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Open Research London

Jenny Molloy - September 21, 2016 in Announcements, Local Groups, OKFN Open Science

Open Research London (ORL) is an informal group formed to promote the idea of sharing and collaboration of research. ORL is a community effort, involving early career researchers and library staff. More volunteers are welcome and needed!

Check out their web page here >>

More information

Contact: @OpenResLDN if you’d like to get involved in the group, to propose a talk, host a talk at your institution, or would like to know more…

Twitter: @OpenResLDN follow us to keep up-to-date with meeting announcements!

Next Meeting: 3 October 2018, 6-9pm. Francis Crick Institute. Further details coming soon.

Ideas? Comments? Contact us on openresldn@gmail.com or on Twitter @OpenResLDN

 

Open Science Policy Platform – Open Science Working Group Representative

Jenny Molloy - March 22, 2016 in Announcements, OKFN, OKFN Open Science

The following is an application submitted by Jenny Molloy to join the Open Science Policy Platform as a representative of Open Knowledge International and the global Open Science Working Group.

I am writing to apply for membership of the Open Science Policy Platform as a representative of Open Knowledge International and their global Open Science Working Group. This community was founded in 2008 and includes interested people and organisations from a broad spectrum of open science stakeholders including researchers, students, librarians, policy makers, funders and citizens who are interested in greater access to the mechanisms and outputs of science. Our mailing list reaches over 800 members from across the globe with a strong European grouping and active local representatives, affiliates or groups in UK, Germany, Austria, France, Finland, Italy, Spain and Sweden. Open Knowledge also has a vast network of over 20 working groups and over 40 local chapters or groups who collectively represent one of the largest and most influential grassroots communities in open data: from education to government to transport to hardware.

I was a founding member of the open science working group and became the volunteer global Coordinator in 2010. During that time we changed our name from ‘Open Data in Science’ to ‘Open Science’ to reflect the widening interest in open access to all research outputs and openness to participation in the scientific process and I watched open science grow from a niche topic of interest to a political priority. I have been involved with numerous community initiatives including promotion of the Panton Principles for Open Science; coordination of community building activities such as the science track at OKFest, the world’s largest open knowledge event; running global calls and local discussion groups and supporting members of the community with their own activities. I have the support of the leadership team at Open Knowledge International and written endorsements from community members via our mailing list, so I am confident that I can credibly represent their perspectives at the Policy Platform. These perspectives are many and diverse, which is exactly the strength of the open science community in that it allows so many voices to access and influence science and science policy.

As an early career researcher whose chosen role is now enabling and facilitating greater openness in the field of synthetic biology, I am acutely aware of the perspectives and needs of my direct peers in addition to my long-standing engagement with the broader open science community. I therefore put myself forward with the following special interests:

  • Open technologies for open science (software, hardware and wetware)
  • Rewards and incentives for open science
  • Education & skills
  • New models for research communication and publishing

I have experience with the European Commission Open Science Agenda having represented Open Knowledge in Brussels in 2013 at a consultation meeting on the Science 2.0 whitepaper. As an active community member and current or recently active scientific researcher I was in a minority of meeting participants and this experience cemented my strong belief that community-based organisations should be represented on official platforms alongside political organisations and formal institutions. I do not currently sit on any other international policy-oriented board but I coordinated working group responses to policy consultations such as the Hargreaves report into copyright exceptions for text and data mining in the UK and I’m a member of the Open Knowledge/ContentMine team in the H2020-funded FutureTDM consortium, who will provide policy recommendations for text and data mining to the Commission. I am a member of the Europe PubMedCentral Advisory Board and am frequently contacted for informal advice on openness in addition to numerous invitations to present or discuss openness in science at events on the national and international level.

My academic interests now extend into science and technology studies in an attempt to better understand the theoretical underpinning and implementation of cultural change in science. However, I am also happy to question the assumptions and goals of the open science agenda, which was necessary in coordinating an IDRC-funded scoping project on ‘Open and Collaborative Science in Development’. This ultimately led to OCSDNet, a network of 15 case study projects around open science in the global South and I have acted an an informal advisor to several of these. An advantage of affiliation with Open Knowledge is that I can also draw on knowledge of existing research on open government data and other areas of open knowledge, which are further advanced from a policy and implementation perspective and so offer a useful set of outcomes and critiques which may be relevant to comparative policies in science. Many similar questions and challenges are faced across the open knowledge movement and greater connectivity could only enrich discussions at the OSPP.

In conclusion, I bring eight years of experience in the open science community, a wealth of knowledge about different players and their interactions and personal dedication to seeing changes towards greater openness in science. I therefore believe that I am a well-placed representative for the segment of stakeholders described above and can bring a researcher, practitioner and community organiser perspective that will be valuable to the OSPP.

Open Science Blog Editors Wanted!

Jenny Molloy - January 5, 2015 in Announcements, Featured

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Do you have 2+ hours a month available to edit and post some fantastic open science content to the Open Science Working Group blog?

We are looking for more editors to join Ann, Scott and Rayna on the blog editing team!

We aim to post at least once a month on events and activities organised by working group members, insights and thoughts from you all on different aspects of open science or the occasional guest blog post from others in the field.

The ideal minimum commitment is to manage/edit/author two blog posts a year but any additional help is much appreciated, for instance in curating the blog by putting together a short series of related posts and requesting guest posts.

More info on the role can be found here

If you are interested:

  • Get in touch with any questions via this thread or science@okfn.org
  • Add you name to the wiki
  • Follow the open science blog queue topic on Discourse to pick up posts as they come in!

More interested in curation than editing?

Check out our discussion on aggregating blog feeds to create a Planet Open Science that Svetlana Belkin is driving forward. This will eventually involve ‘Editor’s Picks’, community tagging and other features.

Would you like your work featured on this blog?

Check out the blog contributions wiki page and get in touch!

Image Credit: 2008-01-26 (Editing a paper) – 31 by Nic McPhee on Flickr, licensed under CC-BY-SA 2.0

Open Training for Open Science

Jenny Molloy - December 21, 2014 in Featured, Reproducibility, Research, Tools

This is part of series of blog posts highlighting focus points for the Open Science Working Group in 2015. These draw on activities started in the community during 2014 and suggestions from the Working Group Advisory Board.

By opensourceway on Flickr under CC-BY-SA 2.0

By opensourceway on Flickr under CC-BY-SA 2.0

The Open Science Working group have long supported training for open science and early introduction of the principles of open and reproducible research in higher education (if not before!). This area was a focus in 2013-4 and grows in importance as we enter 2015 with the level of interest in openness in science increasing at a rapid rate. This post attempts to provide examples of training initiatives in which members of the working group have been involved and particular areas where work is lacking.

  1. Openness in higher education
  2. Strategies for training in open science
  3. The Open Science Training Initiative (OSTI)
  4. Developing Open Science Training Curricula
  5. Incorporating Open Science Training into Current Courses
  6. Conclusion
  7. Getting Involved in Open Science Training

Openness in higher education

Openness has the potential to radically alter the higher education experience. For instance, Joss Winn and Mike Neary posit that democratisation of participation and access could allow a reconstruction of the student experience in higher eduction to achieve this social relevance, they propose:

“To reconstruct the student as producer: undergraduate students working in collaboration with academics to create work of social importance that is full of academic content and value, while at the same time reinvigorating the university beyond the logic of market economics.”[1]

Openness focuses on sharing and collaboration for public good, at odds with the often competitive ethos in research and education. This involves more than simply implementing particular pedagogies or publishing open access articles – as Peters and Britez state bluntly in the first sentence of their book on open education:

“Open education involves a commitment to openness and is therefore inevitably a political and social project.” [2]

This could equally apply to open science. Openness is a cultural shift that is facilitated but not driven by legal and technical tools. In open education, for instance, open pedagogy makes use of now abundant openly licensed content but also places an emphasis on the social network of participants and the learner’s connections within this, emphasising that opening up the social institution of higher education is the true transformation. In open science, a lot of training focuses on the ability to manage and share research data, understand licensing and use new digital tools including training in coding and software engineering. However, understanding the social and cultural environment in which research takes place and how openness could impact that is arguably even more fundamental.

This section will focus on three topics around open science training, offering relevant linkages to educational literature and suggestions for teaching design:

  1. Use of open data and other open research objects in higher education.
  2. Use of open science approaches for research-based learning.
  3. Strategies for training in open science.

Strategies for training in open science

As openness is a culture and mindset, socio-cultural approach to learning and the construction of appropriate learning environments is essential. While the Winn and Neary [1] focus on the student as producer, Sophie Kay [3] argues that this can be detrimental as it neglects the role of students as research consumers which in turn neglects their ability to produce research outputs which are easily understood and reuseable.

Training in evolving methods of scholarly communication is imperative because there are major policy shifts towards a requirement for open research outputs at both the funder and learned society levels in the UK, EU and US. This is in addition to a growing grassroots movement in scientific communities, accelerated by the enormous shifts in research practice and wider culture brought about by pervasive use of the internet and digital technologies. The current generation of doctoral candidates are the first generation of `digital natives’, those who have grown up with the world wide web, where information is expected to be available on demand and ‘prosumers’ who consume media and information as well as producing their own via social media sites, are the norm. This norm is not reflected in most current scientific practice, where knowledge dissemination is still largely based on a journal system founded in the 1600s, albeit now in digital format. Current evidence suggests that students are not prepared for change, for example a major study of 17,000 UK graduate students [4] revealed that students:

  • hold many misconceptions about open access publishing, copyright and intellectual property rights;
  • are slow to utilise the latest technology and tools in their research work, despite being proficient in IT;
  • influenced by the methods, practices and views of their immediate peers and colleagues.

While pre-doctoral training is just as important, the majority of open science training initiatives documented thus far have aimed at the early career research stage, including doctoral students.

The Open Science Training Initiative (OSTI)

Photo courtesy of Sophie Kay, licensed under CC-BY.

OSTI photo courtesy of Sophie Kay, licensed under CC-BY.

Open Knowledge Panton Fellow Sophie Kay developed an Open Science Training Initiative (OSTI) [3], trialled in the Life Science Interface Doctoral Training Centre at the University of Oxford, which employs `rotation based learning’ (RBL) to cement the role of students as both producers and consumers of research through learning activities which promote the communication of coherent research stories that maximise reproducibility and usefulness. The content involves a series of mini-lectures around concepts, tools and skills required to practice openly, including an awareness of intellectual property rights and licensing, digital tools and services for collaboration, storage and dissemination, scholaraly communication and broader cultural contexts of open science.

The novel pedagogical approach employed was the creation of groups during an initiator phase where each group reproduces and documents a scientific paper, ensuring that outputs are in appropriate formats and properly licensed. Next the successor phase sees the reproduced work being rotated to another group who must again validate and build upon it in the manner of a novel research project, with daily short meetings with instructors to address any major issues. No intergroup communication is allowed during either phase, meaning that deficiencies in documentation and sticking points become obvious and hopefully leads to greater awareness among students of the adequacy of their future documentation. The pilot course involved 43 students and had a subject-specific focus on computational biology. Feedback was excellent with students feeling that they had learnt more about scientific working practises and indicating they were highly likely to incorporate ideas introduced during the course into their own practice.

This course design offers great scope for inter-institutional working and as it uses OERs the same training can be delivered in several locations but remains adaptable to local needs. RBL would be more challenging to mirror in wet labs but could be adapted for these settings and anyone is encouraged to remix and run their own instance. Sophie is especially keen to see the materials translated into further languages.

Developing Open Science Training Curricula

OSTI is one of the first courses to specifically address open science training but is likely the first of many as funding is becoming available from the European Commission and other organisations specifically aimed at developing open access and open science resources and pedagogies. Some of the key consideration for teaching design in this space are:

  1. How to address socio-cultural aspects in addition to imparting knowledge about legal and technical tools or subject-specific content and skills training.
  2. The current attitudes and perceptions of students towards intellectual property and the use of digital technologies and how this will impact their learning.
  3. The fast pace of change in policy requirements and researcher attitudes to aspects of open science.
  4. Additional time and resources required to run additional courses vs amelioration of existing activities.
Open science curriculum map at MozFest 2014.  Photo by Jenny Molloy, dedicated to the public domain via a CCZero waiver.

Open science curriculum map at MozFest 2014. Photo by Jenny Molloy, dedicated to the public domain via a CCZero waiver.

There are numerous one-off training events happening around the world, for instance the series of events funded by the FOSTER EU programme, which includes many workshops on open science. There are also informal trainings through organisations such as the Open Science working group local groups. Open science principles are incorporated into certain domain-specific conferences or skill-specific programmes like Software Carpentry Workshops, which have a solid focus on reproducibility and openness alongside teaching software engineering skills to researchers.

There are no established programmes and limited examples of open science principles incorporated into undergraduate or graduate curricula across an entire module or course. Historically, there have been experiments with Open Notebook Science, for instance Jean-Claude Bradley’s work used undergraduates to crowdsource solubility data for chemical compounds. Anna Croft from Bangor University presented her experiences encouraging chemistry undergraduates to use open notebooks at OKCon 2011 and found that competition between students was a barrier to uptake. At a graduate level, Brian Nosek has taught research methods courses incorporating principles of openness and reproducibility (Syllabus) and a course on improving research (Syllabus). The Centre for Open Science headed by Nosek also has a Collaborative Replications and Education Project (CREP) which is an excellent embodiment of the student as producer model and incorporates many aspects of open and reproducible science through encouraging students to replicate studies. More on this later!

It is clear that curricula, teaching resources and ideas would be useful to open science instructors and trainer at this stage. Billy Meinke and Fabiana Kubke helpfully delved into a skills-based curriculum in more depth during Mozilla Festival 2014 with their mapping session. Bill Mills of Mozilla Science Lab recently published a blog post on a similar theme and has started a pad to collate further information on current training programmes for open science. In the US, NCAES ran a workshop developing a curriculum for reproducible science followed by a workshop on Open Science for Synthesis .

NESCent ran a curriculum building workshop in Dec 2014 (see wiki). Several participants in the workshop have taught their own courses on Tools for Reproducible Research (Karl Broman) or reproducibility in statistics courses (Jenny Bryan). This workshop was heavily weighted to computational and statistical research and favoured R as the tool of choice. Interestingly their curriculum looked very different to the MozFest map, which goes to show the breadth of perspectives on open science within various communities of researchers!

All of these are excellent starts to the conversation and you should contribute where possible! There is a strong focus on data-rich, computational science so work remains to rethink training for the wet lab sciences. Of the branches of skills identified by Billy and Fabiana, only two of seven relate directly to computational skills, suggesting that there is plenty of work to be done! For further ideas and inspiration, the following section details some ways in which the skills can be further integrated into the curriculum through existing teaching activities.

Skills map for Reproducible, Open and Collaborative Science. Billy Meinke and Fabiana Kubke's session at MozFest 2014.

Skills map for Reproducible, Open and Collaborative Science. Billy Meinke and Fabiana Kubke’s session at MozFest 2014.

Incorporating Open Science Training into Current Courses

Using the open literature to teach about reproducibility

Data and software is increasingly published alongside papers, ostensibly enabling reproduction of research. When students try to reanalyse, replicate or reproduce research as a teaching activity they are developing and using skills in statistical analysis, programming and more in addition to gaining exposure to the primary literature. As much published science is not reproducible, limitations of research documentation and experimental design or analysis techniques may become more obvious, providing a useful experiential lesson.

There is public benefit to this type of analysis. Firstly, whether works are reproducible or not is increasingly of interest particularly to computational research and various standards and marks of reproducibility have been proposed but the literature is vast and there is no mechanism widely under consideration for systematic retrospective verification and demarcation of reproduciblity. Performing this using thousands of students in the relevant discipline could rapidly crowdsource the desired information while fitting easily into standard components of current curricula and offering a valid and useful learning experience.

The effect of `many eyes’ engaging in post-publication peer review and being trained in reviewing may also throw up substantive errors beyond a lack of information or technical barriers to reproduction. The most high profile example of this is the discovery by graduate student Thomas Herndon of serious flaws in a prominent economics paper when he tried to replicate its findings [5,6]. These included coding errors, selective exclusion of data and unconventional weighting of statistics, meaning that a result which was highly cited by advocates of economic austerity measures and had clear potential to influence fiscal policy was in fact spurious. This case study provides a fantastic example of the need for open data and the social and academic value of reanalysis by students, with the support of faculty.

This possibility has not been picked up in many disciplines but the aforementioned CREP project aims to perform just such a crowd-sourced analysis and asks instructors to consider what might be possible through student replication. Grahe et al., suggest that:

“Each year, thousands of undergraduate projects are completed as part of the educational experience…these projects could meet the needs of recent calls for increased replications of psychological studies while simultaneously benefiting the student researchers, their instructors, and the field in general.” [7]

Frank and Saxe [8] support this promise, reporting that they found teaching replication to be enjoyable for staff and students and an excellent vehicle for educating about the importance of reporting standards, and the value of openness. Both publications suggest approaches to achieving this in the classroom and are well worth reading for further consideration and discussion about the idea.

Reanalysing open data

One step from reproduction of the original results is the ability to play with data and code. Reanalysis using different models or varying parameters to shift the focus of the analysis can be very useful, with recognition of the limitations of experimental design and the aims of the original work. This leads us to the real potential for novel research using open datasets. Some fields lend themselves to this more than others. For example, more than 50% of public health masters projects across three courses examined by Feldman et al. [9] used secondary data for their analyses rather than acquiring expensive and often long-term primary datasets. Analysis of large and complex public health data is a vital graduate competency, therefore the opportunity to grapple with the issues and complexities of real data rather than a carefully selected or contrived training set is vital.

McAuley et al. [10] suggest that the potential to generate linked data e.g. interconnecting social data, health statistics and travel information, is the real power of open data and can produce highly engaging educational experiences. Moving beyond educational value, Feldman et al. [9] argue that open data use in higher education research projects allows for a more rapid translation of science to practise. However, this can only be true if that research is itself shared with the wider community of practise, as advocated by Lompardi [11]. This can be accomplished through the canonical scientific publishing track or using web tools and services such as the figshare or CKAN open data repositories, code sharing sites and wikis or blogs to share discoveries.

In order to use these digital tools that form the bedrock of many open science projects and are slowly becoming fully integrated into scholarly communication systems, technological skills and understanding of the process of knowledge production and disemmination in the sciences is required. Students should be able to contextualise these resources within the scientific process to prepare them for a future in a research culture that is being rapidly altered by digital technologies. All of these topics, including the specific tools mentioned above, are covered by the ROCS skills mapping from MozFest, demonstrating that the same requirements are coming up repeatedly and independently.

Use of open science approaches for research-based learning

There are several powerful arguments as to why engaging students in research-based activities leads to higher level and higher quality learning in higher education and the Boyer Commission on Educating Undergraduates in the Research University called for research based learning to become the standard, stating a desire:

“…to turn the prevailing undergraduate culture of receivers into a culture of inquirers, a culture in which faculty, graduate students, and undergraduates share an adventure of discovery.”

The previous section emphasised the potential role of open content, namely papers, data and code in research-based learning. In addition, the growing number of research projects open to participation by all – including those designated as citizen science – can offer opportunities to engage in research that scales and contributes more usefully to science than small research projects that may be undertaken in a typical institution as part of an undergraduate course. These open science activities offer options for both wet and dry lab based activities in place or in addition to standard practical labs and field courses.

The idea of collaborative projects between institutions and even globally is not new, involvement in FOSS projects for computational subjects has long been recognised as an excellent opportunity to get experience of collaborative coding in large projects with real, often complex code bases and a `world-size laboratory’ [12]. In wet lab research there are examples of collaborative lab projects between institutions which have been found to cut costs and resources as well as increasing the sample size of experiments performed to give publishable data [13]. Openness offers scaling opportunities to inter-institutional projects which might otherwise not exist by increasing their visibility and removing barriers to further collaborative partners joining.

Tweet from @O_S_M requesting assistance synthesising molecules.

Tweet from @O_S_M requesting assistance synthesising molecules.

There are several open and citizen science projects which may offer particular scope for research-based learning. One could be the use of ecology field trips and practicals to contribute to the surveys conducted by organisations such as the UK Biological Records Centre, thus providing useful data contributions and access to a wider but directly relevant dataset for students to analyse. NutNet is a global research cooperative which sets up node sites to collect ecosystem dynamics data using standard protocols for comparison across sites globally, as this is a longitudinal study with most measurements being taken only a couple of times a year it offers good scope for practical labs. On a more ad hoc basis, projects such as Open Source Malaria offer many project and contribution opportunities e.g. a request to help make molecules on their wishlist and a GitHub hosted to do list. One way of incorporating these into curricula are team challenges in a similar vein to the iGEM synthetic biology project, which involves teams of undergraduates making bacteria with novel capabilities and contributes the DNA modules engineered to a public database of parts known as BioBricks.

In conclusion, open and citizen science projects which utilise the internet to bring together networks of people to contribute to live projects could be incorporated into inquiry-based learning in higher education to the benefit of both students and the chosen projects, allowing students to contribute truly scientifically and socially important data in the `student as producer’ model while maintaining the documented benefits of research-based pedagogies. This ranges from controlled contributions to practice particular skills through discovery-oriented tasks and challenges such as iGEM, allowing students to generate research questions independently.

There are significant challenges in implementing these types of research-based activities, many of which are true of `non-open’ projects. For instance, there are considerations around mechanisms of participation and sharing processes and outputs. Assessment becomes more challenging as students are collaborating rather than providing individual evidence of attainment. As work is done in the open, provenance and sharing of ideas requires tracking.

Conclusion

This post has introduced some ideas for teaching open science focusing on the student as both a producer and consumer of knowledge. The majority of suggestions have centred around inquiry-based learning as this brings students closer to research practices and allows social and cultural aspects of science and research to be embedded in learning experiences.

Explicitly articulating the learning aims and values that are driving the teaching design would be useful to enable students to critique them and arrive at their own conclusions about whether they agree with openness as a default condition. There is currently little systematic evidence for the proposed benefits of open science, partly because it is not widely practised in many disciplines and also as a result of the difficulty of designing research to show direct causality. Therefore, using evidence-based teaching practices that attempt to train students as scientists and critical thinkers without exposing the underlying principles of why and how they’re being taught would not be in the spirit of the exercise.

Support for increased openness and a belief that it will lead to better science is growing, so the response of the next generation of scientists and their decision about whether to incorporate these practices into their work has great implications for the future research cultures and communities. At the very least, exposure to these ideas during under- and postgraduate training will enable students to be aware of them during their research careers and make more informed decisions about their practises, values and aims as a researcher. There are exciting times ahead in science teaching!

If you’ve found this interesting, please get involved with a growing number of like-minded people via the pointers below!

Getting Involved in Open Science Training

More projects people could get involved with? Add them to the comments and the post will be updated.

References

  1. Neary, M., & Winn, J. (2009). The student as producer: reinventing the student experience in higher education.
  2. Peters, M. A., & Britez, R. G. (Eds.). (2008). Open education and education for openness. Sense Publishers.
  3. For a peer-reviewed paper on the OSTI initiative, see Kershaw, S.K. (2013). Hybridised Open Educational Resources and Rotation Based Learning. Open Education 2030. JRC−IPTS Vision Papers. Part III: Higher Education (pp. 140-144). Link to the paper in Academia.edu
  4. Carpenter, J., Wetheridge, L., Smith, N., Goodman, M., & Struijvé, O. (2010). Researchers of Tomorrow: A Three Year (BL/JISC) Study Tracking the Research Behaviour of’generation Y’Doctoral Students: Annual Report 2009-2010. Education for Change.
  5. Herndon, T., Ash, M., & Pollin, R. (2014). Does high public debt consistently stifle economic growth? A critique of Reinhart and Rogoff. Cambridge journal of economics, 38(2), 257-279.

  6. Roose, Kevin. (2013). Meet the 28-Year-Old Grad Student Who Just Shook the Global Austerity Movement}. New York Magazine. Available from http://nymag.com/daily/intelligencer/2013/04/grad-student-who-shook-global-austerity-movement.html. Accessed 20 Dec 2014.
  7. Grahe, J. E., Reifman, A., Hermann, A. D., Walker, M., Oleson, K. C., Nario-Redmond, M., & Wiebe, R. P. (2012). Harnessing the undiscovered resource of student research projects. Perspectives on Psychological Science, 7(6), 605-607.
  8. Frank, M. C., & Saxe, R. (2012). Teaching replication. Perspectives on Psychological Science, 7(6), 600-604.
  9. Feldman, L., Patel, D., Ortmann, L., Robinson, K., & Popovic, T. (2012). Educating for the future: another important benefit of data sharing. The Lancet, 379(9829), 1877-1878.
  10. McAuley, D., Rahemtulla, H., Goulding, J., & Souch, C. (2012). 3.3 How Open Data, data literacy and Linked Data will revolutionise higher education.
  11. Lombardi, M. M. (2007). Approaches that work: How authentic learning is transforming higher education. EDUCAUSE Learning Initiative (ELI) Paper, 5.
  12. O’Hara, K. J., & Kay, J. S. (2003). Open source software and computer science education. Journal of Computing Sciences in Colleges, 18(3), 1-7.
  13. Yates, J. R., Curtis, N., & Ramus, S. J. (2006). Collaborative research in teaching: collaboration between laboratory courses at neighboring institutions. Journal of Undergraduate Neuroscience Education, 5(1), A14.

Licensing

Text is licensed under the Creative Commons CC0 1.0 Universal waiver. To the extent possible under law, the author(s) have dedicated all copyright and related and neighbouring rights to this text to the public domain worldwide.

Open Books Image: by opensourceway on Flickr under CC-BY-SA 2.0

Asia-Pacific Open Science Call

Jenny Molloy - December 15, 2014 in Announcements, Featured, Meetings

Asia-Pacific_map1

We are pleased to announce our first ever open science working group call specifically for Asia-Pacific timezones!

Sunday 21 December, 8:00 UTC

(12:00 UTC+4 – 18:00 UTC+10)

Dial-in instructions will be posted on the wiki and call notepad prior to the call.

Check out the open science wiki for more details and please do add your details there, especially if you would be willing to help host a call.

Massive thanks for Ranjith Raj Vasam for taking on the task of organising the first call. We look forward to seeing how the group shapes these calls going forward and look ahead to many more opportunities to bring together the open science community in the Asia-Pacific region.

Congratulations to the Panton Fellows 2013-2014

Jenny Molloy - November 20, 2014 in Featured, Panton Fellowships

Samuel Moore, Rosie Graves and Peter Kraker are the 2013-2014 Open Knowledge Panton Fellows – tasked with experimenting, exploring and promoting open practises through their research over the last twelve months. They just posted their final reports so we’d like to heartily congratulate them on an excellent job and summarise their highlights for the Open Knowledge community.

Over the last two years the Panton Fellowships have supported five early career researchers to further the aims of the Panton Principles for Open Data in Science alongside their day to day research. The provision of additional funding goes some way towards this aim, but a key benefit of the programme is boosting the visibility of the Fellow’s work within the open community and introducing them to like-minded researchers and others within the Open Knowledge network.

On stage at the Open Science Panel Vienna (Photo by FWF/APA-Fotoservice/Thomas Preiss)

On stage at the Open Science Panel Vienna (Photo by FWF/APA-Fotoservice/Thomas Preiss)

Peter Kraker (full report) is a postdoctoral researcher at the Know-Center in Graz and focused his fellowship work on two facets: open and transparent altmetrics and the promotion of open science in Austria and beyond. During his Fellowship Peter released the open source visualization Head Start, which gives scholars an overview of a research field based on relational information derived from altmetrics. Head Start continues to grow in functionality, has been incorporated into Open Knowledge Labs and is soon to be made available on a dedicated website funded by the fellowship.

Peter’s ultimate goal is to have an environment where everybody can create their own maps based on open knowledge and share them with the world. You are encouraged to contribute! In addition Peter has been highly active promoting open science, open access, altmetrics and reproducibility in Austria and beyond through events, presentations and prolific blogging, resulting in some great discussions generated on social media. He has also contributed to a German summary of open science activities every month and is currently involved in kick-starting a German-speaking open science group through the Austrian and German Open Knowledge local groups.

Rosie with an air quality monitor

Rosie Graves (full report) is a postdoctoral researcher at the University of Leicester and used her fellowship to develop an air quality sensing project in a primary school. This wasn’t always an easy ride, the sensor was successfully installed and an enthusiastic set of schoolhildren were on board, but a technical issue meant that data collection was cut short, so Rosie plans to resume in the New Year. Further collaborations on crowdsourcing and school involvement in atmospheric science were even more successful, including a pilot rain gauge measurement project and development of a cheap, open source air quality sensor which is sure to be of interest to other scientists around the Open Knowledge network and beyond. Rosie has enjoyed her Panton Fellowship year and was grateful for the support to pursue outreach and educational work:

“This fellowship has been a great opportunity for me to kick start a citizen science project … It also allowed me to attend conferences to discuss open data in air quality which received positive feedback from many colleagues.”

Samuel Moore (full report) is a doctoral researcher in the Centre for e-Research at King’s College London and successfully commissioned, crowdfunded and (nearly) published an open access book on open research data during his Panton Year: Issues in Open Research Data. The book is still in production but publication is due during November and we encourage everyone to take a look. This was a step towards addressing Sam’s assessment of the nascent state of open data in the humanities:

“The crucial thing now is to continue to reach out to the average researcher, highlighting the benefits that open data offers and ensuring that there is a stock of accessible resources offering practical advice to researchers on how to share their data.”

Another initiative Sam initiated during the fellowship was establishing the forthcoming Journal of Open Humanities Data with Ubiquity Press, which aims to incentivise data sharing through publication credit, which in turn makes data citable through usual academic paper citation practices. Ultimately the journal will help researchers share their data, recommending repositories and best practices in the field, and will also help them track the impact of their data through citations and altmetrics.

We believe it is vital to provide early career researchers with support to try new open approaches to scholarship and hope other organisations will take similar concrete steps to demonstrate the benefits and challenges of open science through positive action.

Finally, we’d like to thank the Computer and Communications Industry Association (CCIA) for their generosity in funding the 2013-14 Panton Fellowships.

SciDataCon2014 Open Science Roundup

Jenny Molloy - November 18, 2014 in External Meetings, Featured, Research, Tools

SciDataCon 2014 was the first ever International Conference on Data Sharing and Integration for Global Sustainability jointly organised by CODATA and World Data Systems, two organisations that form part of the International Council for Science. The meeting was held 2-5 November in New Delhi and I had the pleasure of staying in the peaceful, green campus of IIT-Delhi within walking distance of SciDataCon2014 at the adjacent and equally pleasant Jawaharlal Nehru University (JNU).

It was a jam-packed week but I’ve tried to pick out some of my personal highlights. Puneet Kishor has also blogged on the meeting and there was an active Twitter feed for #SciDataCon2014 .

Text and Data Mining Workshop
Open Data Initiatives
Data from the People for the People
Summary
Bonus slide decks

Photo by Puneet Kishor  published under CC0 Public Domain Dedication

Photo by Puneet Kishor published under CC0 Public Domain Dedication

Text and Data Mining Workshop

On Sunday 2 November I ran a workshop with Puneet Kishor of Creative Commons as a joint venture with Open Knowledge and ContentMine. Armed with highlighters, post-it notes and USB-stick virtual machines, we led a small but dedicated and enthusiastic group of immunologists, bioinformaticians, plant genomics researchers and seabed resource experts through the basics of content mining.

Photo by Puneet Kishor  published under CC0 Public Domain Dedication

Photo by Puneet Kishor published under CC0 Public Domain Dedication

We covered what it means, when it is legal to content mine and more broadly some of the policy and legal frameworks which impact access to and rights of reuse for the scientific literature. We hand annotated entity types in two papers about lion evolution and Aspergillus fungi. This aimed to get people thinking about patterns and how to program entity recognition – what instructions does a computer require to recognise what our brain categorises easily? Swapping over the papers showed 80-90% inter-participant agreement in entity mark-up suggesting a reasonable precision and recall rate for our content mining humans!

Photo by Puneet Kishor published under CC0 Public Domain Dedication

Photo by Puneet Kishor published under CC0 Public Domain Dedication

Everybody managed to scrape multiple Open Access publications and extract species names, we also discussed potential collaborations and had a virtual visitor from afar, Peter Murray-Rust. The overwhelming feeling in the room was once of dismay at the restrictions on reuse of academic content but optimism about the potential uses of content mining – we hope that an excellent collaboration opportunity around phytochemistry will come to fruition!

Legal Implications of Text and Data Mining (TDM)

Open Data Initiatives


Several sessions over the conference highlighted how far we still have to go in terms of data sharing and particularly the challenge of gaining political will required for data sharing for global sustainability. Waltraut Ritter, a member of the active Open Knowledge local group Open Data Hong Kong, presented a paper co-authored with Scott Edmunds and others, making the case to policy makers that open data can support science and innovation. There is no guidance from the Hong Kong University Grants Committee on dissemination of research data resulting from its 7.5 billion HKD annual funding pool. Data sharing was explicitly flagged as low priority in 2011 and on enquiry in 2014 Open Data HK were informed that this assessment had not changed. Arguments to appeal to policy makers are clearly required in these situations and Waltraut expanded on a few during the talk.

Exploring the complexities of sharing data for public health research, Sanna Meherally reported on a qualitative study examining the ethical and practical background to potential research data sharing, involving five sites in Asia and Africa, and focusing on stakeholder perspectives. A key takeaway message was the importance of considering cultural barriers to implementation of funder data policies. Chief concerns raised in interviews were confidentiality, the potential for data collection efforts to be underplayed and the need to give something back to research participants. That the latter point was raised by so many researchers interviewed is encouraging given the title of the next day’s session ‘Data from the people for the people’, which was another focus of SciDataCon.

Data from the People for the People – encouraging Re-use and Collaboration

This double session focused on citizen science projects around topics related to sustainability, including biodiversity and climate change. Norbert Schmidt introduced projects in the Netherlands to monitor air quality while Raman Kumar from the Nature Conservation Foundation introduced a range of bird and plant ecology citizen science projects in India such as eBird, MigrantWatch and SeasonWatch. You can find the full session list here.

Cumulative hours of birding as of Sep 214 through the eBird India citizen science initiative

Most questions raised surrounded the validation of data quality from citizen scientists, which has been addressed at length by several projects. Later presentations and discussions moved to some very pressing matter in participatory science – how to build and retain and community of contributors and how to manage outputs in a way that is accessible to and benefits contributors, a similar point to that raised by Sanna Meherally. Retention of volunteers is a particular issue in longitudinal studies in ecology, as data is required for the same locality over multiple years so repeat volunteering is essential.

Tyng-Ruey Chuang tackled some of these issues in his talk on ‘Arrangements for Data Sharing and Reuse in Citizen Science Projects‘. He asked projects to compare themselves to Wikipedia in terms of openness, participation and tools. For instance, does your project retain or strip metadata from contributed images? Tyng-Ruey also emphasised informed participation – clearly state if citizen contributions are prima facie uncopyrightable or ask agreement for open licensing. This chimed with earlier points by Ryosuke Shibasaki about the need for citizen ownership of contributed data and agency to make informed decisions about its use.

The talk ended with a call to action, as the Open Definition was practically quoted and Tyng-Ruey called for raw data, now! He’s in good company at Open Knowledge!

Arrangements for Data Sharing and Reuse in Citizen Science Projects

Summary

The sessions above are only a small subset of the conversations happening across the whole programme and papers are available online for all sessions. There were many demands for more open data, from Theo Bloom using her keynote to call for the abolition of data release embargos to Chaitanya Baruo revealing that Indian geology students are using US data because India does not make its own data available for open academic research. However, there were also excellent case studies of the reuse of data and its value. It would have been interesting to see some more cross-cutting sessions including all of the data collection and sharing cycle, but that will need to wait for 2016! This is a thoroughly recommended conference for data scientists and managers as well as domain experts and has notable participation from the global South, which is excellent and enriches the perspectives discussed.

Finally, I can only apologise for not being able to report on the Strategies Towards Open Science Panel – I was giving a talk at IIT which clashed with the session, but I’ve no doubt some excellent points were raised which will soon be shared!

Bonus slide decks

I couldn’t attend these sessions, but they’re worth a look! First up Susanna Sansone and Brian Hole on data journals:

Improving openness, transparency and reproducibility in scientific research

Jenny Molloy - October 24, 2014 in Featured, Guest Post, Reproducibility, Research, Tools

This is a guest post for Open Access Week by Sara Bowman of the Open Science Framework.

Understanding reproducibility in science

Reproducibility is fundamental to the advancement of science. Unless experiments and findings in the literature can be reproduced by others in the field, the improvement of scientific theory is hindered. Scholarly publications disseminate scientific findings, and the process of peer review ensures that methods and findings are scrutinized prior to publication. Yet, recent reports indicate that many published findings cannot be reproduced. Across domains, from organic chemistry ((Trevor Laird, “Editorial Reproducibility of Results” Organic
Process Research and Development) to drug discovery (Asher Mullard, “Reliability
of New Drug Target Claims Called Into Question

Nature Reviews Drug Development) to psychology (Meyer and Chabris, “Why Psychologists’ Food Fight Matters” Slate), scientists are discovering difficulties in replicating
published results.

Various groups have tried to uncover why results are unreliable or what characteristics make studies less reproducible (see John Ioannidis’s “Why Most Published Research Findings Are False,” PLoS, for example). Still others look for ways to incentivize practices that promote accuracy in scientific publishing (see Nosek, Spies, and Motyl, “Scientific Utopia II: Restructuring Incentives and Practices to Promote Truth Over Publishability” Perspectives on Psychological Science). In all of these, the underlying theme is the need for transparency surrounding the research process – in order to learn more about what makes research reproducible, we must know more about how the research was conducted
and how the analyses were performed.
Data, code, and materials sharing can shed light on research design and analysis decisions that lead to reproducibility. Enabling and incentivizing these practices is the goal of The Open Science Framework, a free, open source web application built by the Center for Open Science.


The right tools for the job

The
Open Science Framework (OSF)
helps researchers manage their research workflow and enables data and materials sharing both with collaborators and with the public. The philosophy behind the OSF is to meet researchers where they are, while providing an easy means for opening up their research if it’s desired or the time is right. Any project hosted on the OSF is private to collaborators by default, but making the materials open to the public is accomplished with a simple click of a button.

Here, the project page for the Reproducibility Project: Cancer Biology demonstrates the many features of the Open Science Framework (OSF). Managing contributors, uploading files, keeping track of progress and providing context on a wiki, and accessing view and download statistics are all available through the project page.

Here, the project page for the Reproducibility Project: Cancer Biology demonstrates the many features of the Open Science Framework (OSF). Managing contributors, uploading files, keeping track of progress and providing context on a wiki, and accessing view and download statistics are all available through the project page.

Features of the OSF facilitate transparency and good scientific practice
with minimal burden on the researcher. The OSF logs all actions by contributors and maintains full version control. Every time a new version of a file is uploaded to the OSF, the previous versions are
maintained so that a user can always go back to an old revision. The OSF performs logging and maintains version control without the researcher ever having to think about it – no added steps to the workflow, no extra record-keeping to deal with.

The OSF integrates with other services (e.g., GitHub, Dataverse, and Dropbox)
so that researchers continue to use the tools that are practical, helpful, and a part of the workflow, but gain value from the other features the OSF offers. An added benefit is in seeing materials from
a variety of services next to each other – code on GitHub and files on Dropbox or AmazonS3 appear next to each other on the OSF – streamlining research and analysis processes and improving workflows.

 Each project, file, and user on the OSF has a persistent URL, making content citable. The project in this screenshot can be found at https://osf.io/tvyxz.

Each project, file, and user on the OSF has a persistent URL, making content citable. The project in this screenshot can be found at https://osf.io/tvyxz.

Other features of the OSF incentivize researchers to open up their data and materials. Each project, file, and user is given a globally unique identifier – making all materials citable and ensuring
researchers get credit for their work. Once materials are publicly available, the authors can access statistics detailing the number of views and downloads of their materials, as well as geographic
information about viewers. Additionally, the OSF applies the idea of “forks,” commonly used in open source software development, to scientific research. A user can create a fork of another project, to
indicate that the new work builds on the forked project or was inspired by the forked project. A fork serves as a functional citation; as the network of forks grows, the interconnectedness of a body of research becomes apparent.

Openness and transparency about the scientific process informs the development of best practices for reproducible research. The OSF seeks both to enable that transparency, by taking care of “behind
the scenes” logging and versioning without added burden on the researcher – and to improve overall efficiency for researchers and their daily workflows. By providing tools for researchers to
easily adopt more open practices, the Center for Open Science and the OSF seek to improve openness, transparency, and – ultimately – reproducibility in scientific research.

Open science at student conferences

Jenny Molloy - July 1, 2014 in External Meetings

I always really enjoy getting asked to speak at generalist or discipline-specific conferences that are not per se about open science, but the organisers of which recognise that it is a great thing to discuss (and increasingly, a necessary thing). One such opportunity was at the [ID]2 interdisciplinary life science student conference in Oxford last week. I thought I would share my approach and summary here and really hope to hear back from others who have presented on the topic and the kind of discussions that come up in your sessions. For those of us who spend a lot of time talking about open science with a broad range of people, it is really useful to reflect on what aspects different groups relate to and where the really interesting conversations lie.

Here is my slidedeck, it’s a short one (Friday afternoon session!) with a whip through the main aspects of what open means, what falls under the open science umbrella and then three short case studies of projects which represent many different aspects of open science. I chose Open Source Malaria, Open Ash DB and PLUTo, because I felt I knew enough to talk about them for a few minutes and they’re all relevant to the life science interests of the audience alongside their brilliance at using open approaches.

Key to the second half of the session was a discussion, based on the following questions:

  1. Why do you do scientific research?
  2. What are your biggest frustrations?
  3. Do you see scope for greater openness to improve your research or science in general?
  4. What are your reservations?

I emphasised I was particularly interested to find out how the answers to the third question related back to the particular goals, aspirations and barriers that had been identified in the first two questions.

Sticky notes and markers at the ready, the group of 15-20 students split into three and this is what we learned:

  1. Why people were researching science fell into several clusters of answers – pragmatic answers like buying time and paying the rent, intellectual curiosity and the joy of finding things out, personal enjoyment (nice working environment, good coffee!) and wanting to change the world and make a difference.
  2. Biggest frustrations unsurprisingly were slow rates of progress including experiments not working for no apparent reason (I think we can all empathise – for session leaders I would say a tip here is to move people onto the next question quickly before discussion becomes too much of a #phdchat/counselling session!). A lack of openness and slow exchange of information were explicitly mentioned particularly in terms of unpublished algorithms and inability to reproduce other people’s results. There was an interesting dichotomy of an information overload (too much literature/data deluge) contrasted against a complete lack of access to data in some cases. General inertia and conservatism in academia were brought up, some cited a lack of freedom and too much hierarchy whereas others suffered from a lack of direction. Complicated data formats and restrictive formats for submission (e.g. only a Microsoft Word document) caused some lively discussion in the groups. The final frustration listed was (of course) supervisors.
  3. Scope for openness to benefit people’s research was a little under-represented with only four sticky notes once a slight colour confusion had been corrected, but as someone pointed out one of the notes was greater availability of raw data which covers a lot of ground and addresses several people’s frustrations. Publishing negative results was deemed to be a beneficial effect of greater openness. Given that many students in the group work on modeling biological processes, I was surprised that code availability was not brought up but it seems in some areas it isn’t a problem and in others the focus is on the theoretical model rather than the implementations, which neatly led to a side discussion about the level of priority that is given to good software engineering in academia and also the trade-off inherent in documenting research outputs for sharing and reuse versus using that time to create more outputs. All valuable discussions to have.
  4. People were not short of reservations about openness, which was expected. Lack of reciprocation and people cheating the system were brought up as was gaining credit for your work, although other members of the group stated they thought openness would make this easier and get you more recognition and citations. That it’s difficult and time consuming to do openness, to share data and convince collaborators to do the same was a strong feeling and undeniably true. The standard reasons for not being entirely open were all present, as documented extensively in many places including the Royal Society Report Science as a Public Enterprise in their definition of ‘intelligent openness’ – national security, personal privacy and protection of endangered species among others. Additional topics came up in conversation but I will skip over them for brevity.

The overwhelming impression was that there is a clear link between the major frustrations faced by research students and some of the proposed benefits of openness, but more needs to be done to address reservations and make it easier for people to share what they are doing. Students are operating within very different working models, sets of priorities and expected research outputs and these are heavily influenced by their supervisors and the general bureaucracy of research and academia. This means a constant negotiation in terms of where openness might be beneficial to them and that bar is sometimes very high.

There are no ground breaking revelations here, but the more often diverse groups of researchers have the opportunity to engage with each other about these topics, the better for informing their future decisions on how openness will play a role in their research. Feedback suggests that attendees enjoyed the opportunity to discuss these topics with others from a broad variety of research backgrounds so it’s certainly a session I’ll be running again.

I hope other members of the working group can share your own experiences discussing open science with research students. Please take up any opportunity to run sessions like this in your communities and institutes and report back to us on how things go!

Open Science at Tech4Dev 2014

Jenny Molloy - June 10, 2014 in External Meetings, Meetings, Research

Winner of the #LavauxContest photo competition at #t4d2014 from @GabrielaTejadaG

Winner of the #LavauxContest photo competition at #t4d2014 from @GabrielaTejadaG

Denisa Kera and Sachiko Hirosue pulled together a fabulous session at Tech4Dev 2014 #t4d2014 at the SwissTech Convention centre in sunny Lausanne. The conference was organised by CODEV and the UNESCO Chair in Sustainable Technologies and focused on ‘What is essential?’ in technology for development. Many answers to this question discussed throughout the three days converged around collaboration with communities, with many sessions highlighting examples of co-design and co-creation across a range of technologies for development including water, energy, healthcare and ICTs for education. This recognition of and commitment to participation and collaboration in reseach for development relates strongly to work completed by the open science working group and the OpenUCT initiative funded by IDRC (documented here, working paper available online).

The session ‘The Openness Paradigm: How Synergies Between Open Access, Open Data, Open Science, Open Source Hardware, Open Drug Discovery Approaches Support Development?’ covered a range of topics reflecting the breadth of practices that constitute open science but the two key areas of interest were open hardware for science and open data.

First speaker up was Professor Irfan Prijambada from Gadjah Mada University in Yogyakarta, Indonesia, who described the necessity of access to lab equipment for his microbiology research focused on agricultural practices and fermentation. Fermentation is important for alcoholic drinks but also the fermentation of cassava and rice to produce traditional Indonesian foods such as tapei. Further aspects of research in the Laboratory of Agricultural Microbiology centre around soil and water microbiology, including biodegradation and bioremediation in volcanic soils. As any microbiologist knows, the ability to observe small lifeforms and a sterile environment in which to culture and work with them are the two most essential research requirements in the lab. Prof Prijambada described the resultant difficulties of performing research effectively when dealing with obsolete and inadequate research equipment, relying on out of date microscopes with no digital image collection and plating microorganisms on agar in open spaces next to a bunsen burner with no access to a clean hood or laminar flow hood, both standard pieces of equipment for maintaining a near-sterile environment and ensuring samples are not contaminated. To add to these difficulties, applying for funding for equipment procurement at the university can mean a 12 month wait for processing and delivery even if the application is approved. There was a clear need for cheap, rapid and local supply of essential kit.

miCAM v3.2 on display at Tech4Dev. Photo by Jenny Molloy, all rights waived under CC0.

miCAM v3.2 on display at Tech4Dev. Photo by Jenny Molloy, all rights waived under CC0.

Step in Hackteria.org. In 2009 after a workshop in Yogyakarta run by Marc Dusseiller, an active maker and advocate of DIY biology and open source hardware, Prof Prijambada and his lab set about taking a DIY approach to lab hardware by creating their own clean hood and laminar flow hood, initially using a glassfibre filter but now employing a series of HEPA filters. The equipment was constructed in only 2 months for less than 10% of the cost of a commercial equivalent (1.2m IDR vs 15m IDR). Microscopes were constructed from webcams in less that one month costing 750k IDR instead of 7m IDR and were entirely adequate for research needs. Not only adequate, but aquisition of digital images allowed an automated colony counter to be developed. The importance and utility of these microscopes was explained by their developer Nur Akbar Arofatullah, a researcher at Gadjah Mada University, who founded the Lifepatch initiative and along with other hardware projects, has improved the DIY microscopes to the stage where a company is now offering a commercial version of the latest MiCAM v3.2 for those who don’t find DIY appealing. However, hands-on construction remains a key part of the educational aims of open hardware and Lifepatch are using the microscopes and their construction for a range of workshops pitched at different educational levels. Kindergarten students compare the width of their hair in Cyber Hair Wars, elementary students learn about plant and muscle cells, high school students construct their own microscopes while their teachers are taught how to run workshops themselves. University students are enthused with the DIY spirit and encouraged to apply these principles in their own education and research.

One area where Gadjah Mada University excels is community relations. Setting an example for all publicly funded research establishments, staff and students are expected and obliged to work with the community to achieve promotion within the university and there exists a dedicated Office of Research and Community Development. Within this ethos, DIY microscopes have been used to bridge knowledge between the university and community through workshops on sanitation and hygiene which make use of the microscopes and microbiology techniques to analyse water, take handswabs and analyse data on E. coli contamination. Lifepatch have run the Jogja River Project for several years, taking an integrative approach to water quality and river monitoring including participatory mapping and data collection on vegetation and animals all the way through to active clean up operations. Innovation in DIY hardware is rapid at Lifepatch and Gadjah Mada, with other projects including a vortex, rotator for incubating bacterial samples and a pipette stand. As per the example of MiCAM, the DIY approach is still compatible with commercialisation as people can buy pre-built hardware, thus offering the possibility of generating jobs and income but there are many questions around models for these activities which were of interest to the audience but could easily fill an entire session and were not covered in any depth (see reports here and here for an introduction).

In a related talk during a later session at a beautiful UNESCO World Heritage Site, the Lavaux vineyards on the banks of Lake Geneva, Dara Dotz presented on 3D printing open hardware during another session which touched on the creation of jobs and hyper local digital manufacturing capacity in Port au Prince, Haiti. Dara travelled to Haiti for three weeks and ended up staying for a year working for an NGO. She observed problems in water treatment plants and in hospitals which were caused by a lack of supplies and particularly spare parts due to a broken supply chain including long shipping and customs quarantine times, a culture of bribes and poor transport links for distribution. After a friend attended the delivery of 5 babies in one evening and had no option for tying off umbilical chords but using her own gloves, Dara realised that her background interest and contacts in 3D printing could be used to solve some of the issues of obtaining plastic parts and consumables. Having brought a Maker-bot 3D printer into Haiti, Dara trained a group of Haitians with basic education to use the printers and 3D design software and several potential uses were identified, with critical application being umbilical chord clips, splitters for oxygen tubing to allow multiple patients to receive oxygen from the same cyclinder and IV bag hooks to reduce the use of large IV stands which blocked space in already overcrowded wards.

3D Printing Umbilical Cord Clamps for babies in Haiti! from Not Impossible on Vimeo.

There were many considerations and design challenges to be addressed such as ensuring that designs addressed community needs and were designed with, by and for local people. In addition to empowering people to produce there own solutions to address real-time problems, the manufacturing method has the benefit of being on-demand, helping to ensure cleanliness of equipment, provides jobs and is also cheaper than importation of commercial equipment. Umbilical clips can be manufactured for $0.36 compared to $2.69 imported cost, representing a significant saving over time in this resource poor setting. Dara is now applying the same ideas to disaster zone supplies through the NGO fieldready.org and plans extensions to the Haiti project including importing CNC machines to allow manufacture of metal parts, creating a repository of designs for field supplies and increasing the use of recycled plastic waste for non-clinical devices and prototyping.

The Open Source Hardware approach advocated throughout this session is supported by the Open Source Hardware Association (OSHWA), a non-profit aiming to raise awareness of OSHW and to spur innovation by hobbyists, commercial and academic users. Gabriella Levine is President of the OSHWA Board and an artist with an interest in snake biomimicry. She introduced two projects designed for sensing water quality and clearing oil waste – Protei and Sneel, a snake biomimetic robot designed iteratively by Gabriella and documented online.

two sneels together playing from gabriella levine on Vimeo.

PROTEI PRESENTATION VIDEO from toni nottebohm on Vimeo.

These modular sailing and swimming robots allow sensors for oil, plastic waste,temperature, radioactivity and more to be attached and move through the water autonomously or via remote control, taking readings as they go. These concepts have been used in a range of water quality workshops and Gabriella runs hackdays exploring ideas around the design and deployment of water quality monitoring sensors and other hardware, including a water hackathon at Tech4Dev the following day!

With a variety of DIY and OSHW approaches and designs being prototyped and promoted in areas as important as sensors and even medical devices, a major question becomes how to ensure that quality is consistent and devices work accurately and safely. The current systems of quality assurance regulations in various countries are often either complex, expensive, time-consuming and a massive barrier to market entry – or non-existent. Kate Ettinger is working to develop a system for collecting information on quality and accuracy of OSHW projects in an open and transparent way using an open source hardware/software data collection system and an open data approach to making information available. This framework could apply to many projects but Kate used the examples of neonatal incubators and prosthetic limbs, with data being collected to accelerate responsive design and ensure ‘integrity by design’ throughout the development and deployment of open source medical devices.

OpenQRS in 30 Seconds from Kate Ettinger on Vimeo.

From open data for open hardware to open data as a research tool, Nanjira Sambuli from iHub in Nairobi described the use of crowd sourced data during the Kenyan elections in 2013 and contrasted data collected from Twitter and other social networks via passive crowdsourcing with active sourcing organised by Ushahidi. Conclusions presented were that machine learning algorithms are necessary to make collection of large datasets from high volume social networks viable and that there were surprising patterns and voices gathered through passive listening rather than active calls for information. Nanjira presented a framework developed by iHub for election data crowdsourcing emphasising the three V’s – viability, validity and verification.

jb_CrowdsourcingInfographice

Integrity and curation of scientific data was also highlighted in the final talk by Scott Edmunds of GigaScience , during which he described some excellent case studies of the power of openness. One example was increasing the rapidity of disease research during the E.coli outbreak in Europe in 2011, where BGI rapidly sequenced and released the genome as open data. The image of the chromosome map was later chosen as the front cover of a major report from The Royal Society in the UK on openness in science. Another example looked at the great scope for crowd sourcing the collection and analysis of open datasets. Research on Ash Die Back, an invasive tree disease, demonstrated several flavours of citizen science from publicly contributed geo-tagged photos of infected trees for OpenAshDB to gamification of genome data analysis via the Facebook game Fraxinus. It is also clear that citizens are very keen to support local research that is important for them and wish data to be made public to enrich their scientific and cultural heritage. The Puerto Rican “People’s Parrot” genome project took an endangered and much loved national symbol and sequenced its genome to learn more about its uniqueness and evolutionary history. This effort was funded by fashion shows, art projects, concerts, a branded beer and public donations. Scott focused on these successes but also discussed the challenges in increasing open data release, including ensuring researchers get appropriate credit and are incentivised to make their data available.

The BGI sequenced chromosome of the German E.coli outbreak strain.

The BGI sequenced chromosome of the German E.coli outbreak strain.

A common theme running through the presentations was that openness can be effective at accelerating innovation and enabling research in resource-poor settings. In addition, the scope for education and democratisation of the scientific process through involvement of local communities in scientific research and technological innovation has variously led to employment, empowerment and increased opportunities. The challenge now is to establish under what contexts this remains true and work to advocate and support open approaches where they can offer benefits for scientists and citizens in the global South. I hope members of this working group and the rest of the global open science community will be able to contribute to this mission!