part of the WikiSprint group in Geneva

We will use this post, however to recap the day! Fearless hackathon leaders Stefan Kasberger and Rayna Stamboliyska had previously solicited project proposals and votes on favourites, with which they announced what projects would likely be attempted on the day.

Hackdays don’t always go to plan and that’s intentional, people are welcome to start something unexpected. One unintended, good result of mashing up great people and great ideas was the metabolomics scientist who met Daniel Lombraña-González and got into crowdsourcing, citizen science with CrowdCrafting, run on OKF’s PyBossa.

A particularly active and international group held a WikiSprint to improve Open Science related content at the P2P Foundation and on Wikipedia as detailed in those links. You can still contribute! and please do. Pictured above are some of the participants in Geneva, with the photo taken by project leader, Célya Gruson-Daniel @celyagd. Activities were organized with this Etherpad, where you can find more on who got up to what in the WikiSprint.

@MaliciaRogue!

At about the halfway mark, Rayna @MaliciaRogue dropped a few summary tweets:

The Open & Citizen Science workshop is going very nicely: we have an #OpenScienceManifesto coming, an #OpenScienceWiki sprint, (cont) #OKCon

>>> We also have more hardcore statistical stuff going on w friends from OKF Finland organizing R packages for #OpenGov data analysis #OKCon

Last but not least, we have metabolomics scientists interested to involve citizens with #Crowdcrafting cc @teleyinex #OpenScience #OKCon

We will report more soon!

For WikiSprint: Global overview of Open Science initiatives please join us remotely via the coordinating Etherpad (found: https://etherpad.mozilla.org/xpQvKfNv5c) and working either here or on Wikipedia.

For other projects, join us in IRC: #openscience on freenode or via the web at http://webchat.freenode.net/?channels=openscience. Find us on Twitter @MaliciaRogue, @stefankasberger, @openscience, and at #openscience or #OKCon.

Proposal 1

Title: “Open Data in Research: an illusion?”

Details: Despite the dazzling development of the open access movement, open data initiatives in science and research are still trailing in involvement. Additionally, disparities in research data sharing and openness are huge across scientific communities and domains.

Last but not least, formats and licensing terms greatly vary even within specific field. This suggested activity will wrap-up current initiatives and achievements prior to formalizing the challenges ahead. The middle-term goal is to bootstrap connections converging to a true institutional change that leads to more participative, shareable and transparent science: the science of tomorrow.

Support: Open Data enthusiasts, geeks and science nerds welcome.

Comment: Remote participation welcome (IRC, pad). Hashtag: #OpenSciData

Proposal 2

Title: “An inclusive approach to open science”

Details: The discourse in open science often runs along the lines of open vs. closed approaches. In reality though, most researchers act in-between those two extremes. From successful examples such as genomics, we can see that open science is essentially a community effort (cp. Bermuda Principles). Therefore, we (the Austrian chapter of the OKFN) advocate an inclusive approach to open science.

From a community perspective, it is the commitment to openness that matters, and the willingness to promote this openness on editorial boards and program committees. It is therefore important to get as many researchers on board as possible. This approach is _not_ intended to replace existing initiatives but to make researchers aware of these initiatives and helping them with choosing their approach to open science.

The idea of this hackathon is to create a manifesto/declaration for such an inclusive approach. A draft and a first discussion can be found here: http://science20.wordpress.com/2013/06/25/an-inclusive-approach-to-open-science/
We invite contributions from researchers in various disciplines on their experiences with advocating and implementing open science practices. This could be in the form of presentations, lightning talks, or focused discussions.

Support: We mainly need creative minds; designers, illustrators, and animators are welcome as we could produce a short video about the idea.

Comment: N/A

Proposal 3

Title: “Wikisprint: Global overview of OpenScience initiatives”

Details: A few months ago an event was organised to agregate links and knowledge about P2P initiatives. http://codigoabiertocc.wordpress.com/2013/08/07/globalp2p-the-wind-that-shook-the-net/
In partnership with Michel Bauwens of the P2P Foundation and HackYourPhd I’d like to organize a similar event for OpenScience initiative. The P2P Foundation aims to promote and document peer to peer practices in a very broad sense. The collective HackYourPhd federate numerous students, researchers and citizens interested in the production and the sharing of knowledge. Being an administrator on the French Wikipedia, I will likely get support from the Wikimedia communities.

This “wikisprint” will be set up as follow:

1. The idea will be to announce the event a few days ago and invite people on twitter and other plateform to share their initiative with us.
2. We could for exemple use the hashtag #OpenScienceWiki
3. During the hackathon People in Geneva but also elsewhere could help to agregate the links in a wiki, interact with people all around the world and invite them to share their initiatives.
   We can use the P2Pwiki: http://p2pfoundation.net/Spanish_P2P_WikiSprint
   We could also map this OpenSciene initiative in a map http://maps.ubimix.com/hyphdus/
4. We could also visualize all the interaction with the hashtag
   Here is an example of what people have done during the #GlobalP2P event: http://demos.outliers.es/wikiSprint/
5. Once the broad mapping is done on the P2Pwiki, it could serve to enhance several Wikipedia articles on Open Science. The content is currently rather poor: see for instance http://en.wikipedia.org/wiki/Open_knowledge and to a lesser extent http://en.wikipedia.org/wiki/Open_Science. Wikidata — the growing open data repository of the Wikimedia Foundation — could also use some contributions to the topic https://www.wikidata.org/wiki/Q2251455 and https://www.wikidata.org/wiki/Q309823 are empty.
6. Illustrations and dataviz might also be welcome: for instance, graphics of academic publishing economics (figures are rather hard to get).

Support: Designer and programmer are welcome for the visualisation

Comment: Here are some guidelines given by Michel Bauwens to help us organize this workshop.

• it’s important to give some basic how to advice at the beginning of the process
• in each locale, it’s good to have a person that can just wander around and help and stimulate the other people (this makes a big difference)
• we had a permanent rolling hangout, with every hour a different topic to be discussed (it went on for 15 hours or so during the hispanic wikisprint)
• it makes it much more easy if there is a pre-established form, with the tickable tags etc.
• clear delimitation of subject matter, not anything goes , make sure you specify what open science is inclusive of, perhaps some geographic limitation (say Europe) etc..
• choice of tags: one for the event itself, say [[Category:OpenScience Wikisprint]]; one for the topic, so that it continues to live on after the event, say [[Category:Open Science]]
  this can be combined for example with country tags, [[Category:France]] etc.
  (the p2pfoundation.net wiki already has http://p2pfoundation.net/Category:Science for the broader p2p/commons aspects of science, this would allow a more specialized focus)
  I will be also present during this workshop to help the interaction with Wikipedia and the wikipedia community.
• Including Wikipedia within the wikisprint could stimulate global contribution by attracting experienced wiki user. We can create a parallel contribution project (an example: http://en.wikipedia.org/wiki/Wikipedia:GLAM/MonmouthpediA )

Proposal 4

Title: “rOpenGov – R ecosystem for social and political science”

Details: With the avalanche of open government data and other fields relevant to computational social science, new algorithms are needed to take full advantage of these new information resources – to access, analyse and communicate such information in a fully transparent and reproducible manner as part of scientific inquiry or citizen science projects.

A scalable solution will require coordinated effort from independent developers. Hence, we are now building up a community-driven ecosystem of R packages dedicated to open government data and computational social and political science, building on lessons learned from analogous and wildly successful projects in other fields. The site already provides open source R tools for open government data analytics for Austria, Finland, and Russia and we are now actively collecting further contributions.

The preliminary project website is at: http://louhos.github.io/en/ropengov.html

Support: In addition to internet access, the project would benefit from contributions from website designers, scientists and R package developers.

Comment: Distant participation to the hackathon through IRC/Skype is also possible.

Proposal 5

Title: “Crowdcrafting Everywhere”

Details: Crowdcrafting is a straightforward, open source handy tool for citizen science. Unfortunately, Crowdcrafting solely speaks English for now. What about translating it into other languages, e.g. French, Spanish, Russian,…?

Support: Multilingual enthusiasts welcome!

Comment: Remote participation welcome.

Hashtag: #CCEverywhere.

Crowdcrafting’s lead developer, Daniel Lombrana-Gonzalez, will also be with us throughout the whole day.

Proposal 6

Title: Open Access Button

Details: Open Access Button is a browser-based tool which tracks every time someone is denied access to a paper. We want to display this, along with the person’s location, profession and story on a real time, worldwide, interactive map of the problem. While creating pressure to open up scholarly and scientific research, we also want to help people work within the current broken system by helping them get access to the paper they need.

That’s the project summed up really briefly. We built a prototype at the start of the summer and are working towards a launch of later in the year.

Support: tbc

Comment: Waiting for confirmation for founders to join in person. Remote participation will be confirmed soon.

Proposal 7

Title: “Booksprint: OpenScience Guidelines for PhD Students and researchers”

Description: Organize a book sprint to write a guide about how to do open science for researchers or PhD students.

No special skills are needed to participate, if you are a PhD student or a students or know the basic of science from another area. We will share our ideas and experience with open science.

Possible chapters:
* What does it mean to publish in open access?
* How do you go about publishing in open access?
* What is an “Open notebook”?
* How do I organize an open notebook?
* Which other tools are available?
* What tools are missing?
* How do we communicate and better support each other?
etc.

To write the book, we will use Fidus Writer ( http://fiduswriter.org ), an open source, webbased editor that typesets academic writing with citations and formulas, and lets us publish PDFs or ebooks of articles and/or journals without any technical skills. The Fidus Writer team will assist via hangout/chat.

Support: Some designers are welcome to help for figures, and other visualisations.
Internet access has to be available and Google Chrome or Chromium installed on the machines.
Artististic minds are also welcome

Comment: I think it would be a good idea to find a printing solution as well, because to have something in your hands, can be very engaging and it would be great for hackyourpdh to have something to show around. But this could be done afterwards.

Open and Citizen Science in the heart of Europe – Workshop

Thursday 19 September, 10:00 – 17:00 @ Centre Universitaire d’Informatique Université de Genève, Auditorium, Ground Floor

Coordinators: Stefan Kasberger (Open Knowledge Foundation Austria) and Rayna Stamboliyska (Open Knowledge Foundation France), in collaboration with François Grey (Citizen Cyberscience Center / University of Geneva), Margaret Gold/ Brian Fuchs (Citizen Cyberscience Center / The Mobile Collective)

Hacking science makes us happy. If it makes you happy, too, then, this year’s Open Knowledge Conference is the place to be!

Indeed, OKCon 2013 is where an amazing bouquet of insights from Open and Citizen science will converge. But if you thought there would be only food for the brain, you were wrong. A satellite event will take place on 19 September aiming at giving space for everyone to actually get great things done.

With our friends François Grey (Citizen Cyberscience Center/University of Geneva), Margaret Gold and Brian Fuchs (Citizen Cyberscience Center/The Mobile Collective), we have come up with a way allowing everyone to take part to this exciting day.

I have an idea!

We know you do. Hence, we have a dedicated form ready for you to submit a short description of what you are keen to work on. You can also indicate what additional competences you need in order to get your project done.

Idea submission will be running from today until 10 September. Every week, we will be updating everyone (through the Open Science mailing list) telling you about the new ideas submitted. In addition, a community call will be scheduled to discuss and narrow down these ideas so that they actually become feasible within one-day long hands-on sprint.

Working together

The idea of the satellite event is to geek out together. On 11 September, we will be publishing a poll with all ideas so that you can be able to vote for the project you want to work on on Day D. Voting will run until 18 September.

Do not forget to bring your favourite geeking gear (laptop, some flavour of mobile device or a fancy notebook in the perfect 1.0 fashion). We will have WiFi, cookies and fun!

The workshop space can accommodate up to 45 people.
To sign-up, express your interest in the topic and get in touch with the coordinators please write to openandcitizenscience@okcon.org.

1. Open Quake- Welcoming OpenQuake and OpenGEM as new members in Open Science group. 

The Open Quake project summarise discussions at the OKCon Open Science Panel and the issues they face in open data: volunteer computing, licensing and user interfaces. Volunteer-based projects in scientific research can be improved by using a platform like BOINC which allows open-source computing solution. As for interfaces, the actual challenge comes down to making open data usable.

2. Citizen Cyberscience

Francois Grey- on the distinction between open science and citizen cyberscience. Playing with the liminal space between professional and amateurish science, openness should primarily enhance the possibilities for praxis. As Grey states, “I’m not interested in openness as an end in itself, but rather as a means to an end”: in this case, widening the circle of experts. Empowering the „have-nots” is not enough, as access must come along with real opportunities of participation. „In short, Open Science is about making sure there are no locks on the doors to science. Citizen cyberscience is about making sure as many people as possible walk through those doors.”

Original post can be found here.

——————————–
Other Reports from OKCon

Interested in hearing more from Open Knowledge Conference 2011? Below you can find listed reviews, comments on speakers and presentations, but also ideas to be further developed.

·         On his blog, Nikolay Georgiev (Open Source Ecology) brings together the presentations related to Open Hardware, from principles of freedom to FabLabs and RepRap machines. Follow his slideshare, and consider his argument for having different levels of openness for Hardware.

·         Part of the LOD2 team (who presented this year in Berlin the Open Government Data Stakeholder Survey) Martin Kaltenboeck writes more on Andreas Blumauer’s presentation on open data for enterprises. Here.

·         DataMinerUk presents Nicola Hughes’s stand for open data in journalism. Find out why infographics and other interactive tools are only a superficial effort towards data journalism, reading her extracted points from the speakers Simon Rogers, Stefan Candea, Caelainn Barr, Liliana Bounegru and Mirko Lorenz.

·      Here,   James Harriman-Smith maps OKCon2011 around the Open Shakespeare’s annotation system, asking whether subjective opinion can be processed as (open) data as well, in the ecosystem of openness

·        In this post from http://www.lanetscouade.com, Samuel Goëta summarizes top 5 speakers, starting with Richard Stallman’s intriguing talk on fundamental liberties vs. Open Source. (Article in French).

·         For DataOne research, Richard Littauer relates his experience of the OKCon2011, taking the pulse of legal matters. Find out why we will soon need a database of Open Knowledge-relevant lawsuits: https://notebooks.dataone.org/workflows/2011/07/12/okcon-recap/

·         An extensive, critical blogpost from Michael Gurstein. Who is the end-user for whom we fight to open-up data?

·           Stefan Merten offers full details on some compelling presentations, and forecasts a soon-to-come big boom for open hardware. On http://www.keimform.de/2011/report-from-open-knowledge-conference-2011/ and here.

·          Rolf from Open for Change links OKCon presentations on governmental data with the beta version of the Open for Change Manifesto, as a way to better create autonomy, control and empowerment: http://openforchange.info/node/341

·         For details on backstage meetings at OKCon2011, and on how OKF design its organizational DNA, find out more in Peter Murray-Rust article here (also blogged by Glyn Moody).

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):

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

Towards Embedding Open Methods in Chemistry

Anna Croft

Anna discussed her efforts to get open science into the undergraduate curriculum at Bangor University, with both successes and failures.

Abstract

Notes from talk (Jenny Molloy)

Workflow Classification and Open-Sourcing Methods: Towards a New Publication Model

Richard Littauer

Richard discussed the use of programmes such as Taverna and Kepler to create, execute and share scientific workflows leading to greater automation of scientific data analysis and management. He presented the initial findings of the Data Observation Network for Earth study on the uptake and effectiveness of these systems.

Abstract

Slides

Open Palaeontology – Putting fossil data on the web for all to see and use

Ross Mounce

Ross advocates the dissemination of open research data on the web in paleontology, a field which is cautious to adopt this approach.

Abstract

Presentation

Open Access: Closed Discourse or Open Knowledge?

Ulrich Herb

Ulrich aimed to explore and clarify the relationship between the paradigms of Open Access and Open Knowledge. He looked at issues such as the resource disparity between open and closed access scholarly publication, and the social effects at work in the sciences that discourage people publishing in open access journals.

Abstract

Open Science, Open Data, Open Minds: Using smartphones games to study recreational drug use

Caspar Addyman

Slideshare

Caspar described his project using smartphones to gather data on recreational drug use, including data on alcohol consumption and its cognitive effects. The project also follows open knowledge principles.

Abstract

Slides

Project Info

Open Access… but Professionally

Jacek Ciesielski

Jacek believes that OA journals need not be poor cousins of commercially published journals and discussed solutions to encourage OA publishers to be as professional as modern closed publications.

Abstract

Presentation (pdf)

You can view a full list of participants and ideas on the Etherpad, or view a more coherent and permanent record on the workshop Wiki as items are migrated over!

The session kicked off by introducing some successful citizen science projects:

• MalariaControl.net – Distributed computing using volunteer CPU time to run simulations of malaria epidemiology under different parameters and incorporating different control measures.

• Epicollect – A web application for the generation of data collection forms for mobile phone platforms, as well as data collection to project websites.
• QuakeCatcher – brings seismology into homes and schools using internal accelerometers in laptops or external USB accelerometers in desktops to detect earthquakes. Aims to generate the world’s largest distributed network of seismometers.

Following this burst of inspiration, the group then generated a total of nine hack ideas around the topic of generating quality open science/social science data and took forward some of these in four groups

Data Digitiser

A tool for volunteer sourced transcription of data tables from scanned books/papers where OCR and machine automation is not an option. Suggested applications: Brazilian census data, regression tables from economics articles to allow comparisons across multiple articles examining the same variables.

How? See the dedicated Etherpad for a full run down of what was suggested and achieved.

Output: Working demo of user interface! Data Digitiser displays an image opposite a Google spreadsheet ready for transcription, which can be supplemented by a separate metadata form.

Source code available via Github.

BOINC on Phones (Android)

How to take advantage of the computing power of smartphones to run applications such as MalariaControl.net.

How? Port malaria code to Google Android, probably via Android NDK to compile native C/C++ code and then write an Android Java “stub” to do the computation on Android devices (i.e. mobile phones, tablets, etc). On a grander scale we will also need BOINC to run on Android to launch the Android malariacontrol.net

Output: On the way! Far too much to do in one day.

Data Cleaning and Quality Control and Assurance

How to integrate data cleaning and general QA/QC steps with open databases and volunteer networks.

How? That was the question the group set out to answer and they concluded that they’d like to see a web based spreadsheet quality assurance tracker. Ideally this would take the form of an overlaid comment/issue flagging system which could then be checked by the data provider.

Output: Lots of interesting discussions and ideas – a summary of these can be found here.

Geo-tagging

This group discussed the idea of mapping images/photos published on the web using contextual information (detective work) and pattern recognition from satellite images. This is already used in humanitarian crises to do damage assessment and help plan investment for post conflict reconstruction and a version for the tobacco free initiative was planned.

Output: See their discussion and suggestions at the bottom of this Etherpad.

Follow on and getting involved

There is now a new mailing list for people interested in developing apps/tools/datasets etc for open science/open data in science/citizen cyber science.

Sign up here if you’re keen!

Open Science Panel

Francois Grey and Rufus Pollock

Abstract

Video

Wikipedia & Research: The innovative character of Wikipedia research

Mayo Fuster Morell, Daniel Mietchen, Mathias Schindler and Benjamin Mako Hill

Abstract

Proceedings (pdf)

Open Research: Already here or still a distant pipedream?

Cameron Neylon

Abstract

Slideshare

Interview with Cameron on German radio (MP3 in English)

Collaborative platforms for streamlining workflows in Open Science

Konrad U. Förstner

Abstract

Proceedings (pdf)
Slideshare

Citing versioned sources

Daniel Mietchen

Abstract

Talk Wiki (see the Q&A tab for discussion and continue to contribute if you’d like!)

Scholarly Publishing Reform: What Needs to Change?

Björn Brembs

Abstract

Old slides (hoping for updated versions from OKCon soon!)

If you know of further resources or notes on any of these talks, or the Open Science Panel, that you’d like to share then email me at jenny.molloy@okfn.org. I’ll keep the page updated as more ‘official’ resources become available from OKCon.