Commons sharing – buzz at this years Translational Bioinformatics Conference

Our work on a stem cell commons – an as-open-as-you-choose sharing data system for placing stem cell molecular and experimental information into context was shared with the community by Shannan Ho Sui – the program director- at the TBI last week. Tweets #TBI2013 covered it – and tweeted us nicely as they say. Why? because its hard to bring together researchers, their NGS data, the molecular profiles that result and then to combine it in order to find the underlying shared function and meaning and shared interests. The Harvard Stem Cell Institute Stem Cell Commons plans to do just that. Find our presentation here. Genomeweb shout out here.

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The next resignation from an Elsevier Board

Today,  Bart Knols, editor of MalariaWorld and chair of the advisory board followed my resignation with his own decision to resign from the editorial board of Acta Tropica (Elsevier):. MalariaWorld, a project of the Dutch Malaria Foundation, is the world’s scientific and social network for malaria professionals with more than 7300 members from 135 countries. MW promotes Open Access 2.0 (free reading and publishing) to malaria information and publishes the first peer-reviewed OA 2.0 scientific journal: the MalariaWorld Journal.

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Reform is overdue: No longer working for a journal that puts profit over access to research

I resigned today from the board of Genomics, where I have been an associate editor for the last few years. My resignation and my reasons for it are blogged at the UK Guardian.

It is not easy to do this publicly – a good friend heads the board, and I respect him and what the science of the journal seeks to achieve. But now I just think this way of publishing is wrong. Just wrong. My colleagues in South Africa in general don’t have access to the swathe of journals we take for granted in the west. Yet I was working to edit publications that were often written by people who are not in the mainstream western institutions.

How to move forwards?

First and foremost, we need to be able to see everything that our governments have paid us, using our taxes, to research.

Secondly, we need to address the ‘closed shop‘ that is peer review – we need to be able to engage interactively with a larger community, some of which have to be actual experts in the area.

Finally we need to address the tenure issue – High profile publications need to be defined by the actual impact of the work , as opposed to the perceived impact of the journal. These are *different* things.

Posted in African bioinformatics, bioinformatics, Data sharing, genome data sharing, Genomics, open access, open access | 11 Comments

H5N1 surveillance: Shift expertise to where it matters

Jeremy Farrar is someone who “gets it”. He works at the Hospital for Tropical Diseases in Ho Chi Minh City.  He writes in today’s Nature on the need to have expertise at the site of infection. Together with other ‘out there in the real world’ research professionals, he has trained thousands of regional scientists in clinical medicine, epidemiology, microbiology, bioinformatics and other disciplines crucial to monitoring, controlling and understanding infectious diseases and outbreaks. H5N1 is nasty. It kills millions of birds and of course threatens people in pandemic ways as yet unexplored. He makes the hugely important point that  local treatment is impossible when the work requires individuals to fly in and out and to analyse samples in another country. This reflects in the access to flu data – an ongoing debate at several levels. Should new lab-mutated flu strains be published and accessible to all? Should flu data painstakingly generated in Indonesia be used by western labs without recognition of the governments and people who capture it? Flu kills. Its as simple as that. We should stop the bickering about who should and should not access the strain data – and instead concentrate on educating our communities across the world on how better to work together to ensure its control.

Farrar’s model for containing flu is an excellent one. Its robust, cheap and efficient. It trains people locally and it addresses the disease at the site of infection. It needs the support of the global scientific community, not just the Wellcome Trust. We used a similar model for development of approaches to containing public health at the SA National Bioinformatics Institute in South Africa and here. Recognition of the power of these approaches will make a dramatic difference to public health, not only in the developing world, but in the developed world where pandemics are a reality.

Posted in African bioinformatics, bioinformatics, bird flu, Data sharing, genome data sharing, Genomics, influenza, networks, open access, pathways, swine flu | Leave a comment

6 months delayed… but – open access proposed for all US Government funded research

From the GenomeWeb Newsite: – Members of both houses of Congress this week introduced identical bills that would expand public access policies for research funded by taxpayers, such as the one in place at the National Institutes of Health, to include all the major science-funding agencies.

The Federal Research Public Access Act, which has bipartisan sponsors in the US House of Representatives and the US Senate, would require that research funded by federal departments and agencies with annual extramural budgets of $100 million or more be submitted after publication in a peer-reviewed journal.

The bills require that manuscripts be submitted within six months of publication for storage in an accessible repository that would be publicly available online. The poicy will cover  the National Science Foundation, the Department of Agriculture, the Department of Defense, the Department of Energy, and others.

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No access to food means you die quickly. No access to science means you die more slowly.

Teleporting Duplicator makes food freely available

The farmers were sad because they wanted everyone to have food. But what could they do? Letting all their food be freely replicated without the aid of a top distributor was professional suicide

The Guardian’s blog features Mike Taylor who uses a parable for a world where food is cheap and freely available to expose the conflict between access to science and paywalls set up by its distribution. Of all the shrill verbage I have read on the issue of open access I think his piece provides by far the most telling insight. A few snippets are below but the whole post only takes a few moments to read.It leaves an image on the back of the eyelids. The view it provides has made me finally seriously reconsider the whole access to published papers issue. I am an associate editor for the Elsevier journal ‘Genomics‘. I am becoming more and more uncomfortable with this role as I am effectively putting my time into something that I am not sure is going to be an effective investment into the future. I have not left the board, but questions I have raised with the company on open access have not been answered.

With the new machines, anyone who came upon a particularly delicious or nutritious morsel of food could send it to all of his friends. Farmers could send their newly harvested crops directly to other farmers, even those on the other side of the world.

Wait a minute,” said the distributors, “what about us? We’re a valuable part of the supply chain. We add value. It would be much better if we continued to distribute food the old way, with trains and ships. But everyone immediately saw that this was silly. The old technology was obsolete, the new was better in every way. Facing an outcry, the distributors saw that they wouldn’t be able to go on as before, pretending that Teleporting Duplicators didn’t exist.

You can’t just cut us out of the food distribution process”, they said. “It would be much better if farmers and ordinary people were not allowed to operate Teleporting Duplicators. We’ll operate them for everyone, and sell the duplicated food.”

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Cloud Biocumputing just for you

Brad Chapman in my group here published his blog – ‘blue collar bioinformatics’ where he describes the progress being made in online accessible cloud instances (private to you) of analytical environments for bioinformatics.

Look for BioCloud Central where users, having established an Amazon account, can fill out a simple entry form and then get biocomputing ASAP.

Connectivity issues apart, we are finding that (cores performing sequencing are happy to directly upload large datasets to the site, and) processing is simplified for users who cannot program but need to set algorithm parameters in pipelines using galaxy (where galaxy might be hidden or exposed.)
The end users – read biologists – really like the freedom, power, control and low cost. Service providers and researchers alike are using these instances here at Harvard to share data and provide consulting on users datasets. The systems are actively being developed and are also useful for teaching.
Want to keep up on the buzz in bioinformatics? Stop by the Harvard Center for Health Bioinformatics news page for weekly updates.

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