Conclusion</strong></p>

<p>This summary of evidence of the importance of research software to research outcomes illustrates increasing recognition of this fact. This summary could also be useful to encourage the community to consider where additional work could be useful (such as expanding existing surveys in specific countries and disciplines to get a more global scope), and to inspire the recording of more of this information (which could include striking examples that convey the impact of failing to understanding the costs and responsibilities of thoughtful software management).</p>

<p>We encourage readers to submit additional resources to the ReSA resources list, which is publicly available:</p>

<ul>
  <li>Add it directly to the ReSA <a href="https://www.zotero.org/groups/2400609/resa/library">Zotero group library</a> (requires Zotero account).</li>
  <li>Submit an issue in <a href="https://github.com/researchsoft/Resources/issues/new/choose">GitHub</a> (requires GitHub account).</li>
  <li><a href="mailto:info@researchsoft.org">Email</a> it directly to ReSA.</li>
</ul>]]></content><author><name>Michelle Barker, Daniel S. Katz, Alejandra Gonzalez-Beltran</name></author><category term="Research Software" /><category term="Community" /><summary type="html"><![CDATA[(This post is cross-posted on the URSSI blog, the SSI blog and the Netherlands eScience Center blog, and is archived in Zenodo)]]></summary></entry><entry><title type="html">The Research Software Alliance (ReSA) and the Community Landscape</title><link href="https://agbeltran.github.io/posts/2020/03/ReSA-landscape" rel="alternate" type="text/html" title="The Research Software Alliance (ReSA) and the Community Landscape" /><published>2020-03-11T00:00:00-07:00</published><updated>2020-03-11T00:00:00-07:00</updated><id>https://agbeltran.github.io/posts/2020/03/ReSA-landscape</id><content type="html" xml:base="https://agbeltran.github.io/posts/2020/03/ReSA-landscape"><![CDATA[<p>(This post is cross-posted on the <a href="https://software.ac.uk/blog/2020-03-11-research-software-alliance-resa-and-community-landscape">UK Software Sustainability Institute blog</a>, the <a href="https://blog.esciencecenter.nl/the-research-software-alliance-resa-and-the-community-landscape-9b8a6290ebb3">Netherlands eScience Center blog</a> and the <a href="http://urssi.us/blog/2020/03/11/the-research-software-alliance-resa-and-the-community-landscape/">US Research Software Sustainability Institute blog</a>.)</p>

<p>ReSA’s mission is to bring research software communities together to collaborate on the advancement of research software. Its vision is to have research software recognized and valued as a fundamental and vital component of research worldwide. Given our mission, there are multiple reasons that it’s important for us to understand the landscape of communities that are involved with software, in aspects such as preservation, citation, career paths, productivity, and sustainability. One of these reasons is that ReSA seeks to be a link between these communities, which requires identifying and understanding them. We want to be sure that there aren’t significant community organizations that we don’t know about to involve in our work. Also, identifying where there are gaps will help us create the opportunities and communities of practices as required.</p>

<p>When thinking about these communities, it’s clear that in addition to those that focus on software, there are others for which software is just a small part of their interest. Some examples are communities that focus on open science, reproducibility, roles and careers for people who are less visible in research, publishing and review, and other types of scholarly products and digital objects. ReSA also wants to define how we fit and interact with that  broader scholarly landscape.</p>

<h3 id="how-was-this-work-undertaken">How was this work undertaken?</h3>

<p>In September 2019, a <a href="http://www.researchsoft.org/resa-taskforces-join-us/">ReSA taskforce</a> came together to map the software community landscape, consisting of the authors of this blog. This group distributed a <a href="https://docs.google.com/forms/d/1kftKvGAHXIFButQ47Q3WoSCBT0v789tuksiLQkekzt4/viewform?edit_requested=true">survey</a> to <a href="https://groups.google.com/forum/#!forum/research-software-alliance">ReSA google group</a> members to identify other groups interested in software. Other useful sources included:</p>

<ul>
  <li>
    <p><a href="https://github.com/NLeSC/awesome-research-software-registries/blob/master/README.md">Netherlands eScience Center: Awesome-research-software-registries</a> by Jurriaan Spaaks</p>
  </li>
  <li>
    <p><a href="https://github.com/jamespjh/eResearch-meeting-list/tree/master">eResearch-meeting-list</a> by James Hetherington</p>
  </li>
  <li>
    <p><a href="https://rse.ac.uk/community/international-rse-groups/">International RSE groups</a> by the <a href="https://rse.ac.uk/">Research Software Engineering (RSE) Association</a></p>
  </li>
  <li>
    <p><a href="https://docs.google.com/spreadsheets/d/1LNF5_bOkRV-RLIF4HYmu-gOemIa4IdfXEer89fM-Vy8/edit#gid=0">Open Science Grassroots Community Networks</a>, a consortium of 120 networks</p>
  </li>
  <li>
    <p><a href="https://www.software.ac.uk/which-journals-should-i-publish-my-software">In which journals should I publish my software?</a> by Neil Chue Hong</p>
  </li>
</ul>

<p>The taskforce then met to consider the results and how to analyze them. The <a href="https://docs.google.com/spreadsheets/d/15JHqOxR4HIKHYe821IPvbxIuXP1zMjXKGEIJwB-GPqE/edit#gid=0">ReSA list of research software communities</a> is now publicly available as a living community resource, with the version of this list used by the ReSA taskforce in February 2020 and a copy of this post archived in <a href="https://doi.org/10.5281/zenodo.3699950">Zenodo</a>. Suggested additions or corrections are welcome by making comments in the <a href="https://docs.google.com/spreadsheets/d/15JHqOxR4HIKHYe821IPvbxIuXP1zMjXKGEIJwB-GPqE/edit#gid=0">list</a>.</p>

<p>Some of the issues we’ve had in assembling this list are:</p>

<ul>
  <li>
    <p>How much interest in software does an organization need to have to be listed?</p>
  </li>
  <li>
    <p>When is an organization sufficiently research focused to be included?</p>
  </li>
  <li>
    <p>What momentum/scale does an organization need to have so that we consider it relevant in the global picture?</p>
  </li>
</ul>

<p>On the other hand, once we started adding entries to the list, for many we found that we immediately thought of other similar organizations that should be added. For example, some organizations have a geographic aspect, and this led us to think of other similar organizations with different geographic aspects, such as all the national and regional RSE associations.</p>

<h3 id="what-did-we-learn">What did we learn?</h3>

<p>There were a range of interesting outcomes of the analysis:</p>

<ul>
  <li>
    <p>There are many, many communities that support research software, emphasizing the need for a coordinating organization such as ReSA. The importance of community development is captured in articles such as <a href="https://arxiv.org/abs/1811.08473">Community Organizations: Changing the Culture in Which Research Software is Developed and Sustained</a> by Daniel S. Katz et al., which provides an overview of key groups and discusses opportunities to leverage their synergistic activities.</p>
  </li>
  <li>
    <p>There is an increasing (and wide) range of community initiatives. For example, the <a href="https://docs.google.com/spreadsheets/d/1geYQLpJQtzPbhN3UZGSqPGFKNIF-hqXd7PGrwZJzasA/edit#gid=0">Open Science Grassroots Community Networks</a> list has evolved into the Community of Open Scholarship Grassroots Networks (COSGN), whose networks communicate and coordinate on topics of common interest. COSGN has submitted an <a href="https://osf.io/preprints/metaarxiv/d7mwk">NSF proposal</a> to formalize governance and coordination of the networks to maximize impact and establish standard practices for sustainability.</p>
  </li>
  <li>
    <p>The increasing focus on open software makes it hard to separate research and non-research initiatives. As per the points above, it is very hard to define which initiatives are part of the research software community, and which aren’t.</p>
  </li>
  <li>
    <p>Some organizations that were originally data-centric now include a software focus. For example, the Research Data Alliance now includes the <a href="https://www.rd-alliance.org/groups/software-source-code-ig">Software Source Code Interest Group</a>, which provides a forum to discuss issues on management, sharing, discovery, archiving, and provenance of software source code.</p>
  </li>
</ul>

<h3 id="what-are-the-next-steps">What are the next steps?</h3>

<p>We invite readers to continue to add or make corrections to the <a href="https://docs.google.com/spreadsheets/d/15JHqOxR4HIKHYe821IPvbxIuXP1zMjXKGEIJwB-GPqE/edit#gid=0">ReSA list of research software communities</a> by making comments in the list, which will continue to be curated by ReSA. We are also interested to hear from community members who would like to engage with us in writing a landscape paper based on further analysis and work. This could address questions such as what are the axes that create the space, where do the currently-known organizations fit in the space, and are there gaps where no organization is currently working? We also invite readers to consider involvement in other ReSA activities, including <a href="http://www.researchsoft.org/resa-taskforces-join-us/">Taskforces</a>.</p>

<h3 id="conclusion">Conclusion</h3>

<p>The ever-growing number of constituents of the research software community both reflects and demonstrates the increasing recognition of research software. The research software community is now a complex ecosystem comprised of a wide variety of organizations and initiatives, some of which are community networks themselves. Collaboration and coordination across these initiatives is important, to enable the broader community to work together to achieve bigger goals.</p>

<p>ReSA aims to coordinate across these efforts to leverage investments, to achieve the shared long-term goal of research software valued as a fundamental and vital component of research worldwide. Join the <a href="https://groups.google.com/forum/#!forum/research-software-alliance">ReSA google group </a> to stay up-to-date on our activities.</p>]]></content><author><name>Daniel S. Katz, Michelle Barker, Paula Andrea Martinez, Hartwig Anzt, Alejandra Gonzalez-Beltran, and Tom Bakker</name></author><category term="Research Software" /><category term="Community" /><summary type="html"><![CDATA[(This post is cross-posted on the UK Software Sustainability Institute blog, the Netherlands eScience Center blog and the US Research Software Sustainability Institute blog.) ReSA’s mission is to bring research software communities together to collaborate on the advancement of research software. Its vision is to have research software recognized and valued as a fundamental and vital component of research worldwide. Given our mission, there are multiple reasons that it’s important for us to understand the landscape of communities that are involved with software, in aspects such as preservation, citation, career paths, productivity, and sustainability. One of these reasons is that ReSA seeks to be a link between these communities, which requires identifying and understanding them. We want to be sure that there aren’t significant community organizations that we don’t know about to involve in our work. Also, identifying where there are gaps will help us create the opportunities and communities of practices as required. When thinking about these communities, it’s clear that in addition to those that focus on software, there are others for which software is just a small part of their interest. Some examples are communities that focus on open science, reproducibility, roles and careers for people who are less visible in research, publishing and review, and other types of scholarly products and digital objects. ReSA also wants to define how we fit and interact with that broader scholarly landscape. How was this work undertaken? In September 2019, a ReSA taskforce came together to map the software community landscape, consisting of the authors of this blog. This group distributed a survey to ReSA google group members to identify other groups interested in software. Other useful sources included: Netherlands eScience Center: Awesome-research-software-registries by Jurriaan Spaaks eResearch-meeting-list by James Hetherington International RSE groups by the Research Software Engineering (RSE) Association Open Science Grassroots Community Networks, a consortium of 120 networks In which journals should I publish my software? by Neil Chue Hong The taskforce then met to consider the results and how to analyze them. The ReSA list of research software communities is now publicly available as a living community resource, with the version of this list used by the ReSA taskforce in February 2020 and a copy of this post archived in Zenodo. Suggested additions or corrections are welcome by making comments in the list. Some of the issues we’ve had in assembling this list are: How much interest in software does an organization need to have to be listed? When is an organization sufficiently research focused to be included? What momentum/scale does an organization need to have so that we consider it relevant in the global picture? On the other hand, once we started adding entries to the list, for many we found that we immediately thought of other similar organizations that should be added. For example, some organizations have a geographic aspect, and this led us to think of other similar organizations with different geographic aspects, such as all the national and regional RSE associations. What did we learn? There were a range of interesting outcomes of the analysis: There are many, many communities that support research software, emphasizing the need for a coordinating organization such as ReSA. The importance of community development is captured in articles such as Community Organizations: Changing the Culture in Which Research Software is Developed and Sustained by Daniel S. Katz et al., which provides an overview of key groups and discusses opportunities to leverage their synergistic activities. There is an increasing (and wide) range of community initiatives. For example, the Open Science Grassroots Community Networks list has evolved into the Community of Open Scholarship Grassroots Networks (COSGN), whose networks communicate and coordinate on topics of common interest. COSGN has submitted an NSF proposal to formalize governance and coordination of the networks to maximize impact and establish standard practices for sustainability. The increasing focus on open software makes it hard to separate research and non-research initiatives. As per the points above, it is very hard to define which initiatives are part of the research software community, and which aren’t. Some organizations that were originally data-centric now include a software focus. For example, the Research Data Alliance now includes the Software Source Code Interest Group, which provides a forum to discuss issues on management, sharing, discovery, archiving, and provenance of software source code. What are the next steps? We invite readers to continue to add or make corrections to the ReSA list of research software communities by making comments in the list, which will continue to be curated by ReSA. We are also interested to hear from community members who would like to engage with us in writing a landscape paper based on further analysis and work. This could address questions such as what are the axes that create the space, where do the currently-known organizations fit in the space, and are there gaps where no organization is currently working? We also invite readers to consider involvement in other ReSA activities, including Taskforces. Conclusion The ever-growing number of constituents of the research software community both reflects and demonstrates the increasing recognition of research software. The research software community is now a complex ecosystem comprised of a wide variety of organizations and initiatives, some of which are community networks themselves. Collaboration and coordination across these initiatives is important, to enable the broader community to work together to achieve bigger goals. ReSA aims to coordinate across these efforts to leverage investments, to achieve the shared long-term goal of research software valued as a fundamental and vital component of research worldwide. Join the ReSA google group to stay up-to-date on our activities.]]></summary></entry><entry><title type="html">Web standards for describing datasets and profiles</title><link href="https://agbeltran.github.io/posts/2019/02/webstandardsdatasetsprofiles" rel="alternate" type="text/html" title="Web standards for describing datasets and profiles" /><published>2019-02-14T00:00:00-08:00</published><updated>2019-02-14T00:00:00-08:00</updated><id>https://agbeltran.github.io/posts/2019/02/webstandardsdatasetsprofiles</id><content type="html" xml:base="https://agbeltran.github.io/posts/2019/02/webstandardsdatasetsprofiles"><![CDATA[<p>This is blog post was published on the <a href="https://software.ac.uk/blog/2019-02-14-web-standards-describing-datasets-and-profiles">Software Sustainability Institute’s website</a>.</p>

<hr />

<p><img src="https://agbeltran.github.com/images/database_land.jpg" alt="Image of Database Land" /> Image by <a href="https://www.flickr.com/photos/chrisdlugosz/5577388841/">chrisdlugosz</a>.</p>

<p>Supported by the UK <a href="http://software.ac.uk">Software Sustainability Institute</a> Fellowship, I attended the fourth Face-to-Face (F2F) meeting of the <a href="https://www.w3.org/2017/dxwg/wiki/Main_Page">W3C Dataset eXchange Working Group</a> (DXWG) in Lyon, France, at the end of October 2018. Here, I report on how W3C WGs work and the specific outputs we’ve been producing at DXWG.</p>

<p>W3C stands for <a href="https://www.w3.org/Consortium/">World Wide Web Consortium</a> and is an organisation that works to develop web standards through an international community, which is built through a membership approach. Web standards are documents describing web technologies (for example HTML, CSS and XML) for which consensus, fairness, public accountability and quality have been reached. W3C follows a process that is designed to enable getting to that status where a document can be recommended for use, and this is done through Working Groups. Web standards are fundamental to achieve <a href="https://software.ac.uk/blog/2018-12-06-interact-interoperate">interoperability</a>.</p>

<p>Every year, W3C members come together over a week for the Technical Plenary and Advisory Committee (TPAC) meeting. This meeting brings together all the Technical Groups, the Advisory Board, the <a href="https://www.w3.org/2001/tag/">Technical Architecture Group</a> and the Advisory Committee, as well as Working Groups and Community Groups.</p>

<p>As a member of the <a href="https://www.w3.org/2017/dxwg/wiki/Main_Page">W3C Dataset eXchange Working Group</a>, I went to the F2F meeting, in which we continued our work related to the group’s charter to provide the following outcomes:</p>
<ul>
  <li><strong>A revised version of the Data Catalog vocabulary (DCAT)</strong>: The current DCAT Recommendation provides a vocabulary to publish datasets and data catalogs on the web. The working group is working on an update and expansion of the vocabulary, considering multiple new use cases and requirements.</li>
  <li><strong>Guidance on how to publish profiles of other standards</strong>: This document is meant to include a definition of what is meant by profiles and an explanation of one or more methods for publishing and sharing them.</li>
  <li><strong>Content negotiation by Application Profile</strong>: An explanation of how to implement the <a href="http://profilenegotiation.github.io/I-D-Accept--Schema/I-D-accept-schema">expected Internet Engineering Task Force (IETF) Internet-Draft</a> and suitable fallback mechanisms as discussed at <a href="https://www.w3.org/2016/11/sdsvoc/report#conneg">the Smart Descriptions &amp; Smarter Vocabularies (SDSVoc) workshop</a>.</li>
</ul>

<p><img src="https://agbeltran.github.com/images/agb_tpac.jpg" alt="Image of AGB at TPAC" /></p>

<p>To produce this work, we meet weekly in teleconferences online, communicate via a mailing list and collaborate through GitHub, where we keep all of the output documents (see the repository: <a href="https://github.com/w3c/dxwg">https://github.com/w3c/dxwg</a>). We also meet in person from time to time, as it is a great way of progressing the work by focusing on specific issues in intensive meetings that run for two days. As not everyone is able to attend in person, there is always remote connection available and thorough minutes are taken via an Internet Relay Chat (IRC) system. The e-mails and minutes are archived and made public for anyone to follow the work of the Working Group, and public feedback is seeked and welcome at all times.</p>

<p>The whole W3C process is <a href="https://www.w3.org/2018/Process-20180201/">extensively documented</a> and it includes the <a href="https://www.w3.org/2018/Process-20180201/#Reports">development of a series of technical reports</a> until reaching the recommendation status. Working groups then publish a First Public Working Draft for each document, then zero or more revised Working Drafts, a Candidate Recommendation, a Proposed Recommendation and a W3C Recommendation (that can be later edited or amended, if needed). You can see all the W3C standards and drafts on the <a href="https://www.w3.org/TR/">W3C website</a>.</p>

<p>The first step to produce these documents is to gather use cases and derive requirements from them. So, in DXWG, we first produced the <a href="https://w3c.github.io/dxwg/ucr/">Use Cases and Requirements</a> document. The current status of the other documents is as follows.</p>

<p><strong>Revised DCAT.</strong> Up until now, we have produced two working drafts of the revised version of DCAT. The latest working draft is <a href="https://www.w3.org/TR/2018/WD-vocab-dcat-2-20181016/">here</a>. The latest additions are always in the <a href="https://w3c.github.io/dxwg/dcat/">Editors’ Draft</a>. As I mentioned before, the original DCAT vocabulary provided terms to publish datasets and data catalogues on the web. For this revised version, we have been addressing new requirements around cataloguing data services and data distribution services, recording resources provenance, adding recommendations for catalogues that store datasets that are a bunch of files rather than explicitly splitting between a datasets and its different representations in different formats, guidance on how to describe the quality of a dataset, support for data citation, and many other relevant aspects of cataloguing resources.</p>

<p><strong>The Profiles Ontology.</strong> A profile is a set of constraints over one or more standards of information resources. Thus, a profile may extend a standard by identifying new entities, or may  add more restrictions, options, parameters or semantic interpretations to a given standard. In the context of data catalogues, there have been several extensions or profiles of the DCAT vocabulary, but up until now there was no way to formalise profiles and to relate them to the standards they are based on, or to other profiles. In DXWG, we have produced a <a href="https://www.w3.org/TR/2018/WD-dx-prof-20181218/">first public working draft of an ontology for describing profiles</a>, including references to a test suite and to <a href="https://github.com/CSIRO-enviro-informatics/prof-ont-implementation-results">an implementation report</a>. The latest version of the document is the <a href="https://w3c.github.io/dxwg/profilesont/">Editors’ Draft</a>.</p>

<p><strong>Content Negotiation by Profile</strong>. <a href="https://en.wikipedia.org/wiki/Content_negotiation">Content negotiation</a> is a mechanism by which a server may have different representations of a resource (e.g. different versions of the same document) at the same location (or URI) and users or agents can specify what version to retrieve. However, up until now, there was no way for a client to negotiate for content based on what standard it complies with or what profile it conforms to. DXWG produced the <a href="https://www.w3.org/TR/2018/WD-dx-prof-conneg-20181218/">first public working draft</a> of a specification for negotiating the content by profile. As per the other documents, the latest specification is always the <a href="https://w3c.github.io/dxwg/conneg-by-ap/">Editors’ Draft</a>.</p>

<p>If you have comments about these documents, we very much welcome them. To send feedback, you can do it via <a href="https://github.com/w3c/dxwg/issues">GitHub issues</a> and/or by email at <a href="mailto:public-dxwg-comments@w3.org">public-dxwg-comments@w3.org</a>. We are especially looking for feedback around the direction we have taken in the different documents and also if you have any views on what we should prioritise next (you can check the list of open issues we have in GitHub to see the project roadmap). There are many <a href="https://www.w3.org/2000/09/dbwg/details?group=99375&amp;public=1">DXWG participants</a> who worked on these specifications and we look forward to hearing your views about them.</p>

<p>By using these specifications, we hope to enable high standards for describing datasets and profiles, which will contribute to data sharing and research reproducibility.</p>]]></content><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><category term="W3C" /><category term="Web standards" /><category term="Community" /><category term="Interoperability" /><category term="Datasets" /><category term="Profiles" /><category term="Data catalogues" /><summary type="html"><![CDATA[This is blog post was published on the Software Sustainability Institute’s website.]]></summary></entry><entry><title type="html">Interact to Interoperate</title><link href="https://agbeltran.github.io/posts/2018/12/interact-to-interoperate" rel="alternate" type="text/html" title="Interact to Interoperate" /><published>2018-12-06T00:00:00-08:00</published><updated>2018-12-06T00:00:00-08:00</updated><id>https://agbeltran.github.io/posts/2018/12/interact-to-interoperate</id><content type="html" xml:base="https://agbeltran.github.io/posts/2018/12/interact-to-interoperate"><![CDATA[<p>This is blog post was published on the <a href="https://software.ac.uk/blog/2018-12-06-interact-interoperate">Software Sustainability Institute’s website</a>.</p>

<hr />]]></content><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><category term="Interoperability" /><category term="Dagstuhl workshop" /><category term="CW19" /><category term="Community" /><summary type="html"><![CDATA[This is blog post was published on the Software Sustainability Institute’s website.]]></summary></entry><entry><title type="html">The #RSE18 Times</title><link href="https://agbeltran.github.io/posts/2018/09/rse18-times/" rel="alternate" type="text/html" title="The #RSE18 Times" /><published>2018-09-27T00:00:00-07:00</published><updated>2018-09-27T00:00:00-07:00</updated><id>https://agbeltran.github.io/posts/2018/09/rse18-times</id><content type="html" xml:base="https://agbeltran.github.io/posts/2018/09/rse18-times/"><![CDATA[<p>This is blog post was published on the <a href="https://software.ac.uk/blog/2018-09-27-rse18-times">Software Sustainability Institute’s website</a></p>

<hr />

<p>This year I attended for the first time the third edition of the <a href="https://rse.ac.uk/conf2018">RSE conference</a> thanks to the support of the <a href="http://software.ac.uk/">Software Sustainability Institute</a> Fellowship. The conference brings together <strong>Research Software Engineers</strong> (or RSEs) from across the UK and the world.</p>

<p><img src="https://agbeltran.github.com/images/RSE18.jpg" alt="Image of RSE18" /> Image courtesy of Cristin Merritt, WHPC Social Media Volunteer</p>

<p>But what is an <strong>RSE</strong>? In brief, an RSE is someone with a research background, skilled in software development and who cares about applying best practices for software sustainability when producing software needed for research. If you want to know more, check out the <a href="https://software.ac.uk/ssisearch?search_api_fulltext_1=research+software+engineer">blog posts</a> at the <a href="https://software.ac.uk/">Software Sustainability Institute</a>, some of which deal with <a href="https://software.ac.uk/blog/2016-10-07-what-research-software-community-and-should-you-care">the Research Software community</a>, <a href="https://software.ac.uk/blog/2013-08-23-ten-reasons-be-research-software-engineer">the reasons for being an RSE</a>, <a href="https://software.ac.uk/blog/2016-09-30-i-dont-fix-printers-or-do-it-support-im-research-software-engineer">what is not part of the role</a>, and how the role has actually <a href="https://software.ac.uk/blog/2018-04-05-research-software-engineers-and-data-scientists-more-common">a lot in common with that of a data scientist</a>.</p>

<p>At the conference, we were reminded about <a href="https://software.ac.uk/blog/2016-08-17-not-so-brief-history-research-software-engineers">the history of the RSE term</a> and the community around it. The term was coined in 2012 during a meeting of like-minded people in Oxford. The meeting was organised to highlight the importance of both research software and the people that make it possible, whose role and career paths weren’t clearly recognised. A lot has happened since, and it was exciting to hear Christopher Woods announcing the creation of the <a href="https://www.society-rse.org/"><strong>Society of Research Software Engineering</strong></a>. If you want to know more about it, sign up at the website.</p>

<p>The conference spanned over <a href="https://rse.ac.uk/conf2018/programme/">two packed days</a> of activities. A welcoming environment was set from the start with <a href="https://rse.ac.uk/conf2018/diversity-statement/">a code of conduct and diversity statement</a> on the website, plus a reminder about it on the initial session. The importance of this to establish a positive atmosphere cannot be overstated.</p>

<p>Behind the conference there is a growing and bubbling community, as it is evident from Neil Che Hong’s tweet:</p>

<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">314 delegates from 12 countries, with an improving gender balance and a wide range of career stages attending - what a great start to <a href="https://twitter.com/hashtag/RSE18?src=hash&amp;ref_src=twsrc%5Etfw">#RSE18</a> <a href="https://t.co/ue8bwiTY1Q">pic.twitter.com/ue8bwiTY1Q</a></p>&mdash; Neil P Chue Hong (@npch) <a href="https://twitter.com/npch/status/1036534141460856832?ref_src=twsrc%5Etfw">September 3, 2018</a></blockquote>
<script async="" src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

<p>and also <a href="https://twitter.com/hashtag/RSE18?src=hash">all the tweets with the #RSE18 hashtag</a>.</p>

<p>Each morning included two keynote speakers with varying and interesting topics:</p>
<ul>
  <li><strong>Prof Eleanor Robson</strong>(<a href="https://www.ucl.ac.uk/history/people/academic-staff/professor-eleanor-robson">web</a><a href="https://twitter.com/Eleanor_Robson">twitter</a> from UCL gave an inspiring talk about the role that research software played in post-conflict Middle Eastern countries, in reducing researchers isolation and increasing the accessibility to reliable information and research and teaching materials.</li>
  <li><strong>Dr Andrew Fitzgibbon</strong>(<a href="https://www.microsoft.com/en-us/research/people/awf/">web</a>, <a href="https://twitter.com/awfidius">twitter</a>) from Microsoft Research works on computer vision systems and showed us several applications of computer graphics, including his work on making movie magic, and was around to let us use the mixed reality smart glasses <a href="https://en.wikipedia.org/wiki/Microsoft_HoloLens">HoloLens</a>.</li>
  <li><strong>Prof James Howison</strong>(<a href="http://james.howison.name/">web</a>, <a href="https://twitter.com/jameshowison">twitter</a>) from the Information School of the University of Texas at Austin, United States, presented a framework for the discussion of Software Sustainability. The framework provides useful concepts to discuss about software development vs maintenance, the cycle of software/use/impact/resources and how it varies in commercial, open source and research software settings. His slides are <a href="https://doi.org/10.6084/m9.figshare.7043093.v1">here</a>.</li>
  <li><strong>Dr Andreas Fidjeland</strong>(<a href="https://www.linkedin.com/in/andreas-fidjeland-89a47a38">linkedin</a>) is the Head of Research Engineering at Google DeepMind and mentioned that he moved from Academia to Research Software Engineering in Industry and talked about the importance of RSEs to help scientific discoveries and in particular, the work they are doing at Google <a href="https://deepmind.com/">Deep Mind</a>.</li>
</ul>

<p>In the afternoon there were very interesting parallel sessions, which made it very difficult to choose what to attend. The sessions included tracks covering different themes, panels and hands-on workshops.</p>

<p>I found the session on ‘Funder’s perspectives’ very encouraging for those of us who care about research software (and data!). The presentations were by Susan Morell from EPSRC/UKRI and David Carr from the Wellcome Trust.</p>

<p>Susan Morrell mentioned that she wants to be remembered as the person who funded the EPSRC RSE fellowships and showed us the UKRI strategy for Software Infrastructure.</p>
<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr"><a href="https://twitter.com/hashtag/RSE18?src=hash&amp;ref_src=twsrc%5Etfw">#RSE18</a> emerging <a href="https://twitter.com/EPSRC?ref_src=twsrc%5Etfw">@EPSRC</a> recommendations from the software element of the upcoming roadmap <a href="https://t.co/s4WXwghCZP">pic.twitter.com/s4WXwghCZP</a></p>&mdash; Alejandra Gonzalez-Beltran (@alegonbel) <a href="https://twitter.com/alegonbel/status/1036618480915804161?ref_src=twsrc%5Etfw">September 3, 2018</a></blockquote>
<script async="" src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

<p>David Carr mentioned Wellcome Trust’s commitment to <a href="https://wellcome.ac.uk/what-we-do/our-work/open-research">open research</a>, including research data sharing where their main efforts have been up until now, but also research software. He reminded us of the Survey they did on Researchers’ attitudes about open research (<a href="https://doi.org/10.6084/m9.figshare.4055448.v1">Towards Open Research</a>) that they published a couple of years ago.</p>

<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr"><a href="https://twitter.com/hashtag/RSE18?src=hash&amp;ref_src=twsrc%5Etfw">#RSE18</a> summary of <a href="https://twitter.com/wellcometrust?ref_src=twsrc%5Etfw">@wellcometrust</a> survey on researcher attitudes and practices on open research, including data and software as research outputs <a href="https://t.co/jQIKTQo0cK">pic.twitter.com/jQIKTQo0cK</a></p>&mdash; Alejandra Gonzalez-Beltran (@alegonbel) <a href="https://twitter.com/alegonbel/status/1036626109247434752?ref_src=twsrc%5Etfw">September 3, 2018</a></blockquote>
<script async="" src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

<p>For information on the rest of the conference, visit <a href="https://rse.ac.uk/conf2018/programme/">the website</a>, where you should be able to find links to presentations and materials from all the sessions in the near future.</p>

<p>To sum it up, if you are interested in research software, the RSE conferences is a place you will want to be, because as <a href="https://twitter.com/alysbrett">Alys Brett</a> put it, it will top you up of ‘ambitious-yet-practical community spirit for the rest of the year’!</p>

<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">I had a great time at <a href="https://twitter.com/hashtag/rse18?src=hash&amp;ref_src=twsrc%5Etfw">#rse18</a> - welcome top-up of ambitious-yet-practical community spirit for the rest of the year! We even look happy being grilled on how to set up and run <a href="https://twitter.com/hashtag/RSEng?src=hash&amp;ref_src=twsrc%5Etfw">#RSEng</a> groups at the end of two long days :-) <a href="https://t.co/XI8ojGv4ej">https://t.co/XI8ojGv4ej</a></p>&mdash; Alys Brett (@alysbrett) <a href="https://twitter.com/alysbrett/status/1037748298407464960?ref_src=twsrc%5Etfw">September 6, 2018</a></blockquote>
<script async="" src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>]]></content><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><category term="Research Software Engineers" /><category term="RSE18" /><category term="RSE Conference" /><category term="Community" /><summary type="html"><![CDATA[This is blog post was published on the Software Sustainability Institute’s website]]></summary></entry><entry><title type="html">So you want to start a data science institute? Achieving sustainability</title><link href="https://agbeltran.github.io/posts/2018/04/05-so-you-want-start-data-science-institute-achieving-sustainability" rel="alternate" type="text/html" title="So you want to start a data science institute? Achieving sustainability" /><published>2018-04-05T00:00:00-07:00</published><updated>2018-04-05T00:00:00-07:00</updated><id>https://agbeltran.github.io/posts/2018/04/data-science-institute</id><content type="html" xml:base="https://agbeltran.github.io/posts/2018/04/05-so-you-want-start-data-science-institute-achieving-sustainability"><![CDATA[<p>This blog post was published in the <a href="https://software.ac.uk/blog/2018-04-05-so-you-want-start-data-science-institute-achieving-sustainability">Software Sustainability Institute’ website</a>, and includes the conclusions of our discussions at the <a href="https://github.com/alan-turing-institute/RSE4DataScience18">Research Software Engineers for Data Science (RSE4DataScience)</a> meeting at the <a href="https://www.turing.ac.uk/">Alan Turing Institute</a> in London.</p>

<hr />

<p>By R. Stuart Geiger, Alejandra Gonzalez-Beltran, Robert Haines, James Hetherington, Chris Holdgraf, Heiko Mueller, Martin O’Reilly, Tomas Petricek, Jake VanderPlas (authors in alphabetical order)</p>

<p><strong>Data and software have enmeshed themselves in the academic world, and are a growing force in most academic disciplines (many of which are not traditionally seen as “data-intensive”). Many universities wish to improve their ability to create software tools, enable efficient data-intensive collaborations, and spread the use of “data science” methods in the academic community.</strong></p>

<p>The fundamentally cross-disciplinary nature of such activities has led to a common model: the creation of institutes or organisations not bound to a particular department or discipline, focusing on the skills and tools that are common across the academic world. However, creating institutes with a cross-university mandate and non-standard academic practices is challenging. These organisations often do not fit into the “traditional” academic model of institutes or departments, and involve work that is not incentivised or rewarded under traditional academic metrics. To add to this challenge, the combination of quantitative and qualitative skills needed is also highly in-demand in non-academic sectors. This raises the question: how do you create such institutes so that they attract top-notch candidates, sustain themselves over time, and provide value both to members of the group as well as the broader university community?</p>

<p>In recent years many universities have experimented with organisational structures aimed at acheiving this goal. They focus on combining research software, data analytics, and training for the broader academic world, and intentionally cut across scientific disciplines. Two-such groups are the Moore-Sloan Data Science Environments based in the USA and the Research Software Engineer groups based in the UK. Representatives from both countries recently met at the Alan Turing Institute in London for the RSE4DataScience18 Workshop to discuss their collective experiences at creating successful data science and research software institutes.</p>

<p>This article synthesises the collective experience of these groups, with a focus on challenges and solutions around the topic of sustainability. To put it bluntly: a sustainable institute depends on sustaining the people within it. This article focuses on three topics that have proven crucial.</p>

<ol>
  <li>Creating consistent and competitive funding models.</li>
  <li>Building a positive culture and an environment where all members feel valued.</li>
  <li>Defining career trajectories that cater to the diverse goals of members within the organisation.</li>
</ol>

<p>We’ll discuss each of these points below, and provide some suggestions, tips, and lessons-learned in accomplishing each.</p>

<p><em>An Aside on Nomenclature</em></p>

<p>The terms Research Software Engineer (i.e. RSE; most often used by UK partners) and Data Scientist (most often used by USA partners) have slightly different connotations, but we will not dwell on those aspects here (see Research Software Engineers and Data Scientists: More in Common for some more thoughts on this). In the current document, we will mostly use the terms RSE and Data Scientist interchangeably, to denote the broad range of positions that focus on software-intensive and data-intensive research within academia. In practice, we find that most people flexibly operate in both worlds simultaneously.</p>

<h2 id="challenges--proposed-solutions">Challenges &amp; Proposed Solutions</h2>

<h3 id="challenge-financial-sustainability">Challenge: Financial sustainability</h3>

<h4 id="how-can-institutions-find-the-financial-support-to-run-an-rse-program">How can institutions find the financial support to run an RSE program?</h4>

<p>The primary challenge for sustainability of this type of program is often financial: how do you raise the funding necessary to hire data scientists and support their research? While this doesn’t require paying industry-leading rates for similar work, it does require resources to compensate people comfortably. In practice, institutions have come at this from a number of angles:</p>

<p><strong>Private Funding.</strong> Funding from private philanthropic organisations has been instrumental in getting some of these programs off the ground: for example, the Moore-Sloan Data Science Initiative funded these types of programs for five years at the University of Washington (UW), UC Berkeley, and New York University (NYU). This is probably best viewed as seed funding to help the institutions get on their feet, with the goal of seeking other funding sources for the long term.</p>

<p><strong>Organisational Grants.</strong> Many granting organisations (such as the NSF or the UK Research Councils) have seen the importance of software to research, and are beginning to make funding available specifically for cross-disciplinary software-related and data science efforts. Examples are the Alan Turing Institute, mainly funded by the UK Engineering and Physical Sciences Research Council (EPSRC) and the NSF IGERT grant awarded to UW, which funded the interdisciplinary graduate program centered on the data science institute there.</p>

<p><strong>Project-based Grants.</strong> There are also opportunities to gain funding for the development of software or to carry out scientific work that requires creating new tools. For example, several members of UC Berkeley were awarded a grant from the Sloan Foundation to hire developers for the NumPy software project. The grant provided enough funding to pay competitive wages with the broader tech community in the Bay Area.</p>

<p><strong>Individual Grants.</strong> For organisations that give their RSEs principal investigator status, grants to individuals’ research programs can be a route to sustainable funding, particularly as granting organisations become more aware of and attuned to the importance of software in science. In the UK, the EPSRC has run two rounds of Research Software Engineer Fellowships, supporting leaders in the research software field for a period of five years to establish their RSE groups. Another example of a small grant for individuals promoting and supporting RSE activities is the Software Sustainability Institute fellowship.</p>

<p><strong>Paid Consulting.</strong> Some RSE organisations have adopted a paid consulting model, in which they fund their institute by consulting with groups both inside and outside the university. This requires finding common goals with non-academic organisations, and agreeing to create open tools in order to accomplish those goals. An example is at Manchester, where as part of their role in research IT, RSEs provide paid on-demand technical research consulting services for members of the University community. Having a group of experts on campus able to do this sort of work is broadly beneficial to the University as a whole.</p>

<p><strong>University Funding.</strong> Universities generally spend part of their budget on in-house services for students and researchers; a prime example is IT departments. When RSE institutes establish themselves as providing a benefit to the University community, the University administration may see fit to support those efforts: this has been the case at UW, where the University funds faculty positions within the data science institute. In addition, several RSE groups perform on-demand training sessions to research groups on campus in exchange for proceeds from research grants.</p>

<p><strong>Information Technology (IT) Connections.</strong> IT organisations in universities are generally well-funded, and their present-day role is often far removed from their original mission of supporting computational research. One vision for sustainability is to reimagine RSE programs as the “research wing” of university IT, to make use of the relatively large IT funding stream to help enable more efficient computational research. This model has been implemented at the University of Manchester, where Research IT sits directly within the Division of IT Services. Some baseline funding is provided to support things like research application support and training, and RSE projects are funded via cost recovery.</p>

<p><strong>Professors of Practice.</strong> Many U.S. universities have the notion of “professors of practice” or “clinical professors,” which often exist in professional schools like medicine, public policy, business, and law. In these positions, experts with specialised fields are recruited as faculty for their experience outside of traditional academic research. Such positions are typically salaried, but not tenure-track, with these faculty evaluated on different qualities than traditional faculty. Professors of practice are typically able to teach specialised courses, advise students, influence the direction of their departments, and get institutional support for various projects. Such a model could be applied to support academic data science efforts, perhaps by adopting the “Professor of practice” pattern within computational science departments.</p>

<p><strong>Research Librarians.</strong> We also see similarities in how academic libraries have supported stable, long-term career paths for their staff. Many academic librarians are experts in both a particular domain specialty and in library science, and spend much of their time helping members of the community with their research. At some universities, librarians have tenure-track positions equivilant to those in academic departments, while at others, librarians are a distinct kind of administrative or staff track that often have substantial long-term job security and career progression. These types of institutions and positions provide a precedent for the kinds of flexible, yet stable academic careers that our data science institutes support.</p>

<h3 id="challenge-community-cohesion-and-personal-value">Challenge: Community cohesion and personal value</h3>

<h4 id="how-to-create-a-successful-environment-where-people-feel-valued">How to create a successful environment where people feel valued?</h4>

<p>From our experience, there are four main points that help create an enjoyable and successful environment to facilitate success and makes people feel valued in their role.</p>

<p><strong>Physical Space.</strong> The physical space that hosts the group plays an important role to creating an enjoyable working environment. In most cases there will be a lot of collaboration going on between people within the group but also with people from other departments within the university. Having facilities (e.g. meeting spaces) that support collaborative work on software projects will be a big facilitator for successful outputs.</p>

<p><strong>Get Started Early.</strong> Another important aspect to creating a successful environment is to connect the group to other researchers with the university early on. It is important to inform people about the tasks and services the group provides, and to involve people early on who are well connected and respected within the university so that they can promote and champion the group within the university. This helps get the efforts off the ground early, and spread the word and bring on further opportunities.</p>

<p><strong>Celebrate Each Other’s Work.</strong> While it may not be possible to convince the broader academic community to treat software as first-class research output, data science organisations should explicitly recognise many forms of scientific output, including tools and software, analytics workflows, or non-standard written communication. This is especially true for projects where there is no “owner”, such as major open-source projects. Just because your name isn’t “first” doesn’t mean you can’t make a valuable contribution to science. Creating a culture that celebrates these efforts makes individuals feel that their work is valued.</p>

<p><strong>Allow Free Headspace.</strong> The roles of individuals should (i) enable them to work in collaboration with researchers from other domains (e.g., in a support role on their research projects) and (ii) also allow them to explore their own ‘research’ ideas. Involvement in research projects not only helps these projects develop reliable and reproducible results but can be an important source to help identify areas and tasks that are currently poorly supported be existing research software. Having free head space allows individuals to further pursue ideas that help solve the identified tasks. There are a lot of examples for successful open source software projects that have started as small side projects.</p>

<h3 id="challenge-preparing-members-for-a-diversity-of-careers">Challenge: Preparing members for a diversity of careers</h3>

<h4 id="how-do-we-establish-career-trajectories-that-value-peoples-skills-and-experience-in-this-new-inter-disciplinary-domain">How do we establish career trajectories that value people’s skills and experience in this new inter-disciplinary domain?</h4>

<p>The final dimension that we consider is that of the career progression of data scientists. Their career path generally differs from the traditional academic progression, and the traditional academic incentives and assessment criteria do not necessarily apply to the work they perform.</p>

<p><strong>Professional Development.</strong> A data science institute should prepare its staff both in technical skills (such as software development best practices and data-intensive activities) as well as soft skills (such as team work and communication skills) that would allow them to be ready for their next career step in multiple interdisciplinary settings. Whether it is in academia or industry, data science is inherently collaborative, and requires working with a team composed of diverse skillsets.</p>

<p><strong>Where Next.</strong> Most individuals will not spend their entire careers within a data science institute, which means their time must be seen as adequately preparing them for their next step. We envision that a data scientist could progress in their career either staying in academia, or moving to industry positions. For the former, career progression might involve moving to new supervisory roles, attaining PI status, or building research groups. For the latter, the acquired technical and soft skills are valuable in industrial settings and should allow for a smooth transition. Members should be encouraged to collaborate or communicate with industry partners in order to understand the roles that data analytics and software play in those organisations.</p>

<p><strong>The Revolving Door.</strong> The career trajectory from academia to industry has traditionally been mostly a one-way street, with academic researchers and industry engineers living in different worlds. However, the value of data analytic methods cuts across both groups, and offers opportunities to learn from one another. We believe a Data Science Institute should encourage strong collaborations and a bi-directional and fluid interchange between academic and industrial endeavours. This will enable a more rapid spread of tools and best-practices, and support the intermixing of career paths between research and industry. We see the institute as ‘the revolving door’ with movement of personnel between different research and commercial roles, rather than a one-time commitment where members must choose one or the other.</p>

<h3 id="final-thoughts">Final Thoughts</h3>

<p>Though these efforts are still young, we have already seen the dividends of supporting RSEs and Data Scientists within our institutions in the USA and the <a href="http://doi.org/10.5281/zenodo.495360">UK</a>. We hope this document can provide a roadmap for other institutions to develop sustainable programs in support of cross-disciplinary software and research.</p>]]></content><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><category term="data science" /><category term="research software engineers" /><category term="sustainability" /><category term="community" /><summary type="html"><![CDATA[This blog post was published in the Software Sustainability Institute’ website, and includes the conclusions of our discussions at the Research Software Engineers for Data Science (RSE4DataScience) meeting at the Alan Turing Institute in London.]]></summary></entry><entry><title type="html">Research Software Engineers and Data Scientists: More in Common</title><link href="https://agbeltran.github.io/posts/2018/04/more-in-common/" rel="alternate" type="text/html" title="Research Software Engineers and Data Scientists: More in Common" /><published>2018-04-05T00:00:00-07:00</published><updated>2018-04-05T00:00:00-07:00</updated><id>https://agbeltran.github.io/posts/2018/04/more-in-common</id><content type="html" xml:base="https://agbeltran.github.io/posts/2018/04/more-in-common/"><![CDATA[<p>This blog post was published in the <a href="https://software.ac.uk/blog/2018-04-05-research-software-engineers-and-data-scientists-more-common">Software Sustainability Institute’ website</a>, and includes the conclusions of our discussions at the <a href="https://github.com/alan-turing-institute/RSE4DataScience18">Research Software Engineers for Data Science (RSE4DataScience)</a> meeting at the <a href="https://www.turing.ac.uk/">Alan Turing Institute</a> in London.</p>

<hr />

<p>By Matthew Archer, Stephen Dowsland, Rosa Filgueira, R. Stuart Geiger, Alejandra Gonzalez-Beltran, Robert Haines, James Hetherington, Christopher Holdgraf, Sanaz Jabbari Bayandor, David Mawdsley, Heiko Mueller, Tom Redfern, Martin O’Reilly, Valentina Staneva, Mark Turner, Jake VanderPlas, Kirstie Whitaker (authors in alphabetical order)</p>

<p><strong>In our institutions, we employ multidisciplinary research staff who work with colleagues across many research fields to use and create software to understand and exploit research data. These researchers collaborate with others across the academy to create software and models to understand, predict and classify data not just as a service to advance the research of others, but also as scholars with opinions about computational research as a field, making supportive interventions to advance the practice of science.</strong></p>

<p>Some of us use the term “data scientist” to refer to our team members, in others we use “research software engineer” (RSE), and in some both. Where both terms are used, the difference seems to be that data scientists in an academic context focus more on using software to understand data, while research software engineers more often make software libraries for others to use. However, in some places, one or other term is used to cover both, according to local tradition.</p>

<h2 id="what-we-have-in-common">What we have in common</h2>

<p>Regardless of job title, we hold in common many of the skills involved and the goal of driving the use of open and reproducible research practices.</p>

<p>Shared skill focuses include:</p>

<ul>
  <li>Literate programming: writing code to be read by humans.</li>
  <li>Performant programming: the time or memory used by the code really matters</li>
  <li>Algorithmic understanding: you need to know what the maths of the code you’re working with actually does.</li>
  <li>Coding for a product: software and scripts need to live beyond the author, being used by others.</li>
  <li>Verification and testing: it’s important that the script does what you think it does.</li>
  <li>Scaling beyond the laptop: because performance matters, cloud and HPC skills are important.</li>
  <li>Data wrangling: parsing, managing, linking and cleaning research data in an arcane variety of file formats.</li>
  <li>Interactivity: the visual display of quantitative information.</li>
</ul>

<p>Shared attitudes and approaches to work are also important commonalities:</p>

<ul>
  <li>Multidisciplinary agility: the ability to learn what you need from a new research domain as you begin a collaboration.</li>
  <li>Navigating the research landscape: learning the techniques, languages, libraries and algorithms you need as you need them.</li>
  <li>Managing impostor syndrome: as generalists, we know we don’t know the detail of our methods quite as well as the focused specialists, and we know how to work with experts when we need to.</li>
</ul>

<h2 id="our-differences-emerge-from-historical-context">Our differences emerge from historical context</h2>

<p>The very close relationship thus seen between the two professional titles is not an accident. In different places, different tactics have been tried to resolve a common set of frustrations seen as scholars struggle to make effective use of information technology.</p>

<p>In the UK, the <a href="http://rse.ac.uk/community/research-software-groups-rsgs/">RSE Groups</a> have tried to move computational research forward by embracing a service culture while retaining participation in the academic community, sometimes described as being both a “craftsperson and a scholar”, or science-as-a-service. We believe we make a real difference to computational research as a discipline by helping individual research groups use and create software more effectively for research, and that this helps us to create genuine value for researchers rather than to build and publish tools that are not used by researchers to do research.</p>

<p>The Moore-Sloan Data Science Environments (<a href="http://msdse.org/">MSDSE</a>) in the US are working to establish Data Science as a new academic interdisciplinary field, bringing together researchers from domain and methodology fields to collectively develop best practices and software for academic research. While these institutes also facilitate collaboration across academia, their funding models are less based on a service model than in UKRSE groups and more based on bringing together graduate students, postdocs, research staff, and faculty across academia together in a shared environment.</p>

<p>Although these approaches differ strongly, we nevertheless see that the skills, behaviours and attitudes used by the people struggling to make this work are very similar. Both movements are tackling similar issues, but in different institutional contexts. We took diverging paths from a common starting point, but now find ourselves envisaging a shared future.</p>

<p>The <a href="http://turing.ac.uk/">Alan Turing Institute</a> in the UK straddles the two models, with both a Research Engineering Group following a science-as-a-service model and comprising both Data Scientists and RSEs, and a wider collaborative academic data science engagement across eleven partner universities.</p>

<h2 id="recommendations">Recommendations</h2>

<p>Observing this convergence, we recommend:</p>

<ul>
  <li>Create adverts and job descriptions that are welcoming to people who identify as one or the other title: the important thing is to attract and retain the right people.</li>
  <li>Standardised nomenclature is important, but over-specification is harmful. Don’t try too hard to delineate the exact differences in the responsibilities of the two roles: people can and will move between projects and focuses, and this is a good thing.</li>
  <li>These roles, titles, groups, and fields are emerging and defined differently across institutions. It is important to have clear messaging to various stakeholders about the responsibilities and expectations of people in these roles.</li>
  <li>Be open to evolving roles for team members, and ensure that stable, long-term career paths exist to support those who have taken the risk to work in emerging roles.</li>
  <li>Don’t restrict your recruitment drive to people who have worked with one or other of these titles: the skills you need could be found in someone whose earlier roles used the other term.</li>
  <li>Don’t be afraid to embrace service models to allow financial and institutional sustainability, but always maintain the genuine academic collaboration needed for research to flourish.</li>
</ul>]]></content><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><category term="research software engineer" /><category term="data scientist" /><summary type="html"><![CDATA[This blog post was published in the Software Sustainability Institute’ website, and includes the conclusions of our discussions at the Research Software Engineers for Data Science (RSE4DataScience) meeting at the Alan Turing Institute in London.]]></summary></entry><entry><title type="html">Questions &amp;amp; Answers - Profile of Dr Gonzalez-Beltran for the OeRC 10th anniversary</title><link href="https://agbeltran.github.io/posts/2016/06/qs-and-as/" rel="alternate" type="text/html" title="Questions &amp;amp; Answers - Profile of Dr Gonzalez-Beltran for the OeRC 10th anniversary" /><published>2016-06-21T00:00:00-07:00</published><updated>2016-06-21T00:00:00-07:00</updated><id>https://agbeltran.github.io/posts/2016/06/questions-and-answers</id><content type="html" xml:base="https://agbeltran.github.io/posts/2016/06/qs-and-as/"><![CDATA[<p>This blog post was published in the <a href="http://www.oerc.ox.ac.uk/dr-alejandra-gonzalez-beltran">Oxford e-Research Centre’s website</a>, University of Oxford, in the occasion of the Centre’s 10th Anniversary.</p>

<hr />

<p>Dr Alejandra Gonzalez-Beltran, Research Lecturer, talks about her recent Kellogg College Junior Research Fellowship, reporting the statistical methods used in data analysis and the technical challenges around data stewardship.</p>

<h2 id="when-did-you-start-at-the-centre-and-what-was-your-first-role-here">When did you start at the Centre and what was your first role here?</h2>
<p>I joined the Centre in June 2012 as a Senior Research Software Engineer. Now, I am a Research Lecturer. From the start, I have been involved projects related to enhancing and extending the Investigation/Study/Assay (ISA) infrastructure for tracking metadata about biological experiments. Furthermore, I have also contributed to the BioSharing portal of standards, databases and policies in the life, environmental and biomedical sciences *(renamed <a href="https://fairsharing.org/">FAIRsharing</a> since this blog post was published).</p>

<h2 id="what-is-your-background">What is your background?</h2>

<p>I am a computer scientist: after a degree in Computer Science from the Universidad Nacional de Rosario, Argentina (equivalent to BSc + MSc), I was awarded a PhD in Computer Science from Queen’s University Belfast, UK. My PhD work was about efficient ways to access information on a distributed network using probabilistic data structures. Then I worked as a post-doctoral researcher at University College London, UK, collaborating with the UK National Cancer Research Institute, the US National Cancer Institute, the UCL Cancer Institute and others, on methods to find and integrate distributed cancer data as well as best practices to record therapy experiments information.</p>

<h2 id="summarise-the-research-you-are-doing--your-research-interests-in-a-few-sentences">Summarise the research you are doing / your research interests in a few sentences.</h2>

<p>My research interests involve applying Computer Science methodologies to applications in the life, environmental and biomedical domains. In particular, I develop models, methods and software tools for data curation, data discovery, knowledge management, data publication, data analysis looking at enabling data sharing, data re-use and reproducible research.</p>

<h2 id="why-is-this-important-to-the-scientific-community--the-world-at-large">Why is this important (to the scientific community / the world at large)?</h2>

<p>Technological advances have propelled data generation to levels previously unimaginable. Managing the generated data in an efficient way is paramount for the advancement of science, as it would help to avoid duplication of efforts, would enable data sharing and improve data re-use, and would support reproducibility, which requires a detailed description of the methods used, as well as the availability of the software tools yielding the results.</p>

<p>I collaborate with scientists, technologists, service providers, journals and communities developing standards that support data sharing, interoperability, re-use and reproducibility. I hope to contribute to innovative ways of enhancing scholarly communication and the ways in which all the outcomes of research are made available as I believe it would accelerate science and discoveries.</p>

<h2 id="what-would-you-like-to-do-next-funding-permitting">What would you like to do next, funding permitting?</h2>
<p>I would like to explore further the issues around reporting the statistical methods used in data analysis and how these relate to the quality of the data produced. For this purpose, I want to apply the <a href="http://stato-ontology.org/">STATistical Ontology</a> (STATO) we have built to help reporting and reason over (logically connect) the statistical methods applied in different experiments.</p>

<p>Some questions that the ontology can answer:</p>

<p><img src="https://agbeltran.github.com/images/some-questions.png" alt="Image of STATO questions" /></p>

<p><img src="https://agbeltran.github.com/images/some-questions-2.png" alt="Image of STATO answers" /></p>

<h2 id="are-you-involved-in-any-wider-collaborations-why-are-these-important">Are you involved in any wider collaborations? Why are these important?</h2>
<p>I am involved in multiple projects with collaborations in the UK, Europe, the US, China and beyond. These collaborations are crucial for the work we do, as making the data FAIR (Findable, Accessible, Interoperable and Reusable) requires the wide adoption of standards, which per definition have to be agreed by large communities of practitioners and all stakeholders.</p>

<h2 id="what-publication-paper-are-you-most-proud-of-and-why">What publication /paper are you most proud of and why?</h2>

<p>I have published papers on the software tools I have worked on, such as <a href="http://doi.org/10.1186/1471-2105-15-S1-S11">Risa</a> (a tool that bridges the information about an experiment and the data analysis using the R language) and <a href="http://dx.doi.org/10.1186/1471-2105-15-S14-S4">linkedISA</a> (a tool that converts experiments described using spreadsheets to linked data, allowing to search and establish connections between datasets).</p>

<p>These papers are important, but it is also great to apply these tools to specific use cases, demonstrating how the can help in making data reproducible. So, I would highlight a paper for which we collaborated with other researchers and publishers and made recommendations on how to report results to move <a href="http://doi.org/10.1371/journal.pone.0127612">“From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics”</a>.</p>

<p><img src="https://agbeltran.github.com/images/isatab-peer-reproduced.png" alt="Image of Peer-Reproduced Paper" /></p>

<h2 id="have-you-received-any-awards-or-fellowships">Have you received any awards or fellowships?</h2>

<p>I have recently been elected to be a Junior Research Fellow at Kellogg College, which will start in Michaelmas Term (October 2016). This is a great opportunity to increase the links between the Centre and Kellogg College, promote my research and potentially create new collaborations. In addition, I hope to use the fellowship to raise the profile of women in Science, Technology, Engineering and Mathematics by organising seminars and outreach activities.</p>

<p>I have also received a Lockey grant to fund my trip to the <a href="https://save-sd.github.io/2016/">“Semantics, Analytics, Visualisation: Enhancing Scholarly Data”</a> workshop, which I co-chaired, and the <a href="http://www2016.ca/">25th International World Wide Web Conference</a>, which took place in Montreal, Canada, in April 2016.</p>

<p>Previously, I won the <a href="https://orcid.org/orcid-outreach-meeting-may-2013">ORCID codefest</a> that took place at Oxford, UK, on May 2013 and as a prize, got invited to participate in the <a href="https://odin-project.eu/">ORCID and DataCite Interoperability Network</a> (ODIN) codesprint and first year conference at CERN, Switzerland.</p>

<p>And even before that, I won a best paper award for my paper and presentation on <a href="http://www0.cs.ucl.ac.uk/staff/A.Finkelstein/papers/ontologyswat.pdf">“Ontology-based queries over cancer data”</a> at the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences (<a href="http://www.swat4ls.org/2010/">SWAT4LS 2010</a>).</p>

<h2 id="what-do-you-think-the-most-important-issueschallenges-in-your-field-will-be-in-the-next-decade-and-how-is-the-centre-placed-to-address-them">What do you think the most important issues/challenges in your field will be in the next decade and how is the Centre placed to address them?</h2>

<p>There are technical challenges around data stewardship: distinguishing what data to preserve, evaluating data quality, ensuring the accessibility and privacy of confidential data, and providing easy to use tools to help in all of the above. But there are also important social challenges which need to be tackled, which revolve around highlighting the societal benefits of making the research process more transparent, as well as revising the academic credit system, so that instead of seeing it as being a disadvantage, researchers get rewarded for sharing their well-described data and methods.</p>

<h2 id="what-do-you-think-the-centre-does-best">What do you think the Centre does best?</h2>

<p>The Centre’s interdisciplinary nature is definitely what makes us unique compared to other departments across the University. This interdisciplinary nature allows us to have a stimulating working environment with common interest groups (e.g. in linked data or machine learning) while we work applying these methodologies to different domains of application.</p>

<p>Watch Alejandra’s <a href="https://www.youtube.com/watch?v=brZQZrneuD0">presentation on scholarly publishing in the life sciences</a> at the 16th Annual BioInformatics Open Source Conference.</p>

<p><img src="https://agbeltran.github.com/images/youtube-alejandra.JPG" alt="Image of Alejandra's presentation in Youtube" /></p>]]></content><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><category term="statistical analysis" /><category term="fellowship" /><category term="data stewardship" /><summary type="html"><![CDATA[This blog post was published in the Oxford e-Research Centre’s website, University of Oxford, in the occasion of the Centre’s 10th Anniversary.]]></summary></entry><entry><title type="html">Winner of the ORCID Codefest prize</title><link href="https://agbeltran.github.io/posts/2013/05/orcid-codefest" rel="alternate" type="text/html" title="Winner of the ORCID Codefest prize" /><published>2015-12-17T00:00:00-08:00</published><updated>2015-12-17T00:00:00-08:00</updated><id>https://agbeltran.github.io/posts/2013/05/orcid-codefest-prize</id><content type="html" xml:base="https://agbeltran.github.io/posts/2013/05/orcid-codefest"><![CDATA[<p>On 23rd May 2013, I participated in the <a href="http://www.hackathon.io/orcid">ORCID CodeFest</a> (see also the details in the <a href="https://orcid.org/orcid-outreach-meeting-symposium-and-codefest-may-2013">ORCID website</a>) and won the first prize to attend the ODIN Codefest in CERN.</p>

<p><a href="https://www.hackathon.io/isacreator">My project</a> was about adding support to the ISAcreator Java-based tool for searching a user’s ORCID and retrieve all their information based on the ORCID API.</p>

<p>You can read more about the <a href="https://isatools.wordpress.com/2013/05/24/orcid-codefest-2013/">ORCID codefest</a> and about <a href="https://isatools.wordpress.com/2013/05/24/alejandras-project-wins-the-orcid-codefest-prize/">my project</a> in these blog post by <a href="https://twitter.com/antarcticdesign">Eamonn Maguire</a>.</p>

<p>In summary, I added code to search for an ORCID record via a dedicated interface:</p>

<p><img src="https://agbeltran.github.com/images/posts/2013-05-23-orcid-codefest/createnewprofile-orcid.png" alt="Image of create new profile feature with ORCID for ISAcreator" /></p>

<p>and then, the user information is automatically added from the ORCID profile:</p>

<p><img src="https://agbeltran.github.com/images/posts/2013-05-23-orcid-codefest/createnewprofile-searchorcid.png" alt="Image of create new profile feature with ORCID for ISAcreator" /></p>]]></content><author><name>Alejandra Gonzalez-Beltran</name><email>alejandra.gonzalez.beltran@gmail.com</email></author><category term="ORCID" /><category term="codefest" /><category term="hackathon" /><category term="prize" /><summary type="html"><![CDATA[On 23rd May 2013, I participated in the ORCID CodeFest (see also the details in the ORCID website) and won the first prize to attend the ODIN Codefest in CERN.]]></summary></entry></feed>