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

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

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

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!

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.

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

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!

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!

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

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!

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

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.

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.

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.

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!

Chemistry themed lunch!

I have spent the last two days at a meeting run by the Automation and Analytical Management Group (AAMG) of the Royal Society of Chemistry.  As well as being a lovely meeting location (the RSC building Burlington house isn’t your average conference centre- dessert was served in beakers and the rooms are beautiful) the meeting itself has been very interesting.

With topics of talks ranging from new air quality monitoring techniques to the latest deployment of networks of sensors to exciting new citizen science projects and the future of air quality monitoring.

The iSPEX add-on being used to measure aerosol properties

It was this final topic that really caught my attention, a project called iSPEX originating in the Netherlands.  iSPEX is an add-on for your iPhone which allows the user to take measurements of the properties of aerosols. This project is currently being piloted in the Netherlands and has had some great success. On the first national iSPEX measurement day more than 5000 measurements were collected all over the Netherlands. This brilliant response shows the interest that can be generated by citizen science air quality projects.

I personally cannot wait for this project to be extended to other countries as well because I think it’s gadgets like this that really will start to make some headway towards increasing public interest in Air Quality.

Other projects discussed included installing a large network of low-cost air quality sensors at Heathrow airport and another project from Leicester where air quality outreach is also being pushed through funding from the RSC. Overall a very positive meeting demonstrating the interest in networks of monitors and citizen science concepts.

Open science and development were the two key points that brought together a diverse group of over 20 scientists, methodological experts and researchers last week at the University of Cape Town. From the 12–13 September, these experts in their fields gathered for an IDRC OKFN-OpenUCT Open Science for Development workshop to scope possible research areas of open science for development. The focus was on research could be undertaken and to strengthen networks around this broad topic across Africa, Asia, Latin America and the Caribbean.

Day 1 involved discussions around opportunities and challenges for each of the regions represented as well as available resources that could be used and shared. By the end of the day, the group was starting to draw on these potential avenues for exploring open science for development to shape research questions.

Continuing from day 1’s discussions, day 2 focussed on framing these research questions around open science for development. These questions were discussed by breakout groups who selected the top four out of the multitude of those suggested. This selection was no easy task in such a mixed bag of broad, conceptual questions and focused practical questions – a clear indication that there are many potential interesting research questions.

Four key questions emerged that were taken forward in further discussion:

1. What value framework is a prerequisite for open science?
2. How can open science support visibility and communication of science outside formal academic structures?
3. How can open science create education?
4. How can the economic and social value of open science be measured?

Projects that could help to answer these main questions were conceptualised and expanded upon. Some of the broad areas that the suggested projects could address included education, increased public involvement as well as the implication of open science on cost and building value. A regional focus for the suggested projects was thought to be best, largely due to financial and time limitations as well as co-ordination issues. The overarching IDRC-backed research programme will help to create and develop further synergies between any funded projects.

As part of maintaining the momentum created during over the course of the workshop, staying connected and growing the network by bringing other people with diverse perspectives on board are key actions going forward. All of us walked away from this workshop with a greater appreciation for open science and an understanding that, although diverse, open science is united by many similar practises across regions.

We ended with more questions than answers at the end of the two days – just where you should be when you’re scoping possible research questions. What comes next is an OKFN working paper pulling together all the discussion threads, questions and resources raised over the two days, which will inform a call for research proposals for projects involving and investigating open science.

Watch this space as open science spreads across the map!