Wired magazine on open publishing

Biologist Howard Eisen's son tries to put his late father's papers freely online. Hilarity ensues.

Trying to explain open publishing to someone outside the field? “Free Science, One Paper at a Time” in the May Wired tells a compelling story about the need for open publishing, referencing PLoS, academic librarians’ woes, Mendeley, and Michael Weiner’s work on ADNI, through the story of Jonathan Eisen‘s attempt to make his late father’s scientific publications freely accessible online. Very readable, and highly recommended.

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Upcoming talk on Open Science by Michael Nielsen

For those of us interested in open science, Dr. Michael Nielsen will be speaking in San Francisco later this month.  Dr. Nielsen is a leading advocate in this field and his book, “Reinventing Discovery” will be published later this year.  Here’s some information about his upcoming talk:

The net is transforming many aspects of our society, from finance to friendship.  And yet scientists, who helped create the net, are extremely conservative in how they use it.  Although the net has great potential to transform science, most scientists remain stuck in a centuries-old system for the construction of knowledge. Michael will describe some leading-edge projects that show how online tools can radically change and improve science using projects in Mathematics and Citizen Science as examples, and he will then go on to discuss why these tools haven’t spread to all corners of science, and how we can change that. [via]

The wine, beer, and cheese event will be held at the Public Library of Science on June 29th at 6pm.  The event is free and open to the public,but they ask people to RSVP at rshah@plos.org if you plan to attend.

Open Notebook Science

Thinking about our recent posting  regarding project and document management, along with a number of postings on open source data, people might be interested in learning more about a movement that takes open source to a basic level.  As described in Wikipedia:

Open Notebook Science is the practice of making the entire primary record of a research project publicly available online as it is recorded. This involves placing the personal, or laboratory, notebook of the researcher online along with all raw and processed data, and any associated material, as this material is generated. The approach may be summed up by the slogan ‘no insider information’.

While not everyone thinks this is a great idea, a number of labs in a variety of disciplines have begun to embrace the concept.  Similar to the Creative Commons movement, there are a number of ways to implement open science in your lab (with associated logos, of course!).

So, does open notebook science have a place in biomedical research, and does it have a role in translational science?

Further reading:

Open Source Genetics

We’re familiar with open source software and open source data.  Now it looks like we need to add open source molecular biology to the list.

The same concepts that have lead to open source rockin the software world have spawned the beginning of a revolution in biotech. An organization called Biofab, funded by the NSF and run through teams at Stanford and Berkeley, is applying open development approaches to creating building blocks (BioBricksTM from BioBricks Foundation) for the bio products of the future. Now, the first of those building blocks based on E. coli are just rolling off the production line. This, according to the organizers, represents “a new paradigm for biological research.” (via)

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Credit: Penguin Books

When we think of Translational Science, we imagine going from bench to bedside to community.  But what if the research itself is happening in the community?  Meet the Biohackers:

These do-it-yourself biology hobbyists want to bring biotechnology out of institutional labs and into our homes. Following in the footsteps of revolutionaries like Steve Jobs and Steve Wozniak, who built the first Apple computer in Jobs’s garage, and Sergey Brin and Larry Page, who invented Google in a friend’s garage, biohackers are attempting bold feats of genetic engineering, drug development, and biotech research in makeshift home laboratories.

In Biopunk, journalist Marcus Wohlsen surveys the rising tide of the biohacker movement, which has been made possible by a convergence of better and cheaper technologies. For a few hundred dollars, anyone can send some spit to a sequencing company and receive a complete DNA scan, and then use free software to analyze the results. Custom-made DNA can be mail-ordered off websites, and affordable biotech gear is available on Craigslist and eBay.

Is there a place for this movement in the CTSI continuum?

A GitHub of science

A conversation on scientists’ favorite online tools on Quora led to several ideas on online tools scientists wish existed. The most popular was Marius Kembe’s idea:

Github for scientists – a distributed hosting and version control system for all parts of scientific communication, including writing, code, data, and audio/video/images. So that you could build on somebody else’s work by versioning it! Isn’t that what science is meant to be about?”

As a GitHub user in non-biomedical domains, this makes so much sense to me. Marium went on to describe the idea further on his blog:

“GitHub is a social network of code, the first platform for sharing validated knowledge native to the social web…I believe it represents a demonstrably superior way of distributing validated knowledge than academic publishing. How are these even related? Software developers rarely write applications from scratch. Instead, they often start with various modular bundles of open source code…Scientists never begin a research project from an intellectual vacuum. They stand on the shoulders of giants, building on the knowledge contained in previous publications to form a new, coherent finding…Gems on GitHub are not just code.  They also have authors whose relative contributions are automatically catalogued…This impact graph can let you know precisely which developers are responsible for this awesome-ness…By contrast, current Open Science efforts that ask scientists to ‘share all your data’ have not become mainstream, because they do not appropriately reward knowledge producers.”