From the GNU GPL to GISAID's EpiFlu

A few months ago, I wrote about GISAID, which takes a rather interesting and - to readers of this blog, at least - familiar approach to sharing genomic data:

Registered users can upload data relating to sequences, clinical manifestations in humans, epidemiology, observations in poultry and other animals, etc. These data will be accessible to all other registered users, but not to others unless they have agreed to the same terms of use. This maintains confidentiality of the data.

This is, of course, the same as the GNU GPL: do as you would be done by - if you want to use the GPL'd code, you can, but you must share with everyone the results of your work if you decide to share it with anyone.

The GNU GPL was radical in its time, and the GISAID approach with its EpiFlu database, containing flu virus sequences, is also challenging - and meeting its own obstacles:

Today, the GISAID database (which is called EpiFlu) features both genomic and epidemiological data on tens of thousands of virus samples. At least until recently, the project seemed to be working. During the H1N1 outbreak, so many sequences were being submitted so quickly that researchers were literally watching clusters of outbreaks in real time.

Then, in July of 2009, the Swiss Institute of Bioinformatics (SIB) in Geneva, which has managed the database since 2006, removed EpiFlu from the GISAID Web site, making it available only to users redirected to SIB's Web site. SIB claims that GISAID had breached contract by failing to pay its bills on time, thereby relinquishing its rights to the database.

Let's hope that the SIB comes to its senses before it loses more of its credibility as a modern scientific organisation. Its high-handed claiming of "rights" to a commons created by others is simply not acceptable in the 21st century - which, if it has a future, will be one based around precisely the kind of sharing practised by GISAID.

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PLoS Reinvents Publishing and Saves the World

As someone who has been writing about open access for some years, I find myself returning again and again to the Public Library of Science. That's because, not content with pioneering open access, PLoS has time and again re-invented the broader world of scientific publishing. Now, it's done it again:

Today, after several months of work, I’m delighted to announce that PLoS is launching PLoS Currents (Beta) – a new and experimental website for the rapid communication of research results and ideas. In response to the recent worldwide H1N1 influenza outbreak, the first PLoS Currents research theme is influenza.

Note the emphasis on "rapid": this is absolutely crucial, as I've noted before. The current system of publishing papers is simply too slow to deal with pandemics, where speed is of the essence if we're to have a chance of nipping them in the bud. It's good to see PLoS stepping in to help address this major problem.

It's doing it in a very interesting way:

PLoS Currents: Influenza, which we are launching today, is built on three key components: a small expert research community that PLoS is working with to run the website; Google Knol with new features that allow content to be gathered together in collections after being vetted by expert moderators; and a new, independent database at the National Center for Biotechnology Information (NCBI) called Rapid Research Notes, where research targeted for rapid communication, such as the content in PLoS Currents: Influenza will be freely and permanently accessible. To ensure that researchers are properly credited for their work, PLoS Currents content will also be given a unique identifier by the NCBI so that it is citable.

...

The key goal of PLoS Currents is to accelerate scientific discovery by allowing researchers to share their latest findings and ideas immediately with the world’s scientific and medical communities. Google Knol’s features for community interaction, comment and discussion will enable commentary and conversations to develop around these findings. Given that the contributions to PLoS Currents are not peer-reviewed in detail, however, the results and conclusions must be regarded as preliminary. In time, it is therefore likely that PLoS Currents contributors will submit their work for publication in a formal journal, and the PLoS Journals will welcome these submissions.

PLoS Currents: Influenza is an experiment and a prototype for further PLoS Currents sites. It reflects our commitment to using online tools to the fullest extent possible for the open sharing of research results. As with any new project, we will be listening carefully to the reactions within and beyond the scientific and medical communities and welcoming suggestions for improvements.

This is really exciting from many viewpoints. It's pushing the ideas behind open access even further; it's reshaping publishing; and it may even save humanity. (Via James Boyle.)

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Swine Flu in the Nude

This is what the virus really looks like:

1 atgaaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt taaccttcta gaagacaagc ataacgggaa actatgcaaa
181 ctaagagggg tagccccatt gcatttgggt aaatgtaaca ttgctggctg gatcctggga
241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
301 agttcagaca atggaacgtg ttacccagga gatttcatcg attatgagga gctaagagag
361 caattgagct cagtgtcatc atttgaaagg tttgagatat tccccaagac aagttcatgg
421 cccaatcatg actcgaacaa aggtgtaacg gcagcatgtc ctcatgctgg agcaaaaagc
481 ttctacaaaa atttaatatg gctagttaaa aaaggaaatt catacccaaa gctcagcaaa
541 tcctacatta atgataaagg gaaagaagtc ctcgtgctat ggggcattca ccatccatct
601 actagtgctg accaacaaag tctctatcag aatgcagatg catatgtttt tgtggggtca
661 tcaagataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gagggatcaa
721 gaagggagaa tgaactatta ctggacacta gtagagccgg gagacaaaat aacattcgaa
781 gcaactggaa atctagtggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
841 ggtattatca tttcagatac accagtccac gattgcaata caacttgtca gacacccaag
901 ggtgctataa acaccagcct cccatttcag aatatacatc cgatcacaat tggaaaatgt
961 ccaaaatatg taaaaagcac aaaattgaga ctggccacag gattgaggaa tgtcccgtct
1021 attcaatcta gaggcctatt tggggccatt gccggtttca ttgaaggggg gtggacaggg
1081 atggtagatg gatggtacgg ttatcaccat caaaatgagc aggggtcagg atatgcagcc
1141 gacctgaaga gcacacagaa tgccattgac gaaattacta acaaagtaaa ttctgttatt
1201 gaaaagatga atacacagtt cacagcagta ggtaaagagt tcaaccacct ggaaaaaaga
1261 atagagaatt taaataaaaa agttgatgat ggtttcctgg acatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
1381 aacttatatg aaaaggtaag aagccagcta aaaaacaatg ccaaggaaat tggaaacggc
1441 tgctttgaat tttaccacaa atgcgataac acgtgcatgg aaagtgtcaa aaatgggact
1501 tatgactacc caaaatactc agaggaagca aaattaaaca gagaagaaat agatggggta
1561 aaactggaat caacaaggat ttaccagatt ttggcgatct attcaactgt cgccagttca
1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa tgggtctcta
1681 cagtgtagaa tatgtattta a

Amazing what a few As, Cs, Gs and Ts can do.... (Via Common Knowledge.)

Why Pig Flu is Better than Bird Flu: Open Data

As I wrote two years ago, one of the most worrying aspects of bird flu (remember that?) was that virus sequences were not being shared well, which meant that it was hard for experts to track its development and come up with a vaccine. Well, in one respect, swine flu seems to be an improvement over the avian variety:

In contrast to H5N1 bird flu, all the genetic sequences of this H1N1 are being posted on bulletin boards like GISAID, where scientists can access them and compare preliminary analyses.

The GISAID system was set up in 2006 by scientists who protested that H5N1 sequences were not being made freely available.

Here's what the GISAID site says:

This platform is designed and maintained by scientists for scientists from various disciplines e.g. veterinary and human virology, bioinformatics, epidemiology, immunology and clinical analysis etc. From here on, you will find a series of services, including the EpiFlu Database (developed by the Swiss Institute of Bioinformatics in conjunction with other partners of this initiative) providing secure storage and the analysis of genetic, epidemiological and clinical data.

Researchers like you have come together to empower this publicly accessible platform, free-of-charge to all researchers in the world who agree to the same terms, to foster a better understanding of the influenza virus. Following the correspondence letter in Nature, we have all pledged to share the data, to analyze the findings jointly, and to publish the results collaboratively, on the basis of open sharing of data respecting the rights and interests of all involved parties.

One fascinating aspect of this is that to view the data you must agree to the data-sharing that lies at the heart of the site:

Before you can enter, you are required to register and agree to the Terms of Use of our platform, as GISAID implements a particular data-sharing concept that has facilitated the flow of influenza sequence data to the public.

This creates an information commons, just as free software does.

Maybe there's hope for us yet.