Week 10: Progress

My program concluded this past week. And just in time, we got the robot to follow a thin black line and turn around when it reached the end. With a simple input of "Red" or "Green", we can easily direct the platform to one of two directions. The robotics here lays the foundation for what will eventually be a "bacterial brain" interface with a larger robot.

You're probably wondering, "This took them ten weeks? Really?" With no prior knowledge of electronics or programming, we put this thing together with no instructional booklet. So it's a little like putting together a giant Lego set without the instruction manual, and in our case, the programmed code is not visible. In these ten weeks, we learned so much more by messing around with it ourselves instead of immediately going for help, which we never did.

When we refined our program and redid the wiring scheme many times, frustration ensued. But when we tested it and saw the movement as in the video above:

And then we went suit shopping. At the toilet store.

My fellow Scieneer Sean Hardy and I presented these findings and our future plans at the VT Undergraduate Research Symposium on July 31st.

Heading into the VT Inn Ballroom to present. Free food had nothing to do with it.

Sean and I presenting our poster. Our title turned a lot of heads, and students/faculty were wowed by our project and where we're going with it.

The Steppin' Out Festival on August 2/3. Downtown had the largest turnout I'd ever seen, despite the mostly-deserted campus.

High schoolers and old people abound here. In other words, a constant reminder that you're still single.

This program opened my eyes to what research really is. For some, it can be a more concrete series of tasks, such as injecting mice or analyzing data trends. Or in our case, you get a bunch of parts and only an idea of the final product in your head. This project gave me a greater appreciation for that kind of open, out-of-the-box thinking, and I plan on continuing it in the Fall and Spring.

I'm back in Richmond for two weeks until I return on the 18th for MV Band Camp prep. I'll be in Atlanta on the 31st for the kickoff against Alabama. I'll also continue to update on blog-worthy events and my research progress.

Until next time,

Ben

Weeks 8/9 :Wrapping up

We've come a long way from nine weeks ago. After having to program and wire and reprogram/rewire constantly, I can say I've got a greater appreciation for electronics. Our robot more or less follows a line and turns around once it reaches the end.  Now I want to try to take apart everything I see just to find out how it works. Never thought I'd see myself doing this stuff. And that isn't a bad thing.

We'll be presenting our model at the VT Undergraduate Research Symposium with a projected path for future study this Wednesday.

Cheers,

Ben

Floyd, VA: Modern Renaissance Men

I've wanted to be a doctor for a decent amount of time now, time enough to take it seriously. But if a purpose more interesting came calling, I would think about it. Call it fate, but if something were to change my idea of my own future so drastically, I would be open to it.

Guys like Skip Garner and Michael "Buzz" Waitzkin prove that there's more out there than your cookie-cutter careers. Several undergrad researchers and I drove down to Floyd, Virginia to meet the two at Buzz's home up in the Blue Ridge Mountains.

They first showed us into Buzz's office, the headquarters of Genomeon, a genetics company run by the two. They aim to help clients analyze human genomes with specific markers meant to detect microsatellites, repetitive pieces of DNA often indicative of disease. 

Buzz's office was built from wood taken from the multi-acre property. This reminded me of our family friend's cabin up in Boulder Junction, Wisconsin.

But that's not all; Skip has founded several other companies with lofty scientific goals, such Heliotext, BioAutomation, and Xanapath. They range from data search/organization services to selling DNA sequencing/synthesis machine parts. I think he picked a badass name and then just added a more mundane word like "path" or "text" on the end.

Skip spent a decade or so at General Atomics, a nuclear energy company based at the time in California. He worked on projects ranging from nuclear reactors to paint for stealth bombers. Oh, and he was director of the Virginia Bioinformatics Institute (VBI) here in Bburg for several years.

Buzz came from a different background. He went through law school in Stanford, worked as a D.C. public defender, and was brought on as one of President Bill Clinton's lawyers. As he told us, "I never thought I'd be working in the White House because of blowjobs," and said his meeting with Ms. Lewinsky was "a rather unimportant moment in my life." Classy. I would not have been as polite.

Old habits...

Hearing Buzz talk about his forays into different fields, whether it be giving talks at the Duke Business School or founding biology companies with Skip, was reassuring. They didn't fit to any mold, and have been involved in more scholarly and business circles than I can imagine. 

I asked him, "Was there ever a moment for you knew what you wanted to do?" He responded that his father encouraged law school, but he would have preferred med school. He told me, "Don't be so narrow-minded that you pass up everything that comes by you. Take advantage of every good-looking opportunity you get, and see where it leads. Get out there." However, he wished he kept more in touch with his mentors and mentees from his various pursuits. I'll have to remember that one.

Next we toured the art studio of Buzz's wife, Gibby. Her approach is unique; she only uses organic materials, like banana peel fibers and tree lichens. She's putting on a display this fall in Blacksburg that I hope to see.

Gibby picks some of her materials as they grow out of the ground, while others, like banana peels, are ground up into their fibers to make paper.

Water is used frequently to affix some of Gibby's materials. The grate at the bottom left takes any spills into the soil outside.

Gibby's current collection resembled pairs of angel wings, which she said double as a pair of feminine legs. Her enthusiasm with her work made it all the more enjoyable to see.

Buzz gave us a tour around his property before we left for town. Long story short: I'm buying this house if I ever get rich.

That's a Tibetan prayer flag on the right, and you can several in a straight line if you stand near one. The whole lake is man-made as well, back when there weren't as many restrictions on such a project.

This square is the land's own "dig site". 17-18th Century Appalachian families would dig square sections such as these to construct lean-tos for temporary shelter while they built their homes.

Old mason jars and shoe soles are among the relics Buzz has found since he's been here.  The soles, like Joan Rivers, have been estimated at over 100 years old.

Having spent his childhood in Miami, Buzz received this "beach" for his birthday one year. On a side note, I should buy a boat.

We saw the sights in Floyd as well. Bluegrass street performers, plenty of vendors, and great local food. The big attraction is the Floyd County Store, AKA The AARP Convention Center. Local groups play with an open floor for dancing and flatfooting. FloydFest is going be packed in such a small town.

Floyd has only one main street, by the looks of it. It's also the hipster capital of Southwest VA. 

Groups like these line the street. It's funny they always try to outplay each other and crowds come and go accordingly.

Inside the Floyd County Store. You hear that? That's the sound of Duck Dynasty DVD sales going up.

Cheers, 

Ben

Week 7: Fine Tuning

Our line following program is just about done. Uploaded to the robot, it works well and reacts to light-reflective surfaces.

The infrared sensors are attached to the gold-colored board at the front.

Our robot has a perforated board attached in front with two mounted infrared sensors. One sensor on the left controls the direction of the left side wheels, while the right sensor controls the right side.

We numbered the wheels for ease of programming. For example, if the right sensor is off, Wheels 1 and 4 turn backwards while 2 and 3 keep going, causing the bot to turn left.

We start by programming the bot to calibrate to the white paper; if the sensors detect something other than that, the wheels will respond. If a left turn is ahead, the right sensor will come off the line first and detect the black floor, and the bot will turn left by switching its righthand wheels backwards while the left sided wheels continue forward. Once both sensors are aligned on the line again, the bot moves forward.

A crude robot arena to test the edge detection and line-following programs. Come back next week when he fights the Coke machine from the second floor.

 We've created the base program for what will eventually be under the bacteria's control. That stage is still far off, but I can imagine that the IR sensor input will be replaced by the bacterial data, controlling the turns on its own. For example, the bacteria releases a specific protein, which means it wants a certain food source. That signal can translate in code to "turn right" or the like.

Next we'll focus on refining the program, placing the sensors in more effective configurations, and drawing up model pathways.

Cheers,

Ben

Defend your Nuts

When I was younger, I went to baseball games in the Diamond when the Richmond Braves were still around and the Indian poked his head out of the side of the stadium. It's everything you would expect to see at the major leagues, albeit on a smaller scale: the hammered fans and peanut-covered aisles were part of America's pastime.

The Indian statue "Connecticut" usually pokes his head through that white building below the stands on the right. I hear he ended up somewhere along the James River

A lot has changed since then. They're the Richmond Flying Squirrels now, and the whole ballpark management has seen a serious overhaul.

You could see the Richmond skyline from here. And the free t-shirts never seemed to reach you.

I was hoping for a more intimidating name, like the Raptors or Raiders. But the city put the team name up to a public vote. From what I heard at the time, some wiseass thought it would be funny to submit "Flying Squirrels" over 200 times. Other names in contention were Rock Hoppers, Rhinos, and Hush Puppies (...really?).

The joke's on that guy, though, because the Diamond took the name in stride, producing official merchandise and heavily advertising their sleek new mascot. Local advertisements and sponsors are on every support column and wall, professing their love for their new team. If they're trying to build a brand, it's working. I've seen quite a few people in and around Blacksburg wearing their hats.

They were selling "Squirrels gone wild" trucker hats for $5. Those poor, unsuspecting kids. 

What impressed me when I saw a game for the holiday weekend was the family atmosphere. Well-behaved kids with gloves and whole rows of relatives filled the stands, and you're not sitting on dirty concrete slabs with some drunk guy yelling into your ear. Creating this kind of atmosphere takes years, and isn't easy.

Inside the men's bathroom. The world needs more stuff like this.

The food vendors are all high-school/ college kids, and I can't think of a better fit for them. A friend of mine from Tech was at work that night, and makes a killing in tips, while working every other week. Makes me wish I had done it last summer.

My friend Lucas recently got promoted to beer vendor. Such great power has been placed in this young man's hands.

The game itself had its ups and downs, but I wouldn't say this is a place for baseball aficionados. It's the perfect first date, family outing, and friendly get-together all rolled into one convenient place. And the nut puns were kept to a minimum, as disappointing as that was.

They didn't play the Katy Perry song during this show. Thank God.

Cheers,

Ben

Week 5/6: Line Following

It's been a slow two weeks, honestly. We waited for a part for the robot that was integral to its functioning and communication with the Arduino chip, and read up on papers and books while we waited.

But that's the nature of our project. It's not pipetting something twenty million times and filling columns of Excel spreadsheets with measurements. It's not like any lab class here at Tech, where a book guides you step-by-step and more or less holds your hand. We have a concept, and we put the pieces of the puzzle together from there. Some pieces take longer to find than others, but the idea of finishing an entire do-it-yourself project will be a sense of satisfaction all its own. And like my Grandma engraved into my head, always start with the frame and corner pieces; in other words take what you know and build on it.

The wire connections are those frame pieces. They're easy enough to understand, and certain pieces of hardware can ease the programming process. The Adafruit Motorshield is a flat chip placed on top of the Arduino board that allows easier programming and direct control of the wheels' speed and direction. It also comes with a whole slew of resistors and capacitors that must be soldered in. The three black rectangles are H-bridges, chips that allow varying currents in either direction.

The blue boxes are inputs for the DC motors that power the wheels. The orange taped wires come from  a battery pack under the hood that provide the power.

Assigning each motor a specific name, commands such as motorForward(MOTOR_1) can control each wheel independently. But what we want here is autonomous control, since the bacteria will eventually control the robot's direction. We fitted three infrared sensors on a board in front of the robot to allow it to sense dark-colored lines and follow them. This will come in handy when the robot needs to follow a path to a food source dictated by bacteria.

The three IR sensors are the red boxes spaced equally apart on the yellow-gold board. They send data to the shield/Arduino, which will rotate the robot accordingly via the motors.

We'll be refining the line-following program in the next week, while eventually getting a bacterial interface hooked up. It wouldn't be any fun if this was easy. 

Cheers,

Ben

It Takes a Village

I thought this place would have nothing to offer over the summer in terms of festivals and concerts. Who's even here for that? Are there enough people to make it a sizable event? Do businesses even bother coming out during the summer?

The Summer Solstice Fest in downtown Blacksburg proved me wrong: I've seen crowds just as big before at Relay for Life and Gobblerfest(more on that in the fall), among others. The town came alive, galvanized by all the local businesses and musicians coming together to put on a truly unique festival.

Early afternoon at the festival. The event stretched at least three blocks of  Main Street and more.

From a business perspective, Summer Solstice is an effective springboard for small companies or organizations to make themselves known and spread awareness through free stuff, the universal college student attractant, and unusual activities and games. Some showed interesting ideas:

This neighborhood committee set up a sandbox in one of the alleys right outside Starbucks. Kids play, and their parents get the sales pitch. How they cleaned up all this is beyond me.

Cabo must use the same sand guy. A DJ and plenty of lighting provided a great nightlife scene, giving off that bar by the beach feel.

This artist is an engineering professor who has been "doing sketches on the side" for about nine years. He was doing quick caricatures with a comic-book like feel to them (Think early Walking Dead Comics).

Another neighborhood complex set up this water balloon launching game, which was completely free. Never before have I heard such small children talk so much smack.

A Women's Fitness Club offered a water bottle to anyone who could do 20 pushups. If you're wondering, this was pushup #183.

 Some attractions were more legitimate than others. I didn't even know the flea circus was a real thing, but apparently it is. And it was as ridiculous as you can imagine. I learned that Flea Circus ringmasters come from a long sequence of fathers pressuring their sons to take up their flea-covered mantle. He fired a flea from a cannon. He had one wave a flag. He had another swing on bars. I felt bad for the little kids in the front row who bought into all of it. But at least he had a quirky, borderline creepy enthusiasm; I was about to leave due to the overwhelming smell of corn.

If he said "I hope this doesn't BUG you" one more time, I was about to start the Great Blacksburg Riots of 2013.  

Definitely check out The Next Three Days Blacksburg Website if you're in town. The site shows the schedule of restaurant specials, concerts, and other events for, you guessed it, the next three days.

As a dog lover, I appreciate how every local Blacksburg event is dog friendly; the sheer amount of them and their good behavior are impressive. The Solstice Fest had a petting zoo and a dog parade along Main Street. I was too busy  D'awwing to take pictures, and I only ended up getting two. Sorry.

For her talent, she played "Somewhere Over the Rainbow" on ukelele. It's a shame she lost to the  Dachsund that rolled over for ten consecutive hours.

"Hey, my eyes are up here."

Later that night, the concerts got into full swing. For an event like this, I figured the acts would be too few to last til midnight. Wrong again. And these groups weren't campy garage bands, either; you could tell they had put thought and time into their setlists. Clearly, the hosting radio channel brought in the cream of the local crop.

Everyone funneled toward the stage as the night winded down.  While the day was chock full of kids in Angry birds shirts, many more adults came out for the night concerts.

The Alexander Black House is currently under renovation/restoration on Draper road. A model of Victorian architecture, it'll also be a museum and cultural center.

The Alexander Black House should be almost twice the size of what it is now when it's finished. It provided a great backdrop for the festival, and will hopefully become a centerpiece for events in the future.


Cheers,

Ben

Week 3/4: Programming Made (Sort of) Easy

Figuring out wiring and circuitry is only half the battle; these systems need to be told what do, along with all the specifics that go with those actions. We're programming a small robot to perform certain commands, and once we have it down, we'll build a larger one. Here's where the biology comes in: instead of a small microchip giving commands, it'll be bacteria acting as the robot's brain.

For programming, we've been using Arduino, a microcontroller board that acts like a mini-computer with its own power source.

We used the Arduino UNO, but there's also the Leonardo,  Lilypad (a circular platform),  Nano, Yun, and many more. They offer different sizes, power sources, and functionality.

The UNO is about the size of a playing card, and uses its own type of code as a simpler substitute for C++, a notoriously hard code to understand.

I won't go into the nitty gritty specifics of the code, but it's a lot more straightforward. Assign a device (LED, sensor, motor) to a one of thirteen ports, and you can control under what circumstances the devices are powered through the Arduino.

Using a do-it-yourself Arduino kit with next to no instructions, we were able to put together a moving robot with four-wheel drive  and an ultrasonic sensor that could execute various commands as given by the computer; move forward, move backward, turn right and left, rotate the sensor, and record distance via ultrasonic echoes.

All four motors are connected to the Arduino through the breadboard, as is the motor rotating the sensor on the right.

Right now, the motors for the wheels are controlled by the computer; enter a positive value for moving forward, negative for reverse, and two other arbitrary variables for turning. Speed is controlled by the value entered: the higher it is, the faster the wheels move.

The circuit on the breadboard with the black chip is called an H-bridge, which can direct current in either direction. This is what allows the wheels to spin one way or the other.

Our next step is to have the sensor take over this job; much like the bacterial interface we'll install, it will send distance data to the Arduino and eventually the motors to move in a certain direction. Once we figure out the basic skeleton of the code and wiring, it's just a matter of making sure the bacteria fit in.

It's hard to see here, but we've used an H-bridge already built into a breadboard/chip to use less space. If  you take the tape off, the whole thing doesn't fall apart, I promise.

Was that not the most entertaining and interesting post ever? Maybe I'll search for the Holy Grail next week and write about that to make up for it.

Cheers,
Ben

'Burg to 'Burgh: Day 3

Carnegie Mellon University barely touches UPitt, and yet the campus has such a different feel to it. Surrounding by buildings and open quads, you wouldn't know you were in a densely populated city. Of course,  today Pittsburgh was back to its "usual" weather of cloudiness, humidity, and rain. Blacksburg, take notes.

Our workshop was held in Hamerschlag Hall, which sounds more German than Otto von Bismarck eating schnitzel in a fresh pair of lederhosen. The building houses most of the engineering department and its labs, and while getting lost, I came across a huge conference room/lab that looked just like the UN. No shortage of funding here.

Hamerschlag Hall would fit in just fine in D.C. There's also five floors below this one, with windows facing out towards the rest of the city.

We met Dr. Ruder's colleague Lina Gonzalez and several interested CMU undergrads on D floor, four floors below the hall's entrance. This workshop was meant to explain the idea behind soft lithography, an effective method for creating microfluidic devices.

Lithography was originally used in the art world: professional lithographers, sometimes students of famous artists, could effectively recreate a work by laying layer upon layer of ink and other material until the image is completely rendered. These students then sold their work; the better the quality of their re-creation, the higher the buying price.

Now this technique has been adapted to craft microfluidic channels, as seen in "lab on a chips". There's about five steps in the process, and if you're not careful in any step, or leave your material on a hot plate for too long, you have to start over. A warning:

I apologize if I get too technical. But the man who passes the judgment should swing the sword.

The dimensions of the channel itself are sketched out on AutoCAD, sent out to a company with a high-resolution printer, and the transparency is promptly returned. Next, the master template is made on a silicon wafer with SU-8 photoresist, a very viscous polymer. 

A series of UV and hot plate treatments follows, and then a developer solution is added along with several other reagents. Placed in a vacuum,  the photoresist polymer not bound to the silicon wafer is washed away, leaving only the AutoCAD design. The duration of UV and hotplate exposure it critical; the thinner the channel, the shorter the treatment time.

The wafer/photoresist solution in a vacuum.

That's developing solution in hand on the left. It washes away the portion of the photoresist not exposed to the UV light, AKA everything but the master mold.

Next, we added PDMS (Polydimethylsiloxane) to the master mold template and mixed gently. The mixture was then heated to "cure", or harden, the PDMS polymer. The section of the polymer was isolated and the PDMS layer, now with the channel pattern imprinted was peeled from the wafer.

A special kind of needle was used to poke holes at ends of the channels for adding nutrients, treatments, and the like. But the side of the hardened PDMS with the imprinted channel is open to the air. To fix this, the PDMS and a clean glass coverslip were placed in a plasma cleaner, which cuts off a small layer of electrons from the surface. Now, the PDMS and the glass can covalently bond, forming an airtight system. It was impossible to pull apart with sheer force.

The final product. That white circle is a needle insert, and you can see the branching of the channels  as transparent lines.

We got to keep the channel above as a keepsake, it makes a really good . And the CMU crowd were welcoming folks, too. The workshop gave us a great start for how we can re-create and use something like this for our own projects.

Cheers,

Ben

'Burg to 'Burgh: Day 2

We headed into the Steel City early Sunday morning, coming in through the Fort Pitt Tunnel. The mountains surrounding the place bear a resemblance to those around Blacksburg in that you can see them miles ahead, but steep cliffs from the result of blasting dot the Pittsburgh perimeter.

That pointed building ahead is called Fifth Avenue Place, a shopping and office complex. The mast at the top sways  a good three feet in high winds.

 We passed through the University of Pittsburgh several times due to its central location, much like VCU in Richmond. It has more quads and recreational fields of its own though, and its buildings blend in with the cityscape, save for one:

The Cathedral of Learning has 43 floors with public access to the  36th. Despite the name, no religious events are held here.

The first few floors are the equivalent of Tech's Torgersen Bridge, a quiet study area for students, while the higher levels house offices for the Honors Program, Study Abroad, etc. A few students were at work, but we mostly saw visitors like us walking around.

I wonder how that old Headmaster is doing these days. Oh wait...

From the 36th floor. The Carnegie Museums are on the left, with a quad for communications majors on the right.

Our first stop was the Carnegie Museums of Art and Natural History, both located in the same building. We didn't have time to visit the Carnegie Science Center or the Andy Warhol Museum, also in Pittsburgh. I can only appreciate a soup can for so long.

The Natural History Museum progressed in an evolutionary fashion, from dinosaurs all the way up to modern mammals and other cool things that can kill you.

The windows in the back show the museum's library, with over 132,000 volumes.

  Among the displays I recognized a model of a T. rex skeleton  I had seen before: "Jane", which I saw on exhibit when I was 14 at the Burpee Museum in Rockford, Illinois, where my mom's family is from. The actual "Jane" in Rockford is the best preserved and most complete skeleton in existence of a juvenile T. rex. My sister is also named Jane, who is also a cold-blooded reptile (sometimes).

Plenty of other animal exhibits from around the world were on display, such as this one:

A French naturalist and taxidermist witnessed this badass scene and recreated it in the late 1800s, entitled "An Arab Courier Attacked by Lions."  The courier has killed the lioness here with a shot to the head.

It's probably thanks to this guy that Barbary lions are now extinct. And yet, the public and art world of 1898 thought this was so discomforting and unsuitable for display that the Carnegie Museum acquired it for only $50.

The art museum has everything you would expect and then some; a giant statue room, a large atrium with casts of famous buildings and sculptures, and art pieces sorted by style and civilization. Japanese prints, Renaissance art, and Hindu idols were all there.

The modern art section is another story. If you've seen Banksy's documentary "Exit Through the Gift Shop," then you know how confusing modern art can be. It's not supposed to make sense. You're not supposed to piece together a story or find an underlying meaning from it. Scratching your head and wondering what the hell you're looking at is the point.

The first exhibit in the modern art section. I think I did something like this in third grade and got a C+.

Slenderman has really let himself go.

Yes, this is a looped video of a cat drinking milk. And yes, this is in the modern art section.

A more artsy piece called the "Walking Man".  It sold at auction for *Raises pinky  to mouth* $100 million dollars! But this isn't the only one; there are five more models.

After giving up trying to figure out what everything meant, we took a wooden gondola up to Mount Washington, which offers many high-end restaurants and homes along with a great view of the Pittsburgh skyline. Unfortunately, we weren't dressed for the occasion.

The gondola during its 300 foot descent. The red building below is an old train station converted into a shopping and tourist center.

 From the top of Mt. Washington. Heinz field is centered here, home of the Pittsburgh Steelers. Nice try, Bane.

Our workshop at Carnegie Mellon started early the next morning, so we left after eating to rest up and read over some papers. Pittsburgh has a lot to offer, and it can't be covered in a single day. A Pirates/Steelers game in town would definitely make a great second trip.

Cheers,

Ben