16 September 2009

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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Carla Del Rio said...

Glyn, unfortunately SIB has not as yet come to their senses and appears to loose more of its credibility with their blatant behavior to phish for GISAID user names and passwords on the SIB website now called OpenFlu. They appear to be defiant and have failed to notice that absolutely no one is depositing sequence data since SIB cut themselves off from the GISAID website. What is disturbing us is that SIB is still offering data from GISAID users, data that is neither theirs nor data from the public domain. Perhaps the wheels of justice grind differently in so-called ‘neutral’ Switzerland, as SIB continues to flagrantly violate many rules of ethics and law. My image of Heidi’s Switzerland has greatly suffered from this ordeal.

Fortunately though for GISAID, the German Government - I read this morning http://shar.es/1KQgV - has announced to permanently host their database. We wish the GISAID initiative the best of luck and are happy to see that they have been resilient and successful in getting right back on top of the game. Thank you GISAID people for hanging in there!

Glyn Moody said...

@carla: great news - I've now tweeted it:


thanks for letting me know