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.
Regular readers will know I am a great believer in the potential of Web2.0 tools to enable rapid aggregation of loose networks of collaborators to solve a particular problem and the possibilities of using this approach to do science better, faster, and more efficiently. The reason why we haven’t had great successes on this thus far is fundamentally down to the size of the network we have in place and the bias in the expertise of that network towards specific areas. There is a strong bioinformatics/IT bias in the people interested in these tools and this plays out in a number of fields from the people on Friendfeed, to the relative frequency of commenting on PLoS Computational Biology versus PLoS ONE.
Putting these two together one obvious solution is to find a problem that is well suited to the people who are around, may be of interest to them, and is also quite useful to solve. I think I may have found such a problem.
The Illumina next generation sequencing platform developed originally by Solexa is the latest kid on the block as far as the systems that have reached the market. I spent a good part of today talking about how the analysis pipeline for this system could be improved. But one thing that came out as an issue is that no-one seems to have published detailed analysis of the types of errors that are generated experimentally by this system. Illumina probably have done this analysis in some form but have better things to do than write it up.
The Solexa system is based on sequencing by synthesis. A population of DNA molecules, all amplified from the same single molecule, is immobilised on a surface. A new strand of DNA is added, one base at a time. In the Solexa system each base has a different fluorescent marker on it plus a blocking reagent. After the base is added, and the colour read, the blocker is removed and the next base can be added. More details can be found on the genographia wiki. There are two major sources of error here. Firstly, for a proportion of each sample, the base is not added successfully. This means in the next round, that part of the sample may generate a readout for the previous base. Secondly the blocker may fail, leading to the addition of two bases, causing a similar problem but in reverse. As the cycles proceed the ends of each DNA strand in the sample get increasingly out of phase making it harder and harder to tell which is the correct signal.
These error rates are probably dependent both on the identity of the base being added and the identity of the previous base. It may also be related to the number of cycles that have been carried out. There is also the possibility that the sample DNA has errors in it due to the amplification process though these are likely to be close to insignificant. However there is no data on these error rates available. Simple you might think to get some of the raw data and do the analysis – fit the sequence of raw intensity data to a model where the parameters are error rates for each base.
Well we know that the availability of data makes re-processing possible and we further believe in the power of the social network. And I know that a lot of you guys are good at this kind of analysis, and might be interested in having a play with some of the raw data. It could also be a good paper – Nature Biotech/Nature Methods perhaps and I am prepared to bet it would get an interesting editorial writeup on the process as well. I don’t really have the skills to do the work but if others out there are interested then I am happy to coordinate. This could all be done, in the wild, out in the open and I think that would be a brilliant demonstration of the possibilities.
Oh, the data? We’ve got access to the raw and corrected spot intensities and the base calls from a single ‘tile’ of the phiX174 control lane for a run from the 1000 Genomes Project which can be found at http://sgenomics.org/phix174.tar.gz courtesy of Nava Whiteford from the Sanger Centre. If you’re interested in the final product you can see some of the final read data being produced here.
What I had in mind was taking the called sequence, align onto phiX174 so we know the ‘true’ sequence. Then use that sequence plus a model with error rates to parameterise those error rates. Perhaps there is a better way to approach the problem? There are a series of relatively simple error models that could be tried and if the error rates can be defined then it will enable a really significant increase in both the quality and quantity of data that can be determined by these machines. I figure splitting the job up into a few small groups working on different models, putting the whole thing up on google code with a wiki there to coordinate and capture other issues as we go forward. Anybody up for it (and got the time)?
One of the strong messages that came back from the workshop we held at the BioSysBio meeting was that protocols and standards of behaviour were something that people would appreciate having available. There are many potential issues that are raised by the idea of a ‘charter’ or ‘protocol’ for open science but these are definitely things that are worth talking about. I thought I would through a few ideas out and see where they go. There are some potentially serious contradictions to be worked through. Read more »
I am thinking about how to present the case for Open Science, Open Notebook Science, and Open Data at Science in the 21st Century, the meeting being organised by Sabine Hossenfelder and Michael Nielsen at the Perimeter Institute for Theoretical Physics. I’ve put up a draft abstract and as you might guess from this I wanted to make an economic case that the waste of resources, both human and monetary is not something that is sustainable for the future. Here I want to rehearse that argument a bit further as well as explore the business case that could be presented to Google/Gates Foundation as a package that would include the development of the Science Exchange ideas that I blogged about last week. Read more »
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. Read more »
Following on from my post there has been lots of discussion both in the comments to the post and also support and ideas on other blogs. I also had a good talk (I know, face to face, how archaic :) with Jeremy Frey about the idea. Here I want to collate a few of the comments and ideas. Read more »
A whole series of things have converged in the last couple of days for me. First was Jean-Claude’s description of the work [1, 2] he and Brent Friesen of the Dominican University are doing putting the combi-Ugi project into an undergraduate laboratory setting. The students will make new compounds which will then be sent for testing as antimalarial agents by Phil Rosenthal at UCSF. This is a great story and a testament in particular to Brent’s work to make the laboratory practical more relevant and exciting for his students.
I received the rejection letter late last week but hadn’t got as far as posting about this yet. Given the referee’s comments this was not surprising. We were ranked 20 out of 21 proposals that were considered by the panel. This is not nearly so bad as it sounds. The story as that there were over a hundred proposals so to actually get to the panel wasn’t a bad thing in its own right. The other positive thing to take from this is that the referee’s comments were very clear about what the problems were: too much discussion of the type of things we would like to do, and not enough about how we would get more people involved, or how we would disseminate information. Basically it wasn’t focussed well as a Network application, which is not suprising in light of the fact that I had never been involved in one before so I didn’t really know what is was ’supposed’ to look like.
We are allowed the resubmit the grant in six months time and I would be inclined to do so. The original proposal document as well as the final submitted version (there are significant differences - I needed to cut a lot to make it fit) is still available for viewing or editing and it ought to be possible to re-jig it over the next six months in light of the referee’s comments.
p.s. Am using Zemanta which looks potentially like a great tool in principle for getting more consistency into the use of tags and linking the information up. Something I am very much in favour of. However it appears to have decided that this post is about Volkswagens. Go figure.
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?
