Software and research: the Institute's Blog

DifferenceBy Daniel S. Katz, Assistant Director for Scientific Software and Applications at NCSA

Reposted with the author's permission. This article was originally published in Daniel S. Katz's blog

This blog is based on part of a talk I gave in January 2017, and the thinking behind it, in turn, is based on my view of a series of recent talks and blogs, and how they might be fit together. The short summary is that general software reproducibly is hard at best, and may not be practical except in special cases.

Software reproducibility here means the ability for someone to replicate a computational experiment that was done by someone else, using the same software and data, and then to be able to change part of it (the software and/or the data) to better understand the experiment and its bounds.

I’m borrowing from Carole Goble (slide 12), who defines:

  • Repeat: the same lab runs the same experiment with the same set up
  • Replicate: an independent lab runs the same experiment with the same set up
  • Reproduce: an independent lab varies the…
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Charteris Land, EdinburghBy Shoaib Sufi, Community Lead.

Every year once the Fellowship starts, we get the Fellows together to give them the opportunity to learn about the different parts of the Institute (Training, Community, the Research Software Group, Policy, Communications and the Directorate) so they can better understand how we operate and how to interact with us to produce a good working relationship and better outcomes for their Fellowship.

This year we were in the lovely city of Edinburgh at Charteris Land, University of Edinburgh.  The Institute is headquartered in Edinburgh and it is where three of the new Institute 2017 Fellows are based, making it an ideal location for holding the inaugural. With 18 new Fellows, 14 were there in person, two connected via Skype, one sent a video and only one could not be involved.

The Institute Director, Neil Chue Hong gave an introduction to the Institute, its teams and how it operates; he highlighted Fellows as…

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ICMStalksBy Raniere Silva, Software Sustainability Institute, Hans Fangohr, University of Southampton.

From the 16th to the 20th January, the International Centre for Mathematical Sciences  hosted the Computational Mathematics with Jupyter Workshop organised jointly by the OpenDreamKit and CoDiMa projects where GAP, Singular, SageMath, Jupyter users and developers met for experience sharing talks and coding hackathons.

The workshop kickstarted with Mike Croucher asking the provocative question "is your research software correct?" Mike covered the reproducibility crises that, in his own words, can be partially solved with:

  • Automation (aka learn to program)

  • Writing code in a (very) high-level language

  • Getting some training

  • Using version control

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By Raniere Silva, Community Officer.Laptop on the beach.

The first phase of Google Summer of Code 2017 launched on January 19th and by participating as an open source project or mentor you could help make this edition the best one so far. This is an opportunity to have that change to your IDE that you have dreamt of for months, remove the bottleneck in your data analysis pipeline or test a new idea by the end of August.

Google Summer of Code (GSoC) allows projects to download developers! We at the Institute think that it’s a great opportunity for those working with research software to be a part of the wider open source community either by mentoring students (who are paid by Google to work on open source projects during the summer) or by suggesting project ideas. The first phase of the programme is when mentoring organisations can apply to participate in GSoC: the deadline is February 9, 2017 17:00 (GMT). In this phase, mentoring organisations start to collect project ideas and identify mentors; in this post we will list some ways you can contribute to GSoC's.

I want to lead my project / organisation’s application

If you are part of an open source software project, or an organisation…

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DIHDYou find yourself stranded on a beautiful desert island. Fortunately, the island is equipped with the basics needed to sustain life: food, water, solar power, a computer and a network connection. Consummate professional that you are, you have brought the software packages you need to continue your life and research. What software would you choose and - go on - what luxury item would you take to make life easier?

Today we hear from Liz Allen, Director of Strategic Initiatives, F1000, and Visiting Senior Research Fellow at the Policy Institute at King’s College London.

I feared that I might be the most unqualified person to have been invited to contribute to this blog. Having read previous entries, I checked with Simon (Hettrick) at the Software Sustainability Institute to see whether he seriously wanted a contribution from me, and I received the encouraging reply “it's not really about the software, but about what the software says about you.” So assuming that the Institute isn’t seeking to dumb down its excellent work, and that at least one person wants to know what my choices of software say about me, here goes...

The first thing I would need is the ability to write. I would record my daily trials and tribulations and, while it might not be fashionable, would need…

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