openaccess
jwilbanks | May 18, 2009Open Knowledge Foundation have released a short guide to open data as part of the open data commons project.
I have my philosophical disagreements with OKF on some issues - and they with me! - but they're the kind of disagreements that come from people on the same side of the fence. We all want open data, and we want it now.
Moments like this are good to step back and focus on our agreements. We agree that data is a little weird, and that we need more research on how to best treat the law around the data. We agree that public sector information needs to be free - in fact, Rufus Pollock has…
jwilbanks | May 18, 2009(note - I have edited this post to add in Rufus Pollock, who I left out primarily because I wasn't sure he would endorse the ideas in this post - Peter notes that he was not only at the meeting but essential, so I'm happy to add these edits!)
Peter Murray-Rust has posted some essential reading for anyone interested in open data in the sciences. He follows onto Cameron Neylon's post whose title I have quoted in my own title here.
Peter summarizes an informal summit meeting held lest week in the UK by a group of folks interested in open science and open data, including Rufus Pollock of the…
jwilbanks | April 22, 2009The Tropical Disease Initiative has released a "kernel" for open source drug discovery. It's been published in both Nature Biotechnology (ugh, subscription required) and in PLoS Neglected and Tropical Diseases (yay, open access fulltext under CC-BY).
I am not steeped enough in the reality of drug discovery to make believable statements about how much this means for those actually on the ground looking for cures. I do know that drug targets are only the first step on a really long road to drugs in patients, and Derek Lowe has written a very informative post on this topic over at In the…
gregladen | April 13, 2009It is a ground breaking company, it is a bookstore that is mega mega like few other companies are. It is a bookstore that is a huge corporation. Think about that for a second. Think about bookstores in the old days then think about this thing, Amazon Dot Com. A bookstore that is leading the way in mega cloud computing. It has one of the most effective ways ever of interfacing with its customers. It has become the go to place for many people for the purchase of almost anything one can imagine being delivered by mail. Amazon Dot Com is a thing the likes of which we have not seen before…
jwilbanks | April 9, 2009Michael Nielsen gets it right, again.
This is what I'm on about when I talk about ontologies and object-orientation of knowledge. In science, the code is the knowledge. Unlike computer programming, the code is locked up PDF and XML formats, and behind firewalls and copyrights (at least in code you could write your own if you knew what you wanted.). On top of that, ontologies are a royal pain in the ass.
But it's worth it - if the pain is big enough. Standard ontologies and common names mean we at lest get a speck of modularity in database aggregation, for example. You can do some cool stuff…
jwilbanks | April 6, 2009I don't like getting into blog back and forths, but this post from the Information Research folks really deserves a reply of its own. I believe this is an honest piece of confusion, and it's likely the result of FUD from the traditional publishing community. I invite the Information Research folks to contact me if they have questions about how Open Access works from a legal perspective so that we can counter any unwarranted fears about how to make the sharing involved easy and legal - we're here to help.
From the post:
If the author retains copyright, as Information Research authors do, it is…
jwilbanks | April 1, 2009Big FriendFeed chatter on the interwebs yesterday about JoVE "moving" to a closed access model.
This is being covered extensively on the FF conversation so I won't dredge through the points there - if you want to see the arguing and JoVE responses, head over there.
What's interesting for me is the lack of conversation about the importance of licensing. There is a reason Open Access talks about copyrights in the definitions. Let's go back and remember:
By "open access" to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy,…
gregladen | August 13, 2008From Sex, Genes and Evolution, a story of publishing in PLoS Open Access Journal:
My lab has taken its initial journey on the PLoS ONE train.
Yesterday, our paper entitled "An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis" was published in PLoS ONE. It's a updated and detailed report on the ongoing work in my lab to generate and curate an "inventory" of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life…
gregladen | July 6, 2008 OA pillars The following are excerpts from the journal Nature regarding the Public Library of Science. These were located with a simple search for the phrase "Public Library of Science." For each item, I provide the source, and a selected bit of text. I have no selection criteria to report, but I do have a reason for doing this: To give an interesting view of the history of PLoS as a concept and an entity, and to some extent, the reactions to PLoS from various quarters.
I ignored passing reference to PLoS or redundant items.
Personally, I find this textual sequence fascinating. I…
gregladen | March 6, 2008Late last month, I put up a quick post, New-generation antidepressants do not produce clinically significant improvements in depression, that addressed a PLoS published metastudy of interest.
I was careful to use the phrasing from the paper as the title of my post, and to provide only the author's summary, because I knew this was a tricky issue. I could have read the paper carefully and reported my opinion on it along side the information from the paper (a practice known as "blogging on peer reviewed research), but I did not have the time or interest to do so, yet I knew many of you would…
gregladen | December 18, 2007I wanted to point out two interesting posts both having to to with the nature of knowledge, or as we call it here in Minnesota (where the "k" in "Knute" is proudly pronounced).
The first is The Problem with Google's Knol Initiative (aha, you see, there's that "k" again...). This is about Google's idea of starting up it's own version of Wikipedia. Pierre Far of BlogSci questions the wisdom of Google's approach. The Google version of a wiki that is an encyclopedia promises to be better because it will recruit, and rely on, expertise. However, Far suggests that this could backfire, and asks…
gregladen | November 27, 2007We are told that "the Million Book Project has exceeded its goal of digitizing one million books by 2007. " Well, I can think of a million books that I'd never want to look at, and I can think of a million books that I would give up my life to preserve. Or your life, at least.
Which million does the Million Book Project address? And how? And why?
I don't know about why, but I am deeply offended and seriously worried about the "how" part ... about the fact that the very first words you encounter if you go to the US site of the million book project are:
"Use Internet Explorer to....." (…