David Perez-Suarez

26215728419_e6bd12a04a_z.jpgBy Raniere Silva, Software Sustainability Institute, Yo Yehudi, InterMine, Cambridge University, David Pérez-Suárez, University College London.

The Mozilla Festival, or MozFest for short, is “an annual gathering of passionate thinkers and inventors from around the world who meet to learn from each other and help forge the future of the web" as described in the Mozilla Wiki. It started in 2010 in Barcelona but has been hosted in London since its second edition, in 2011. The event is a multi-massive-parallel session of debates and workshops. We attended the gathering to share ideas with Mozilla Open Leaders and other attendees interested in open science. Keep reading to find our top six highlights of MozFest 2017.

Open science public park

Some unconferences only have a open agenda, but others reinvent the whole space where it is happening. MozFest is in the second group, as you can see from the photo montage below. The photo in the right shows Naomi Penfold's activity, called…

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Software use in researchBy Daniel S. Katz, University of Illinois Urbana-Champaign, Robert Haines, Research IT, University of Manchester, David Perez-Suarez, Research IT Services, UCL, Alexander Struck, Humboldt-Universität zu Berlin

Nowadays, software is used in most research. But how the software is created, used, and what it depends on are not well understood questions. The importance of such knowledge varies based on the motivation of the reader. On one side, we could be interested in the impact of the software, how many times it has been used and by who. This type of analysis could come, for example, from funding bodies and organisations to reward the creation of something and help its sustainability, from institutions who hire people behind that software, or from the software authors to get an understanding of the needs of their users or simply to get credit for their work. Another motivation may be trying to understand the research being carried out with a particular software or set of tools either for purely academic purposes (e.g., by historians and scholars of science) or with a commercial perspective (such as by intellectual property teams from universities for the monetisation of the software). Some other purposes have to do with reproducibility and provenance: for example, how do we know which calculations need to be repeated if a bug is discovered in a particular version of software?

Looking for software in research is one of many topics…

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

Last year Raniere found out that the GNOME User and Developer European Conference (GUADEC) 2017 would be hosted in Manchester and that he should attend. Early this year, during Science Together, Raniere mentioned GUADEC to David Pérez-Suárez and we agreed to show up at the conference to find out what we could learn from GNOME about onboarding newcomers and best software development practices.

Onboarding Newcomers

GUADEC

All open source projects struggle with onboarding newcomers. And, most of the time, driving yourself to the first contribution is a journey that will have old source code, out-of-date documentation, undocumented culture and other rocks on the way. Thankfully, many contributors to open source are working collaboratively with other…

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Seductive Data

By Eilis Hannon, University of Exeter, Martin Callaghan, University of Leeds, James Baldwin, Sheffield Hallam University, Mario Antonioletti, Software Sustainability Institute, David Pérez-Suárez, University College London.
 

This post is part of the Collaborations Workshops 2017 speed blogging series.

In our daily work we may, at some point, need to access data from third parties that we wish merge or compare with some data that we have generated or obtained. Invariably we may turn to Google to find pertinent data sources. Domain experts may be able to refer us to data sources or in part there are keywords that can unlock what you are trying to find on the web. Alongside, we can filter results using advanced Boolean operators.  In order to make sense of the results, we can consider a number of factors, such as top links and domains that are most relevant to the topic. For specific domains, there will be known and trusted data providers, e.g. the Gene Expression Omnibus (GEO) or the…

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SciTogBy David Pérez-Suárez, University College London.

Originally published at sciencetogether.online.

Why #SciTog

Since I finished my PhD, I’ve worked on various large e-infrastructure projects which aimed to build bridges between various research sub-disciplines within solar system physics. All these projects were doing a great job for researchers in one area to know the effects (or the source) in a different place. That helps a lot to get the bigger picture and to find out interesting events in an easier manner than before. However, I think that’s just the beginning. A researcher specialised in one area may not understand exactly what’s happening in a different one. We were helping researchers to discover data in other domains but not to connect them with the experts in those areas.

Due to my involvement in open source projects and online communities like Software Carpentry, I knew such a thing was possible with the current tools available. But, why were we not using them? That thought embarked me on this adventure, which is not finished, but its first chapter has just concluded.

Getting there...

As part of my Software Sustainability Institute Fellowship, I organised…

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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…

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MentoringBy Raniere Silva, Software Sustainability Institute, David Pérez-Suárez, University College London, Stian Soiland-Reyes, University of Manchester.

Ian Holmes said on Twitter:

"You can download our code from the URL supplied. Good luck downloading the only postdoc who can get it to run, though".

Ian's quote raises awareness that those working on research software need to use best practices, such as version control, testing and documentation, in their daily work because otherwise, other researchers, developers or even the authors themselves will have difficulty getting hold of the software or making it work. Keeping software effort in your research project for a long period of time can be challenging, especially if you don't have access to a big budget; this is also true for many open source projects.

To help the open source ecosystem, Google has a programme called Google Summer…

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Image by CASTLE ROCK INNOVATIONS.By David Perez-Suarez, University College London, Phil Bradbury, University of Manchester, Aleksandra Nenadic, University of Manchester, Laurent Gatto, Cambridge University, and Niall Beard, University of Manchester.

A speed blog from the Collaborations Workshop 2016 (CW16).

Remote collaboration: challenges in Human-Computer-Human interactions.

Tools that were mentioned during the discussion: GitHub, BitBucket, GitHub issue tracker, Skype, Google Hangouts (but max participants in Skype/Google Hangouts), Google Docs, spreadsheets, Jira, todo lists, time sheets, DropBox, … but are tools really the problem?

Use cases: coding, remote teaching, writing papers, large open-source development.

We started our discussion with a list of tools and use cases from our own experience: GitHub, BitBucket, GitHub issue tracker, Skype, Google Hangouts (but max participants in Skype/Google Hangouts), Google Docs, spreadsheets, Jira, todo lists, time sheets, DropBox, … for situations like coding, remote teaching, writing papers, large open-source development. Despite the availability of these tools, some being really good, we were left to wonder whether the tools were really the problem, here?

How is the Team…

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A fast speed blog from the Fellows 2016 inaugural meeting.

by Craig MacLachlan (Met Office), Terhi Nurmikko-Fuller (University of Oxford), David Pérez-Suárez (University College London), Heather Ford (University of Leeds)

How do researchers in an interdisciplinary environment, with different skills and experiences pick collaborative tools that best fit their needs? There are literally hundred's of choices[1], thus we set out a list of 5 considerations to help you.

 

Documentation. High quality documentation and tutorials can really improve user experience and buy-in from users. Nobody wants to use a tool that is poorly documented or spend time trawling for answers to problems.

Data restrictions and security. Groups or institutes involved in the collaboration may have existing data storage rules, for example prohibiting data storage on cloud platforms. The sensitivity of the data may also…

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Post Doctoral Research Associate, Solar physics group,  UCL Department of Space and Climate Physics, Mullard Space Science Laboratory, University College London

Interests

I'm a open-source software advocate! But as a researcher this includes open science, and I believe the future of science depends on open access, open review, open software and open data. As a scientists or developer I do most of my work collaboratively, enjoying testing new collaborative tools and finding new ways to improve collaborations.
 

Research

I'm a solar physicists, that type of astronomy that studies our closest star: the Sun. I've been characterising various features that appear on the Sun such as sunspots, bright points or coronal holes by using image processing techniques. At the moment I'm working in the development of an algorithm to detect automatically big waves on the sun - solar tsunamis - observed from ground based telescopes. The detection of such waves provides us with a method of characterisation of Coronal Mass Ejections- big explosive events that can cause auroras on Earth but also disruptions in electrical and communication systems (space weather). 
 
I'm one of the core developers of SunPy, a project that tries to remove a 20-year dependency on the solar physics community of a very expensive software library…
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