Drafting proposals in the open – sketching out project ideas

[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

Recapitulation

“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.

The course is scheduled around a series of workshops, each focusing on a different aspect of the proposal-writing process:

• 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.

The Architecture of Access to Scientific Knowledge from Lessig on Vimeo.

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.

The approach, though initially focused on contemporary literature, could likewise be applied to legacy literature – a start in this direction has already been made, as discussed here.

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.

Drafting proposals in the open

[By Fabiana Kubke and Daniel Mietchen, Original post in

http://www.science3point0.com/evomri/2011/04/26/drafting-proposals-in-the-open-a-practical-test/]

This is the first of a series of initially 5 posts in which we – Fabiana Kubke^[1], 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.” ^[2]

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^[3]

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 [4].)

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^[5].

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 ^[6]

The general scheme of how we think of the bigger picture is here ^[7]:

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 26^th, 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 ^[3]

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”^[6] (emphasis added)

The proposal

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.

[1] Disclosure: Fabiana Kubke is a member of the advisory panel of Creative Commons Aoteaoroa New Zealand

[2] Wald, C. (2010). Scientists Embrace Openness. Science. doi:10.1126/science.caredit.a1000036

[3] 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.

[4] Radder, H. (2010). The commodification of academic research : science and the modern university. Pittsburgh  Pa.: University of Pittsburgh Press.

[5] An article along these lines of thought sits in SpeciesID and in Nature Preceedings.

[6] 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)

[7] 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

‘Tis the season…

…to file my Annual Performance Review.

Nothing makes me shiver as much as the Dean’s email reminding us that it is time to file our Annual Performance Reviews (APRs). This year shivering does not begin to express the feeling I got upon receiving that email.

What have I achieved this year? ‘Nothing’ was the first thing that came to mind. This was followed by a profound state of panic!

But wait, there is more….

This has been probably the most difficult year of my entire life. Those who know me will also know that I have had really difficult years. So this is not a light statement. It has been filled by personal and professional crises, nights with no sleep, anxiety, and the health issues that come with all that. So back to my APR – Nothing. (This does not help my sleep issues)

Or so I thought until I realised I was looking for ‘measures of performance’ in the wrong places. So yes, the papers are still being written and haven’t been submitted, I haven’t attended any ‘scientific meeting’, I haven’t received any new grants. I could go on.

But crises did not just ‘happen’. Mine came about because this has been a year in which my way of thinking and doing things has been challenged to its roots. Deep, deep roots. So perhaps, I have a lack of sense of achievement because I am looking in the wrong places.

Sure. I didn’t go to any ‘scientific meetings’. But this is where I did go to: Science Online 201o, the Linux Conference, KiwiFoo, SciFoo, the Data Matters workshop, the eResearch conference. I also became an Academic Editor for PLoS ONE and became more engaged with the discussions about science on social networks like Twitter and FriendFeed. And I have to say, I learned more about ‘Science’ this year that in my entire career. And I was reminded not just of why I got into science in the first place, but also what kind of scientist I wanted to become.

I also attended couple of workshops and conferences on innovative teaching, I completed my first year in a degree in education, became involved with WikiEducator, and was reminded not only why I got into teaching in the first place, but also what kind of teacher I wanted to become.

I also became engaged with a variety of issues. From Public ACTA, and OpenLabour, to olpc and Creative Commons. And I was reminded of the kind of citizen I thought I was to become.

I guess with great moral crises also comes great change. So I am actually looking forward to next year, when I hope that all the struggle of 2010 will pay off in the form of positive change and positive action.

To all of you out there that gave me the chance to talk to you, who offered your ideas and listened to my ramblings, who helped me organize my thoughts, formulate my goals and provided me with guidance and support, my most sincere Thank You.

As for my APR, it will be hard to fill. Can I just say:

‘This year I learned’?

 

Opening up [I think]

What does it mean, in science, to be open?

I don’t know.

by Darwin Bell

I wrote a while back, that while I endorse the principles of ‘openness‘, I struggle with the issue of ‘how‘. Since then I have been trying to listen and learn. [Or, better said, shut up and listen.] I started trying to see what hurdles I encountered trying to work exclusively on Open Source Software. I joined the Learning4Content course at WikiEducator. I started looking into platforms that would fit my needs as an open lab notebook. I tried to follow the Open Science Summit. I listened hard at sessions at SciFoo Camp. I went to some New Zealand open data discussions. I became an Academic Editor at PLoS ONE. I joined the panel of the Creative Commons Aotearoa New Zealand.

And after several months of ‘listening’ the one thing that keeps popping in my head is:

kubke, you ain’t gonna figure it out by yourself.

The loudest message that I heard is, perhaps, that there is not a single, simple, one-size-fits-all answer, and that it just may come down to fumbling through until we figure it out.

So, I decided to fumble.

I am taking in Summer students this summer to work on a project that I will try to make as ‘open’ as possible.

I am leaning towards a few things:

• I am pretty sure I want to give Mahara a go as a platform for the day-to-day ‘lab’ stuff.
• I am pretty sure I want to regularly put as much as I can into my space in OpenWetWare.
• I am pretty sure I want to try to shift my imaging to Open Source Software (e.g., Osirix, ImageJ, Cell Profiler)
• am pretty sure I want to put the work out there as it is being gathered.

What I am not so sure about is how this will work. It will be a steep learning curve, but one thing that I am hoping is that by giving it a go I may begin to get the answers.

And hopefully some of the smart people out there might give me a hand and help me steer the boat in the right direction.

Software Freedom Day[s] are here!

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?

Software Freedom Day celebrates free and open source software (FOSS), and there are several events happening in New Zealand spread over the weekend. As the site says:

‘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

By Josh Brancroft on Flickr

aturday and Sunday in Wellington, Christchurch, Auckland, Hamilton and Tauranga.

Friday 17^th September, 2010

You can come from 4-6 pm to Albany Senior High School, the first open source high school and see what they are doing.

Saturday 18^th 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 19^th 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!