Open Science

By Jenny Molloy, University of Cambridge.

Introduction by Raniere Silva, Software Sustainability Institute.

Chris Anderson, in his book "Free: The Future of a Radical Price", explores the transformation on business imposed by the spread of cheap computation power and data transfer. This same factors changed how we do research. Pre-prints, data share, code share have more common than you’d think. Unfortunately, scientific hardware is still a barrier for many researchers who don't have access to the tools required for their investigation. We are very excited to share the “Gathering for Open Science Hardware's Roadmap”, originally published at, "for providing global access to scientific hardware by 2025 through open source designs, collaborative research and new manufacturing techniques, including 3D-printing."

The following text was first posted at the Gathering for…

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Open Science, that is, the trio of open access, open data, and open methods, is not a new concept in the scientific world. Despite the fact that Budapest Open Access Initiative is more than 15 years old and the level of openness among researchers rises continually, there is still a long way before open science becomes so ubiquitous we simply call it “science”.

A significant step for humanities, a discipline not commonly associated with rigorous scientific methods, is the creation of the Open Science Interest Group (OSIG) within the largest archaeological community of the Society for American Archaeology. In the recently published manifesto, Ben Marwick, the group creator, argues that an adoption of practices preached by the open science movement can significantly benefit individual scholars as well as the discipline as a whole. At first, the Interest Group will focus on "incentivizing open practices by issuing Center for Open Science (COS) badges for Open Data and Open Materials for display on qualifying posters and slide presentations at the SAA Annual Meeting and other professional venue" and "conduct workshops using Software Carpentry and Data Carpentry pedagogy and materials".

Archaeologists interested in supporting the Society for American Archaeology Open Science Interest Group are welcome to subscribe to…

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Open access academiaBy Jon Hill, University of York, and Software Sustainability Institute Fellow.

A controversial title, but one I hope to explain! When running a couple of workshops later last year, I spoke at length on a number of aspects of open science. This included software sustainability, data and software licensing, collaboration and manuscript writing. I was inspired by this fantastic paper posted on ArXiv from Greg Wilson et al. I will caveat this text with the fact I am not a lawyer and none of the text below should be taken as legal advice.

After running these two workshops—“Tools for Constructing the Tree of Life” and “Good enough practice in Computational Geography”—and speaking to the attendees, I realised there is a disturbingly large gulf between those involved in the open science movement and the rest of academia. Many participants knew the words 'open access' and 'open source', but conflated the ideas and didn't link any licences to these terms. There was also a lot of confusion on what licences to use and which were appropriate, as well as the concept of copyright. Unfortunately, academics have to rely on the lawyers…

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As part of the ongoing public consultation on the midterm evaluation of Horizon 2020, the Free Software Foundation Europe published and submitted to the European Commission its Position paper for the endorsement of Free Software and Open Standards in Horizon 2020, the biggest EU Research and Innovation programme.

Because software is a vital part of today's scientific research, the FSFE believes that Open Access policies promoted in the framework of Horizon 2020 should also explicitly cover the publication of software under Free Software licences. This way, the EU will truly support Open Science.

If you would like to contribute your views, please read more about how to participate in the public consultation and how to share the FSFE's position paper, here:

The consultation, run by the European Commission is open for everyone until 15th January 2017.

Mozilla Science Lab has open applications for the Mozilla Fellowships for Science programme in its 2016 edition. Applicants with a passion for open source and data sharing, already working to shift research practice to be more collaborative, iterative and open, should apply before July 16th, 2016, at 5:00 am. Fellows will spend ten months starting September 2016 as community catalysts at their institutions, mentoring the next generation of open data practitioners and researchers and building lasting change in the global open science community.

Mozilla Science Lab is a community of researchers, developers, and librarians making research open and accessible. They empower open science leaders through fellowships, mentorship, and project-based learning.

For further information and how to apply, please visit Mozilla Fellowships for Science.



The Open Science Prize is a partnership between the Wellcome Trust, the US National Institutes of Health (NIH) and the Howard Hughes Medical Institute to unleash the power of open content and data to advance biomedical research and its application for health benefit.

It invites teams to propose or refine technical infrastructure that makes innovative use of open data or that advances open science more generally, though with a focus on biomedicine.

The awards will be made in two phases: 6 at $80k each in Phase 1, and in Phase 2, $230k for the winning team among these 6.

Teams must have at least one member each inside and outside the U.S., and team members can be individuals, groups or legal entities (e.g. a GLAM, a company or a city). The abstracts of the submissions will be public, and openness beyond that is strongly encouraged.

Deadline for submissions to Phase 1 is February 29, 2016.

For more information about the background behind the Open Science Prize, see:

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By Simon Hettrick, Deputy Director and Policy Lead.

This is the third in a series of blog posts taking you behind the scenes at the Institute. Today, we here about the recent activities of the Policy team.

Thus far in 2015, the efforts of the policy team have mainly been focused on providing data and support for the Institute’s funding bid for a second phase. With this out of the way, July has seen the policy team re-focusing on research. We’ve also had time to catch up with our Research Software Engineer campaign and added a new member of staff.

Surveying further

In October 2014, we ran a nationwide survey to determine researchers’ views on software. We were keen to quickly analyse and publish these results and get the preliminary message out. Due to staff availability, we ended up conducting this first pass analysis in Excel. Although we published our analysis, Excel is not the best package for transparency, which is why we rightly received opprobrium from open-data advocates. But we reasoned that our approach would be acceptable as long as we repeated and extended the work in a more transparent manner in the future.

Our new starter this July, Olivier Philippe, arrived with some serious R skills and was immediately tasked with making the survey analysis…

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By Shoaib Sufi,Community Lead.

This is the second blog post highlighting the activities of the Institute over the last month. Today it's the turn of the Community team to talk about their work.

It’s been a busy time as ever in the Community team. We have interesting blog posts published from community members, informative workshops in the pipeline, and some exciting upcoming news about the team. Read on to find out more.

Community updates

We published an informative and reflective blog post by Institute Fellow Mike Croucher of Walking Randomly fame. Mike speaks about the dangers of thinking your software is correct and what you can do to feel more confident that it is. And if you have seen 2001 you know bad code can be quite dangerous...

Fellow Boris Adryan reported on his trip to promote "Better Software, Better Research" to Eclipsecon 2015 and gives an introduction to the Eclipse Science group which aims to make science software interoperable and interchangeable.

At the Institute we are very interested in open science and open data so in the spirit of openness we made the…

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The Center for Open Science has grants available to connect their open source Open Science Framework (OSF) with the tools and services that researchers use, in particular Dryad, BitBucket and Zenodo. 

The free, open source Open Science Framework (OSF) connects services across the entire research lifecycle to promote research efficiency and reproducibility. For example, OSF is integrated with storage providers, Dropbox, Amazon S3, figshare, GitHub, Google Drive, and Dataverse, and citation management tools Zotero and Mendeley. However, there are hundreds of tools and services that researchers use everyday to create and manage research protocols, collect and analyze data, author manuscripts, submit and review articles, track impact, and search and discover others research.

Grants for $8,000 - $10,000 for this work are available. Proposers must commit to making all code available as open source with an Apache 2.0 license. Applicants may propose working on multiple integrations. Proposals will be accepted on a rolling basis, but no later than August 12, 2015 at Midnight EDT. Decisions will be made quickly so that teams can receive funding and initiate their work.

See for more details and link to apply.

By Megan Potter & Tim Smith, CERN.

For Open Science, it is important to cite the software you use in your research, as has been mentioned in previous articles on this blog. Particularly, you should cite any software that made a significant or unique impact on your work. Modern research relies heavily on computerised data analysis, and we should elevate its standing to a core research activity with data and software as prime research artefacts.  Steps must be taken to preserve and cite software in a sustainable, identifiable and simple way. This is how digital repositories like Zenodo can help.

Best practice for citing a digital resource like code is to refer to a digital object identifier (DOI) for it whenever possible. This is because DOIs are persistent identifiers that can be obtained only by an agency that commits to the obligation to maintain a reliable level of consistency in and preservation of the resource. As a digital repository, Zenodo registers DOIs for all submissions through DataCite and preserves these submissions using the safe and trusted foundation of CERN’s data centre, alongside the biggest scientific dataset in the world, the LHC’s 100PB Big Data store. This means that the code preserved in Zenodo will…

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