Tag: lab book as feed

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What are the services we really want for recording science online?

There is an interesting meta-discussion going on in a variety of places at the moment which touch very strongly on my post and talk (slides, screencast) from last week about “web native” lab notebooks. Over at Depth First, Rich Apodaca has a post with the following little gem of a soundbite:

Could it be that both Open Access and Electronic Laboratory Notebooks are examples of telephone-like capabilities being used to make a better telegraph?

Web-Centric Science offers a set of features orthoginal to those of paper-centric science. Creating the new system in the image of the old one misses the point, and the opportunity, entirely.

Meanwhile a discussion on The Realm of Organic Synthesis blog was sparked off by a post about the need for a Wikipedia inspired chemistry resource (thanks again to Rich and Tony Williams for pointing the post and discussion out respectively). The initial idea here was something along the lines of;

I envision a hybrid of Doug Taber’s Organic Chemistry Portal, Wikipedia and a condensed version of SciFinder.  I’ll gladly contribute!  How do we get the ball rolling?

This in turn has led into a discussion of whether Chemspider and ChemMantis partly fill this role already. The key point being made here is the problem of actually finding and aggregating the relevant information. Tony Williams makes the point in the comments that Chemspider is not about being a central repository in the way that J proposes in the original TROS blog post but that if there are resources out there they can be aggregated into Chemspider. There are two problems here, capturing the knowledge into one “place” and then aggregating.

Finally there is an ongoing discussion in the margins of a post at RealClimate. The argument here is over the level of “working” that should be shown when doing analyses of data, something very close to my heart. In this case both the data and the MatLab routines used to process the data have been made available. What I believe is missing is the detailed record, or log, of how those routines were used to process the data. The argument rages over the value of providing this, the amount of work involved, and whether it could actually have a chilling effect on people doing independent validation of the results. In this case there is also the political issue of providing more material for antagonistic climate change skeptics to pore over and look for minor mistakes that they will then trumpet as holes. It will come as no suprise that I think the benefits of making the log available outweigh the problems. But that we need the tools to do it. This is beautifully summed up in one comment by Tobias Martin at number 64:

So there are really two main questions: if this [making the full record available – CN] is hard work for the scientist, for heaven’s sake, why is it hard work? (And the corrolary: how are you confident that your results are correct?)

And the answer – it is hard work because we still think in terms of a paper notebook paradigm, which isn’t well matched to the data analysis being done within MatLab. When people actually do data analysis using computational systems they very rarely keep a systematic log of the process. It is actually a rather difficult thing to do – even though in principle the system could (and in some cases does) keep that entire record for you.

My point is that if we completely re-imagine the shape and functionality of the laboratory record, in the way Rich and I, and others, have suggested; if the tools are built to capture what happens and then provide that to the outside world in a useful form (when the researcher chooses), then not only will this record exist but it will provide the detailed “clickstream” records that Richard Akerman refers to in answer to a Twitter proposal from Michael Barton:

Michael Barton: Website idea: Rank scientific articles by relevance to your research; get uptakes on them via citations and pubmed “related articles”

Richard Akerman: This is a problem of data, not of technology. Amazon has millions of people with a clear clickstream through a website. We’ve got people with PDFs on their desktops.

Exchange “data files” and “Matlab scripts” for PDFs and you have a statement of the same problem that they guys at RealClimate face. Yes it is there somewhere, but it is a pain in the backside to get it out and give it to someone.

If that “clickstream” and “file use stream” and “relationship” stream was automatically captured then we get closer to the thing that I think many of us a yearning for (and have been for some time). The Amazon recommendation tool for science.

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Third party data repositories – can we/should we trust them?

This is a case of a comment that got so long (and so late) that it probably merited it’s own post. David Crotty and Paul (Ling-Fung Tang) note some important caveats in comments on my last post about the idea of the “web native” lab notebook. I probably went a bit strong in that post with the idea of pushing content onto outside specialist services in my effort to try to explain the logic of the lab notebook as a feed. David notes an important point about any third part service (do read the whole comment at the post):

Wouldn’t such an approach either:
1) require a lab to make a heavy investment in online infrastructure and support personnel, or
2) rely very heavily on outside service providers for access and retention of one’s own data? […]

Any system that is going to see mass acceptance is going to have to give the user a great deal of control, and also provide complete and redundant levels of back-up of all content. If you’ve got data scattered all over a variety of services, and one goes down or out of business, does that mean having to revise all of those other services when/if the files are recovered?

This is a very wide problem that I’ve also seen in the context of the UK web community that supports higher education (see for example Brian Kelly‘s risk assessment for use of third party web services). Is it smart, or even safe, to use third party services? The general question divides into two sections: is the service more or less reliable than you own hard drive or locally provided server capacity (technical reliability, or uptime); and what is the long term reliability of the service remaining viable (business/social model reliability). Flickr probably has higher availability than your local institutional IT services but there is no guarantee that it will still be there tomorrow. This is why data portability is very important. If you can’t get your data out, don’t put it in there in the first place.

In the context of my previous post these data services could be local, they could be provided by the local institution, or by a local funder, or they could even be a hard disk in the lab. People are free to make those choices and to find the best balance of reliability, cost, and maintenance that suits them. My suspicion is that after a degree of consolidation we will start to see institutions offering local data repositories as well as specialised services on the cloud that can provide more specialised and exciting functionality. Ideally these could all talk to each other so that multiple copies are held in these various services.

David says:

I would worry about putting something as valuable as my own data into the “cloud” […]

I’d rather rely on an internally controlled system and not have to worry about the business model of Flickr or whether Google was going to pull the plug on a tool I regularly use. Perhaps the level to think on is that of a university, or company–could you set up a system for all labs within an institution that’s controlled (and heavily backed up) by that institution? Preferably something standardized to allow interaction between institutions.

Then again, given the experiences I’ve had with university IT departments, this might not be such a good approach after all.

Which I think encapsulates a lot of the debate. I actually have greater faith in Flickr keeping my pictures safe than my own hard disk. And more faith in both than insitutional repository systems that don’t currently provide good data functionality and that I don’t understand. But I wouldn’t trust either in isolation. The best situation is to have everything everywhere, using interchange standards to keep copies in different places; specialised services out on the cloud to provide functionality (not every institution will want to provide a visualisation service for XAFS data), IRs providing backup archival and server space for anything that doesn’t fit elsewhere, and ultimately still probably local hard disks for a lot of the short to medium term storage. My view is that the institution has the responsibility of aggregating, making available, and archiving the work if its staff, but I personally see this role as more harvester than service provider.

All of which will turn on the question of business models. If the data stores a local, what is the business model for archival? If they are institutional how much faith do you have that the institution won’t close them down. And if they are commercial or non-profit third parties, or even directly government funded service, does the economics make sense in the long term. We need a shift in science funding if we want to archive and manage data in the longer term. And with any market some services will rise and some will die. The money has to come from somewhere and ultimately that will always be the research funders. Until there is a stronger call from them for data preservation and the resources to back it up I don’t think we will see much interesting development. Some funders are pushing fairly hard in this direction so it will be interesting to see what develops. A lot will turn on who has the responsibility for ensuring data availability and sharing. The researcher? The institution? The funder?

In the end you get what you pay for. Always worth remembering that sometimes even things that are free at point of use aren’t worth the price you pay for them.