Over at The Life Scientists room on FriendFeed (thanks to Bill for introducing me to the site), Pierre has posted a link to the Elsevier Article 2.0 Competition.  The details are scarce at the moment, but enough to pique my interest:

We will provide contestants with access to approximately 7,500 full-text XML scientific articles (including images) and challenge each contestant to be the publisher. In other words, each contestant will have complete freedom for how they would like to present the scientific research articles contained in the Article 2.0 dataset.

And there are prizes to be won as well:

First Prize:  	$2500
Second Prize: 	$1000
Third Prize: 	$500

I’m really hoping that I’ll be able to put together an entry. I’m not as familiar with Xquery as I should be, but I’ve got a couple of months to learn I suppose. I’ve already started brainstorming a pile of ideas of course. It’s what I do best.

I’m not sure if the rules will allow for teams, but I think it would be really great if some of the Open Access proponents could work together to generate a really fine product which relies on the many OA resources that are available on the internet. It’s a prime opportunity to demonstrate the value added by opening up the articles in this way.

There has been a lot of heat on the net over the past few days as the Associated Press went after a blog for posting “blockquotes” and has declared that they will levy fees against anyone who quotes more than 5 words of one of their articles.  The predominant opinion seems to be that quoting an AP article falls under the terms of Fair Use, and that it’s ludicrous for them to charge for the privilege.  The AP disagrees:

AP considers taking the headline and lede of a story without a proper license to be an infringement of its copyrights

As I’m sure you can guess, I fall in with the crowd that believes the AP is just being ridiculous. First of all, I’m not sure that the headline of an article is a “Creative Work” (can I call this the Wilbanks Postulate?) Take this headline, for instance (for which I’m likely to be fined I suppose, as it’s over 5 words):

Obama opts out of public campaign finance system

Copyright 2008 Associated Press

This is a statement of fact, not a truly creative work.  I fail to see how one can copyright this and have a legal leg to stand on.

Secondly, a short excerpt clearly falls within the realm of Fair Use, especially given the link back to the article itself.

The problem is that the AP spends a lot of money writing their articles in the first place, and deserves to get some return on them of course.  If a blog comes along and copies the content wholesale, then this is a problem that needs to be addressed.  From my point of view, this looks like an “old media” company backlash against “new media”; an attempt to subvert and stretch copyright law past the breaking point.  They’ve worsened the situation by propping up a shill who claims to negotiate for all bloggers.  I hope that the AP comes to their senses and realizes that cracking down on spam blogs who are scraping their content is a completely different matter from squashing Fair Use and open discussion of world events.

Two items not related to Open Access (at least in a scientific sense) today that I think you’ll enjoy.

One of the largest “social media” sites (an my personal favorite), Reddit, today announced that they would make about 95% of their code open source, including the algorithm which determines the stories that make the front page.  They’ve got a Trac site set up at code.reddit.com interfaced with a Git version control system.  The code appears to be largely built on Python.  I could definitely see this being leveraged to create some interesting science-related applications.

The second item is completely for fun, although xenobiologists might enjoy it as well.  Spore is an upcoming game from Will Wright, the creator of The Sims, and it looks like it’s going to be great.  The player starts out as a single-celled organism in a pool and has to evolve up to a spacefaring civilization.  The game has been in development for a long time, to the point that some people thought it might end up as Vaporware.  Now, however, it has a release date for September.  Even though the full game isn’t out yet, the Creature Creator portion was released yesterday, both as a free trial and (soon?) a $10 full version.  At first I thought it was weird to release the character creation part of a game as a standalone product, until I got to play with it.  It’s really amazing, but also hard to describe.

When you create a new creature, you start with a randomly shaped blob, which is the creature’s body.  You can move it and reshape it, then start adding parts to make your critter.  The parts you add and the conformations you place them in all influence how the creature acts and moves.  I’m really shocked at how seamless and simple it is.  Once you’re happy with your creation, you can easily upload it to the Sporepedia, a conglomeration of everyone’s aliens.  You can also make a video and send it to YouTube with a few clicks.  The quality of the YouTube videos could be better; I feel like there is a compression issue to work out. Nevertheless, here is one I made:

I can’t really describe how much fun it is to play, so you’ll just have to check it out yourself. If you make any creature videos, link them up in the comments :)

According to my Wordpress dashboard, this will be the 100th post here at PA.  I’m fairly pleased with the response that the blog has gotten so far, and I feel like my decision to keep the focus tightly on Open Access was a good one.

I have to admit feeling a bit like I’m both preaching to the choir and shouting into the wind at the same time.  Most of the comments come either from a dedicated core (awesome) or others in the OA movement who I presume are getting pings from Google hits (also great).  At some point though, I’d like to start hooking into that next layer; people who might be interested in doing more things with OA but don’t know how or are unfamiliar with all of the great options.  We can sit here all day and pat one another on the back for a point well made, but it’s the public-facing products and discussions that will really make a difference.  By this I mean the things that you’re already familiar with; sites like OpenWetWare, journals like PLoS, public talks by proponents of OA, etc.

You might say I’m interested in expanding PA’s deliverables.

At the moment I’m sort of investigating some of the projects that are already out there.  To be honest, I do feel like the OA movement is in some ways disjointed, in that there are many projects which are being maintained by small groups and have relatively narrow impact.  This isn’t necessarily bad - this is the sort of “grass roots” community-based enthusiasm that many causes would love to have.  I’m more interested, however, in applying whatever minimal force I can bring to bear in a way that has more widespread effects.  I’m not sure what this is yet, but I’m thinking hard about it.

Once again, thanks for reading.  It still amazes me that one person pecking away at a laptop keyboard can engage in these discussions in a (hopefully) productive way.  I look forward to continuing the conversation with all of you.

If you’re in science, you have probably heard of J. Craig Venter.  He was the head of the private effort to sequence the human genome, and has since pushed forward with research in a wide variety of fields.  It’s abundantly clear that Dr. Venter has done marvelous things for science.

The thing that always amazes me is that whenever I read a story on him in the popular press, they invariably refer to him as Maverick Scientist J. Craig Venter.  I don’t even think I would have noticed it once or twice, but the occurence in every article is really amazing.  I’m not trying to say it isn’t true; Dr. Venter has done many “maverick” things, including coding his own name (as well as other people and organizations involved in the work) into a recent synthetic genome.

But it just makes me laugh that everyone refers to him as “maverick”.  Look, it’s here in this interview, the very first one I looked at today in “researching” (I use the term lightly) this post:

Here it is again.  And again.  These are only the web-accessible links from his Wikipedia page, which remarkably does not itself include the word “maverick”.
So I have to ask what is the source of this phrase? Is it just lazy reporters copying previous articles? Does Dr. Venter’s official biography include the wording?

I have some readers who have met him (full disclosure: I have not).  Is he really a “maverick” or is he just openly ambitious and confident?

Anyhow, I don’t mean much by pointing this out, besides the fact that it just seems odd to me.  Also, I hereby request that any reference to myself be phrased “the dashingly handsome Open Access blogger, PA”.

Here is a short introduction video:

And a link to the original post over on the SC blog.

The more time I spend delving into the Open Access community, the more I realize that it is deeper and more organized than I would have thought in the not-so-distant past.  Not only are there many people who spend a fair portion of their day thinking of ways to make the practice of science more open, the people I’ve encountered are frankly brilliant.  Where someone like myself might have a somewhat naive vision reminiscent of the peace love & happiness campaign, those who are truly driving the causes of Open Access are remarkably grounded and realistic.

Now, I’m not saying this merely to kiss some butt (although I did apply for a position at PLoS today, so there is definitely some gluteal smooching at work), but because I feel like the leaders of the movement have done a great job addressing potential “problems” of OA adoption.  Of course there are some concerns that need to be refined and worked out as thing go along, but it seems to me that most of the “deal breakers” have been resolved in a way that should satisfy those who matter - the people doing the science.

In light of this, why is the adoption of Open Access not proceeding even faster than its already heady pace?  Perhaps from my side of the fence, where all things Open Access appear logical and highly desirable, I simply can’t comprehend why others might not agree.  Part of me wonders, though, if apathy doesn’t play a part.

Let me draw an analogy here with cable T.V.  I’m sure most of us remember the days when over the air broadcast TV was about the only game in town.  It was cheap, but the selection was limited and quality could have been better.  Then cable came along, and you could get a much greater selection and a higher quality picture.  People signed up in droves.  Over time, though, the programming degenerated, content was diluted, and costs kept rising.  Since this happened over time, it wasn’t necessarily strongly noticed by those who had the service, and there was no one incident that led to people giving up on it.  The average family kept cable because they didn’t really think there was another choice; cable had become ubiquitous.  Now we are at a point where we see people abandoning cable for things like the internet or home DVD rentals.  Even those who keep cable want increasing control over it, in the form of DVRs.  The costs of cable are out of proportion with the benefits, especially when there are newer, cheaper, and in some ways better communication media available.

I think there are some parallels to be drawn here with the state of STM publishing.  The machinery of a large publishing house was really necessary in order to produce a high-end product (by this I mean science journal) and to distribute it.  Over time, however, the journals kept raising prices, to a point where it has become painful for universities to keep up their subscriptions.  Unfortunately, there is little choice - your faculty and students need access to the literature to be effective researchers.  Now, Open Access has come along and shown a way to reduce costs, largely by relying more on web technology to deliver content and removing cost overhead associated with maintaining tight content locks.  The open distribution of the information is not only good for the library’s bottom line, it’s good for science and the world as a whole.  The groundswell of Open Access is growing, and the only ones who stand to lose are publishing companies who refuse to admit it.

So my question is why more scientists don’t get behind OA.  Some of it I think is an unwillingness to take what is viewed by many as a gamble; tenure might come easier if you just fit in with the mold and publish in “accepted” journals.  It’s the same motivation that drives people to Starbucks rather than the great corner coffee shop.  It’s just inertia - why make an effort to find and publish in an OA journal when the “standard” ones are out there?  Largely its an informational issue - we need to extoll the benefits that OA publishing has over locked-down journals.

I should close by saying that I’m not in any way deriding the progress of OA.  I think it’s clear that huge strides have been made, especially in the last year or so.  Much like a member of the audience watching a juggler, once I’ve seen him do 3 pins I immediately want to see 4.

The latest issue is all about Science Commons, and since some of the articles are republished from the SC blog, I’m even quoted in it (much to my surprise).

From John Wilbanks’ introduction:

One of the reasons I believe so deeply in the commons approach (by which i mean: contractually constructed regimes that tilt the field towards sharing and reuse, technological enablements that make public knowledge easy to find and use, and default policy rules that create incentives to share and reuse) is that I think it is one of the only non-miraculous ways to defeat complexity. If we can get more people working on individual issues — which are each alone not so complex — and the outputs of research snap together, and smart people can work on the compiled output as well — then it stands to reason that the odds of meaningful discoveries increase in spite of overall systemic complexity

The newsletter is a 37 page PDF, and you can download it here.

The time has come to make a decision.  Perhaps it is past time, but here we are.  I’ve been putting this off for some time because it is one of the most important and most difficult decisions I’ve ever had to make: do I try to power through and get my Ph.D., or do I write up what I have and move on with a Masters degree?  The issue is that neither solution is without drawbacks, of course.

I had some tough conversations with several groups of friends this weekend (it just seemed like everyone wanted to talk about it).  These made me realize that I’ve been sort of doggedly remaining on autopilot, when I should have been spending more time thinking about how to resolve my situation.

Since I like to obtain input from as many sources as possible before making big decisions (I research everything to death), I thought I’d lay the situation out and see what you have to say.

Read the rest of this entry »

Using web-based tools to manage labs is a key interest of mine.  I believe that these tools are more or less already available, and would greatly aid investigators who are already spread thin due to competing demands on their time.  This is why I’ve made calls for open source LIMS packages as well as taken some initial steps towards building one myself.

My efforts to create a system have not had a high sense of urgency about them.  There are several reasons for this; it will be some time before I have to worry about this myself (if ever), I have other work to do which is actually related to my Ph.D., and because I tend to get discouraged when I run into programming challenges that I can’t handle quickly.

The whole thing has become more important to me, however, since one of my good friends (who posts in the comments occasionally as The Argonaut) is preparing to begin his career as a tenure-track professor.  He needs a solution, and rather soonish.  I’m not sure if I’ll be able to create something functional in the time period he’s got before he starts his job, so I thought I would try to cobble together a list of already-available technologies that I think are really useful, and can be installed today.

First of all, set up a Google Calendar.  Use it.  Post everything there, and share it with your lab.  I’ll repeat this - use it.  It’s easy to think of taking the time to list what you are doing on a calendar as an inconvenience and waste of time, but it’s invaluable (both for your own scheduling as well as your students).

Install some sort of version management system.  Trac + Subversion is a good way to go.  This sort of system is used very often in software development, but I think it has applicability to any project, including research projects.  The system is designed to assign and monitor workflow of a project - just think of it as a file folder of your progress, in every project going on in the lab.  Trac has a built-in Wiki, which you can use to store protocols and other lab-wide documents that you’d like to share.  You can use Subversion to get version control of your grants and papers, rather than dealing with endless iterations of new word documents.  It’s becoming more trendy to use a distributed version control system, so you might look at using Git as opposed to Subversion.  Both should integrate with Trac, although Git requires a plugin (makes sure to check out the entire trac-hacks site, as there are many useful plugins there).

If Trac seems too daunting, you can try out MediaWiki, the software that runs Wikipedia as well as OpenWetWare and many other great sites.  The version control isn’t quite as rigorous (you’re left looking at page edit histories), but it’s a bit more user-friendly.

So at this point you have a calendar and project management running.  This is a pretty solid base, and you’re blowing most labs out of the water as far as organization.  I would leverage the wiki functionality of Trac to build in some other things like inventory management as well.

The last thing you probably want is a public-facing website.  You have several options here, although a content management system (CMS) of some type is going to make life a lot easier.  If you just want a simple website, you can use blogging software such as Wordpress, or MovableType.  These are relatively easy to install, theme, and update with new content.  If you’re looking for something more powerful, you may consider the free and open-source Drupal.  It’s more complicated to use, but also has a lot more functionality.

If you can manage to get all of these running and convince your lab to use them, congratulations!  It will probably take some time to become familiar with using each of these systems, but for the most part they are accessible to novices.  The effort it takes will be well worth it.  Of course, it would be best if all of these functions lived under one roof, rather than split across 3 or 4 different software packages.  This is the goal of a LIMS, and I should probably GB2W on my pet project…