Archives for the month of: November, 2012

The Test

My group hoped to create a sensor network as part of our final project in sensitive buildings.  As a first test, we followed the example found in chapter 5 of Wireless Sensor Networks.  We configured two XBees to be routers in AT mode, and one XBee to be a coordinator in API mode.  We also configured our two router XBees to send out analog data from AD02 every 1000 milliseconds.

To test out our wireless setup, we breadboarded each of the router XBees and added a photoresistor (the example uses a temperature sensors, but we had these lying around).  We made sure to incorporate a voltage divider circuit on the photoresistor, as XBees require analog values to be between 0 and 1.2 volts.

We plugged our coordinator XBee into the computer (via an XBee Explorer) and ran the example Processing sketch.  We were able to see data!

We brought our setup to 240 Central Park South to test our range.  We left the coordinator in the conference room and brought the sensor into the lobby hallway on the first floor.  We were definitely able to communicate close to the window, but another router might provide some extra coverage on the ground floor.

The Real Deal

For our final setup, we added an Arduino into the mix since we wanted to do some preprocessing before sending our data to iDigi  Michael breadboarded some op amp + mic circuits to pick up sound data, and attached some great indicator LEDs.  He wrapped it all up in a modified Radioshack project box.

Here’s the inside:

sensor-box-inside

 

Which fits nicely inside the box (labels by moi!):

sensor-box-with-mic

 

 

Notice that we wrapped the mic in latex to protect it from the elements.  Our plan was to install two microphones in the building, one in the conference room and one in an abandoned apartment building on the second floor (facing Columbus Circle).  We stuck the mic in the conference room out of the window, but decided to keep the other mic inside as there was no good way to protect it from the wind near that particular window.  Here’s a setup in action:

sensor-box-columbus-circle-1

 

Sending our data to iDigi

Here’s a very simple code example to send data to the XIG/iDigi data stream.  This code is keeping count of the sound spikes above a certain threshold, then sending that data to a data stream entitled “counter”.  Our final version is modified, but this is the basic idea.

/* Code by: Alex Olivier
* Example to send sensor data to XIG
*
*
*/

int spike_counter;
int threshold = 542;
int[] names = {”

void setup(){
Serial.begin(115200);
counter = 0;

}

void loop(){
// send a counter value every second
int micValue = analogRead(A0);

if (micValue > threshold){
//increment spikes
spike_counter++;
delay

}
String name = “spike_counter”;
String units = “spikes”;
String post_message = “idigi_data:names=” + name + “&values=” + counter + “&units=” + units;

Serial.println(post_message);
delay(3000);
counter++;
}

 

And here’s some of the data posted on iDigi:

idigi-graph

 

 

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This week in Understanding Genomes, we were asked to run a pBLAST search on a chicken protein to determine its function and similarity to human proteins.  We watched a tutorial video on the proper way to do a pBLAST search beforehand.  Here is the sequence:

MAFVPDLDVLESSSLSEETFYGPSCLCLQKKPRLDSEHTTVDVQVTVRKGRGARSFRRAAVLVVAMTKLL
RRPRSRDFADSDLSALLEEVFEPVTFQRLESSYAGAPAFRYTRSQSFDIFDINQKCFVLESPTQLVALHL
QGPSSSQKVRLNIALYRPRGPRGSAGTGQMPVALGIKGYKLYMSCVMSGTEPTLQLEEADVMRDIDSVEL
TRFIFYRLDSPTEGTTRFESAAFPGWFICTSLQPRQPVGITNQPDQVNIATYKLSGR
Here’s a model of the chicken protein:
In the video, I learned a few things that were definitely helpful.  First of all, the video recommends to search the “Reference Proteins” database rather than the default “Non-redundant protein sequences” database, which actually contains many redundant sequences.  Secondly, the video explains how to read the “E value” of the resulting search.  We are told that e values on the magnitude of 1e-10 are considered good matches.
I ran a pBLAST on the chicken protein and searched only for human matches.  I got 15 results with a low E value.
The top results was an “interleukin-1 beta proprotein”.  It is a cytokine, or cell-signaling protein, that is produced by macrophages.  It is processed to its active form by capsase 1.  According to the report, this protein helps mediate our body’s inflammatory response, as evidenced by some of the related journal articles.
The highest homo sapien match to our chicken protein shows 73/212 exact amino acid matches and 107/212 similar matches.

Sheiva and I did our ethnography assignment at our classmate Jacki Steiner’s apartment on Wall Street.  We decided to explore how Jacki’s space expresses her personal identity.

Jacki is 25 years old.  She’s originally from Florida, but moved to Providence to attend RISD.

The first thing that struck us about Jacki’s room was how coordinated it seemed.  All furniture (her desk, bed, dresser, and bookshelf) was sleek, modern, and black.  Her linens (bedsheets, a curtain hung to cover her windowed door, etc.) were a deep purple.  She even had a black and purple toned painting of the Manhattan skyline.  The painting was small, clean, and framed in a sleek black frame.  She later informed us that she purchased this painting from a street vendor.

Jacki has a lot of books in her bedroom, which are organized into two main locations.  The makeshift bookshelf on top of her dresser contains many books relating to typography and design.  Jacki went to RISD, so some of these books were from her time spent there.  Her other bookshelf contains a few books for pleasure (books about Batwoman, wolves, etc.) as well as books about sexuality.  Jacki told us about her organizational scheme, but it is also pretty apparent.

Her desk is neat as well, complete with a chair and printer. She has a few trinkets around her room, including a postcard with a schnauzer dressed as a biker and a leather Pirates of the Carribean cuff.  She told us that she has a schnauzer named Mongo at home in Florida.  It seems like Jacki’s trinkets remind her of home.

Jacki’s room appears very adult, with small touches of nostalgia.  It seems like she aspires to live in a somewhat controlled and organized environment as well as present a mature but well-designed exterior.

Pics coming soon!