Building Blogs of Science

Digital skills and scholarship for researchers 5 – getting funded

Posted in Environment and Ecology, Health and Medicine, Science, Science and Society by kubke on September 20, 2016

Almost a year had past since that first conversation between Kaitlin Thaney, Nick Jones, Cameron McLean and myself where we asked:

‘what would Software Carpentry look like if it was delivered as a university course?’

A number of conversations and workshops were had that kept indicating that the thirst and need for this was there, that there wasn’t a clear solution in place, and that the solution was not going to be easy to produce. We knew what we wanted the house to look like, but we needed to find an architect. And of course, money to pay them.

Enter Nat Torkington

Card sorting at Foo Camp CC-BY-NC-SA Titine on Flickr

Nat organises an unconference called KiwiFoo. He invites a bunch of people to a retreat north of Auckland and lets the awesome happen. In 2015 I was invited, and, by pure luck Kaitlin Thaney was invited too as she was around that time in Australia for a software carpentry instructor training around ResBaz Melbourne. Also invited were Nick Jones, director of NeSi which had recently become the New Zealand institutional partner of Software Carpentry, and John Hosking, Dean of the Faculty of Science, University of Auckland.

The words that Kaitlin Thaney said at one of our meetings came back as if from a loudspeaker: You need to engage with the University Leadership. You need to think strategically.

And KiwiFoo gave us that opportunity.

Kaitlin, Nick and I brought John Hosking into the conversation, and his response was positive. We tried to exploit the convergence as much as we could over that weekend – there are not that many chances to get to sit with this group of people in a relaxed environment and without interruptions or the need to run to another meeting. We had each other’s full attention. And exploit we did.

Back in Auckland, Nick suggested that I talk about the project to the Centre of eResearch Advisory Board. The Centre of eResearch at the University of Auckland is helping researchers with exactly these kinds of issues. Next thing I know, Cameron McLean and I are trying to get everything we learned through the workshops into something more concrete. I talked to those details, and when the Board asked: ‘how can we help you’ I did not know what to say.


Luckily, Nick Jones, as usual came to the rescue. We had a chat, and decided to work with me on higher level thinking. I was still missing the big picture that we could offer the leadership. Watching Nick’s thinking process was a humbling joy. I think I learned more from that session than what I did in all the Leadership programmes I was part of. I realised also how far I was from getting to where we needed to get. What is the long term vision? What are the gaps? Why do we need to fill them? How are you going to manage change?

At this meeting we saw we needed to engage with CLeaR, the organisation that provides Professional Development for staff and the group has a lot to offer in instructional design. We had already agreed that this training project should not be focused solely on students, but, rather, should have a broader scope. We produced an initial outline of what we were proposing, and invited Adam Blake from CLeaR to join the conversation and contribute to this document.

I was invited again to the eResearch Advisory Board, and this time I was better prepared. The timing was also perfect. The application window for the Vice Chancellor’s Strategic Development fund was open and I now knew what I needed: support to put an application through. We built a team of key project advisors, each who could contribute something quite specific: Adam Blake, to advise on course structure and to provide support to do the research on the course, Mark Gahegan, Director of the Centre for eResearch, Poul Nielsen, from the Auckland Bioengineering Institute, Nick Jones, from NeSI, and myself as the Project Lead, and the intention of hiring Cameron McLean as project manager. We worked on the application and backed, by the eResearch Advisory Board, it went in.

Our proposal was to develop a training suite, based on Software and Data Carpentry that could be used to be delivered to students and staff in different formats, to support a ResBaz in Auckland in February 2016, and to run a pilot course for students about to enter the research lab on second semester in 2016. We knew our bottleneck was time – people’s time to do the work. We asked for $150,000 in salaries.

In September we got the email: your application has been approved….


The Vice Chancellor’s fund was giving us initially a limited amount of money with the rest of the money contingent on the approval of a needs analysis by the eResearch Advisory Board.

We accepted the offer and hired Cameron McLean as Project Manager (by now he was a trained Software Carpentry Instructor and had submitted his PhD thesis and was waiting for his viva). First order of business, a needs analysis.

Time to go to the library.

Scientific publishing, with a twist

Posted in Health and Medicine, Science, Science and Society by kubke on June 13, 2012

Every now and then something happens that gets me all excited about what comes next.

Today, it is the launch of PeerJ

Image provided by Peter Binfield

Over 10 years ago I was approached by someone at a scientific conference who told me they were launching something that was to be called the Public Library of Science (PLoS), where people could publish their results and make it freely available to anyone, anywhere. The catch: authors paid for the publication cost. I wasn’t sure what to think of it. Yes, I would be totally behind it, and thought the ethos rocked but was not sure how they would get authors to pay for things they would otherwise be able to publish for ‘free’*.

Soon after that I moved to New Zealand and PLoS fell off my radar. Until 2006 when we decided to submit a paper to PLoS Biology. We got a letter back saying that we should instead submit to a new Journal they were launching: PLoS ONE, and that is where the paper got published. I immediately fell in love with PLoS ONE. But I had to wait over 3 years to become an Academic Editor, after meeting I think Steve Koch at Science Online 2010.  Another decision I am proud of.

Image provided by Peter Binfield

In 2009 I was visiting family in Minnesota, and decided to delay my return to New Zealand to attend SciBarCamp in Palo Alto. I had just been to my first unconference (KiwiFoo) and decided to give SciBarCamp a go. Best decision I ever made. It was there I first met Peter Binfield (0f PLoS ONE fame) and Jason Hoyt (who are responsible for PeerJ). There were many things that were said at that un-conference, but I vividly recall Jason’s session on Mendeley and Peter’s session on the future of publishing.

Well, it has been 3 years since then and now is the time for PeerJ.

What is special about it? It does not seem to be ‘another Open Access Journal’ but rather a completely different way of thinking of how authors and journals work together to put scientific results out there. It appears, to me and from what information I have access to, as a partnership. Scientists pay a membership fee and that allows them to publish there. For Free**. In return they commit to providing at least one review a year. Seems like a fair deal. I still find it amazing that at this time and age the majority of published science is ‘read only’. (Shocking, I know!) so I am keen to see how the post-publication interaction with the article (and the pre-publication record) will look like.

It is the sense of ‘partnership’ that I am also attracted to (and got me all excited). I have for some time been thinking whether there should be an ‘Open Science Society’ with its own journals, similar to other societies. A membership fee would subsidise the journal, and everything would be open access. Well, PeerJ is not exactly that, but it comes quite close. I actually like the idea of membership (with its perks) because it makes me the scientist care about that journal in a slightly different way. I am not sure whether Peter and Jason had this ‘partnership’ in mind, but it might just end up becoming that. And that might be a huge game-changer.

Well, we’ve come a long way since the first scientific journal was published back in the 1600’s, and not much had changed since then, other than the font. PLoS changed the game, and they did that so well that they are now one of the biggest scientific publishers. And it is now the turn of PeerJ.

I have a lot of respect for both Peter Binfield and Jason Hoyt (since I first met them in 2009). And I also see that they have Tim O’Reilly in their governing board (someone that deserves an un-interrupted series of hat tips as well).

So, paraphrasing a SciBarCamp question…

What would scientific publishing look like if it was invented today?

We might just be about to find out.

*Well, we still pay to see the article. And in many cases we pay costs of publishing like colour figures, etc. But we tend to not think too much about that. Oh, yes, and of course we transfer our copyright – lest Wikipedia make something interesting with them.
**Different membership levels have different publishing privileges. But you can visit the site to get that nitty gritty.

Drafting proposals in the open – sketching out project ideas

Posted in Health and Medicine, Science, Science and Society by kubke on May 4, 2011

[also posted in] 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.

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.

Science lessons from 8 year old children

Posted in Science, Science and Society by kubke on December 22, 2010

[Cross posted from Talking Teaching]

Ed Yong in Not Exactly Rocket science alerted me to an article published in Biological Letters Biology Letters from the Royal Society. I will not discuss the content of the article, Ed Yong has (as usual) done a wonderful job. I would like instead to share the ‘concept’ of the article.

The article reports on some research that shows that bumble-bees use both colour and spatial relationship in their foraging behaviour. But enough about that. What is unique about this article is that the research was conducted by a group of school children. It is also unique in that it is written by a group of school children (in their language). And the icing on the cake are the figures: pencil coloured; no fancy graphic software.

This is, in my opinion, authentic teaching at its best. And authentic learning. And while we are at it, authentic publishing.

So what have I learned from this group of children? That, as they say, science is fun. And that teaching science, whatever the student age group, can be made fun and authentic and can get children motivated.

The background reads:

Although the historical context of any study is of course important, including references in this instance would be disingenuous for two reasons. First, given the way scientific data are naturally reported, the relevant information is simply inaccessible to the literate ability of 8- to 10-year-old children, and second, the true motivation for any scientific study (at least one of integrity) is one’s own curiosity, which for the children was not inspired by the scientific literature, but their own observations of the world.

I could not agree more. I love biology because I ‘played’ with biology as a child. I was fortunate enough to have a father who never answered my question with ‘I don’t know’ without following that up with ‘but lets try to find out’. As a child my father valued my questions and my curiosity, more so about things he didn’t have an answer for. And I will always be grateful to him for that. For my teachers, well, that was a different issue: rather annoying having a pupil in the class that just refused to overcome the ‘why?’ stage.

And these children have been given a great gift by being it let known that their thoughts and ideas have value. And that, once that barriers that have to do with the specific language of the scientific literature are withdrawn, their ideas and thoughts can bring about new knowledge.

These children will also grow up having learned a few fundamental things about science: How an idea is brought into shape, how scientific questions are narrowed, and the hard work and discipline that is needed to see an experiment through. Oh yes, and that no matter how good an idea may be, reviewers may still reject your grant.

None of this they could have learned from a science textbook.

The editors of the Royal Society should also be commended for not requiring that the manuscript adjust to the traditional publishing formats and allowing the authentic voice of the children to come through. This paper should become obligatory reading in science classes. If nothing else, children will recognise their own voices and curiosity in the reading, and, who knows, other groups of children with innovative teachers may teach us (adult scientists) another thing or two.

P. S. Blackawton, S. Airzee, A. Allen, S. Baker, A. Berrow, C. Blair, M. Churchill, J. Coles, R. F.-J. Cumming, L. Fraquelli, C. Hackford, A. Hinton Mellor1, M. Hutchcroft, B. Ireland, D. Jewsbury, A. Littlejohns, G. M. Littlejohns, M. Lotto, J. McKeown, A. O’Toole, H. Richards, L. Robbins-Davey, S. Roblyn, H. Rodwell-Lynn, D. Schenck, J. Springer, A. Wishy, T. Rodwell-Lynn, D. Strudwick and R. B. Lotto (2010) Blackawton bees. Biology Letters DOI:10.1098/rsbl.2010.1056

[Open] Science Sunday – 15.08.10

Posted in Environment and Ecology, Health and Medicine, Science, Science and Society by kubke on August 15, 2010

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.