Open Access Pioneer Award: George Garrity for his work on Standards in Genomic Sciences journal

A few days ago I got a message that made a big impact on my publication record in PubMed Central.  My number of publications there went up by 85 in one fell swoop (see below for the list ...).  Did I publish 85 new papers yesterday?  No.  But a journal in which I have been a co-author on many papers recently finally showed up in Pubmed Central.  The journal is called Standards in Genomic Sciences.  The journal's scope is:

The goal of SIGS is to serve as an open-access, standards-supportive publication for rapid dissemination of concise genome and metagenome reports that comply with the emerging MIGS/MIMS standards, detailed standard operating procedures, meeting reports, reviews and commentaries, data policies, white papers and other gray literature that is relevant to genome sciences but currently absent from the scholarly literature.

Lots of jargon, I know.  But you can ignore that.  The reason I am writing here is that this journal is a place to publish what could be called "genome sequencing data reports."  These reports are a way for data producers to describe, in a formal manner, their sequencing project - and to share - in a formal manner - not only the data but also metadata about the organism(s) sequenced and the methods used.  As sequencing gets cheaper and easier, we need places for people to publish these types of "data papers" to both produce a citable unit with a DOI relating to the data, and to also share the details of the data production in a way that a simple Genbank entry does not.

One aspect of the papers in this "SIGS" journal is that they are being done in a way that is compliant with sets of standards for sharing metadata about the organism and the project.  I confess, when I first heard about these standards developments, I was bored almost to tears.  But now I realize that this is a very important aspect of getting the most out of genome data.  If people who sequence a genome not only release the sequence data, but also a table of information about the project, such as information about the organism (e.g., aerobic vs anaerobic, location of isolation) and about the data production (e.g., sequencing methods used) then people will be able to do high throughput analyses of these features.  Then we will not just be looking at sequence but also connecting these sequences to organismal features.  Right now that is very hard to do since genome data is rarely accompanied by machine usable information about the organism that has been sequenced.

Anyway - long story short - there will be a paper published in this journal for each genome being produced as part of the "Genomic Encyclopedia of Bacteria and Archaea" project that I have been coordinating at the DOE Joint Genome Institute in collaboration with the DSMZ.

Today I am writing to recognize the people connected to this movement - the people who created the standards, the people who created and run the journal, and the people writing papers for this journal.  All of them are to be commended for their vision and their dedication to openness.  Thus I am giving George Garrity the EIC of SIGS  my "Open Access Pioneer Award" for creating SIGS, making it an open access journal,  for keeping it running and for getting its papers into Pubmed Central and soon Pubmed.   Many others should be recognized too for their contribution to SIGS (see the whole list of founding members here).  I also should recognize Nikos Kyrpides from the DOE JGI who helped coordinate the writing and submission of these papers along with Hans Peter Klenk from the DSMZ.  Without them, these papers would never have gotten out there.  Plus I think some credit goes to Michigan State University and the Department of Energy which apparently are sponsors of SIGS


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Open Access Pioneer Award: Bob Shafer HIV DB

Bob Shafer, an Associate Professor at Stanford, is fighting to make information about HIV freely available. He runs a database called HIVDB that aims to make information about HIV drug resistance available to the broader community. And he has been doing this for years (note - I worked with Bob when I was a PhD student and he was getting HIVDB started - we even wrote a paper together where I helped him do some phylogenetic analysis of HIV). For that alone, Bob deserves an Open Access Pioneer award. But I am giving him one here for a fight he has taken on recently.

You see, a company called Advanced Biological Laboratories, S.A has been suing Shafer and Stanford over a patent dispute. The company seems to be trying to claim to have rights over many (or maybe they think all) uses of using computers to help doctors make medical decisions. And they have been trying to get people to license their IP/software for doing this and one way they appear to be trying to get "users" is by suing them. And Bob is one of the people they have sued.

Sadly, Stanford University appears to have given in to the lawsuits even though their validity is debatable (see The Fight of His Life which provides some of the details - Hat Tip to Bill Hooker and FriendFeed for highlighting this article) and Bob has been left hanging on his own. Instead of caving to the lawsuit and shutting down HIVDB or making it less openly available or requiring people to say they will give commercial rights to Advanced Biological Laboratories for anything they develop using the DB. And rather than cave to the lawsuits Bob is fighting back - with a website called harmfulpatents.org and with a set of letters and communications. Mind you, I know little about IP/patent laws or the legal issues behind this dispute. But if this lawsuit leads to the shutting down or restriction of HIVDB that would be proof enough to me that Advanced Biological Laboratories and the legal system that supports them is doing a disservice to the progress of science.

For his efforts in keeping HIVDB open I am giving Bob Shafer a Open Access Pioneer Award.

For more on this story see

• The Other Dr. No: HIV Researcher Fighting the IP Pirates
  
• The Patent Fight of His Life
  
• New Stanford list of HIV mutations vital to tracking AIDS epidemic

Open Access Pioneer Award: Rick Prelinger, Image Access

Just saw an interesting article in the UC Davis "Dateline" newsletter about Rick Prelinger who is the founder of the Prelinger Library in San Francisco (and see their blog here). He gave a talk at Davis and thus they wrote an article about him here.

Some good lines from the article include

Rick Prelinger’s biggest thrill is “mainstreaming" historical documents for public consumption.

But getting history into the hands of the average citizen is no easy task, the archivist says.

Overbearing copyright issues and rampant commercialism, he argues, threaten the free exchange of information on which a knowledge society — especially its libraries — depends.

...

Rather than concern themselves with rigid lending policies or copyright protections, library systems should focus on “more product, less process” to better serve patrons, Prelinger said.

...

“If the Google book deal is approved without any changes, we could soon lose 100 million books that society doesn’t know what to do with,” said Prelinger, referring to “orphan works,” or works under copyright, but whose owner is not known.

....

On the other hand, archives are empowering, Prelinger said. “Let’s open up the past. Interesting things happen when we do so.”

In general since Prelinger has been pushing for more openness in libraries and in images, I am giving him an "Open Access Pioneer Award".  Sorry I missed the talk but glad I read the article.  

Open Access Pioneer Award #4: Carl Malamud and Public.Resource.Org

This is not about science but I think this guy deserves an award.  I just read an interesting and funny story in the S.F. Chronicle (Sebastopol man puts code manuals online) by Matthew Stannard about Carl Malamud who has been putting building codes, plumbing codes and other codes online at Public.Resource.Org.

Basically, he is doing this because many of the codes are only available for a fee.  He says

"Not everybody is going to read the building code, but everybody who wants to should be able to without putting 100 bucks in the slot," Malamud said. "Primary legal materials are America's operating system."

And though his work has been questioned by some (who would like to make money off of the codes) he appears to be on solid legal ground. 

"It's very clear in American law that you can't get intellectual property protection for law," said Pamela Samuelson, co-director of the UC Berkeley Center for Law and Technology. "Law belongs to everybody."

So for this work, I am giving Malamud by Open Access Pioneer Award (#4).  Keep up the good work.

For more see (among many):

• Tech activist takes on governments over 'copyrighted' laws
  
• Peter Suber's posts on Malamud and Public.Resource.Org
  
• Another profile of Carl Malamud
  
• Carl Malamud - Liberating Law
  
• On Being Open: CNET Profiles Carl Malamud, iLibrarian Interviews ...
  
• Article about Carl Malamud's Crusade for Open Law
  
• Carl Malamud Speaks Volumes about Public Access to California ...

Open Access Pioneer Award #3: Joe Derisi

So I was reading the web page of WTOP radio, which I used to listen to all the time in DC and somehow still have their page near the top of my bookmarks. And there was a headline I could not resist. It said: "Malaria Researcher Wins Heinz Award." As I know a few people studying malaria here and there I had to check it out. And indeed, one of the winners of the award is Joe Derisi, from UCSF, who I know reasonably well and like very much. I am very pleased to see him win one of these Heinz Awards

The Heinz Site says "Joseph DeRisi receives the Heinz Award in Technology, the Economy and Employment for his extraordinary breakthroughs in detecting both new and existing viruses."

In addition to his science they say

"Joseph DeRisi has made breakthrough discoveries in the laboratory that have provided clarity and insight into the detection of some of the world's most threatening viruses as well as distinguished himself as a generous and tireless advocate for the free and open sharing of scientific research. With a brilliant mind and expansive heart, he has ennobled the field of science."

Here here. Derisi is one of the true pioneers of Open Science, not only promoting Open Access publishing but also promoting open sharing of methods, equipment, data, and everything. And, not that he needs another award (to go with his Heinz, his HHMI position, and his Macarthur among many things), but I am giving him my Open Access Pioneer Award #3 for his firm commitment to open science.

Open Access Pioneer Award #2: R. Preston McAfee

Great article in the LA Times on August 18 by Gale Holland about "Free digital textbooks." (see Free digital texts begin to challenge costly college textbooks in California)

The article discussed some issues in open source textbook publishing including in particular R. Preston McAfee's work on creating a free online economics textbook. McAfee is a professor at Caltech and is a self described right winger.

"I'm a right-wing economist, so they can't call me a communist," McAfee said.

And he goes on to say

"What makes us rich as a society is what we know and what we can do," he said. "Anything that stands in the way of the dissemination of knowledge is a real problem."

The article discussed other open source educational materials including:

• Merlot, from Cal. St. Universities which is a "a searchable collection of peer-reviewed, online multimedia materials."
• Connexions, from Rice University , which "stores free, open-licensed educational materials in fields such as music, electrical engineering and psychology.
• OpenCourseWare from MIT which includes "virtually its entire curricula online -- video lectures, problems sets and exams for more than 1,800 courses in 33 disciplines."
• Wikibooks, a collection of editable textbooks
• The Digital Marketplace, from Cal. St. U. which is a "website for selecting, comparing, sharing, approving and distributing both open-source and commercial online educational materials."

Now, I am not saying here there is not a place for textbooks in the normal model (I have one).  Unlike basic science papers, for which the cost of making a presentable paper is relatively low, the cost of producing a textbook can be very very high.  Thus I think publishers are welcome to work with authors to come up with their own models for how to publish the texts.  But nevertheless, the more we can get good open source textbooks out there, the better off we will be.  And thus, for his role in promoting the release of what seems to be a high quality open source textbook, I am giving R. Preston McAfee my second "Open Access Pioneer Award.

Hat tip to Jeremy Peterson and Eilleen Hamilton for pointing this out.

An Open Access pioneer - Trent Reznor

Normally, everything I write about here is at least indirectly connected to science in some way. However, today I am drifting into the world of music. The New York Times had an article a few days ago about Trent Reznor (Trent Reznor’s Frustration and Fury - Take It. It’s Free). Trent, the brains behind the band Nine Inch Nails (full disclosure - I am a fan of his music), has been railing against the constraints of the music industry for year.

And now he is going even further and in essence putting his music into the public domain as much as possible (see his web site NIN.com for more detail). For example

"Mr. Reznor even posts online all the raw digital tracks from Nine Inch Nails albums for anyone to remix. “I’m done with them,” he said. “Why not?”

And he is doing this even though the $$$ for producing his music does not come from the government. He does it in part because he wants his ideas and music to spread and he wants to contribute to musical development. There are obvious parallels between what he (and others) are doing in music and those who develop Open Source software and those who release their data and publications to be as free as possible. I know I am not the first to discuss this, but just thought I would put it out there.