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.

Here is a short introduction video:

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

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…

Donna Wentorth has published an interview with Lorrie Lejeune (of OpenWetWare) over at the Science Commons blog.  It is interesting, and highlights the “non-standard” thought processes going on at OWW:

To paraphrase what we state on the OWW wiki, some users of OpenWetWare think that the best thing to happen would be if somebody “stole” your idea and finished the work before you. Then you could go work on another idea. Good researchers usually have more ideas than they have time to explore, and having more people exploring those ideas will in the end benefit your research.

I am really happy that OWW is around and attracting users (the interview cites approximately 4000). I think it’s a good project with laudable goals. As of now, I do think it’s a bit limited by being so wiki-centric. Wikis are great for certain content, and not so great for others. I’d like to see them implement some other technologies in order to improve site navigation/usability, as well as to add new and interesting features to the toolkit. This would probably require a major reorganization of the current site, however, and I’m not sure if it’s feasible at this time. My gut feeling is that when the site was started as a collaboration between two labs, it just wasn’t designed to be as scalable as it could be. This isn’t anyone’s fault, but it means that they might have to go through some growing pains in order to make the service more attractive to an even broader community.

I also found something of specific interest to me (and perhaps you) in the interview; a link to an open guide/beginning of a book on using Python to do science. If you need me, I’ll be reading it.

Via AiE&S, I found an article in the esteemed Chronicle of Higher Education discussing the prevalence of digital manipulation of figures in scientific articles. This is an issue of interest to be, because I’m something of an amateur digital manipulator myself.  For years I’ve taken part in online Photoshop contests, and even won small monetary prizes here and there for my efforts.  One of the reasons I do this (in addition to how much fun I have with it) is the potential for applying the skills I learn to my work.  Mostly by this I mean my web design hobby, but knowing your way around Photoshop really helps when making presentations or other science-related graphics.  The problem is that there is a very fine line between making something look nice and altering the scientific meaning.

Papers are starting to employ tools to look for digital tampering:

New tools, such as software developed by Mr. Farid, are helping journal editors detect manipulated images. But some researchers are concerned about this level of scrutiny, arguing that it could lead to false accusations and unnecessarily delay research.

I have to say I fall on the side of the “concerned researchers” here. In my experience, you tend to have two groups of people. There are those who understand image manipulation, its strengths and weaknesses, and when it can be appropriately implemented. Then there are others who don’t understand what’s going on and tend to think that if you even open your TIFF file in the program you’ve just sabotaged it’s scientific validity. I worry that we will end up with a situation of photoshop = bad, and that’s simply not true at all. As a matter of fact, the very description of the software being employed indicates that this is already the path we’re heading down:

The software looks for patterns in the digital code underlying an image. When files are opened and altered in Photoshop, for instance, codes are added that Mr. Farid’s software can detect.

I can hardly think of a single image I haven’t opened in such a program (I usually use The Gimp though).  Almost every figure needs at least to be cropped, have a label or two added, and saved out as different formats.  Does that mean every figure in my papers will be throwing up flags?

To be fair, it seems like the journals themselves are still taking a level hand for the most part:

So far the journal’s editors have identified 250 papers with questionable figures. Out of those, 25 were rejected because the editors determined the alterations affected the data’s interpretation.

10% rejection because of altered meaning seems to indicate that the vast majority of digital editing is not scientifically harmful.

And, as we so often see, Open Access may lend a hand in solving the problem:

One new check on science images, though, is the blogosphere. As more papers are published in open-access journals, an informal group of watchdogs has emerged online.

“There’s a lot of folks who in their idle moments just take a good look at some figures randomly,” says John E. Dahlberg, director of the division of investigative oversight at the Office of Research Integrity. “We get allegations almost weekly involving people picking up problems with figures in grant applications or papers.”

I’m not sure that I approve of the online witch-hunt oversight scenario this seems to set up, and this type of method won’t detect image tampering prior to publication (or at least online availability).

It’s a sticky problem, to be sure.  It’s clear that image manipulation programs allow for data falsification that is almost indetectable to the human eye, especially when done by an expert in the use of the software.  These same programs (and largely identical usage of the programs) can pull new scientific information out of otherwise useless images.  In my opinion, specific alterations should be mentioned in the figure captions.  I do this when I present figures at group meeting, for instance noting that I’ve adjusted contrast for easier viewing.  I wouldn’t mind in these cases a requirement to submit both images to the journal, so that they can judge for themselves the validity of the manipulation.  I just don’t want scientist to be discredited simply because they are trying to, with the best of intentions, improve communication of their findings.

When Mrs. PA successfully defended her thesis, I thought it might finally light a fire under me to push through whatever I needed to in order to finish up here so we could get on with our lives.  Instead, I’ve found myself in a more or less continuous state of ennui.  I have no motivation or interest to work on my thesis project.  Partly it’s because I don’t really believe that it will ever generate results, and therefore I don’t really see the point of even trying.  I know that this sort of defeatism is not unusual among graduate students, but I’m having a hard time yanking myself out of it.  I can’t even manage to use the reasoning “just finish it and you can get out of here” as enough impetus to apply myself.

On some level I feel like my reserve of “well it didn’t work that time, let’s tweak the parameters and try again” has just run out.  The “reward” from a scientific standpoint is more or less the same whether I actually do the experiments or not, because the experiments never work.

I think this is made worse by my particular situation.  Most graduate students at this stage would have enough data to just sort of drag themselves across the finish line.  Since I had to change projects, I’m left sitting in the middle of a pile of half-completed projects and seemingly intractable problems with each of them.

I really wish I could think of a way to snap myself out of this funk.  I know that it’s not helpful in any way.

When I started out as a graduate student, in the dark distant past, I chose to work on a protein that we didn’t yet have in our lab.  One of my first goals was to acquire the gene and clone it into our expression system.  After reading some literature, I found one group who had mentioned getting the gene from another, and so I thought I had my opportunity.  I emailed the group who is on record as having supplied it and asked for the gene.  They replied “sure, no problem”; I waited.  Months.  Occasionally I would send off another email, but I didn’t want to seem too pushy.  They were doing me a favor, right?  In the meantime I worked with the mouse version of the gene.

Finally, the envelope came with the gene.  They didn’t provide any real information, but I went ahead and designed my PCR primers and got to work cloning it.  For months.  For some reason, my cloning reactions just weren’t working really well.  I struggled with PCR, digestions, ligations; it seemed like every step of the way was bogged down for some reason.  Eventually I managed to wrangle the gene into a vector and get a good sequence read.  At this point it became abundantly clear why I had been having so much trouble - the end of the gene was missing.  It turns out the lab I had gotten it from had used an enzyme in their own cloning that clipped the sequence short.

In retrospect, I probably should have figured this out much sooner.  The clues were all there, but as a young graduate student I was sure that an established lab would send me the proper gene, and I was just doing something wrong.

It turns out that around this time, another graduate student mentioned that they had bought the gene for their protein for something like $80 (the fee for this particular repository has since been raised to $120), which is just about as close to free as you could hope for.  It turned out that the same place carried my gene.  Of course I bought it, and within weeks my cloning was successful.

When people like John Wilbanks talk about developing these repositories, this is the type of situation they are looking to improve.  The old system, of asking a “favor”, little to no verification, and no real motivation for expediency or quality control is really shockingly bad.  It’s amazing to me that it’s taken this long to sort of start generating significant interest in validated, standardized, open repositories.  The clones, cell lines, mice, etc that we generate in great quantities need a better method of sharing and distribution than some antiquated version of quid pro quo.

This weekend, Mrs. PA and I went out to dinner in town (where, coincidentally, I had one of the best beers I’ve ever tasted).  During the meal, we had a wide-ranging conversation on the difficulties of running a successful lab group.  The training you get as an undergraduate, graduate students, and post-doc does little to prepare you for many of the duties you undertake as a professor.  Teaching, grant-writing, and personnel management are areas that you spend a lot of time working in as a professor but likely have little to no exposure to prior to this position.  Indeed, the level of multitasking it takes in order to be effective as a Principal Investigator at a major research institution is rather astounding.  What tends to happen, in many cases, is that some facet of the position is left to its own devices.  Often this is the personnel management side of things.

We realized that there is already a position, prevalent in industry, which could help ease the burden on professors - the “Principal/Senior Scientist” job.  I did an internship at GiantPharm one summer, and worked in a small group.  There was a leader of the group, but his office was actually in another building on a hallway with other group leaders.  My interaction with him was sort of minimal.  I did, however, spend a lot of time talking to my immediate supervisor.  He was a long-time employee, Ph.D., and incredibly intelligent.  If I was stuck on a task or needed further direction, his office was always open.  Since he was doing research of his own, it was easy to chat with him informally about the work and hash out new ideas.  If I were a professor, I’d love to have someone like this in the lab.

In academia, there are sometimes “Research Scientists” working in a group.  In my experience these tend to be glorified (more or less permanent) post-docs.  They are focused on their own project, and could often not care less about mentoring graduate students or ensuring that the lab is running smoothly (as long as it doesn’t significantly impede their work they are ambivalent).  It’s worth noting that post-docs themselves frequently have a similar attitude.

I think that there is some room here.  Why not delegate some of the roles typically shouldered by a single P.I.?  For instance, the P.I. can focus on “the big picture” (where is the research going, what are our major findings, what is going on in the community), getting money, and their teaching duties.  In the meantime, you can bring in a scientist to be the “research lead”.  By this I mean the person who is in the lab working on a project, but who also oversees the day-to-day activities.  If a graduate student is having trouble getting their affinity column to work, they can go to the Scientist.  This person could be responsible for some of the management of the lab as well - if a student isn’t showing up to work, they can talk to them and/or elevate the situation to the P.I.

Now, I’m not a professor.  I’m sure there are some issues with this plan (or else why wouldn’t it be implemented).  Some that come to mind:

• Funding - you are going to have to pay this Scientist more than you pay a post-doc.  $50,000/yr?  Somewhere in that ballpark is my guess.  It’s roughly equivalent to one post-doc plus an additional graduate student.  I don’t think that this is too onerous.
• Appearance of laziness - Will other faculty members think that you are unable to “handle” being a professor if you have to hire someone else to share the workload?  I’m not really sure about the answer here, but I’d hope this could be minimized.
• What about the Scientist’s career? Won’t they get unhappy and leave?  In my perfect world, the candidate would be someone who has completed their Ph.D. but is uninterested in some of the aspects of joining a faculty.  Perhaps they just don’t like writing grants and want to work at the bench, but aren’t fond of industrial work either.  There are people out there like this, trust me.  They would be thrilled to have a position like the one I’m talking about here.

I’m sure there are other problems, and I hope you’ll bring them up in the comments.  If you are in a faculty-like position, I’d really like to hear your thoughts on this.  Do you see the utility of hiring such a researcher?  Why is it not done?

Those not intimately involved in science sometimes think that a given researcher is fully versed in the entire body of knowledge their field has ever produced.  For instance, since I am a biochemist, I should be able to perform MacGyver-esque transformations of household products into psychedelic drugs at a moment’s notice.  Also, since I’m a biochemist, I am fully familiar with the migratory patterns of african swallows.  Of course those of us who are involved with science know that this is definitely not the way of things.  In truth, science is incredibly specialized, almost to the point of balkanization.  Even when I go to our weekly biochemistry seminar, at times it can be a stretch to wrap my head around anything deeper than a basic understanding of the work being presented.

Of course, the reasoning for this is that the things we study are remarkably complex, and it’s often necessary to immerse yourself deep into the intricacies of a given system in order to make advances in understanding.

The problem that I have with this specialization at the moment is that it makes finding a job pretty tough.  It’s abundantly clear from most postings that the hiring party has a very specific candidate in mind that has a very particular skillset matching the duties they will be expected to perform.  As a job candidate, this makes me feel like I’m locked into doing the exact same types of experiments on the same systems indefinitely.

Professors seem to have some ability to break out, but it’s still tough.  In some ways, they are even more restricted - funding agencies aren’t very likely to give someone money to do something that they’ve never done before.  On the other hand, once the money is in hand, the investigator has more leeway to use whatever tools are necessary (including those that they might not have a history of using before).

My question is to those who are in science - how do you deal with this in finding jobs?  Is this a problem in your field?  If you are in the position of hiring, do you always look for candidates that will be ready to run your experiments on day 1 due to prior experience, or do you just look for the best overall candidate, even if they may need some training?

In the last post, I went over some of the POV-Ray basics. The toughest part of actually using POV-Ray to render figures of proteins is importing the structure into the rendering package - the complex geometry of the macromolecule has to be translated to the system of simple objects understood by POV-Ray.

As I was looking into some software packages that can output .pov files, I came across another raytracing program called Tachyon which is included (sort of) in the latest version of VMD.  The example images made using the ambient occlusion lighting capability of Tachyon made my jaw hit the floor.  Instead of babbling on about ways to get POV-Ray to play nice, I’ll go over how to get and use VMD/Tachyon.
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