Thursday, January 10, 2013

Running Bundler on Ubuntu 12.04 64-bit

This post is mostly a note to myself so that I remember how to do this next time I upgrade or reinstall my system. But, perhaps it will be of use to others.

The program Bundler is one of a suite of programs that are very useful for photogrammetry on the desktop computer or laptop. Being a devoted Linux user, it's important to me to be able to run my software where and how I want it. Unfortunately, Bundler does not play well in 64-bit Linux (I am running Ubuntu 12.04-64 right now, in support of processing large data sets), generating segmentation faults upon attempts to execute. This is a fairly well-known problem (I found three or four pages mentioning this), but it can be tough to track down the solution. Fortunately, I found it here. What follows is essentially a short list of what I did to fix the error (with a general description of how I set up my system).

  • Set up BundlerTools (a package including Bundler and other programs necessary for photogrammetry), using scripts at the BundlerTools website. I installed it into my home folder ("home/username/BundlerTools").
  • Per the directions here, I installed ia32-libs and liblapack3gf:i386. The first one was already installed, just as a note. Code was:
    • sudo apt-get install ia32-libs
    • sudo apt-get install liblapack3gf:i386
  • Then, following these directions, I copied (found in BundlerTools/lib) to my /usr/lib folder, and made the file executable. Commands were:
    • sudo cp /home/username/BundlerTools/bin/ /usr/lib/
    • sudo chmod 755 /usr/lib/
  • And that did the trick!
To run Bundler, I navigate to the directory where I have all of my images. Then, I use the command:
  • /home/username/BundlerTools/ --resize-to 200
    • [or resize to whatever size you want - I set it small for a very quick test run; thus, it could be 200, 1200, 2400, 6000, or whatever size is desired]

Wednesday, November 28, 2012

Mostly moving. . .

Along with Sarah Werning and Shaena Montanari, I have a new blog over at the PLOS blogs network. We're The Integrative Paleontologists - go check it out! For the most part, I'm going to be moving my activity over that-away from here on out. . .the occasional post outside the domain of TIPs will still land here, though.

Wednesday, November 14, 2012

The 2012 Paleo Project Challenge

Everyone has an unfinished project. Most of us have at least a half dozen. Those partly finished manuscripts, paintings, data sets, and preparation projects. Oh, we started out with good intentions. Maybe we even poured a productive week into it. But then, the honeymoon glow faded. Something else got in the way. The field season, or teaching duties, or another more pressing project, or a grant deadline, or just plain old life circumstances, interrupted us.

Luckily, all of that work doesn't have to go to waste. Why not finish up that project? What are you waiting for? Heck, what am I waiting for?

Regular readers of this blog may remember that Dave Hone and I instituted the "Paleo Paper Challenge" (PPC) back in 2009, in an effort to shame all of us into cleaning our (figurative) research plate. We had pretty remarkable success - although not everyone (including ourselves) were able to finish everything we wanted to, most folks made some major progress. Some papers even made it into publication, in venues like Journal of Vertebrate Paleontology and PLOS ONE. Not too shabby.

Not wanting to rest on our laurels, it's time to kick things off for 2012. As before, Dave and I want to pursue a "bigger tent" approach. Why limit the PPC to just academic research? Let's open it up to all paleo enthusiasts! Preparators, artists, researchers, bloggers. . .after all, paleontology does not survive on publication alone. Thus, we are happy to kick off:

The Paleo Project Challenge
Do you have a paper that just needs the finishing touches before it heads off to publication? Is there some half-prepped fossil sitting in a cabinet in the lab? Have you started and finished a big blog post half a dozen times, but never pulled the trigger? Is that masterpiece rendering of a liveTylosaurus still sitting on the easel? Stop sitting around, and finish it!

Here are the rules:
1) Indicate your willingness to participate in the Paleo Project Challenge (PPC) in the blog comment section. You should at a minimum indicate the category it falls under (paper, blog, art, or whatever), and the project (if you can - we totally understand the need for secrecy in some cases!).
2) Do the work! You have until December 31, 2012. Remember, we're all watching.
3) Once you're done, celebrate!

Let's get to work!

My Commitments
1) Write up the ODP results. [yes, for real this time!]

What are you going to do? Chime in below in the comments section!

Note: This post is largely recycled from my post back in 2010. In the interest of laziness--which really is the impetus behind the PPC--that 2010 post is given with only slight modification.

Wednesday, June 13, 2012

PeerJ—What Does It Mean for Paleontology?

For those following open access issues, the arrival of PeerJ has been hotly anticipated (see this link round-up). We all knew Pete Binfield--someone with years of experience in academic publishing and, until recently, publisher of PLoS ONE--was associated with the project, so it wasn't likely to be a half-baked scheme. The big day of announcement finally arrived yesterday, and things look even more innovative than expected. So, what does this mean for us paleontologists?

First, a little background on PeerJ. It's a new journal, falling squarely in the online and open access (CC-BY) categories. Editorial criteria are similar to those for PLoS ONE (scientific and methodological soundness count; perceived impact or splashiness don't). All of this is pretty typical; but the rest ain't.

One of the most common fears of open access publishing is that it can cost a lot of money for authors, a particularly big concern in an underfunded field like paleontology. Free open access journals (like Palaeontologia Electronica) and fee waivers (as for PLoS ONE) can fill the gaps, but most mandatory open access fees are otherwise unaffordable for the typical paleontology lab budget (assuming there is a budget for the lab). PeerJ attempts to fill in this gap, while paying for the costs of open access. Things get pretty interesting as a result.

The conventional open access model is to pay per publication; once a paper is accepted, you pay the $2,000 or $1,350 or whatever to subsidize production costs. PeerJ front-loads this in a unique way; each author pays a one-time membership fee, which is then good for life! Depending on what category of membership you buy, you then can publish one, two, or an unlimited number of publications yearly. These lifetime membership fees are quite reasonable, too. They start at $99, and culminate at $259 (fees go up slightly after September 1). Fee waivers are available for those in developing countries.

So what's the catch? Members are expected to review one paper yearly (either as a full-blown peer reviewer, or as a post-publication commenter). Additionally, each author on a paper (up to the twelfth author) must be a member. How does that translate financially? Let's say I want to publish a paper, and have three co-authors. Assuming each of us is only publishing in PeerJ once a year, that translates to $99 per person. With four total authors, the cost is $396. If one of my co-authors and I later publish another paper, the cost for that one is $0. Same cost for the third paper. That's three open access articles for $132 each. This is definitely an encouragement to continue publishing with PeerJ.

Other good things
PeerJ is pretty savvy, and has covered its electronic bases (see their FAQ). The journal will be edited by an independent academic editorial board, an author's membership category doesn't factor into decisions, and content is archived via CLOCKSS. The journal has plans to get an impact factor (which will take three years) and to get indexed in the major services. These are all carefully thought-out, and within (or exceeding) professional standards for publishing.

As another incentive, PeerJ offers a preprint service (free if you only post one a year). Physicists have arXiv, where they can post unpublished manuscripts for community commentary. However, there isn't really such a central repository for the biosciences (especially since the demise of Nature Precedings). Thus, PeerJ is filling a community need (even if we paleontologists don't yet realize the advantages of preprints).

What's needed now?
This journal is surely within the realm of interest for paleontologists, and those of us who support open access publishing will follow it pretty closely. Because the journal has yet to officially launch, some details are still hazy. In order to be of maximum use to paleontologists, I hope to see the following things (in roughly ascending order of difficulty):
  • Clear guidelines for nomenclatural acts. These should follow recommendations from the ICZN and ensure that any new species erected within PeerJ are valid.
  • A clearly designed, paleontology-specific ethics policy. Standards should be in line with those used by organizations such as the Paleontological Society and Society of Vertebrate Paleontology, and ideally would mandate that all specimens discussed in PeerJ are reposited in appropriate institutions. The last thing the journal needs is to be filled with papers on illegal Chinese specimens or thinly-veiled advertisements for fossils on the commercial market.
  • A strong editorial board with a respected paleontologist (or paleontologists). In order to get community buy-in, we need to see that the person who handles our manuscripts is qualified, trustworthy, and fair. Paleontologists are also rather skittish; we won't publish in a new venue unless someone else tests the waters first (judging by the pattern in PLoS ONE).
  • Strong impact factor and community perception. We all hate impact factors (or at least say we do, right before hitting the submit button on that article for Nature which we know will be rejected but hey we have to try anyhow just in case), but it's sadly a reality for those who want to get jobs and grants. Early-career scientists are likely to be a little wary of submitting their very top stuff to PeerJ, at least until the journal is a little more established. It sucks for the researchers and for the journal, but that's just the way it is. PLoS ONE faced a similar hurdle (and still does, to some degree), and only time can defeat it. Positive word-of-mouth will also help immensely.
Given the experience of the staff at PeerJ with academic publishing, I have all confidence that these issues will be addressed when the formal editorial guidelines are announced. Open access is changing the way paleontologists do business; whether directly or by influencing other publishers, PeerJ will surely push that change a little more in the right direction.

Thursday, April 26, 2012

A Paleontology-Specific Impact Factor for PLoS ONE

The threads at SV-POW! are hopping right now, particularly with one commenting on open access in Journal of Vertebrate Paleontology. One question that came up is how much, if at all, the impact factor of PLoS ONE (4.411 for 2010) indicates the reach of paleontology papers in that journal. In other words, if PLoS ONE just published paleontology papers, what would its IF be?

Naturally, I had to calculate it out. I used the standard IF formula, and looked just at citations in 2010 for papers published in 2008 and 2009. Citation counts were derived from Web of Science, which is linked to from each individual article at the PLoS ONE website. Articles under consideration from 2008 and 2009 were harvested from the PLoS ONE Paleontology Collection; one or two articles in there were only tangentially paleontological, but I kept them in anyhow just for consistency.

I calculated a "paleontology IF" of 3.317 for 2010 - a little lower than 4.411 for the overall journal but still higher than in other more field-specific publications. So, not too shabby.

This omits the issue of whether or not impact factors are worth anything, but I won't delve into that here. Love it or loathe it, we scientists still like to talk about IF!

Wednesday, April 18, 2012

Introducing the Dental Microwear Image Library

Dental microwear, seen in the tiny pits and scratches on a tooth, provides lots of detailed data for inferring diet and chewing behavior in animals. Analyses are often conducted by digitizing highly magnified images of the tooth surface and counting up and classifying the various microscopic features. Animals with a certain percentage of pits and scratches may have browsing habits, whereas those with another profile may be grazers. By measuring extant animals with known diet, we can (hopefully) infer the diet of extinct animals.

Dental microwear; modified from figure 3 in Mihlbachler et al., 2012
In this age of increasingly open science, microwear studies can be problematic. A cornerstone of science is reproducibility - yet, inter-observer variation and error can greatly affect measured data. Furthermore, one study alone may generate dozens or hundreds of images. Even if you wanted to re-analyze teeth, it's pretty tough - how could you get access to the necessary images? Ideally, we want a world where anyone can access the raw image data, make their own observations, double-check published analyses, and add new data for comparison.

Thus, a new project - called the Dental Microwear Image Library, or DMIL - may change things. Assembled by Brian Lee Beatty and Matthew Mihlbachler, the website aims to become a clearinghouse for dental microwear images. This will allow greater standardization of analyses and hopefully better interpretations of paleoecology and diet for extinct organisms and modern organisms. The first data (from a recent paper in Paleontologia Electronica) are now posted, along with many other data sets.

Brian Lee Beatty (who blogs at The Aquatic Amniote and tweets as @Vanderhoofius) was kind enough to answer a few questions about the DMIL. Thanks, Brian!

Was there a particular moment or incident that inspired you to build the DMIL? If so, what was it?
As we set out to test and develop the method that Nikos Solounias and Gina Semprebon started, we found ourselves frustrated by not only the lack of information on methods that were given in most microwear papers, but also the inability for people to check their work. Interobserver error is a major cause of problems for microwear, and the only way for anyone to be aware of those differences is if they compare interpretations of microwear surfaces, not just their numbers on a spreadsheet. The DMIL was the only possible solution to the need to share such images.

How has community response been so far? Is there any particular type of skepticism that you're working to overcome?
The DMIL hasn't yet come up against skepticism, but our first paper on this method that uses it has.

What license, if any, are the data housed under? Or is it on a case-by-case basis?
There is no license for the data. We want it to be completely open-access and simply available.

How would you envision the DMIL 10 years from now? What goals might you have for the long-term?
We hope it will be a place that people can use to learn how to use the methods we are continuing to develop. I most sincerely hope that it will not only be home to our own data, but also be a place for others to deposit their data using similar methods so that more work of this sort is available in a similar, comparable format.
Authors of the recent paper in PE, along with a research assistant. Photos courtesy of Brian Lee Beatty.
For more information, check out the DMIL, or read the recent paper (open access) about the work.

Mihlbachler, Matthew C., Beatty, Brian L., Caldera-Siu, Angela, Chan, Doris, and Lee, Richard, 2012. Error rates and observer bias in dental microwear analysis using light microscopy. Palaeontologia Electronica Vol. 15, Issue 1;12A,22p.

Thursday, April 5, 2012

Open Access in the UK - Comment Now!

The Research Councils UK (an umbrella organization overseeing much of the public scientific funding in that country, as well as funding for the arts and other worthy ventures) is soliciting comments on a new open access policy [PDF]. No matter what your opinion on open access, please comment. Mike Taylor, writing at SV-POW!, has further information and instructions.

Even if you don't live in the UK, it is worth letting the Research Councils know how you feel about the policy. Why? Because science (and scientific publishing) is inherently an international endeavo(u)r. I collaborate with colleagues in the UK all of the time, and many of the best papers I read these days have their origin across the pond. But, as with most scientific literature, access sometimes ain't easy. A more open scientific literature helps all of us, and each accessible paper raises the country's profile in the scientific community. Funding agencies always want more bang for their buck (or pound), and improving accessibility is one great way to do that.

So, drop a line to by April 10 and use the subject "Open Access Feedback." Even a short sentence of support will do. Or three short sentences, as I did (basically using the argument in the paragraph above). Make your voice heard!