First you’ll have to install Imagemagick. This should be as easy as a sudo apt-get install imagemagick. Of course you need perl, but that’s standard on any linux install. Now here’s the perl script:

use Cwd;
$some_dir = cwd;
print $some_dir."\n";
opendir(DIR, $some_dir) || die "can't opendir $some_dir: $!";
system("mkdir small");

while ($_ = readdir(DIR)) {
next if($_ =~ /^\./ || -d "$some_dir/$_" || /\.pl/);
print ":convert -resize 800 -quality 80 $_ small/$_"."\n";
system("convert -resize 800 -quality 80 $_ small/tn_$_");
}
closedir DIR;

Steps

1. Save the above script as resize.pl (copy and paste it into a new text document).

2. Adjust the image width (800 in the example) and quality (80 in the example), and put the script in a folder.

3. Put all the images you want to resize into the same folder.

4. Open a terminal, cd to the folder, and type

perl resize.pl

That’s it! This will make a subfolder called small and put the newly resized images in there.

If you’re not happy with the file size, just do it again, it will overwrite anything. I find this little script really useful — you can now email however many pictures you want. You can also use this script to make thumbnails for a web site: just set the size to 200 or 300, lower the quality a bit, and you can get images that are around 30K each.

Details

Unfortunately, I wasn’t impressed with the shakes. While I enjoyed the atmosphere of Franklin St. and the tiny drugstore, the experience as a whole left something to be desired.

We ordered strawberry and peach shakes, but neither one was anything out of the ordinary. In fact, I think I can make a better shake at home with my immersion blender. The shakes were quite thin (they don’t even bother giving you a spoon–you drink it with the straw), although you can “upgrade” to a thick shake for an additional $0.75. The flavor selection was only decent: they had about 6 flavors of ice cream (including butter pecan and mint chocolate chip) and about 6 mix-ins (mostly candy bars, like butterfinger or snickers). But probably the most disappointing thing about the shakes was that they simply didn’t have much flavor. Maybe we just went on a bad day–it was almost as if the establishment decided to cut back on the mix-ins to save money. The shakes were mostly vanilla ice cream and milk, with a tinge of flavoring.

We also ordered a side of cheese fries, which likewise weren’t great. Whenever I order cheese fries I have visions of a pile of fries smothered with real, melted cheese. That’s way they should be done. Unfortunately, I have yet to find a place that serves the real deal in North Carolina. Instead, I end up with a plate of fries covered in artificial nacho cheese sauce. If that’s you’re thing, you’ll probably love the cheese fries at Sutton’s. Does anyone know of a place where they serve real melted cheese?

The Bottom Line

Overall, the place wasn’t bad, and the prices were low. But I’m not adding Sutton’s to the list of great milkshakes in Durham.

Links

• Best Milkshakes near Durham, North Carolina

You can really just show up for the free entertainment, but to make the night more of an outing, many local businesses (like Locopops) show up to sell food. These companies subsidize the concerts to get people to come out and buy food. There are usually several options, including some outdoor grilling, and there’s always Mellow Mushroom. Or head over to nearby Brightleaf Square before the concert where there are more options.

Seating on the grassy area can be limited, but usually there’s place to squeeze in if you show up just a bit early. If you want to be close enough to actually see the performers, though, you’ll probably want to be there before the concert starts. Guests bring lawn chairs or blankets and often have picnics, either purchased or brought from home, to accompany the music. Since the Campus is surrounded by buildings, the sun is low enough in the sky to not be too much of a bother.

I think this is a great event, and a steal at $0, especially because you’d pay top dollar for a similar quality of entertainment elsewhere.

Links

• Concert Schedule 2010

I’ve decided that my goal for this summer is to find the best milkshake joints near Durham (that includes Chapel Hill, Raleigh, Cary, and Morrisville). I’ll visit every place I can find that serves milkshakes and then I’ll post my opinion here. After doing a bit of searching online, I’ve started a list of places to try. I’m willing to look at either chains or independents. Throughout the summer, I’ll try to visit each of these places. The goal will be to finalize a list of places that really stand out, and by the end of the summer I’ll put these restaurants in ranked order based on how good their milkshakes are. Here’s my list of nearby establishments that serve milkshakes:

Milkshake Joints to Try

1. Sutton’s Drug Store, Chapel Hill
2. Goodberry’s Frozen Custard, Durham/Cary
3. Cook Out, Durham/Cary
4. Circus Family Restaurant, Cary
5. Maple View Farms, Chapel Hill
6. Chick-fil-A, Durham
7. The Loop, Durham/Chapel Hill
8. Sonic, Raleigh
9. Chargrill, Durham
10. Elmo’s Diner, Durham
11. NC State Creamer @ DH Hill Library, Raleigh

If there are other places you think I need to add to the list, please let me know in the comments. I’m definitely looking for your advice for other places I’ve left out. I’m hoping the list will continue to grow as people make suggestions.

As I visit these places and write reviews, I’ll link to the updated posts. Going into this, I think the popular favorite on the web might be Cook Out. I’m not surprised–Cook Out is great place for thick shakes, and they have lots of options. But I think there might be smaller or less popular places around that can do even better. I guess only experience will tell for sure!

“Cellcraft”, as in “Starcraft” ?

When I heard the name “Cellcraft”, I immediately thought of Starcraft, possibly due to the impending release of Starcraft 2. Of course, this was probably the intent of the authors of the game. I was a bit excited, imagining a real-time strategy game where you build mitochondria to power armies of proteins, or rally the immune system to fend of viral invaders. Call me a nerd, but wouldn’t it be sweet to have a game on par with Starcraft that had a cell biology theme? Unfortunately the actual game seems to be built in Flash, so you have some idea of what it will be like. Even so, I think this is a great idea for teaching biology, though I was perhaps disappointed that it’s no SC.

I guess I’ll probably take a look at it when it gets released, though, just for fun. The most recent blog post says it’s in “alpha” stages and being tested in the classroom. Supposedly the final release will be open for all to play. Who knows, maybe I’ll be using something like this in a biology class I teach in the future. This reminds me Times Attacks, the multiplication tables video game that teaches times tables in a doom-style first-person-shooter. Right now, these seem like novel ideas, but kids these days are so attached to computers in some form that this may be the only way to get them to learn things in the future.

1. Waller Family Farm
2. Jean’s Berry Patch

Last year we went to Waller Family Farm, located about 3 miles outside of Durham city. There were plenty of strawberries and the prices were reasonable ($1.35 per pound as of May, 2010). We’ve also considered Jean’s Berry patch, which is currently advertising the same price. I think the strawberries are even cheaper this year than they were last year. Maybe this has something to do with the Cheap Strawberries weather issues? If you’re looking for other farms, there’s a great site at the News and Observer with a U-pick strawberry farm locater. There are 26 such farms in the areas surrounding Raleigh-Durham! Whichever farm you choose, make sure you get out there while the strawberries are still around!

Reasons to pick your own strawberries:

1. Prices are lower when you pick your own.
2. Picking strawberries is fun (once a year, that is).
3. Your money stays local and benefits a community business.
4. You’re not contributing to the environmental costs of shipping from California or Florida (or South America!).
5. They’re fresher — you can eat them the same day they’re picked!

We usually pick way more than we will eat and then make strawberry freezer jam, which we then ration out for the rest of the year. Not only is it less expensive, but it’s better tasting than strawberry jam you can find at the store. We save money by not buying jam, we get to pick extra strawberriess, and we get to enjoy delicious jam year round. It’s a win-win-win situation. If you’re looking for a recipe, just do a search for Strawberry Freezer Jam and you’ll find something.

Details:

I stayed in Loop B of the family campsites area of the Rolling View campground on a Friday evening in April. I had no trouble finding a walk-up campsite, though the sites with lake views were all occupied so I ended up more internal. The site was nice but small, with barely enough room for a couple of 2-man tents. Each site has a picnic table and a fire pit. They sell wood at the entrance station for a ludicrous $4 per bundle, so get some from craigslist before you go if you want a fire. The tent sites in this area were too close together, so there wasn’t much feeling of privacy. Most annoying to me was that at least 2 other visitors decided it was appropriate to play music loud enough for the rest of us to hear. This went on until curfew at around 10 pm, when things quieted down a bit. One other thing is that this park is in a flight path. I noticed the planes, but didn’t find them too bothersome since they didn’t come by very often.

There are some short trails nearby that are easy to find on the map. I hiked down to check out a couple of swim beaches, which seemed very nice and were amazingly empty. The lake water wasn’t too cold, so I was surprised that such a nice place wasn’t overcrowded with swimmers.  I also found a “community building” near the “boat beach” that could apparently be leased for larger group get-togethers. This facility seemed nice, with a large room, attached kitchen, and ample supply of folding chairs. There’s also a group campsite nearby, which was completely empty the night I was there. I did have some difficulty finding flat areas to pitch tents, though. I encountered a few others on the trails but mostly the place was pretty quiet.

The bottom line:

• Campsites in Rolling View were small and noisy.
• The park itself is very nice and not too crowded in April.
• It would be worth it to check out other camping areas, including group camping.
• It’s definitely a great place for day hikes, swimming, or boating.

Links:

• Official Site: http://www.ncparks.gov/Visit/parks/fala/main.php
• Maps and Directions: http://www.ncparks.gov/Visit/parks/fala/directions.php
• Another Review: http://camping.about.com/od/campgroundreviews/fr/ucpcg696.htm

[J]obs themselves are a form of education. In hard times, of course, young people take what jobs they can get. In better times, they should look at the array of jobs available not simply from the standpoint of money and convenience but from the standpoint of their own further growth. If young people are willing to think hard about their own abilities and interests, and then to look at available jobs as opportunities for self-development, they can look forward to years of learning and growth as rewarding as anything a college student might experience. (p. 104, Excellence).

This statement resounded with me. I think that the mentality of the typical American is that jobs are sources of income, not forms of education. I find this unfortunate. I prefer Gardner’s standpoint (shared by other notable people including Robert Kiyosaki and Jim Rohn). I’ve tried to select the work I do on the basis of what I will learn. Of course, you can’t completely disregard the paycheck…but within reasonable limits, I think you’re better off taking a lower-paying job that improves you than taking a high-paying job that doesn’t.

For example, I would take an internship that pays $10/hr in an interesting field over a job that requires and provides no training but pays $20/hr. I believe that the training and learning can easily be worth more than the difference in pay. I no longer consider the hourly rate the most important factor in evaluating employment opportunities. Instead, I consider the skills I will learn and the experience I will gain as a result of my time invested.

I think that one of the big problems is that bad writing is accepted (in science fields). For example, it almost seems expected that scientific papers are written in the passive voice. I, for one, find this to decrease readability. I have been thinking a lot about this lately and wondering what I can do to improve it. I am working on developing a workshop for scientific writing that will address this.

In the mean time, I’ve joined American Journal Experts, a paper editing company that proofreads journal articles for non-native english speakers. This has been an interesting experience for me. This company offers proofreading services. I think this is important as well, but I also think that we need a fundamental change in writing philosophy in order to make meaningful changes.

I’ll be writing more about this in the future.

What is allelic imbalance?

• A difference in the expression between two alleles.

Humans are diploid organisms, which means we have 2 copies of each gene. Normally, these two copies are expressed at the same level. This means that the mRNA transcript from the mother and the transcript from the father will have roughly the same number of copies. Sometimes, however, this is not the case. When the ratio of the expression levels is not 1 to 1,  we call it “allelic imbalance”. There are a variety of reasons why the expression may vary between the alleles. “Gene imprinting,” when environmental factors silence either the maternal or paternal allele, is one case. If one allele is silenced completely, then there will be an extreme case of allelic imbalance. Other scenarios may increase or decrease expression of one particular allele only slightly, resulting in imbalance to a lesser degree. Cis-acting mutations may alter regulation for just one allele through a change to promoter/enhancer regions (transcription factor binding sites), or even through 3′ UTR mutations that affect mRNA stability or microRNA binding.

A good source for further information (if you have a subscription) is Detection of Allelic Imbalance in Gene Expression Using Pyrosequencing