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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Enter the Bio-Hackers

Let's hope there are some white hat bio-hackers working on this too....

Indonesia Hoards Bird 'Flu "Intellectual Property"

You had any doubts about whether intellectual monopolies were a good thing? Try this:

Indonesia is refusing to provide bird flu samples to other countries, companies and the World Health Organisation. Scientists and the WHO have expressed serious concerns about the ban, which they say hampers efforts to avoid a pandemic.

The move could set a precedent for international efforts to control the spread of viruses. Until now, countries have shared virus samples with the WHO, which then provides them to vaccine manufacturers.

In a highly unusual display of patriotism, the Health Minister, Siti Fadillah Supari, claimed Indonesia "owns" the bird flu strain which has spread across the nation, infecting tens of millions of chickens and killing at least 63 people.

Yesterday's announcement of a deal with the pharmaceutical company Baxter comes shortly after Indonesia condemned an Australian research breakthrough that could result in the production of a vaccine within months.

So as the cytokine storm kicks in, and you slowly drown in the fluid that was your lungs, hold on to this comforting thought: you and those you love may die, but the sacred IP virus will live on. (Via Technocrat.)

Will Lack of Open Access Wipe Out the World?

A few months ago, I asked whether lack of open access to avian 'flu data might hinder our ability to head off a pandemic; now it looks like lack of open access could lead to the destruction of civilisation as we know it. If that sounds a little far fetched, consider the facts.

The US is the largest single polluter in terms of carbon dioxide: according to the US Environmental Protection Agency, "In 1997, the United States emitted about one-fifth of total global greenhouse gases."

The EPA plays a key role in determining the US's environmental actions: "the Agency works to assess environmental conditions and to identify, understand, and solve current and future environmental problems; integrate the work of scientific partners such as nations, private sector organizations, academia and other agencies; and provide leadership in addressing emerging environmental issues and in advancing the science and technology of risk assessment and risk management."

To "assess environmental conditions and to identify, understand, and solve current and future environmental problems; integrate the work of scientific partners such as nations, private sector organizations, academia and other agencies" clearly requires information. Much of that information comes from scientific journals published around the world. Unfortunately, the EPA is in the process of cutting back on journal subscriptions:

The U.S. Environmental Protection Agency is sharply reducing the number of technical journals and environmental publications to which its employees will have online access, according to agency e-mails released today by Public Employees for Environmental Responsibility (PEER). This loss of online access compounds the effect of agency library closures, meaning that affected employees may not have access to either a hard copy or an electronic version of publications.

...

In addition to technical journals, EPA is also canceling its subscriptions to widely-read environmental news reports, such as Greenwire, The Clean Air Report and The Superfund Report, which summarize and synthesize breaking events and trends inside industry, government and academia. Greenwire, for example, recorded more than 125,000 hits from EPA staff last year.

As a result of these cuts, agency scientists and other technical specialists will no longer have ready access to materials that keep them abreast of developments within their fields. Moreover, enforcement staff, investigators and other professionals will have a harder time tracking new developments affecting their cases and projects.

So, we have the organisation whose job is to help determine the actions of the world's worst polluter cut off from much of the most recent and relevant research, in part because much of it is not open access.

No OA, no tomorrow, no comment. (Via Open Access News.)

Bird 'Flu vs. Open Source, Open Data

IBM pushes all the right buttons in this announcement of an open source, open data project to predict and help stem the spread of infectious diseases - like bird 'flu.

Central to the effort will be the use of advanced software technologies, elements of which IBM intends to contribute to the open-source community, that are designed to help share information on disease outbreaks electronically and use it to predict how diseases will spread.

And

Ultimately, those plans could include development and distribution of more effective and timely vaccines as IBM taps into knowledge gained through a planned collaborative initiative known as "Project Checkmate," in which IBM and The Scripps Research Institute propose to conduct advanced biological research on influenza viruses. The collaboration is designed to predict the way viruses will mutate over time using advanced predictive techniques running on high performance computing systems, such as IBM's BlueGene supercomputer, allowing effective vaccines to be developed by drug-makers, drawing on the immunology and chemistry expertise at Scripps.

Blue Gene runs GNU/Linux in part, so maybe open source will really save the world. (Via Boing Boing.)

Will Data Hoarding Cost 150 Million Lives?

The only thing separating mankind from a pandemic that could kill 150 million people are a few changes in the RNA of the H5N1 avian 'flu virus. Those changes would make it easier for the virus to infect and pass between humans, rather than birds. Research into the causes of the high death-rate among those infected by the Spanish 'flu - which killed between 50 and 100 million people in 1918 and 1919, even though the world population was far lower then than now - shows that it was similar changes in a virus otherwise harmless to humans that made the Spanish 'flu so lethal.

The good news is that with modern sequencing technologies it is possible to track those changes as they happen, and to use this information to start preparing vaccines that are most likely to be effective against any eventual pandemic virus. As one recent paper on the subject put it:

monitoring of the sequences of viruses isolated in instances of bird-to-human transmission for genetic changes in key regions may enable us to track viruses years before they develop the capacity to replicate with high efficiency in humans.

The bad news is that most of those vital sequences are being kept hidden away by the various national laboratories that produce them. As a result, thousands of scientists outside those organisations do not have the full picture of how the H5N1 virus is evolving, medical communities cannot plan properly for a pandemic, and drug companies are hamstrung in their efforts to develop effective vaccines.

The apparent reason for the hoarding - because some scientists want to be able to publish their results in slow-moving printed journals first so as to be sure that they are accorded full credit by their peers - beggars belief against a background of growing pandemic peril. Open access to data never looked more imperative.

Although the calls to release this vital data are gradually becoming more insistent, they still seem to be falling on deaf ears. One scientist who has been pointing out longer than most the folly of the current situation is the respected researcher Harry Niman. He has had a distinguised career in the field of viral genomics, and is the founder of the company Recombinomics.

The news section of this site has long been the best place to find out about the latest developments in the field of avian 'flu. This is for three reasons: Niman's deep knowledge of the subject, his meticulous scouring of otherwise-neglected sources to find out the real story behind the news, and - perhaps just as important - his refusal meekly to tow the line that everything is under control. For example, he has emphasised that the increasing number of infection clusters indicates that human-to-human transmission is now happening routinely, in flat contradiction to the official analysis of the situation.

More recently, he has pointed out that the US decision to base its vaccine on a strain of avian 'flu found in Indonesia is likely to be a waste of time, since the most probable pandemic candidate has evolved away from this.

The US Government's choice is particularly worrying because human cases of avian 'flu in North America may be imminent. In another of Niman's characteristically forthright analyses, he suggests that there is strong evidence that H5N1 is already present in North America:

Recombinomics is issuing a warning based on the identification of American sequences in the Qinghai strain of H5N1 isolated in Astrakhan, Russia. The presence of the America sequences in recent isolates in Astrakhan indicates H5N1 has already migrated to North America. The levels of H5N1 in indigenous species will be supplemented by new sequences migrating into North America in the upcoming months.

Niman arrived at this conclusion by tracking the genomic changes in the virus as it travelled around the globe with migrating birds, using some of the few viral sequences that have been released.

Let's hope for the sake of everyone that WHO and the other relevant organisations see the light and start making all the genomic data available. This would allow Niman and his many able colleagues to monitor even the tiniest changes, so that the world can be alerted at the earliest possible moment to the start of a pandemic that may be closer than many think.

Update: In an editorial, Nature is now calling for open access to all this genomic data. Unfortunately, the editorial is not open access....

Open Data - Good; Open Access - Bad?

Great story in Nature about data mashups - the mixing together of data drawn from disparate sources to create a sum greater than the parts.

This approach is not new: it lies at the heart of open source software - where chunks of code are drawn from the specialised databases known as hackers' brains and stitched together - and open genomics. Indeed, bioinformatics represents a kind of apotheosis of the mashup - see, for example, the way in which data from many researchers is pulled together in a genome browser like Ensembl.

Data mashups are more recent, and have started to gain popularity thanks to Google Earth. This provides a useful and conceptually simple scaffolding for other data to be brought together and displayed - like Nature's own avian flu mashup.

A pity, then, that this paean to the virtues of open data is not itself freely available under an open access licence. (For the benighted, the indispensable Open Access News has a long quotation that conveys the essence.)