[also posted in http://www.science3point0.com/evomri/2011/05/03/drafting-proposals-in-the-open-sketching-out-project-ideas/] This post is licenced under a CC0
“Professionally our methods of transmitting and reviewing the results of research are generations old and by now are totally inadequate for their purpose.” Vannevar Bush, 1945
As announced last week, we – Fabiana Kubke and Daniel Mietchen – are currently participating in the Getting your CC project funded course at Peer-to-Peer University, and have decided to draft our proposal collaboratively and in the open. Part of our motivation is our (and others’) perceived need for making scientific information more useful by positioning it where it can be easily found, used, linked to, repurposed, and updated.
The introductory meeting of the course took place on April 26 (UTC) via Skype. We have since incorporated some of the feedback we got so far, and in this post – which Claudia Koltzenburg helped us draft – we will outline the next steps in the hope to entice others to get involved as well.
- May 3, Workshop 1: How do we move from having an idea to realizing those ideas in terms of having aims, and goals?
- May 6, Workshop 2: Which funding bodies are there that can give financial support, and how do we find appropriate sponsors for our project?
- May 10, Workshop 3: How can we structure our proposed work in terms of tasks and how do we make a realistic timeline?
- May 17, Workshop 4: Knowing how long time we estimate, and the resources we need, how do we put together a reasonable budget?
- May 24, Workshop 5: What happens after the funding period is over? How do we make the project sustainable?
- May 31, Workshop 6: What would we look at when reviewing another proposal.
The grant proposals are to be drafted in parallel to these workshops until June, when the proposals produced will be peer-reviewed, and professional feedback will be provided to increase the chances of getting funded. In preparation for today’s workshop, we will use this post to explore the aims and goals of our project(s).
The candidate projects in a nutshell
The ideas submitted as part of the application for the course all center around what could be thought of as an Encyclopaedia of original research, which shall therefore be the default focus of the grant proposal (as idea 1). Two smaller projects (ideas 2 and 3) build on idea 1 but are more specific and could thus be integrated into a proposal about idea 1, or developed independently, whereas idea 4 is wider in scope than idea 1. We expect the final scope of our grant proposal to be defined more precisely before attending Workshop 3.
“In the academy [..] we need to recognise an ethical obligation [...] which is at the core of our mission which is universal access to knowledge.” Larry Lessig, in the video embedded below, which is CC-BY-licensed.
Idea 1: The primary aim of the Encyclopaedia of original research (henceforth EOR) is to arrange the existing scientific literature in a way that allows it to become dynamic in nature. The primary goal is to develop a platform that is able to capture and archive the open scientific literature such that the original work is being preserved (like at arXive or PubMed Central) but becomes dynamically and collaboratively editable (like at OpenWetWare). By way of such a platform, scientists and others could share their knowledge more effectively than through papers: Work on related matters could be more easily identified and conceptualized, and so could gaps in knowledge. Besides the possibility for direct editing, facilities for annotation, commenting and other ways of interaction with the community of researchers in the field would ensure the widest possible peer review.
The Encyclopaedia of original research combines two of the principles for open science that have been put forward by Science Commons: it takes the “Open Access” literature and recognizes that it too – like data – is a lost opportunity “without structure and annotation”. The characteristics of the platform that would contain the encyclopaedia are complex: it needs to track individual contributions to enable proper attribution, the content needs to be granular enough to be able to be cite individual elements within an entire piece, individual pieces of works or elements within it need to be able to be dynamically linked, indexed and contextualized, and the metadata needs to be structured to enhance discoverability, an attribute that is essential for reuse. The user interface also needs to be suitable for the different technological levels of knowledge or levels of comfort appropriate for individual scientists, so that technology is not a barrier for adoption and/or contribution.
We expect that the encyclopaedia will benefit science by helping to avoid duplication of research efforts (and related funding), providing a faster means of updating information otherwise delayed by prevalent publication cycles or not deemed “worthy” of formal publication (practical example case) and promoting the open discussion of research findings in light of new evidence.
Idea 2: The aim here is to take advantage of such a repository to facilitate the delivery of scientific and health-related information to remote areas where this information may not be readily available but where access to it is essential for the well-being of those communities. What we imagine is that the above EOR could incorporate (or lead to) lay summaries (similar to AcaWiki of the scientific literature or such as those that already exist in blogs) as part of its knowledge base and both the original research as the lay summaries can be translated to local languages. Specific content that is relevant to specific world regions (e.g., malaria in Africa, Chagas in South America) can be bundled in formats that are compatible with existing local technology. One way to at least partially achieve this goal is to bundle region-relevant information so that it can take advantage of ongoing deployments associated with the One Laptop Per Child (OLPC) project and where it can reach the communities that would benefit most from that research.
Idea 3: The aim here is to take advantage of the infrastructure of the EOR (and part of the information contained within it) to complement (or support) digital collections not typically considered part of the scientific “literature”, e.g. from museums or databases. Take, for example this artifact from the Matapihi digital collection. The interaction of the user with the digital object could be enhanced by linking it to different representations of the same specimen (say, an MRI scan), or to relevant scientific information pertaining to similar specimens. It could further be brought back to life by linking it to other cultural artifacts: for instance, ‘Have specific works of poetry or music been inspired by these types of specimens?’, or ‘Are there local traditions or myths that are associated with the artifact?’, or ‘Is there a personal notebook of the individual who brought this specimen to where it is? As an example, this other digital object from the New Zealand National Library presents not just the artifact but the cultural context of what the object represents and how it relates to the local cultural heritage.
The fate of these ideas will depend on how the grant writing develops; the project as a whole could be shrunk to either of these projects (or similar ones), or these projects could be spinned off or retired.
Idea 4: The project could in principle also be expanded in scope, e.g. to test the efficiency of open versus traditional science. However, in order to produce a competitive grant on this big issue, we would require considerable support from beyond our current team of three.
The next steps
By May 10, we will need to identify in a first instance the type (or types) of funding bodies that would be suitable (at least in principle) to fund and/or sponsor the project. We would like to invite feedback and suggestions for that part of the process as well. For that purpose, we have set up a page on Wikiversity were we will be aggregating the relevant feedback we receive, and draft the next blog post in this series.
We would also like to invite feedback on which platform would be most suitable for the drafting of the full proposal. Different wiki spaces seem to be appropriate, as are Google Docs, but the idea of drafting it on GitHub is also on the table.
[By Fabiana Kubke and Daniel Mietchen, Original post in
This is the first of a series of initially 5 posts in which we – Fabiana Kubke, Daniel Mietchen, and anyone interested to join us – are planning to reflect on a number of projects related to science in the digital age. We have applied for (and admitted to) the Getting your CC project funded course at P2P University that started today and is scheduled to help participants on their way to submission-ready grant proposals by mid-July.
Default to open
The underlying assumption is that open collaborative environments would have a positive impact on science and the relationship between science and society.
“I definitely believe that science in general is more effective the more open people are,” says evolutionary biologist Jonathan Eisen of the University of California (UC), Davis, who keeps much of his research open. “There are unquestionably risks for people that come with [openness], but the benefits to society are enormous. Given that taxpayers are paying for our work, I think that the default should be to be open unless you can prove that it’s a bad idea.” 
The ultimate goal of defaulting to ‘open’, as Eisen suggests, requires suitable (and sustainable) collaborative environments with low adoption barriers. The initial focus must therefore be on how to ‘build’ those environments (or on how to re-purpose existing technology to serve this goal).
Reusing and repurposing existing knowledge
“Knowledge emerges only through invention and re-invention, through the restless, impatient, continuing, hopeful inquiry human beings pursue in the world, with the world and with each other.” Paulo Freire
What we want to address is how to encourage the re-use and re-purposing (Freire’s re-invention) of scientific knowledge through collaboration between the scientific community and the wider society. This ‘invention and re-invention’ is currently hindered by the traditional systems through which science operates: closed notebooks, manuscripts behind pay-walls, no access to the primary data, etc., and especially copyright and licensing limitations. This inevitably leads to duplication of efforts that could otherwise be avoided if the processes were to be made more open. (See also .)
One place to start is by making existing scientific literature licenced under Creative Commons (or other open licenses) available in ways such that it can be edited, updated, commented upon and re-purposed. The goal is to shift the scientific literature from its current static format to a more dynamic one that is more aligned with both how science is done and how information is used.
The bigger picture
“Increasing the number of things you have can be useful, but increasing the amount of knowledge you have can be transformative.” Clay Shirky 
The general scheme of how we think of the bigger picture is here :
We see science as providing information; but that information can only be transformed into knowledge when the different spheres of society can interact with it in a usable manner. One crucial initial step is to make the information available in a way that allows diversifying the ways in which information/knowledge is being put to use so that it can have the desired transformative effect.
How are we planning to achieve (some of) this?
One proposal on how to achieve openness in scientific information was led by Daniel Mietchen and took the shape of the COASPedia project that aimed to “demonstrate to the scientific community that scientific articles published online under CC-BY-licenses can be arranged in a different and — importantly — more efficient manner than those published in classical journals.” The COASPedia project – initially presented at COASP 2010 – was a finalist in the Wissenswert initiative of Wikimedia Deutschland, but did not get funded.
We have now signed up (and were accepted into) a course on “Getting your cc-project funded”, run by P2PU. The course starts on April 26th, and we will be working on expanding on the original project during the course and after and drafting a proposal to get the project funded. To be admitted into the course we had to offer 3 ideas; each will specifically be described (and opened for discussion) in each of the following posts. They all sit around the concept of a basic repository (whatever shape this may take).
“Hence, in the name of the ‘preservation of culture and knowledge’ we have a system which achieves neither true knowledge nor true culture.” Paulo Freire 
This basic framework of our ideas for the course is not too different from what was proposed in the original COASPedia proposal: What we would like is for information to become useable, findable, and linkable while still capturing not only the original work but also the different contributions and their authors (i.e., preserving the cultural heritage of science). The 2 other ideas sit more specifically around how the usability, findability and linkability can help transform the way we relate with the information at hand.
The ultimate goal is not simply a modernisation of the way that information is made available, we also hope to capture the possibilities that this modernisation affords to improve the outcomes of science as a whole – with respect to how it interacts with society, how it becomes transformed into knowledge, and how it becomes part of our cultural heritage. Or in Shirky;’s words:
“what matters now is not the new capabilities we have but how we turn those capabilities, both technical and social, into opportunities” (emphasis added)
In the spirit of openness, we will keep the entire drafting process as open as possible, so as to invite feedback and other contributions from early on.
In order to help us identify the platforms that are best suited to a collaborative writing process of this kind, we will use this series of blog posts to experiment a bit with several potential drafting environments.
An aggregated view of the project will be maintained at https://tuhura.fmhs.auckland.ac.nz/mahara/view/view.php?id=295.
Footnotes and references:
We will link directly where possible, and use the endnotes mainly to store the metadata of some key references.
 Wald, C. (2010). Scientists Embrace Openness. Science. doi:10.1126/science.caredit.a1000036
 Quote was taken from Freire, P. (1985). Pedagogy of the oppressed. Harmondsworth Middlesex: Penguin. A website devoted to this work (http://www.pedagogyoftheoppressed.com/) has useful information on both the author and the text.
 Radder, H. (2010). The commodification of academic research : science and the modern university. Pittsburgh Pa.: University of Pittsburgh Press.
 In Shirky, C. (2010). Cognitive surplus : creativity and generosity in a connected age. London: Allen Lane. (ISBN 978-1-846-14218-5) (see book review here)
 This mindmap began as a discussion with Tabitha Roder over a NZ olpc testing session in Auckland. These ideas were thrown into a prezi and the derived mindmap now includes modifications suggested by Claudia Koltzenburg
A little while ago I started an experiment: can I operate my academic and personal lives by using only open source software?
I often hear the argument that while open source software is ok to fit some needs, it falls short of what it can deliver when it comes to some demands of the academic job. I have always agreed with this position until I asked myself: Based on what do I say that it is so?
So I became my own guinea pig. I installed ubuntu on my netbook (well, the royal I, it was really Tom Parkers from the olpc volunteer community who did that for me), and started adding software that I need for work. I will start sharing my experiences over time on this blog, but I will also bring my computer to Software Freedom Day on Saturday in Auckland to show what I am doing.
What is Software Freedom Day?
‘The principles behind FOSS are underpinned by the users’ freedom to run, copy, distribute, study, change and improve the software. You can read more about the four freedoms on the GNU website.’
The events kicked off yesterday in Warrington and there are more events today Friday, S
Friday 17th September, 2010
Saturday 18th September 2010
From 10 am to 4 pm we will be at Orion Cafe in Mt Eden in Auckland showing the one laptop per child computers, 3D printers, android phones and a lot more, including some presentations. And we have Sugar on a Stick to give away, but bring an empty 1G or 2G usb stick in case we run out of them.
Or if you are in Hamilton just drop by the Centre Place Mall.
Sunday 19th September 2010
Wellingtonians will have lots of fun stuff from 10 to 5 p at the Victoria University Pipitea Campus. The event is also free but you need to Register! (if your kids are coming, make sure you register them separately!) And they even have some Live music!
If you live near Tauranga, from 11 am to 3 pm activities will be happening at St Mary’s School.
And Christchurch will be sharing the FOSS love at the South Library ICT Learning Centre in Beckenham
Visit the sites, and get all the details of what each place is offering. There is plenty to feed the geek inside us!
News hit the stands about a new research collaboration to find biological markers for Alzheimer’s disease (read the stories in the New York Times and the Wall Street Journal). (HT @atreolar on Twitter). One thing that sets this collaboration apart was that the work being done would have researchers
“share all the data, making every single finding public immediately, available to anyone with a computer anywhere in the world.”
The advantages of sharing data were made clear with respect to this project in the article:
“Different people using different methods on different subjects in different places were getting different results, which is not surprising. What was needed was to get everyone together and to get a common data set.”
And this is a very strong argument for data sharing. But as interesting as the story itself is, I find more interesting some of the issues it identified with respect to scientists sharing data at such a wide scale. Specifically this paragraph brought back some things to mind:
“At first, the collaboration struck many scientists as worrisome — they would be giving up ownership of data, and anyone could use it, publish papers, maybe even misinterpret it and publish information that was wrong. “
This (with different grammatic construction) is the argument floating around. We (scientists) may all see the advantage of data sharing, but are we willing to ‘give it up’?
If you ask scientists many of us would probably say that we do science for a specific purpose: try to help find a cure for a disease, solve some environmental problem, to contribute to human culture through the creation of knowledge. Data sharing makes us put our money where our mouths are.
But is it that easy?
I would argue it isn’t. Even when we may be willing to put our data out there, to have others use it and interpret it, there is a reality we still need to face: our hiring and promotion committees. And these look at our scientific output as ‘papers published’.
There has been a lot of chatter on what the values of the papers are: should impact factor matter? Should we be looking at article level metrics? But either still look at the papers. Should we stop valuing papers and start valuing datasets?
I brought this issue up at the Data Matters MoRST meeting I attended. The current PBRF system is incompatible with data sharing. It still measures ‘output’ as individual papers. And whether I like it or not, my University’s funding (and my ability to survive in the system) depends on me satisfying these criteria. So to promote data sharing, this too needs to change.
I wonder what would happen next time I apply for promotion if instead of listing my publications on my CV I were to list my ‘datasets’: This is the data I have generated (and made public), and this is how it has been used by me and by others. Wouldn’t that be a real measure of the impact of my work? Does it really matter ‘who’ used the data to advance knowledge? Or in other words, has the time come for ‘Data Level Metrics’?
Perhaps if we gave data the same hierarchy as papers when it comes to evaluating performance, people may quickly learn that by putting the data out there the impact of our work may be easily increased (and measured). And we may be quicker to put it out.
On other news:
The Open Science Summit‘s opening session are now online thanks to ForaTV. It was a great opening session to be at, and I am glad I managed to make it there. Unfortunately I wasn’t able to stay for the rest of the meeting.
At the same time that this was happening, the government of New Zeland released its Open Access and Licencing Framework (NZGOAL). You can read about it on the Open Knowledge Foundation website, which has links to all of the documents. This is indeed good news for data sharing in New Zealand. And when I returned from my trip I found an email from The Creative Commons Aotearoa New Zealand informing me that I had been selected as a member of the CCANZ Advisory Panel.
I want to thank CCANZ for allowing me to be part of this panel, it is indeed an honour and I look forward to the good things that promise to come out of it.
Thursday saw a meeting on ‘Data Matters: Making the Most of Publicly-Funded Research Data ‘ organised by the Ministry of Research Science and Technology. The event was tweeted under the #ResearchDataMatters hash-tag on twitter, and I wrote my notes on my FriendFeed page.
The day consisted of a number of topical talks (great all of them) and a couple of brainstorming sessions by the individual tables. Julian Carver, who moderated the event did a wonderful job keeping us busy while sticking to the time schedule. It was indeed a great day filled with new ideas, and more importantly, new solutions.
It was clear that the room was filled with the vibe that opening the research data was not only important but also the direction in which we should move. The arguments in favour of this happening are quite compelling, and New Zealand can look inwards and abroad to find support for that position. There were also great examples of what New Zealand is doing in that respect, and that is also encouraging.
The central emerging theme that I think emerged from the day was that the questions about sharing data has moved from the if to the how domain. And the how is not an easy issue to solve, and one that occupies the time and thoughts of many advocates of open data. I think that these issues can be grouped into three broad categories: Ethical, Cultural, and those related to archiving.
In a way these are the ones that are relatively simpler to solve and probably encompass a narrow area of research primarily associated with Health (or other human) data. One of the concerns that was raised was that ethical approval and consent around the gathering of health data is bounded to specific studies that limit the ‘use’ of the data. A second concern is associated with privacy. I see these as relatively minor, since there are protocols in place for privacy, and ‘use’ can be redefined in the consent forms.
Cultural issues in the scientific community are a slightly higher hurdle to overcome, because it requires two things: a ‘buy in’ from the research community and a (I think) rather profound behavioural change that makes data archiving the default. There are heaps of issues around this, and I will probably leave it at that and come back to it on another post.
There was a general consensus that data should be shared. As Penny Carnaby said, if we invest in something because we think it is important, then we should also be thinking on how to preserve that knowledge. Or, what is the point of creating stuff if you then go ahead and delete it?
I also had the feeling that there was a general consensus that ultimately, it is not just about putting data on the web. Data is only useful if it can be discovered and as useful as how easily it can be re-purposed. But making data available in a meaningful reusable way is hard to do. Here is where my brain explodes, and where most of the talking centred around on the day.
There were a few things, however, that stuck with me and kept floating in my head as I took my flight back to Auckland.
One was a suggestion brought up by Andrew Treolar from the Australian National Data Service, about the need to make the data a ‘primary object’. Us researchers tend to think of the ‘paper’ as the end product, but he suggests this is a hierarchy that should also apply to the data. He suggests that data sets should be given a DOI, in the same way that manuscripts have, and this has several advantages. Not only does the data itself become a primary object, but the mechanisms to linking relationships between DOIs are already in place to create relationship and track citations between objects. DOIs have a further advantage and that is that attribution to the original source is inevitable. This idea solves at least in the interim some complex issues around data sharing.
A second point also brought up by Andrew Treolar, is that open data will probably be used to answer questions that are different to those for which the data was generated. This means that we researchers need to think of the description of the data beyond its original intention to facilitate re-purposing. And this is difficult, because how can I know what details will be needed when the question has yet to be posed? The minimum requirement would be to ensure that the data is properly described at least in terms of its origins and the steps through which it was obtained.
One of the things I also really took back with me was Penny Carnaby’s description of the work that the National Library of New Zealand has been doing around archiving of digital objects. She described the work done for the National Digital Heritage Archive (you can read about it here and here). The way I understand it, this system could provide viable solutions to some of the issues surrounding data archiving.
There is obviously a lot of work to be done, but it was encouraging to be in a room filled with people willing to be honest about the challenges, yet still enthusiastic about the road ahead. I will be interested in hearing what the follow-ups of Thursday’s meeting are, in particular the position of the funding bodies that were present in the room.
Megathanks to Jonathan Hunt and Julian Carver who made it possible for me to be there