Software and research: the Institute's Blog

WORBy Rebecca Lawrence, Managing Director at F1000

This blog was first published on the F1000Research blog on 15th November 2016

The first articles have gone live on Wellcome Open Research today; 15 of them in total, with more submissions in the pipeline. The breadth of articles received so far starts to show just how broad these outputs can and should be (not just traditional narrative research articles). It also shows benefits of using such a platform for researchers across career stages, from those just starting out to more experienced and tenured researchers. This is a fantastic start!

Wellcome Open Research uses the publishing model we have developed and run for almost four years on F1000Research, namely immediate publication with mandatory inclusion of the supporting data, followed by transparent invited peer review, complete with full versioning.

This platform fundamentally changes the relationship between the different parties involved in research to support collaboration, openness, and rapid access to findings and data. In this approach, the funder Wellcome is formally the ‘publisher’ i.e. the owner of the platform; F1000 is the contracted service provider who…

Continue Reading

GSOC blogBy Raniere Silva, Software Sustainability Institute, David Pérez-Suárez, University College London.

The Google Summer of Code (GSoC) is a programme run by Google to sponsor the development of open source projects by university students between June and August (see our previous post Downloading Developers: The Google Summer of Code). After the summer, Google sponsors some GSoC mentors to meet in Sunnyvale, California, for a two-day summit where they can discuss what went well and what can be improved.

When we discovered that we would attend the summit (Raniere represented NumFOCUS and David represented Open Astronomy), we were happy to know in advance that a familiar face would be present. The summit kicked-off on a Friday.  Mentors arrived in their respective hotels with their many (figurative) hats—not all attendees make their living from their projects (we don't). The summit followed the unconference style and its schedule for the next two days started to take form the same Friday night. To propose a session, participants needed to write their…

Continue Reading

Automated assembly line

By Mike Jackson, Software Sustainability Institute

Continuous integration frameworks build and test our software, so we don't have too (well, we do, but they do it too!) As part of my work on automated testing to boost recipy's confidence, I've had my first experience of AppVeyor, a continuous integration service for Windows, and it was good!

Growing up in Scotland, I endured an oft-repeated peak and trough of emotion when watching BBC television. A new drama or comedy would be trailed by an enthusiastic announcer, anticipation would rise at the forthcoming delights, only to be dashed upon the rocks of the announcer's concluding words "...except for viewers in Scotland". I've noticed a similar trait in the world of research software where phrases such as "...except for Windows" or "...except for Internet Explorer" occur frequently enough to be noticeable, along with their fellow "works on Linux/UNIX", leaving "Windows" unsaid. So, having used Travis CI, a deservedly-popular Linux-based open source continuous integration framework for projects hosted on GitHub, it was refreshing to see that there's a similar service for Windows, AppVeyor.

I'd first used Travis CI when…

Continue Reading
Gaia artist's impresion
Gaia artist's impression. Credits: ESA/ATG MEDIALAB;
Background Image: ESO/S. Brunier, June 2013

By Francesca De Angeli, in collaboration with Marco Riello, Gregory Holland, Patrick Burgess and Paul Osborne.

This article is part of our series: A day in the software life, in which researchers from all disciplines discuss the tools that make their research possible.

On 19 December 2013, at 09:12:19 UTC, a spacecraft containing the Gaia satellite was launched from Europe's Spaceport in French Guiana. The Gaia satellite reached its stable operational orbit around L2 (approximately 1.5 million km from the Earth) about one month later. Since then, a continuous stream of data has been downloaded for further processing on ground. This data includes broad-band photometry and low-resolution spectra for all sources brighter than magnitude 20 and high-resolution spectra for sources brighter than magnitude 16.

The Gaia focal-plane assembly is the largest ever developed for a space application, with…

Continue Reading

Nasa picture of LondonBy Olivia Guest, Software Sustainability Institute Fellow

The Open Data Science Conference, ODSC, was held for the first time in London on October 8th and 9th. As far as I understand, it has its roots in the US and has only recently expanded to another continent. I’m not sure what I expected as I was still very much recovering from PyCon UK (yes, I’m a lightweight). However, I had noticed that quite a few talks were on packages I and/or colleagues use (e.g., TensorFlow, scikit-learn, etc.) so I was excited to see how and what they’re used for  by others.

The first talk was delivered by Gaël Varoquaux, a core developer of scikit-learn, joblib, and other Python packages. He touched on a number of important issues. Firstly, he defined what a data scientist is as  the combination of statistics and code, and,…

Continue Reading