Tag: Open Science PSB09

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Reflections on the Open Science workshop at PSB09

In a few hours I will be giving a short presentation to the whole of the PSB conference on the workshop that we ran on Monday. We are still thinking through the details of what has come out of this and hopefully the discussion will continue in any case so this is a personal view. The slides for the presentation are available at Slideshare.

To me there were a couple of key points that came out. Many of these are not surprising but bear repeating:

  • Citation and improving and expanding the way it is used lies at the core of making sure that people get credit for the work they do and making the widest range of useful contributions to the research community
  • Persistence of identity, and persistence of objects (in general the persistence of resources) is absolutely critical to making a wider citation culture work. We must know who generated something and be able to point to it in the long term to deliver on the potential of credits.
  • “If you build it they won’t come” – building a service, whether a technical or a social one, depends on a community that uses and adds value to those services. Build the service for the community and build the community for the service. Don’t solve the problems that you think people have – solve the ones that they tell you they have

The main point for me grew out of the panel session and was perhaps articulated best by Drew Endy. Identify specific problems (not ideological issues) and make process more efficient. Ideology may help to guide us but it can also blind you to specific issues and hide the underlying reasons for specific successes and failures from our view. We have a desperate need for both qualitative data, stories about successes and failures, and quantitative data, hard numbers on uptake and the consequences of uptake of specific practice.

Taking inspiration from Drew’s keynote, we have an evolved system for doing research that is not designed to be easily understood or modified. We need to take an experimental approach to identifying and solving specific problems that would let us increase the efficiency of the research process. Drew’s point was that this should be a proper research discipline in it’s own right, with the funding and respect that goes with it. For the presentation I summarised this as follows:

Improving the research process is an area for (experimental) research that requires the same rigour, standards (and funding) as anything else that we do

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Final countdown to Open Science@PSB

As I noted in the last post we are rapidly counting down towards the final few days before the Open Science Workshop at the Pacific Symposium on Biocomputing. I am flying out from Sydney to Hawaii this afternoon and may or may not have network connectivity in the days leading up the meeting. So just some quick notes here on where you can find any final information if you are coming or if you want to follow online.

The workshop website is available at psb09openscience.wordpress.com and this is where information will be posted in the leadup to the workshop and links to presentations and any other information posted afterwards.

If you want to follow in closer to real time then there is a Friendfeed room available at friendfeed.com/rooms/psb-2009 which will have breaking information and live blogging during the workshop and throughout the conference. I will be aiming to broadcast video of the workshop at www.mogulus.com/cameron_neylon but this will depend on how well the wireless is working on the day. This will not be the highest priority. Updates on whether it is functioning or not will be in the friendfeed room and I will not be monitoring the chat room on the mogulus feed. If there are technical issues please leave a message in the friendfeed room and I will try to fix the problem or at least say if I can’t.

Otherwise I hope to see many of you at the workshop either in person or online!

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Open Science Workshop at Southampton – 31 August and 1 September 2008

Southampton, England, United-Kingdom

Image via Wikipedia

I’m aware I’ve been trailing this idea around for sometime now but its been difficult to pin down due to issues with room bookings. However I’m just going to go ahead and if we end up meeting in a local bar then so be it! If Southampton becomes too difficult I might organise to have it at RAL instead but Southampton is more convenient in many ways.

Science Blogging 2008: London will be held on August 30 at the Royal Institution and as a number of people are coming to that it seemed a good opportunity to get a few more people together to have a get together and discuss how we might move things forward.  This now turns out to be one of a series of such workshops following on from Collaborating for the future of open science, organised by Science Commons as a satellite meeting of EuroScience Open Forum in Barcelona next month, BioBarCamp/Scifoo from 5-10 August and a possible Open Science Workshop at Stanford on Monday 11 August, as well as the Open Science Workshop in Hawaii (can’t let the bioinformaticians have all the good conference sites to themselves!) at the Pacific Symposium on Biocomputing.

For the Southampton meeting I would propose that we essentially look at having four themed sessions: Tools, Data standards, Policy/Funding, and Projects. Within this we adopt an unconference style where we decide who speaks based on who is there and want to present something. My ideas is essentially to meet on the Sunday evening at a local hostelry to discuss and organise the specifics of the program for Monday. On the Monday we spend the day with presentations and leave plenty of room for discussion. People can leave in the afternoon, or hang around into the evening for further discussion. We have absolutely zero, zilch, nada funding available so I will be asking for a contribution (to be finalised later but probably £10-15 each) to cover coffee/tea and lunch on the Monday.

Zemanta Pixie

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Somewhat more complete report on BioSysBio workshop

The Queen's Tower, Imperial CollegeImage via Wikipedia

This has taken me longer than expected to write up. Julius Lucks, John Cumbers, and myself lead a workshop on Open Science on Monday 21st at the BioSysBio meeting at Imperial College London.  I had hoped to record screencast, audio, and possibly video as well but in the end the laptop I am working off couldn’t cope with both running the projector and Camtasia at the same time with reasonable response rates (its a long story but in theory I get my ‘proper’ laptop back tomorrow so hopefully better luck next time). We had somewhere between 25 and 35 people throughout most of the workshop and the feedback was all pretty positive. What I found particularly exciting was that, although the usual issues of scooping, attribution, and the general dishonestly of the scientific community were raised, they were only in passing, with a lot more of the discussion focussing on practical issues. Continue reading “Somewhat more complete report on BioSysBio workshop”

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Open Science at PSB – Call for submissions

What Shirley said:

The call for participation for the Open Science workshop at PSB 2009 is now up! We welcome anyone with an interest in open science to submit proposals for talks. Note that although space is limited for talks and demos, anyone who registers for the conference can present a poster, so we also encourage poster submissions!

Please if you are interested in submitting a talk or poster get in touch. We would like to have a good and robust discussion with a range of perspectives on a range of topics. We are limited with respect to the time available so there will be some tough decisions to make. Nonetheless, please do get in touch; we would very much like to have a good representation of posters as well as talks. If there is interest then we can organise an unofficial session on the side of the meeting to take things further, perhaps towards ‘Open Science 2009’  a meeting in its own right?

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A quick update

I have got very behind. I’ve only just realised just how far behind but my excuse is that I have been rather busy. How far behind I was was brought home by the fact that I hadn’t actually commented as yet that the proposal for an Open Science session at PSB that was driven primarily by Shirley Wu has gone in and the proposal is now up at Nature Precedings. The posting there has already generated some new contacts.

On Tuesday I gave a talk at UKOLN at the University of Bath. Brian Kelly kindly videoed the first 10 minutes of the presentation when my attempts to record a screencast failed miserably and has blogged about the talk and on recording talks more generally for public consumption. Jean-Claude does this very effectively but this is something we should perhaps all be more putting a lot more effort into (and can someone tell me what the best software for recording screencasts is?!?). I got a lot of the talk on audio recording and will attempt to record a screencast when I can find time.
The talk was interesting; this was to a group of library/repository/curation/technical experts rather than the usual attempt to convince a group of sceptical scientists. Many of them are already ‘open’ advocates but are focused on technical issues. Lots of smart question on how do you really manage secure identities across multiple systems; how do we make data on the cloud stable for the long term; how do you choose between competing standards for describing and collating data; fundamentally how do you actually make all this work. Interesting discussion all in all and great to meet the people at UKOLN and finally meet Liz Lyon in person.

The other thing happening this week is that tomorrow and Friday we are running a small workshop introducing potential users to our Blog based notebook. Our aim is to see how other people’s working processes do or don’t fit into our system. This is still focused on biochemistry/molecular biology but it will be very interesting to see what comes out of this. I will try to report as soon as possible.

Finally; I think there is something in the air. This week has seen a rush of emails from people who have seen Blog posts, proposals, and other things writing to offer support, and perhaps more crucially access to more contacts.

And further on the PLoS front the biggest story in the UK news on Tuesday morning was about the paper in PLoS Medicine reporting on the results of a meta-study of the effectiveness of SSRIs in treating depression. I woke up to this story on BBC radio and by the time I gave my talk at 10:30 I’d had a chance at least to read the paper abstract. If I’d been on SSRIs this could be really important to me. Perhaps more to the point, if I were a doctor realising I’d be fielding phone calls from concerned patients all day, I could have read the paper. This story tells us a lot about why Open Access and Open Data are crucial. But more on that in another post sometime…I promise.

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PSB Session – Final call for support

If you’ve been following the discussion here and over at the One Big Lab Blog you will know that tomorrow is the deadline for submission of proposals for sessions at PSB. Shirley Wu has done a great job of putting together the proposal text and the more support we can get from members of the community the better. Whether you can send us an email saying you would like to be there, will commit to being there, or (most preferred) can commit to submitting a presentation it will all help. Don’t get too hung up on the idea that talks have to be ‘research’. This can include the description of tool development (including services), quantitative studies of the impact of open practices, or just a description or review of a particular experience or process.

The proposal text is visible at: http://docs.google.com/Doc?id=dv4t5rx_33fpxx9pw5 and if you want editing access just holler or leave some comments here or at One Big Lab.

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More on the PSB proposal

Shirley Wu has followed up on her original proposal to submit a session proposal for PSB. She asks a series of important questions about going forward on this and I thought I would reply to these here to widen exposure.

I think it is worth going for a session and I am happy to lead the application but there may well be better people; Jean-Claude, Antony Williams, Peter Murray-Rust, Egon Willighagen to get to lead it depending on focus. I think the important question to ask is whether we can generate enough research papers to justify a session. I believe we can and should and I will commit to generating one if we go ahead, but we need at least another 3-4 to go ahead I think.

So, to answer Shirley’s questions:

1. What should be the focus of this session on Open Science? (first, frame it as a traditional PSB session, then perhaps as a “creative” session)
2. What kind of substantial/technical/research papers can be written about Open Science?
3. Who are the major players in the field? Who would the session chair invite to submit a paper?
4. Who is willing to help write/organize the actual proposal and session?

Given it is a computing symposium I would say that it should focus on tools and standards and how they effect what we can, or would like to do. This also gives us a chance to provide research type papers describing such tools and standards and investigating their implementation. So we could write papers describing different implementations of Open Notebooks and critical analysis of the differences, the organisation of Open Data, standards for describing data, and social and cultural aspects of what is happening etc etc.

People to invite to write papers include Jean-Claude Bradley, OpenWetWare group, Egon, Peter MR, Deepak Singh (willing to write a review/scoping type paper?), Antony Williams (ChemSpider), Simile Group (www.simile.mit.edu), other repository, data archival groups, Nature Publishing/PLoS/PMC/UK-PMC to describe systems, Heather Piwowar to analyse what happens, and social sciences groups that are becoming interested in what is going on.

Finally, as I say, I am willing to help, but as you can see time becomes a constraint for me and things have a habit if getting left to the last minute. If anyone else would like to step in to lead then I am more than happy to be a co-chair.  If no one else is available I am happy to lead. I at least have the advantage that I can probably source the resources so that I can get there!

I am going to tag this “Open Science PSB09” if that seems a good tag to aggregate around.