Friday, January 30, 2015

Office name plate using Arduino Nano, LED backpacks (Adafruit)

My laboratory/office is located in the basement of Biology Department building which is difficult to find because there are many offices. I decided to make my name plate to be more visible using Arduino and LED packs.

- List of items
  1. Arduino Nano (Here)
  2. 4 character LED (Here)
  3. 8x8 LED matrix (Here)
  4. Power adapter
  5. Jumper wires
  6. Breadboard
  7. Potentiometer
I also used CNC router (from HackRVA) to carve my name and spaces for the LED matrix.
Matt, helping me to carve my first CNC project
Then, I connected Arduino Nano with the two LED backpacks.
Testing LEDs
 It turns out that the 8*8 LED backpack is way more powerful (or functional) than I originally thought because I can scroll a sentence (although I don't know how many characters I can use).

I use a potentiometer to control the display.
The window is not really clear transparent but still I can see my name and LED characters clearly.

I thank Aron, Matt, and other HackRVA members for helping me to build, learn, and do electronic work!



Wednesday, December 31, 2014

Arduino Duemilanove + GSM shield, trouble and solution

If you are a beginner in Arduino,  GSM shield, and have failed to use those for sending/receiving SMS, or calling/receiving a call, I can give you a bit of help. Maybe a lot depends on your previous skill level.

You will be able to find a lot of instructions for Arduino Uno + GSM shield. But for any reason, I could not find one good instruction explaining Duemilanove + GSM. Now, after I figure it out, it makes sense because Uno and Duemilanove are almost identical. However, although Arduino experts would understand this GSM instruction without a question, there are so many things which do not make sense to me at all, such as: (and I strongly believe that it is not just my fault as you can see below)
Figure 1. On the left (GSM shield), it clearly says that 'pins 0 & 1' are not connected! HOWEVER, when you connect the GSM shield onto Duemilanove, the GSM pins 0 & 1 are mounted onto the Duemilanove pins 0 & 1. As you can see in Figure 2!
Figure 2. See the bottom left side of picture (right above orange half circle). As you can see, I connect the GSM pins 0 & 1 with the Duemilanove pins 0 & 1. Why, why, and why the official instruction says "not connected"? I really want to know why they mentioned it. But I can confirm that you NEED to connect them. 
Also, there is one more weird instruction I found (please see Figure 3) below:
Figure 3. Check out the difference of TX/RX labels between pictures from the official website (left) and mine (right). Although left official picture says that Pin 2 = RX, actually, my shield Pin 2 is labeled as TX. 
In Figure 3, the pin 2 is actually labeled as GSM TX (not GSM RX as shown in the official website). I was extremely confused. But please ignore the difference. Just mount the GSM shield to Duemilanove.

I also had a problem with Sim card. I need to explain more about this problem. I don't have a phone using the same size of Sim card. I purchased Sim card from the Ebay and activated on AT&T GoPhone website. As soon as you activated the card (by adding Sim card number and IMEI number of the GSM shield), it automatically changed the Sim card Pin number!!Very annoying!!!!! At this point, only way you can add money to the card is by calling the company. However, you still need a phone using the Sim card to have a PIN number. I called three time, and all AT&T representatives ask me for finding a AT&T phone to get a PIN number. You may think we can receive the number by connecting the shield and Arduino to our computer. However, to run the Arduino 'ReceiveSMS.ino', we need to type 'pinnumber' which I didn't have.

So, what I recommend is simple: just go to AT&T store and explain that you need PIN number. I ended up replacing the SIM card.

Finally, I found that we need to type pin number in Arduino IDE (instruction). On the second line of the instruction, if you have PIN number (e.g., 1234), you need to remove quotation marks!!!!
So, instead of below
#define PINNUMBER ""
you need to type
#define PINNUMBER 1234

The PINNUMBER command line is the only line you need to change. I found some instructions to remove the pin number, but I don't know yet.

I hope this instruction help you.
Figure 4. This image shows another side of Figure 2. 

Wednesday, December 18, 2013

Scientific communication

Many agree with the expression 'A picture is worth than a thousand words' in scientific papers. I like a paper with a summarizing diagram at the end of discussion because it helps me understand main findings of the paper. But I wonder why I have not seen any scientific paper with a drawing, that's not just with boxes or arrows but with actual drawing. Even if we can add a drawing in a paper, I would be in big trouble because I cannot draw well yet all. 
Small pond with many cattails

Bioluminescence lagoons in Puerto Rico 2

It was way more brighter than I thought!  
Laguna Grande
For a week-long intense field work, more than 15 undergraduate students and 7 instructors had worked together to conduct various experiments, including environmental monitoring, phytoplankton and zooplankton metabolism, and sediment-water nutrient flux, in Laguna grande, Puerto Rico. I would like to share pictures showing a time line of our experiments. 
Collecting sediment cores
Sediment core samples collect at three sites (tape colors indicate sites) 
Set up incubation for light-dark experiment
Collect water samples 
We had also monitored water properties throughout the lagoon and, interestingly, there was a wide range of difference in depth, salinity, oxygen, and turbidity. I did not expect such a big difference in all aspects of ecosystem properties in the small ecosystem from the head (near the channel of the Caribbean Sea) to the other end (near mangrove forest) of the lagoon. Our preliminary sediment-water flux results also suggest that there was 5-fold difference between sites in the flux of respiratory products, such as ammonium and dissolved inorganic carbon. In fact, this experience makes me think that I want to do whole ecosystem study similar to 'Ecology of a New England salt marsh (Nixon & Oviatt 1973).' It was too short period to fill all processes into the diagram but hopefully I can work there again in near future.
Uncompleted conceptual diagram
Most of all, I would like to thanks all participants and Drs. Moser and Cornwell in the program for providing me the wonderful research experience in the Caribbean island.

Saturday, June 1, 2013

Bioluminescence lagoons in Puerto Rico

I have traveled many cities in the US to participate in oceanographic research and conferences but didn't have a chance to travel outside this mainland. Now, I will be in Puerto Rico (PR) in June 2013 and help Puerto Rican undergraduates who want to learn aquatic science.

The title of this National Science Foundation funded project is:
Undergraduate Research Experiences in Estuarine Processes

Drs. Moser (director at Maryland Sea Grant College), Harris, Cornwell, and Pierson (faculties at University of Maryland Center for Environmental Science) have been collaborating with Puerto Rican scientists and conducting preliminary studies in bioluminescent lagoons in PR.
In the upper right corner of the country, bioluminescent lagoons are located in the city of Fajardo and the lagoons are surrounded by mangrove forest. Inorganic matter produced or released from mangrove trees are known to be consumed by dinoflagellates which emit bluish color.

The lagoons are now heavily protected due to detrimental effects of tourism in the country and a lot of efforts has been made by individual and groups to protect this environment. However, only a handful number of research has been conducted and we have no clear understanding of this amazing plankton reaction and the effect of changing environmental conditions. We hope that our collaboration not only enhances our understanding in the ecosystem but also increases awareness of this vulnerable environments. Also, I personally hope that I can improve my teaching skill through an interaction with local students. I will keep posting this project as it progress.   

Saturday, May 11, 2013

KIOST-NOAA lab opening ceremony




I have been invited as a guest speaker for KIOST (Korea Institute of Ocean Science and Technology) and NOAA workshop in Vienna, Virginia. KIOST director Dr. Kang and other KIOST staff visited from Korea and shared our interests in ocean environments. I have honestly never met this many Korean scientists before but this meeting absolutely broadens my view in oceanography.

NOAA-KIOST collaboration seems to focus on ocean observation and the exchange of oceanic technologies. For examples, IMET (Institution of Marine Environmental Technology) in Baltimore has been working together with KIOST for about a decade. And it is really pleasure to hear that Korean government invests lots of money to all sorts of oceanographic division.

Wednesday, December 19, 2012

Conceptual Diagram

One of most respected scientists at University of Maryland Environmental Sciences is Walter Boynton, who has devoted almost entire his life to restore Chesapeake Bay. He emphasizes drawing conceptual diagrams so much, and I also draw a lot to clarify my research idea. One of examples is shown below and this is about nutrient cycle in estuary although it is not completed. It can be very complex but also simple depend on the purpose of diagram. I need full pictures of nutrient cycles because I want to estimate net ecosystem metabolism, which I want to talk in near future. In short, net ecosystem metabolism is a combination of 'plant' and 'animal' metabolism and it shows the balance of ecosystem by subtracting them each other.  
Conceptual diagram