Archive 2012

PeerJ pulls off a hat trick Fabiana Kubke Dec 03

No Comments

It is December 3.

It is the birthday* of John Backus, Richard Kuhn, Anna Freud, Carlos Juan Finlay, and, why not, Ozzy Osbourne.

It is also the day that PeerJ starts receiving manuscript submissions. I talked about PeerJ before and why I was so enthusiastic about its launch. Over the last while I have been experiencing PeerJ as a user.

Some of us academic editors were able to do some website testing for the article submission site, and I have to say I am impressed. Truth be told, the most painful part of submitting a paper has been, in my experience, being confronted with those horrid manuscript submission sites. When I started working in science there were no computers. We typed (yes, remember the typewriter?) our manuscripts, printed our pictures in the dark room, drew our graphs by hand with rotring pens and letraset and put the lot in an envelope. With a stamp. And walked the envelope to the Post Office.

Then came the electronic submission, and it seems that those who designed those sites knew that our high motivation level to submit would make us be able to endure their site’s, well, unfriendliness (oh and those dreadful pop-up windows!). They were right. Our motivation to submit a paper is high enough that we overlook the nuisance of the submission system – it is not a factor in the decision of where to submit. I find myself sometimes putting an entire afternoon aside just to upload the files on their system, and I have become accustomed to this, I have been doing it for years. And I know that any submission or editorial task will have to wait until I am at my desktop computer because navigating those sites on my netbook or my tablet is, well, not worth the effort

So needless to say, opening up the PeerJ system was nothing more than a yay moment. Finally someone thought about me, me, me.

The first thing I loved was that I just need to login to my account at and from there I have the links to whatever I need: my profile, my manuscripts, my reviewer dashboard and my editor dashboard. None of that looking for the email that has the web address for the editorial manager system; even my tired old brain can remember that url. Even better, I can do that from my netbook, my tablet, my mobile phone, because the site loads really nicely in all my devices. The plus side of this is that when I think about checking something I can just go ahead and do it. Easily


Submitting the manuscript was a completely new experience. In my opinion they have done a few things right: a good visual (and intuitive) toolbar (text comes up on mouse over) and a hint box at the right of the screen.


As I moved from one page to another, the hintbox was always there to answer most of my questions, or send me to the instructions to authors – again, with a really nice and intuitive layout.


I never found myself second guessing what it is what I needed to do, or how to do it. And for that PeerJ deserves a hat tip.

But one of the things that impressed me the most, were the requirements under the “Declarations” section. There are a lot of things there that impressed me. Firstly, the detailed description of the Animal Ethics (not just that your University Committee approved it), the request for agreement for people to be acknowledged, the declaration of conflict of interest and any type of funding, etc. I think this is a good thing. I found it tedious at first. But when I started thinking about it more, I think this is a great step for better scientific standards. And I hope they keep on having those requirements, and hope more journals follow suit. And a second hat tip for contacting all of the listed authors to inform them someone has submitted a manuscript with their name on it. I am still shocked some journals still do not do this!


I am now acting as an academic editor for another manuscript, and the experience from that end is no different. The system is simple and intuitive which makes my job easier. From an editor’s point of view what I liked the most was the page where I had to choose/load reviewers. I had on that page a list of suggested reviewers by the authors and those that authors opposed, so there was no need of navigating different windows to get that information. Made a mistake and want to get rid of a reviewer? Just click on the trash can. On that page, also nicely visible are the links to tools to help me find reviewers (JANE, PubMed and Google Scholar). Now what was a really nice touch (lke the links weren’t enough!) was that clicking on any of those links automatically ran a query for me based on title and keywords of the article – one less thing for me to do (unless I need to for some reason). So another hat tip for that – and I think that rounds up the hat trick.

Now, what a bright idea – make the system user friendly! You’d think those in the Science Publishing system would have already figured that out, eh?



More on Open Access Week Fabiana Kubke Oct 25

No Comments

It has been a busy Open Access Week for me. My last (well almost last!) duty is today at 4:00 pm at the Old Government House at the University of Auckland.

Stratus has organised a panel and invited me to participate, and I have just uploaded my upcoming presentation to Slideshare. If you have a chance, we would love to see you there!

Oh, and thanks to Nat for 4-short-linking my previous post!

Hello Open Access Week 2012 Fabiana Kubke Oct 22

No Comments

So, it is Open Access Week, so I thought I should drop by and tell you what I have been up to other than collecting swag.

It has been a very busy time. Heaps of things have happened and I am thrilled of how much louder the conversation about Open Access has become. So what I thought I might do on this post is link to some of the stuff that I have been doing over the past year.

Back in July, Cameron Neylon and I ran a Workshop on Open Research in the New Zealand context as part of the eResearch Symposium. It was great. There was a great crowd and Cameron did an excellent job moderating, and all we learned and gathered is being shared here. I think that one of the take-home messages from that workshop was the need to build a solid community of practice and communicate more actively with each other.

The symposium ran a bit after the Finch Report was released and PeerJ came out of the closet. So while Cameron and I were at Wellington we got a chance to chat about Open Access with Peter Griffin on the Sciblogs podcast.

Flew back to Auckland and hardly caught my breath before heading to Net Hui. Matt McGregor from Creative Commons Aotearoa New Zealand had asked me to participate in a panel on ‘Open in Tertiary’. I said yes. Then he texted me to ask me to do a radio interview about the panel with bFM. Have you ever tried to a radio interview over a mobile trying to find a quiet spot in Sky City? Well, this is what that sounds like.

Not long after I get a phone call from Radio New Zealand while I am on the bus. Dodgy connection. I was sick so I also had a dodgy brain. Nonetheless, kudos to the reported who managed to seep through the nonsense generated by a sickly brain and make something of it. The recording is here, and I was surprised to find that the clip also interviewed Peter Gluckman and Cameron Neylon.

All throughout the year, a bunch of us have also been busy organising a conference for next year on Open Research. You can find info on the conference on this site. And yes, we will take your money so just contact us if you can support us.

And I am currently going through the nominations for the New Zealand Open Source Awards – this year featuring Open Science. The finalists should be made known soon. Some great nominations!

And today begins Open Access week, and so back to work.

I already published a post in Mind the Brain on my experience as an Academic Editor in PLOS ONE, and another post appears in Creative Commons Aotearoa New Zealand site on the cultural heritage of science. Matt McGregor, our CCANZ lead has aggregated a wonderful collection of posts on their site – worth going onto the OA week page and read them!

I will be in two panels, one at Waikato University on Tuesday and one at University of Auckland on Thursday, and of course I will be stalking Alex Holcombe as much as possible while he is visiting Auckland.

So if you have a chance to come meet and greet, I am sure that by the time this week (and this year!) is over, I will be welcoming that drink! You can find activities for Open Access near you at the Creative Commons ANZ site.

A personal thank you note to Peter Griffin Fabiana Kubke Oct 07

No Comments

When Victoria Costello contacted me to join the blog ‘Mind the Brain’ over at the PLoS blogging network, I was thrilled.

I love PLoS. I heard of them back when they were just starting, and have since contributed as an author and an academic editor. I have met both online and in real life people I respect and admire who are or were involved with PLoS. I also have a lot of respect for what PLoS has achieved not just as a publishing platform but for the role they play in the Open Access movement. Joining the PLoS blogging network? Heck, yeah!

Church Door

Image by By doc(q)man, licensed under CC-BY

Then there is Sciblogs.

I met Peter Griffin back in 2009 I think, and it would not be long before he, Dacia Herbulock  and I would be sitting over a coffee discussing what was to become my blog. It was to be my first blogging experience (one that was made easier by Keith Ng’s blogging advice, and Peter’s continued words of wisdom). And so this blog was born. I might never have started blogging had it not been for Peter, and I am grateful to him for helping me find my voice. So after receiving Victoria’s invitation I rang him.

There were many possible scenarios how this might have played out. It wasn’t like Peter had not pinged me before asking why I wasn’t posting for a while. It isn’t like other blogs haven’t been archived. It is not like I bring a significant proportion of traffic to Sciblogs. Yet, Peter offered nothing but support and encouragement with the PLoS venture. And when my first post was published, he tweeted it from both his personal and the Science Media Centre account, and even highlighted it in the Science Media Centre’s newsletter. In short his response was, well, extra-ordinary.

So, I thought a hat tip was well-deserved. So there, Peter, a big thanks for not forcing me to make what would have been a very difficult choice.

New Zealand Open Source Awards Fabiana Kubke Sep 25


When I was contacted to be a judge for the New Zealand Open Source Awards, I was elated. When I was told there was to be an Open Science category, I could not contain my joy.

Open Science Logo

by gemmerich, on Flickr CC-BY-SA

The New Zealand Open Source Awards celebrate everything that is good about Open Source – mainly the opportunity to share and build on each other’s achievements. As a scientist I don’t feel the need to be told why this is good. After all science builds on the achievements of others and no project can be considered completed until the results are shared.

But how and when we share seems to be where we get stuck in the discussion.

Almost by definition, Open Science is about sharing early and without barriers. This (I think) makes science better: we make replication easy, we avoid duplicating efforts, and we make sure that any mistakes we made can be corrected, openly. It is a no-brainer to me. So having an Open Science category this year I think is absolutely fantastic! There are great Open Science projects in New Zealand that I wish will receive the recognition they deserve.

One thing I like about the NZ Open Source Awards is that they recognise openness in many areas (government, education, arts, business, science) – not just software. And raising the awareness of the impact of open source projects is a good step towards adopting that philosophy.

This year I am abstaining from nominating since I am a judge, so I am asking all of you to go down to the website before October 3 and nominate your favourite project. There are plenty to choose from, and I hope we can reward some well-deserving ones.

Scientific publishing, with a twist Fabiana Kubke Jun 13

No Comments

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.

#OAMonday Fabiana Kubke May 22

No Comments

If you are on twitter you might have seen that hashtag. And if you are a tax payer then we need you!

By Ian Bloomfield, CC-BY

A petition has been lodged at the White House ‘We the People’ asking for all tax-payer generated scientific results to be made freely available.

This is how it works – If we get 25,000 signatures by June 19, then it will go to the Obama Executive Office. So you see, we do need you!

If you think you should have access to what you pay us the scientists to produce, then please go and sign the petition.

Read more about this petition here

Kiwi foo’s eye view of Open Science Fabiana Kubke Feb 13


I just came back from another amazing kiwi foo. I have talked about it before, so I will not bore you with the details of what kiwi foo is all about. This time, unlike other years, I went with a very focused view of what I wanted to achieve. And it was as stimulating as ever.

Over the past year, I have gone into a rather quiet reflexion of what ‘open science’ is and how to make it work. I have become increasingly frustrated with a model of science that increasingly rewards self-promotion rather than knowledge sharing. And the emerging theme of my reflexion was ‘context’.

If we want a ‘global’ open science, the formula for adoption needs to be able to adapt to local personal, institutional, social, political, economical and legislative contexts. I may be wrong, but I think many of us who support open science struggle at times with how to make it work in the particular contexts in which we need to operate.

As I was struggling with the frustration of the commodification of science over the past two years, I started thinking about the open source community.  I can’t blame universities for encouraging scientists  to produce revenue at a time when public funding for education are research appear to be in constant decline. So I went to Webstock a year ago to try to learn more about how open source projects generate revenue. After all, their business models are built around giving their ‘product’ away for free, something that is well aligned with the ethos of science. One of my highlights at kiwi foo was a conversation with Don Christie from CatalystIT, a company that produces high quality open source software. I am looking forward to continuing this conversation and exploring how these business models can be adapted to the different demands and constraints for science. I got a lot of insight from him, and am hoping he and people like him can help us move forward.

On the second day (or rather the first long day) there were a few sessions that centered around science. Great things came out of it, and it would be impossible to name everyone that provided insight. Nick Jones, Leonie Hayes, Alex Holcombe , Alison Stringer and I partnered in crime and ran a couple of sessions where we hashed a few issues around. I personally wanted to explore what Open Science meant in the New Zealand / Australia context (I can’t speak for the others’ motivations!).  I think that the local context in NZ/OZ is slightly different than in the Northern hemisphere and there are some things that differentiate this region. Perhaps we can/should capitalise on that.

For example, you will never see a ‘Research Works Act’ bill here, because we don’t seem to have Open Access mandates. Instead, we have NZGOAL and AUSGOAL which are frameworks for data licencing. The Australians have ANDS and NZ has eResearch, all focused on the data. Tim O’Reilly mentioned the PantonPrinciples  in this context – but the Panton Principles (which I have personally endoresed) cannot be exported ‘as is’ to Australia and New Zealand because neither Creative Commons Aotearoa-New Zealand nor CC-Australiahave CC0, for example.  Software hopefully will not be covered by patents is covered by copyright (not patents) in NZ*, so maybe we can capitalise on that to develop tools for open science. New Zealand has a Treaty of Waitangi, and any local open science needs to respect and work constructively to meet our treaty obligations. Lets add to that, that different research groups are going to be subject to obligations related to the international treaties their countries have signed up to. We all have different copyright restrictions and freedoms, we have different systems that determine how to assign funding, and different mandates and guidelines, and are at different points of our careers with different job securities.

So, how do we make open science work within these diverse contexts? We can all agree on the philosophy, but perhaps we need to also agree that the implementation will take different shapes. I think wee need to continue the global conversation and continue to support each other, but we also need to start working locally in smaller groups to ‘make things happen’. And the battles we choose to fight perhaps should be aligned with local contexts so that we can each capitalise on our strengths. I loved having this dialogue at kiwi foo, getting great insights from a diverse group, and mainly feeling that this is something for which we have support.

The rest of the things that happened at kiwi foo will slowly seep into future posts.

I would really like to thank Jenine, Nat Torkington and Russell Brown for putting kiwi foo together (and inviting me!), my partners in crime Alex, Nick, Alison, and Leonie for their hard work on the sessions, all the attendees for their contributions and especially Tim O’Reilly for providing us with valuable insights. You all have complicated my life, but I look forward to a 2012 of hard work and of ‘making things happen’.


*Edited on 16/2/2012 to reflect the correction made by @kayakr (thanks for that!). I was thinking of this bill: (which is probably the one that @kayakr refers to as pending legislation)

Network-wide options by YD - Freelance Wordpress Developer