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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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.