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Open science & development goals: round up & the way forward

Jenny Molloy - September 23, 2013 in Collaborations, External Meetings, Meetings, Research

This is a post by the team at OpenUCT (post by Sarah Goodier, photos by Uvania Naidoo) and will soon be published on the OpenUCT blog.

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.

day2_1

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.

day2_2

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!

day2_3

Open science & development goals: shaping research questions

Jenny Molloy - September 13, 2013 in Collaborations, events, External Meetings, Guest Post, Meetings, Research

This is cross-posted from the OpenUCT blog.

What do we include in our definition of open science? And what is meant by development? Two key questions when you’re discussing open science for development, as we were yesterday on day one of the IDRC OKFN-OpenUCT Open Science for Development workshop.

Participants from Africa, Asia and Latin America and the Carribbean have gathered at the University of Cape Town in an attempt to map current open science activity in these regions, strengthen community linkages between actors and articulate a framework for a large-scale IDRC-funded research programme on open science. The scoping workshop aims to uncover research questions around how open approaches can contribute to development goals in different contexts in the global South. Contextualization of open approaches and the identification of their key similarities and differences is critical in helping us understand the needs and required frameworks of future research.

Several key themes, which generally provided more questions than answers, came up throughout a day packed of presentations, discussion and debate: strategic tensions, inequalities, global power dynamics, and the complexity of distilling common challenges (and opportunities) over large geographical areas. Some of the key strategic tensions identified include the balance between the “doing” of open science as opposed to researching it, as well as the tension between high quality research and capacity building at an implementation level. Both tensions are centred on inextricably linked components which are important in their own right. This brings up the question of where should the focus be? Where is it most relevant and important?

The issue of inequality and inclusivity also featured strongly in the discussions, particularly around citizen science – by involving people in the research process, you empower them before they are affected. But this begs the questions: How open should citizen science be? Who takes the initiative and sets goals? Who is allowed to participate and in what roles? With regard to knowledge, a small number of countries and corporate entities act as gatekeepers of the knowledge produced globally. How should this knowledge be made more accessible? Will open scientific approaches make dialogue and knowledge distribution more inclusive?

By the end of the first day’s discussion, the workshop had surfaced opportunities and challenges for each of the regions, but many questions still remain in terms of how to address the complex issues at hand and bring together the complex and disparate components of open scientific activity. Day two of the workshop will be focused on articulation of research problems, possible areas of activity and the structure of the envisioned research programme.

Join the discussion via Twitter via #OpenSciDev.

by SarahG (Pictures by Uvania Naidoo)

Open Science for Development

Jenny Molloy - July 20, 2013 in Announcements, Collaborations, events, External Meetings, Meetings, Research

OpenSciDev_logo

We are delighted to announce that OKF is collaborating with the OpenUCT Initiative at the University of Cape Town in an International Development Research Centre funded project to develop a southern led research agenda for open science for development.

We hope to use this as an opportunity not only to explore research into open science but also to really push community building efforts in the global south and identify a strong network of open science advocates and practitioners – maybe setting up some new local open science groups along the way!

You can read more in our project proposal.

A small group met in London last week to set the ground work for a larger workshop in Cape Town 11-13 September 2013 and the results of that meeting will be available online shortly.

We hope you are as excited about this opportunity as we are and in the spirit of the exercise we will be making both the process and outcomes as open as possible. Therefore, if you would like to apply to participate in the Cape Town meeting please send jenny.molloy@okfn.org a brief half page introduction to yourself including answers to the following questions:

Why is this project of interest? What expertise and experience do you bring? What would you like to see come out of this project?

Preference will be given to participants from developing countries in order to further the aims of the project and full funding will be provided.

There is a short deadline of 24 July 2013 so please spread this invitation through your networks, particularly contacts you might have in the global south. If selected, we will organise travel and flights as soon as possible.

OpenSciDev_Funders

Citizen Science Open Technical Workshop on Google+ Hangout

Theodora Middleton - January 29, 2013 in Collaborations, events

It’s our pleasure to invite you to join the Citizen Science Open Technical Workshop to be held Wednesday 30th January 16:00 CET virtually using Google Hangout.

You can attend the meeting and send all your comments in this Youtube channel or this twitter account.

Over 2 hours, we’ll have expert talks and open discussions about technologies for volunteer computing and thinking projects like:

  • BOINC, the popular volunteer computing desktop middleware used in scientific projects like Seti@Home where volunteers donate their computing resources for analyzing radio telescope data, Einstein@Home where you could help analyzing weak astrophysical signals from spinning neutron stars, or CERN’s LHC@Home where the users help the physicists to develop and exploit particle accelerators like CERN’s Large Hadron Collider.
  • BOSSA, a distributed thinking framework for creating scientific projects where the volunteers perform tasks that require human intelligence, knowledge, or cognitive skills. An example of this technology is the project Transcribe Bleek & Lloyd where the volunteers help to transcribe Bushman hand written documents.
  • PyBossa, the OKFN’s framework for volunteer thinking projects where volunteers could participate in scientific applications like Feynman’s Flowers where the volunteers help to study how molecules interact with the surfaces they are stuck to, ForestWatchers.net where the users can help to detect deforested areas from satellite images in forests, or for example helping in damage assessment cases like with the Pablo Typhoon or oil spills by Shell experienced by the company in the Niger Delta (Nigeria).
  • Furnivall, a framework for distributed volunteer science. It helps to organize batches of tasks, collect them form volunteers and it does all the related housekeeping.
  • Ourgrid a grid middleware based on a peer-to-peer architecture. This middleware enables the creation of peer-to-peer computational grids,
  • and other technologies.

The speakers are:

  • David Anderson (Univ. Berkeley),
  • Daniel Lombraña (CCC),
  • Francisco Sanz (BIFI),
  • Eduardo Lostal (Ibercivis),
  • Francisco Brasileiro (Univ. Fed. Campina Grande),
  • Candida Silva (Univ. Coimbra),
  • Juanjo Molinero (software developer).

The workshop is co-organized by the Ibercivis Foundation and the Society as Infrastructure for e-Science project funded by the European Commission under FP7.

Ross Mounce on “Open Palaeontology” @OKCon Berlin 2011

Maria Neicu - August 11, 2011 in Collaborations, OKCon, Panton Principles

The following is a guest blogpost by Ross Mounce, currently a PhD writing on “The Importance of Fossils in Phylogeny” at the University of Bath, in UK. As his approach includes application of informatics techniques to palaeontological data, Ross’s research interests are also oriented towards Openness in Data, Access and Science. Ross attended the Open Knowledge Conference in Berlin, 2011, where he gave a talk on Open Palaeontology.

Ross Mounce:

“A few weeks ago, I gave a talk at the Open Knowledge Conference 2011, on ‘Open Palaeontology’ – based upon 18 months experience as a lowly PhD student trying, and mostly failing to get usable digital data from palaeontological research papers. As you might well have inferred already from that last sentence; it’s been an interesting ride.

The main point of my talk was the sheer stupidity/naivety of the way in which data is supplied (or in some cases, not at all!) with or within research papers. Effective science operates through the accumulation of knowledge and data, all advances are incremental and build upon the work of others – the Panton Principles probably sum it up far better than I could. Any such barriers to the accumulation of knowledge/data therefore impede the progress of science.

Whilst there are numerous barriers to academic research (access to research papers being perhaps the most well-known and well-publicised), the issue that most aggravates me, is not the access to these papers, but the actual papers themselves – especially in the digital context of the 21st century. They are only barely adequate (at best) for communicating research data and this is a major problem for the future legacy of our published work… and my research project.

My PhD thesis title is quite broad: ‘The Importance of Fossils in Phylogeny’. Given this title and (wide) scope, I need to look at a lot of papers, in a lot of different journals, and extract data from these articles to re-analyse; to assess the importance of fossils in phylogeny; to place them on a meta-scale. There are long established data formats for the particular type of data I wish to extract. So well established and easy to understand there’s even a Wikipedia page here describing the most commonly used data format (nexus). There exist multiple databases set aside specifically to host this type of data e.g. TreeBASE and MorphoBank. Yet despite all this standardisation and provisioning for paleomorphological phylogenetic data – far less than 1% of all data published on, is actually readily-available in a standardised, digital, usable format.

In most cases the data is there; you just have to dig very very hard to release it from the pdf file it’s usually buried in (and then spend unnecessary and copious amounts of time, manually reformatting and validating it). See the picture below for a typical example (and yes, it is sadly printed sideways, this is a common and silly practice that publishers use to inappropriately squeeze data matrices into papers): 7BHO

I hope you’ll agree with me that this is clearly absurd and hugely inefficient. As I explain in my presentation (also available below this post) the data, as originally analysed/used, comes in a much richer, more usable, digital, standardised format. Yet when published it gets stripped of all useful metadata and converted into a flat, inextricable and significantly obfuscated table. Why? It’s my belief that this practice is a lazy unwanted vestigial hangover from the days of paper-based (only) publishing, in which this might have been the only way in which to convey the data with the paper. But in 2011, I can confidently say that the vast majority of researchers read and use the digital versions of research papers – so why not make full and proper use of the digital format to aid scientific communication? I argue, not to axe paper copies. But to make sure that digital versions are more than just plain pdf versions of the paper copy, as they can and should be.

With this goal in mind, I set about writing an Open Letter to the rest of my research community to explain why we need to richly-digitise our published research data ASAP. Naturally, I wouldn’t get very far just by myself, so I enlisted the support of a variety of academic friends via Facebook, and (inspired by OKFN pads I’d seen) we concocted a draft letter together using an Etherpad. The result of this was a fairly basic Drupal-based website that we launched http://supportpalaeodataarchiving.co.uk/ and disseminated via mailing lists, Twitter, Academia.edu as far and wide as we possibly could, hoping just hoping, that our fellow academics would read, take note and support our cause.

Surprisingly, it worked to an extent and a lot of big names in Palaeontology signed our Open Letter in support of our cause; then things got even better when a Nature journalist (Ewen Callaway) got interested in our campaign and wrote an article for Nature News about it, which can be found here. A huge thanks must go to everyone who helped out with the campaign, it has generated truly International support, as can be demonstrated on the map below:

(View Open Letter Signatures in a larger map)

It’s far too soon to know the true impact of the campaign. Journal editorial boards can be very slow to change their editorial policies, especially if it requires a modicum of extra effort on the part of the publisher. Additionally, once the editorial policy does change at a journal, it can only apply to articles submitted from henceforth and thus articles already in the submission pipeline don’t get affected by any new guidelines. It’s not uncommon for delays of a year between submission and publishing in palaeontology, so for this and other reasons, I’m not expecting to see visible change until 2012, but I think we might have helped get the ball rolling, if nothing else… The Paleontological Society journals (Paleobiology and Journal of Paleontology) have recently adopted mandatory data submission to the Dryad repository, and the Journal of Vertebrate Paleontology has also improved their editorial policy with respect to certain types of data, but these are just a few of many journals that publish palaeontological articles. I’m very much hoping that other journals will follow suit in the next few months and years by taking steps to improve the way in which research data is communicated, for the good of everyone; authors, publishers, funders and readers.

Below you can find the Prezi I used to convey some of that (and more) at OKCon 2011. Huge thanks to the conference organisers for inviting me to give this talk. It was the most professionally run conference I’ve ever been to, by far. If the conference is on next year – I’ll be there for sure!” Ross Mounce

The invited talk, given on Friday 1st July 2011 at the Open Knowledge Conference (Berlin) by Ross Mounce: Open Palaeontology on Prezi

Wikimedian in Residence on Open Science

Jenny Molloy - July 26, 2011 in Collaborations

Congratulations to working group member Daniel Mietchen on becoming the first Wikimedian in Residence on Open Science

Daniel at Rencontres Wikimedia France (1)

His appointment is announced in this blog post from Wikimedia, which encouragingly stresses the importance they place on open science:

“The open science movement is fighting to make scientific research – especially publicly funded research – more transparent, freely accessible and reusable. The goals of open science are closely aligned with our mission, yet for years there has been little institutional contact between our movement and initiatives such as Open Access and Open Data. Joining forces with individuals and organizations who are working to promote a culture of openness in the scientific community should be high on our agenda.”

This joining of forces is already underway as the project is hosted by the Open Knowledge Foundation Germany, where OKF will act as a partner for the provision of content and external expertise in Open Knowledge and particularly Open Data.

You can read more about Daniel’s plans in his introductory blog post here and interview with the Wikipedia Signpost. There are also plenty of opportunities to get involved, as detailed in his call to the working group for input. This is a fantastic collaborative opportunity so we hope plenty of people are able to contribute!

[1] Thesupermat, Wikimedia Commons under CC-BY-SA

New Mailing List for Open Science Apps and Tools

Jenny Molloy - July 1, 2011 in Collaborations, Tools

After the exciting collaboration between developers and scientists at the Open Science and Social Science Workshop on Wednesday (see the introductory blog post, Etherpad and the post event report for the full story!) a new mailing list has been created for people interested in developing apps, tools and datasets around open science, open data in science and citizen cyberscience.

We hope to get a good crowd of people from the OKF and organisations such as the Citizen Cyberscience Centre to follow on the great work here in Berlin and generate some really useful projects to facilitate open science in all its forms.

Sign up here and get developing!