Protichnoctem

New post: Thematic focus and other considerations in science blogging

noreply@blogger.com (Matt BK) — Thu, 03 Nov 2011 16:27:00 +0000

New post over where everything will be someday: Thematic focus and other considerations in science blogging.

Wanted: Geologic maps (formation contacts) of South America countries, ideally for use in GIS

noreply@blogger.com (Matt BK) — Fri, 12 Aug 2011 17:43:00 +0000

Here's a good ol' plea for help from the scientific community. As my questions to "the scientific community" via Academia.edu have gone unnoticed, I'm posting this out here to see if anyone else searching for the same thing has had any luck.

I'm building a GIS (geographic information system) model to determine the possible biogeographic districbution of a genus through time. What I need for this, since the fossils are from South America, is a good geologic map, either of most of the continent or of the countries of Brazil, Argentina, Ecuador, and Peru. Hunting around online hasn't shown me anything that I want to shell out a bunch of money for, site unseen, and I'm honestly trying to avoid having to scan paper maps and register them (additionally, I haven't been able to access our worldwide collection of paper geologic maps recently).

1:500,000 or 1:100,000 would be great, but I'd even take 1:1,000,000 at this point. I need something with formational contacts so I can plot possible distributions.

So that's the challenge of the day: have any geologists in South America discovered a good source for this type of material? Would you be willing to share or trade?

Snapshot: Crossing at DeMers Ave/S. Columbia Rd Interchange

noreply@blogger.com (Matt BK) — Tue, 08 Mar 2011 19:53:00 +0000

Trying to keep the words to a minimum, but here is an intersection in Grand Forks that I find particularly worrisome, especially for people to whom cycling/commuting is new. This crossing is the primary avenue between the University of North Dakota (to the north) and points to the southeast. The protected sidewalk on the S. Columbia Rd. overpass is used by riders because the traffic on the often exceeds 35 mph and people are not used to cyclists. See map at bottom of post.

Most problematic: drivers merging onto the northbound onramp and off the southbound offramp. They do not expect to stop because all they have is a yield sign. Drivers merging on are especially dangerous because they have little need to yield most of the time, and see little reason in signaling.

Suggested solution: Unsure. Would be nice to straighten out the crossing (will have to take a photo now that it's snowed again) to make it easier for people on the path, but something needs to be done to prevent merging drivers from running into riders and drivers stopped at the red light from stopping in front of the pedestrian cutout ramps (on the crosswalk).

View Larger Map

Total time on this post: 46 minutes.

Need a geologic time scale? Use TimeScale Creator!

noreply@blogger.com (Matt BK) — Sun, 06 Mar 2011 17:19:00 +0000

I didn't know this existed until today, so I'll give it a little promotion. I was in the midst of building my own in Illustrator by tracing the official 2009 timescale from stratigraphy.org (the PDF has font issues on my computer, apparently).
TimeScale Creator
Overview

We'll see how it works for my 2011 UND Scholarly Forum poster. Wish me luck.

EDIT: Had some problems saving the image as a PDF in Mac OS 10.6.6 (Snow Leopard), but saving as SVG works fine. If a save seems to fail, you need to restart the program and try again. Using version 4.2.5.

Trying to Focus on Specimen Databasing

noreply@blogger.com (Matt BK) — Fri, 21 Jan 2011 18:30:00 +0000

This post will explore some fairly specific topics, but I hope the thought process will be instructional (or inspiring) to others. Additionally I think it's worthwhile to talk about the concepts of specimen/biological collection database management with reference to funding, not schemas and platforms.

At the UND Department of Geology and Geological Engineering, a small number of us have been pursuing an overall upgrade of the paleontological specimen and lithotype collection consisting of improved facilities (compactor cabinets) and a comprehensive online database. We've applied for funding from NSF and been denied twice, and the project would be dead in the water except for the quarter-time assistantship I'm receiving from the Dean's office at the School of Engineering and Mines. Development has been slow, mostly due to the conversion between the existing databases (stored as flat text files) and the online system (I will not mention the name of the new system because events today have made me question (again) the cost/benefit ratio of utilizing it), and I've been importing locality data so we can use the new system to analyze locality distribution, among other things.

The question today is how to proceed. As useful as locality data are to paleontological and geological researchers, locality information is, at its core, supplementary to the specimens themselves. (I'll avoid an argument right here: I believe that locality data are essential to proper context, and I'm not advocating the dissociation of these data from specimens.) Specimens are the core of the paleontological sciences, and it is from specimens and their assigned taxonomic identities that researchers work toward understanding past life. Rather than browsing locality lists and then looking at specimens, given a database most researchers will search by taxon or in special cases by specimen number, and then they will look at the associated locality data. In my opinion, we've been doing it wrong.

The above point regards usability, and I promised to talk about funding issues, so here we go: in order for such an online database (and more importantly, the effort to digitize specimen data and provide specimen imagery) to keep getting funding, it needs to be usable so it will be used! That's the whole point. If the Dean (or any other UND administrator) wants to put us on the map for having a world-class collection, we need to get the data out there that people want, we need to tell them about it, and we need to encourage them to use it. From the administration's perspective, numbers are going to determine how successful we are: number of unique visitors the online database gets every year, number of publications that reference specimens held in our collections, and number of researchers who visit or request material loans.

What can I do today that will improve our chances? In my opinion, we need to improve usability by others before we can improve usability by ourselves. This means a focus on specimen-data entry, the postponement of certain analytical capabilities we (as UND researchers) would like, and beginning with those specimens referenced in peer-reviewed articles, dissertations, and theses. These specimens have already gotten the most attention and they are likely to get more attention in the future because of their "published" status. The associated material can come next, and then we can start adding data systematically. At this point, to show that this is possible and that it shows our research collections in a good light, we need to get the bare bones online first and follow with everything else later.

That's what I think, and what I will discuss with others here later today. Has anyone else come across such a crux of funding issues? How about with specimen collections that are even less sexy than ours (which are primarily freshwater mollusks, and are pretty darn sexy in my opinion)? Am I on the right track, or should we back this train up again?

Things It Would Be Great To See Finished (part 1) - Bicycle Routing Map for GFK

noreply@blogger.com (Matt BK) — Sun, 09 Jan 2011 22:45:00 +0000

I'm always trying to organize myself a little bit more. Unfortunately, this means not being able to take the time to do (all by myself) everything I think would be totally awesome.

Excuse me while I take my pizza out of the oven.

The first of the many things I would like to highlight is my idea for an online bicycle routing map for the cities of Grand Forks, ND and East Grand Forks, MN. Obviously, these are small towns and don't warrant the attention of people who like to develop maps on a large scale, but since I'm here and want to encourage people to ride more, I'd like to see it happen. This idea stems from my Advanced GIS class at the University of North Dakota, during which I built an (offline) routing map that integrated the streets, paths, and bike lanes to try to study specific routing problems in the city.

I discovered (last spring semester it was) that the mapping service Cloudmade was utilizing Open Street Map to do similar things for projects such as Ride the City. I began adding things via GPS tracks towards the end of the summer (I spent most of the spring and summer in a wheelchair/on crutches), but have not had time recently to add any more or work on the specific details. It would be great if anyone else in the area was interested in collaborating (competing?) on making OSM as reflective of the real-world as possible.

Not only this, but I've constructed an example of what the interface could do, with some tweaking. See the example here, [seems not to work in Opera 11, hmm] and remember that I'm not responsible if you get lost. Specifically, I'm not sure how the routing algorithm works, how it weights streets, and how it can be customized. It would be great if someone could help me with this or explain it to me. The link above has a list of project goals.

The point? For anyone who is not a bicycle commuter, even in a city as small as Grand Forks, the prospect of getting between points A and B is a daunting one. You need to deal with traffic, you need to look at intersections a certain way, and you may need to bend the law (or think you need to) in order to get where you are going (to follow a sidewalk under an underpass, for example). A routing map specifically aimed at cyclists and took into account some of the oddities of this particular city ("mistakes in planning", let's say) would make this step of commuting a little bit easier and maybe help people make it farther than down the block.

I'm open to questions, comments, and offers of help (or desires to take over the project completely). I don't know of a similar project in the works for this area.

Tell Abstract Authors You Love Them

noreply@blogger.com (Matt BK) — Fri, 17 Dec 2010 18:00:00 +0000

Abstracts, posters, meeting presentations: great for organizing your thoughts, great for meeting new people, lousy for getting you motivated. A typical scenario: you've just finished a poster at the last minute, had it printed minutes before you were due to leave for your conference, gone to the conference, saw lots of talks, got lots of new ideas, and then had to deal with all the stress of coming back to "real life" and all the work that piled up while you were away. Seems like a perfect time to rest on your laurels and let that poster ride a little longer (after all, you really did put a lot of effort into it, and it came out generally okay, right?).

There are those who are extrmely driven, seem to have enough time to do everything they set out to do, and even complete the Paleo Project Challenge every year. Then, there are the rest of us. Just a reminder during this holiday of seasons that for every ounce of inspiration you are lacking to finish things up on that particular project that's been sitting around, data-heavy, for a few years and needs to be shaped up into manuscript form, there are probably dozens of people in your field who feel the same way. Why not give them a bit of extra encouragement for the coming year?

So, my own challenge to keep the science flowing: if you come across an abstract in your research that seems promising but has no later published version, especially if you aren't acquainted with the author, drop them a friendly line. Tell them how much you appreciated the effort and that you're waiting for the paper. Let them know you'd love to see the data in print. If you take five minutes of your time doing this, maybe we'll all get the benefit--plus, who doesn't like being praised for work they had abandoned for the assumption of lack of interest?

Clever abstract artists may find a way to monetize this, if the data are interesting enough. With a little PayPal encouragement, who knows what can be accomplished?

Looking for Inspiration in the End of a Project

noreply@blogger.com (Matt BK) — Wed, 15 Dec 2010 18:50:00 +0000

It's the time of year again where I get a break from classes and from being in North Dakota in general, and get to go visit the folks for a few weeks and get some down time. "Down time" being, for a graduate student, the opportunity to get some serious work done without the distractions of classes, advisors, people down the hall, etc.

One of the projects I want to get mostly completed by the time I return in January is to produce two graphics based on literature and museum data concerning my family-level taxon of study. The first of these will be a range chart of the fossil and modern genera (if not species...we'll see), the second a map showing where all of these taxa can be found. To the commonfolk (i.e., anyone who has never tried this before) this might seem easy, but it's really going to take a lot of digging through old papers, searching PDFs, and racking up a heck of a list for interlibrary loan next semester. I rediscovered earlier this week that although there may be a lot of information out there on my taxon, some authors didn't do the best job of organizing what they knew.

Now, you might ask me why I want to use a great deal of my "break" time to do research. The first reason is that I would like to graduate somewhat soon, and the time for, well, wasting time is over. The second reason is something I had to come up with myself for motivational purposes: I want to help people understand things, and to do that I need to be able to make good graphics.

"Infographics" have been the hot new thing for a couple years now, and Tufte will tell you over and over again that you need to include what data are needed and eliminate the stuff that doesn't matter. I would also argue that things need to be aesthetically pleasing to be educational, something to which I attribute the use of such soothing colors in introductory textbook diagrams. The point I am trying to make is that I need practice in this area, and I might as well practice now, at the beginning of my dissertation, than at the end when all I will want to do is hand-scribble a diagram, scan it, and call it good enough to hand in.

Optimally, my goal is to make these figures (my range diagram and global distribution map) not only good enough to include in a peer-reviewed journal article but good enough to print out as posters and hang on the wall! This is the goal toward which I am striving: I want someone in a similar research area to be able to use my work as a visual reference, and I want someone who has no clue about my research area to be able to look at it and say "oh yeah, I see how this can be useful." For a great example, see the "Unionoida cum Grano Salis" poster from the Mussel Project.

Goals like "aesthetically pleasing" and "understandable" are intangible and hard to quantify, but that's also not the entire point--sure, I'll be happy to get as close as I can, but my real reason is the second motivation I listed above. If I can picture the future where I'm done with the figures, they look good, and I publish them so others can use them, it makes the drudgery of collating occurrence data that much more bearable--and if that is what gets good science done, let's do it.

First winter training ride 2010/2011

noreply@blogger.com (Matt BK) — Mon, 29 Nov 2010 02:11:00 +0000

I just got back a while ago (:-P) from my first "official" training ride of the winter season. It snowed the weekend before Thanksgiving, but I was returning from the Smithsonian and missed out on the freshie powder, then was busy all week aside from commuting. This evening I finished what I was doing in time to get some real training in.

(All You Haters Stud My Tires)

The temperature when I returned (a little before 7 PM) was 17 F (-8 C), so it's balmy by Grand Forks standards (or it will be by March!). There was an 11 MPH (17 km/hr) breeze from the north, but it definitely (to my out-of-shape body) felt like a lot more than that. I did the pedestrian bridge loop (to north bridge to south bridge and back) on my mountain bike, following the Greenway path. The path is nicely plowed for the most part, so much so that once my light died I could still see well enough to not endo over any piles of snow kicked up by the snowmobiles (the clear sky may have helped in this regard; nothing like following a black ribbon through a white wilderness).

As I said, the wind being from the north I got a bit of a workout, followed by a long period of speed, followed by my realization that I had forgotten how much of a workout I'd had at first, once I got to turn back into the wind. The weather was nice, and I think I dressed appropriately, which is always something of a challenge for me. I tend to run hot, which up until recently has resulted in me winding up drenched by the time I get to school since I wear a down jacket. I finally bought a clip-on pannier/shopping bag that I can throw my messenger bag into and not have to carry it on my back, so it's much easier to regulate my temperature while commuting.

Anyway, back to tonight: the image below shows what I was wearing, with a list in case people are interested. I was warm enough with the tailwind, but the headwind sections were somewhat chilly on the knees and arms. I tried out vapor barriers for my feet for the first time since I have chronically cold toes in the winter; they may have worked, or it may have been too warm for me to feel the difference. Any time I can step off the bike and not feel like I'm standing on two frozen lumps of flesh is a good day.

(All You Haters Wash My Shorts)

"RED" snowboarding helmet (from Play It Again Sports)
Smith goggles and neckwarmer (from Ali!)
bike shorts from inside baggy mtb shorts
Teko socks from END-AR 2009
plastic bags from phonebooks
cheap Nike mtb shoes
wool mittens (knitted by Mum) inside Swedish mitts from Midwest Mountaineering
North Face fleece (from Ali's parents)
Cloudveil pants (from Ali)
Under Armour coldgear shirt (from a guy I ran with at SLU)

My other equipment could use an upgrade (maybe someone could by me this?), especially my front lighting system. I bought this light when I first got my mountain bike in eighth grade (thankfully the frame has proven large enough!). It runs a single incandescent bulb, I have no idea what the candlepower is, and uses 4 D batteries. It also seems to be having a lot of trouble in the cold this year :-(

(All You Haters Velcro My Batteries)

Since I'm trying to limit the whole blog post production time (BPPT) to a half-hour or less, I'll only throw up one more photo of my new camera sweater. I'm not sure it works to keep things warm so the batteries last longer, but my buddy Mario (now Cat 2 road, congrats!) uses a similar setup for his power meter, and considering he's an electrical engineer, it can't have deleterious effects. I've been taking some decent winter commuting videos, so hopefully they'll make it up eventually.

(All You Haters Sweater My Camera)

Happy riding!

Ride distance: 16.2 km
Ride time: 45:11
Average speed: 21 km/hr

Trouble-Free Upgrading Between Opera Nightly Builds in Mac OS 10.6

noreply@blogger.com (Matt BK) — Thu, 21 Oct 2010 15:02:00 +0000

(If you can't tell from the title, I've been reading too much Lifehacker lately.)

As alluded to before, I've been using Opera for a month or so now because Camino decided it was going to suck down all my CPU. Since only the nightly build at the time had the feature I wanted (bookmark bar, works well so far), I was forced to travel into "the land of no automatic updates." Fortunately, I figured out how to keep all of my settings, bookmarks, and even open tabs when upgrading. Note that these steps may not be necessary, since everything might end up hunky-dory all by itself.

Steps:
1. You're probably getting your nightly builds from here. Why they use a blog (with anonymous commenting disabled, no less) for getting feedback on builds is beyond me. In any case, you should download the nightly you want to use.
2. Back up your bookmarks and your ~/Library/Preferences/Opera Preferences * folder just in case. You can also move your current Opera application bundle out of Applications and onto the desktop just in case.
3. Install the new version by opening the DMG and dragging the application bundle to your Applications directory. Don't start the browser yet.
4. Copy the files you backed up from your Opera Preferences folder into the most recent Opera Preferences folder (there might be a version change which changes the folder name; just today I went from 10.7 to 11.0 on the folder name even though I'm using the last build of 10.
5. Start Opera (the new version). Hope things work.

Hope this helps somebody, or at the very least sets them on the right track.

Life as a Race/Event Coordinator

noreply@blogger.com (Matt BK) — Sun, 17 Oct 2010 15:06:00 +0000

I was recently (last month) elected to be the Race/Event Coordinator for the UND Cycling Club. This is a position I've more-or-less held in some capacity for the past few years, since I've been trying to get more events happening ever since I got hooked up with the club back in 2008. Now that I can someday put this on my resume (ha!), I'm taking it more seriously, but at this point I'm receiving more help than opposition than any time in the past.

I intend to add "event coordinating" to the list of things I blog about here. Over the next year you will be subjected to the problems I encounter, the triumphs of successfully navigated paperwork, and hopefully even some good feedback about what else can be done in Grand Forks for this organization and others.

One of my inspirations in this pursuit is Andy Magness, director of END Racing, choreographer of the only adventure racing in the state, and top-notch yoga instructor. If I can get to the point where I can orchestrate an event with half the participants, half the sponsors, half the press, and half the general excitement surrounding it of any of the events Andy has organized over the last few years, I'll be flying high.

As someone who is naturally not outgoing, event coordinating is a big deal to me for that reason: I have to interact with people, I have to know what's going on, and I have to think of things nobody else does, answer questions that nobody would ever come up with, and do it all with volunteers who would much rather be racing than volunteering (but we're working on that this year; I'm committed to this role, even if it means I don't get to participate in the 'cross series [beginning Halloween in Riverside Park], the icebike series [announcement coming soon!], or even another collegiate road race weekend).

Most importantly, I need to be able to take the (sometimes nebulous) ideas presented by club members and turn them into a workable event. The best mind we've had for this is Dave Cardarelli, who will finally be graduating this December. Whether we've been organizing UND's 2010 NCCCC road race weekend (complete with conference criterium championships), alleycat races that aren't boring, or Grand Forks' first ever (?) icebike race, Dave has either known what to do or shouted the rest of us down when we disagreed, which generally amounts to the same thing. Now that I've got this role on my shoulders, I hope I can measure up.

So far this fall I've been in contact with more people than ever to get some last-minute fall events into place and think about the future:

We're starting a three-race cyclocross series (UND's Fall Classic, to be expanded next year) on Halloween. Instrumental in the planning of this race so far have been my geology colleague Ted Bibby as well as Dave; so much so that I have yet to visit they race course they've supposedly devised, even though I've delivered a map to the city with our request for a special events permit.
For the long term, I've been working with riders in Fargo, Sioux Falls, and Winnipeg to organize a winter icebike series next February, as well as keeping in contact with Andy Magness to make sure we won't interfere with END-IT (which as scheduled stands to be the light at the end of the tunnel of a month of winter racing if all goes to plan).
It hasn't been nailed down yet whether we'll be hosting "Too Flat, Too Furious" again next spring, but if our roster expands as much as I hope it will, we shouldn't have a reason not to (more riders, in my mind, means a larger volunteer pool and more people invested in making sure the event goes off without a hitch). We'll be talking about this down the road as people start dropping like flies around January.
We failed to organize a late summer mountain bike series this year (although getting a 'cross series in before the snow is a nice bonus), but I hope to get it rolling for sure in mid-August: six weeks of mountain bike racing at Turtle River State Park followed by six weeks of cyclocross (which could alternate between TRSP and the Grand Forks Greenway, to say nothing of finding a friendly farmer who will let us use a cornfield).
Beyond? Well, let's not get ahead of ourselves :-)

As a final note, this isn't about me: it's about the club and what we can do for people in Grand Forks. Cycling, running, and even adventure racing events have been on the rise since I moved here in January 2006. I intend to make this trend continue, so if you have any ideas for events, improving events, or collaborating, get in touch.

From Landscape XYZ Point Data to *.STL to Rapid Prototype (part I)

noreply@blogger.com (Matt BK) — Fri, 01 Oct 2010 04:23:00 +0000

Considering I haven't sent the finished model to be vetted by the Professor who runs the rapid prototyping machine, this can only be the first part of hopefully a short series.

To continue my quest to use laser scanning to model and then reproduce important fossils, I was given a sample dataset to format correctly and then send over to the Mechanical Engineering Department to test out their rapid prototyping machine. This dataset is a landscape model (I believe based on a DEM) made of point data in an XYZ file. To explain, the surface is made up of a series of points positioned by x-axis, y-axis, and z-axis triplets. In the end, I needed a solid model in *.STL format. Although I was told to use AutoCAD for this, I think I've found another (free) way.

I planned to import the data file into the free, open-source point-meshing program Meshlab v. 1.2.3 and manipulate it there, but I needed to change the file format correctly first. Originally, I used the MS-DOS program xyz2vrml.exe (from this useful site) to convert the data text file into a *.WRL (VRML) file, but then I realized I could just change the file extension and Meshlab would be able to read and import the points (this of course only works if your data file just has a different extension than Meshlab expects, not if the data are a different type).

Adding point landscape data to Meshlab.

To convert the point data to a mesh (TIN) surface, I used the Surface Reconstruction: Ball Pivoting filter (in the Remeshing, simplification and reconstruction menu) with the default settings (world unit: 0.0, perc on 0.0, clustering radius: 20, angle threshold: 90). To see the result I had to click the Wireframe button in Meshlab to get a surface made of triangles. The file was saved in *.3DS format.

Wireframe after meshing.

The *.3DS file was then imported into Google Sketchup for modeling. Although the mesh seemed to act like a single object, attempting to use certain tools made me realize that it was being manipulated as a collection of triangles, which meant I couldn't use such things as the Push/Pull tool to extrude the surface down to a lower plane to create a solid model. Luckily I found a Sketchup plugin to let me do something similar (available here). The Curviloft plugin allowed me to fill in space between a rectangular base (easily drawn in Sketchup) and the meshed landscape surface above it.

Adding mesh to Google Sketchup.

I used the Skin Contours tool on each of the four remaining sides to achieve a solid model. To do this, I drew a line connecting the corner of the base rectangle to the corner of the mesh above it. Once a side had been marked this way, I used the Skin Contours tool to select each edge of what the new face was going to be and clicked the checkbox. In order to select adjacent mesh edges, the Extend Selection toolbar button needed to be on, and the Stop Prolongation button needed to be off.

Adding a base and connecting it to the mesh at the corners.

One side completed.

To get the final file format correct (I'm hoping), I had to export the model from Sketchup as a COLLADA (*.DAE) file, then into Meshlab, and then use Meshlab to save into *.STL. I was told that my *.STL file needs to be "solid," but I'm not sure whether this simply means "no holes" or whether there is a trick to completely fill the model with some virtual material (Unobtanium? Adamantium?). I'll send this model to the Professor of Rapid Prototyping (not his real title, unfortunately) and see what sort of feedback he has. Tune in next time for the exciting conclusion!

The finished model in Google Sketchup.

Total project time (including learning Sketchup and Meshlab and designing the workflow): several hours.
Writeup time: 1.5 hours

ND EPSCoR State Conference 2010 in Grand Forks

noreply@blogger.com (Matt BK) — Wed, 29 Sep 2010 21:17:00 +0000

I spent this morning and early afternoon at the North Dakota EPSCoR 2010 State Conference. EPSCoR (Experimental Program to Stimulate Competitive Research) is a federally funded program to fund states that need additional infrastructure in order to improve their research output. It is funded competitively, and then those funds are distributed within the state towards research projects, facilities, and scholarships. I learned today that North Dakota is the only state that has been funded continuously since the program's inception in the early 80s. Part of this is supposedly because the state agrees up front beforehand to match the federal money given, something I guess other states aren't able to do.

The posters (graduate student research projects) were generally very good, although a lot of walking was involved to see everything because of placement on the walls down the main corridor of the Alerus Center. Several of my Geology and Geological Engineering colleagues presented posters, most of them luckily in high-traffic areas. A lot of the material was biochemical in nature, which tended to make me (since I'm not a chemical biologist) gloss over some things I probably shouldn't have; I would suggest to EPSCoR that in the future the posters be arranged more according to topic, which might have the added benefit of getting students from different institutions to talk to each other about their similar topics.

I've scanned the poster session program (includes abstracts), and for general entertainment I shot some photos, shared below.

A geologist explains his project.

Breakfast, the introductory speaker, and some of the many posters were on display in this room.

Student posters went all the way down the hall.

A biologist explains her work.

Lunch was surprisingly good for being free.

To do: make sure I have a list here of all the GGE students who presented.

Problems with Tiddlywiki with Opera 10.70 (build 9047) for Mac

noreply@blogger.com (Matt BK) — Tue, 28 Sep 2010 18:22:00 +0000

At some point in the last few days (actually it looks like since the 18th of September), Opera has quit being able to save my TiddlyWiki files--in fact it appears that all the notes I made for my dissertation on Monday have disappeared, even though I thought I was autosaving. I'm more than slightly miffed about this.

At present, it looks like TiddlyWiki works fine in Safari and Camino (the browser from which I just switched because it uses up most of my CPU). In Opera, however, I get this error:

The original file 'empty.html' does not appear to be a valid TiddlyWiki

and the file will not save. For some reason, the dialog box asking for permission for the security certificate has also stopped appearing, while in other browsers it comes up for each new TiddlyWiki file I open.

I've looked into this as much as I wish but I cannot find a solution. The problem may be with Java (somehow?), or with this particular build of Opera (I think I am on a nightly build because I wanted some of the new functionality). In any case, I'm stymied by the lack of ability to really manage the security certificates, especially when they don't pop up. I'll be using Safari as my TiddlyWiki browser until I figure out what the issue is or things suddenly start working again in Opera.

Laser-Scanning Small Objects with a Leica Scanstation

noreply@blogger.com (Matt BK) — Thu, 23 Sep 2010 17:45:00 +0000

As previously mentioned, we have a Leica Scanstation here at UND that is used for scanning large areas for geomorphology projects. I borrowed it yesterday to try out how it did at close range. Although I probably don't need to say this, things did not go as well as well as planned.

First, the setup:

Since we're neither scanning a large area nor worrying about repeatability, there was no need for a leveled tripod or targets. The metal base of the scanner is designed for these sorts of applications, so no harm is being done by setting it down on the table like this. The bricks are used to keep the specimen up in front of the scanner, and the computer runs the whole setup. You can see the Triceratops "model" and the gastropod (snail) specimen as well, to judge their size:

I'll skip over the mechanics of scanning, except to mention that the Leica licensing system is still giving us problems; under one Windows 7 account I couldn't access the license but under another I could. Such is life with computers!

The problems came from trying to scan at very fine detail. The scanner was set up just under 0.5 m from the objects being scanned, and the resolution (density of scanning points at that distance) was varied as I tried to make things work.

At 0.1 mm point spacing, I ran into this problem (gastropod):

Hitting the limit of the resolution causes this weird striping pattern. This might be okay if the surface were accurately represented, but at this point you lose depth perception as well: the scatter on those stripes averages around 9 mm between the front "surface" and the back, meaning that the surface itself (if I modeled this scan) would vary that much. Not so good.

At 1 mm point spacing, things were better but not so great (gastropod):

The stripes are toned down, but the error is just too large for a decent 3D model to be produced :-(. With 1 mm spacing between points, even if the points were a surface rather than a cloud, this is about the smallest object I would try to scan with it.

Finally, fellow graduate student Ted wanted to try out the Triceratops model. With 1 mm spacing, this is what we got:

Although I'm sure the morphology is incorrect in the details, such a scan fits in nicely with the current horned dinosaur publishing extravaganza going on.

Final verdict: while the Leica Scanstation is good for some things, scanning small fossils is not one of them.

New END-AR video!

noreply@blogger.com (Matt BK) — Wed, 22 Sep 2010 15:19:00 +0000

For Sale: Geological Survey Professional Papers

noreply@blogger.com (Matt BK) — Tue, 21 Sep 2010 18:35:00 +0000

Off-topic: GoPro Sport Videos

noreply@blogger.com (Matt BK) — Tue, 21 Sep 2010 13:48:00 +0000

It's not science, but it could be used for science, if I had to chase down fossils or something. Since that's not really an option, I've been using my GoPro Helmet Hero (the original, non-HD version) to capture some cool things but haven't had a chance to blog. Here's a video from END-IT, the Extreme North Dakota Iceman Triathlon, back in March. The disciplines were nordic skiing (doubletrack classic for the most part), cycling (some of it on snowmachine trails), and trail running. Per the END Racing creed, there was a bit of adventure thrown in. At the end we had to sled down a hill and run back up three times.

I ended up getting second overall in this race, which is far beter than how I had expected to do since I'm not a strong nordic skier. If you watch the raw footage, you can actually see where I messed up tactically--since I was wearing a camera on my head, I had to switch mounts twice (once between the ski and cycle legs and then once again between the cycle and run legs). If I hadn't wasted that time, I may have been able to win overall--but then you wouldn't have this cool video now, would you?

Since I haven't posted about this camera before, I'd like to say a few things. I love it for what it lets me do, but it could be designed slightly better. A lot of people complain about battery usage, but I've been having success lately with rechargeable NiMH AAs rather than lithiums. It would be great to have more of an indication from behind whether the camera is recording or not, and recording without a date on the files is annoying. Also mentioned by others is the amount of recording you can do at once; I applied this firmware update and haven't had any problems (it will let you record for twice the normal time in one file and use a larger memory card). I honestly think it's a great little camera; it's rugged and waterproof, it records video, it's fisheye so you can see a lot more, and you can strap it onto yourself in a variety of ways. Thumbs up.

Researching Laser Scanning and Rapid Prototyping of Fossils

noreply@blogger.com (Matt BK) — Sun, 19 Sep 2010 00:51:00 +0000

This post is a summary of my research over the past few days; I'll continue to update it or make new posts as necessary.

Introduction
One of the growing subfields of paleontology is the digitization of fossil material via 3D laser scanning. There are several reasons to do this: protecting valuable specimens from potentially destructive handling, making virtual models available for morphometric analysis, and producing physical replicas of specimens, either for sharing with other institutions or for performing physical tests relating to size and shape. Two disparate technologies must come together for all of the above to come to pass: first, a scanning system to accurately digitize specimens (via laser or, in some cases, photography) so that they can be visualized and manipulated on-screen; second, a rapid prototyping system that can accurately reproduce objects with fine detail and accuracy to the original model. I am concurrently researching both of these technologies to determine the options we have at my institution.

Specimens and Detail
The collection at UND comprises mostly invertebrate fossils, and of those a great many are freshwater mussels and gastropods. Generally these objects are a good size to scan and do not have "important" morphological features that are very small; however we currently have two graduate students studying mammals via teeth and one student studying microsnails. These items range to several millimeters, so when it comes to detail we need to be pushing the edges of the technology as much as we can afford, in order to get good data. (I don't have to worry as much since I'm studying normal-sized mussels, but in paleo as in everything else, the more decimal places, the better.) It would be excellent if we could capture surface features less than 0.1 mm in height.

Laser Scanning
Several systems are available for digitizing physical objects; I am focusing on laser scanning because it can produce virtual models of highly detailed objects that are very accurate to the original. Other methods of creating 3D models are photogrammetry and to a lesser extent morphometric probes that record the position of landmarks in three dimensions but not the intervening surfaces.

Build-your-own scanning systems:

DAVID

MakerScanner

Cyclops

These systems generally utilize a line laser and a webcam to digitize objects, although the Cyclops uses a "shadow line" and the DAVID can use both. The object is digitized by the interpretation of the bright laser line (or dark shadow line) on the image pulled from the webcam: the position of the surface is calculated based on the known relationship between the laser and the camera or the laser and the background. From my rough experience (earlier this summer with DAVID and just today with a hacked version of MakerScanner), it is quite difficult to get a really good scan, although some of the planeless scans done by people on the DAVID forum are amazingly good. If you want a good scan, you can do it, but you're going to use up a lot of time and effort getting to that point. I will be playing with replicating a MakerScanner some more over the next few days and hope to report on the results.

"Cheap" scanning systems:

NextEngine

Currently, only the NextEngine scanner is priced "cheaply" when it comes to laser scanning. For $2,995 you can get the basic package, and for $995 more you can get even better precision. I've seen a lot of commentary on this scanner, and all of it good, but I'm not sure it will capture enough detail for our needs. The "dimensional accuracy" is +-0.0005", or about 0.0127 mm. That's pretty darn good, but will it work for us? We'll have to go visit someone and see.
- http://palaeo-electronica.org/2008_2/134/index.html
- http://reporting.journalism.ku.edu/fall08/adler-noland/2008/11/ku-geologist-preserves-dinosau.html

Expensive scanning systems:

I had a larger list of these systems a couple months back, but since that information is probably out of date by now, I'll refrain from posting it. Most of the issues I remember running into are: cost (of course), intended use (if they're designed for reverse engineering, will they work for fossils?), and, well, cost. Now, I'm all for getting the top-of-the-line scanner so you can do the most awesome digital models possible, but paleo is one of those disciplines in which you do what you can with what you have, because the cashflow isn't always the steadiest. On this note, we do have a Leica Scanstation in the department that I have experience with scanning landscape features; I will be testing it out soon to see how well it can do with closeups on small items.

All in all, more research needs to be done on the available laser scanners to see which is best suited for our purposes. I will be posting as I can talk to people about their experiences.

I'll leave things there for today and pick up in a little while with the next section: rapid prototyping.

Design and the science and what's to come

noreply@blogger.com (Matt BK) — Fri, 17 Sep 2010 13:47:00 +0000

The new Blogger template designer is quite good. I'm still trying to find something I'm the most happy with, however.

Some changes in content may be coming down if I find the time, but the purpose of this blog will remain the same: documenting ideas I find interesting and recording things I've learned that may be useful to others. There will continue to be code snippets and blockquotes from various sources, but I hope to tighten things up and provide a bit more analysis as I go.

Possible topic ideas for the near future*

Planning to finish up the project from NAPC last year (freshwater mussel shape change over distance)

Experiences with small-scale laser scanning (not only DAVID but MakerScanner, something I just found yesterday)

More videos of science in action (including wind tunnel studies and rooftop apparatus)

My fascination with trace fossils

The total-body experience that is trying to build a useable specimen database

Making my thesis code available

Off-topic interests may include

Cycling in and around Grand Forks, ND

Book reviews not relating to science (but I will try to relate them in some way)

Video from various excusions that were more athletic than academic

If anyone has suggestions for other topics, I'm open and ready to discuss things about which I may know more than the average person. Post me a comment and I'll see what I can do.

*Motiviating myself by telling other people what my plans are. Sometimes it works.

The CRAPL: license your academic code

noreply@blogger.com (Matt BK) — Tue, 14 Sep 2010 14:36:00 +0000

Matt Might (who knows when) came up with a license for academics to release code used for research. You all know the code: it barely works, comes with little documentation, and you're really embarrassed every time someone asks to see it in relation to a publication. The solution? The CRAPL--the Community Research and Academic Programming License.

He says "Academics rarely release code, but I hope a license can encourage them," and I am strongly encouraged. Although I've "published" the code used in my MS thesis in an appendix, it's not available for download anywhere. When I have a few hours sometime I plan on getting things moving with this. For the good of science!

Dynamic DNS notes

noreply@blogger.com (Matt BK) — Fri, 20 Aug 2010 01:24:00 +0000

Dynamic DNS is a system where you update the nameserver every time the IP address changes, so you don't lose links.

I'm using freedns.afraid.org right now because it lets me use my own domain name (protichnoctem.com) for, well, free.

I set the nameservers in GoDaddy, then set cron to run wget every hour (of the "Direct URL" on this page)to update the nameservers with the current IP address. I know this is much more often than my IP address changes, but if it should change I'd like the domain name not to be broken for more than an hour (a cron wget is a fairly light task anyway).

If it works, I will be happy.

Difficult Concepts

noreply@blogger.com (Matt BK) — Wed, 18 Aug 2010 20:38:00 +0000

Traditional dispersal: A pair of goats wanders over a mountain.
Geodispersal: A mountain wanders under a pair of goats.

Making SFTP work

noreply@blogger.com (Matt BK) — Fri, 07 May 2010 20:45:00 +0000

Beyond creating a new user, you need to add their name to the bottom of /etc/ssh/sshd_config:

AllowUsers user1 user2 user3

Restart SSH:
# /etc/init.d/ssh restart

Ubuntu and Time Capsule

noreply@blogger.com (Matt BK) — Thu, 22 Apr 2010 17:29:00 +0000

Looks like they've fixed the problem with SMB shares breaking. This fstab entry is currently working for me:

# Athena on Puck
192.168.1.1/Athena /media/Athena cifs auto,user,pass=password_goes_here,nounix,noserverino,rw,iocharset=utf8,file_mode=0777,dir_mode=0777 0 0

Ubuntu version 9.10

EDIT: At first I had the relevant line commented out (//), sorry about that. "192.168.1.1" is the IP address of your Time Capsule. Make sure your firewall will allow access on the correct port (set in Time Capsule setup on the Mac).