Friday, June 29, 2012

Week 3 Day 5

This morning we finished up our artificial stream system and it is running great!




We dealt with some water level issues in the beginning but we have that pretty well worked out now. We will fill and drain the system a couple of times until the water is running clean before we actually add the fish. This is the general idea, though!



Exciting stuff! We also presented a progress report to the other RET teachers and some of the UNT staff. Below you will find the presentation we gave as well as the demo of the stream the RET group was given.



Here is the Demo!

Thursday, June 28, 2012

Home

This is a link to a documentary called Home that could be used to provide some background for a "big idea." Thanks Lori!


Week 3 Day 4


This morning we had a meeting with Dr. Hoeinghaus to catch him up on the project. He was very enthusiastic about the progress we have made with the sensor cluster and is excited that we may be able to start field testing as early as next week (assuming the Otter Box shows up and Yixing banishes the last of the gremlins from the pH probe.) He is also sending us a research grade pH probe so that we can take comparison readings to help us sort out what might be going on with our probe.

We also talked some more about the possibility of setting up streaming video. We discussed some of the difficulties involved in setting up the system as well as looking at the best ways to get around those. It looks like that is still a project that we will push out to next year. We still have a stretch goal this year of putting together a proposal for that project so the UNT RET team can begin gathering the tools and equipment necessary.

After having the general discussion about setting up the streaming video Dr. Hoeinghaus went into more detail about his vision for ways to utilize the wireless sensor network and the possibilities for the streaming video. Once we get the sensor clusters packaged in the enclosure the potential for use is really only limited by your creativity. The most straight forward use is putting a large hanging hook on the device itself so you can hang it off the side of any tank and dangle the probes in for readings. Alternately you could mount it on a post in a lagoon, place it in a bouy, either tethered or free floating, mount it on an R/C boat and cruise around... There are any number of deployment methods. One goal for future study would be to find smaller probes to increase the number of areas you could deploy in as well as allowing for better monitoring of microzones in the water. Once the device is deployed and broadcasting the data can be uploaded to the internet with relative ease (assuming there is an internet connection available at or near the site) and then the data is available anywhere. Some of the specific instances Dr. Hoeinghaus referenced when discussing the utility of that level of access involved situations in Brazil where a test site might be a three hour boat ride away from you base, or when roads between you and a test site get washed out. It would also be helpful, and possibly more cost effective, to have team members who were not in the field access the data through the internet and begin crunching numbers.

A final use for the internet access to field date involved sharing a limited data set with schools so they could use real world data in the classroom. This idea ties in with why he is so interested in live streaming video. Dr. Hoeinghaus would like to provide a way for students everywhere to be able to remotely access some of these field sites to see what research is going on in the real world. It might even be possible to do webinars and/or a remote classroom type of situation where high school students could be given a tour of the research sites and then ask questions of the scientists doing the study.

In other news, Yixing thinks he has the problem with the pH probe isolated. It appears there is some interference that occurs when you run the pH probe and the DO probe concurrently. The initial thought he had was that it might be because they are drawing from the same power source. He is going to create a transformer to split the single 5 volt DC output to two channels. If that fails I suggested the possibility of inserting a switching call in the code so that the pH and DO probes would alternate when they are on. The first solution works if the problem is in the power draw on the circuit side. The second solution works if the problem involves the current flow through the probes and the sample water.

We also finished sealing the joints in the table top model. We have a three part solution because we REALLY don't want the water to leak once we started this bad boy up considering it is in a computer lab. We sealed the gaps between the guttering for the riffle and the edge of the tubs with J-B WaterWeld and let it dry. Next, we coated the joint on both sides with Loctite Marine Epoxy and let it set. After that we put a layer of waterproof repair tape over the joint. If it still leaks...well, no one can say it was because we weren't thorough. Tomorrow morning we will clean the gravel, install the pump and fill the system with water. Wish us luck!

Literature Review

Here is what Lori has come up with so far on the Literature Review:


Literature Review



Monitoring water quality through a telematic sensor network and a fuzzy expert system
Hatzikos, Bassiliades, Asmanis and Vlahavas

The article introduces an expert system that monitors seawater quality and pollution through a sensor network called Andromeda. This system is used to monitor sensor data collected from monitor stations. The data is then used to tell whether water is suitable for different uses, such as swimming. The goal of this system is t help authorities in the fight against pollution in the aquatic environment. This expert system determines when certain pollution limits have been exceeded and flags up alerts. The use of this system could someday help to monitor pollution on a worldwide basis.

Environmental Wireless Sensor Networks
Corke, Wark, Jurdak, Hu, Valencia, Moore

The article explains why there has been slow progress in using WSN. The WSN hype was triggered by the availability of low-cost low-power feature-rich microcontrollers and single-chip radio transceivers. Scientists expected a high level of system integration, performance, and productivity. The WSN is just one-part of a complex system that includes internet links from the WSN to a server, databases, and web presentation tools. Each component is critical for success and each was underestimated. It was assumed that servers were always up. Performance of the WSN has many aspects. A gap in any one of the aspects lead to gaps in the data gathered.

Environmental sensor networks in ecological research
Rundel, Graham, Allen, Fisher, Harmon

Environmental research is undergoing technological revolution as interfaces develop between environmental science, engineering and informational technology. Advances have been made possible by decreasing cost, size and weight, and improved reliability, of sensing hardware and software. The internet allows for increased connectivity to transmit and share data, with this development, an array of sensor networks are emerging to address ecosystem issues. New designs of sensor networks allow for the observation of systems in near-real time from local sources and remote sensing data streams. Ecological sensor networks are at the core of major new efforts to address issues of global change and environmental stability.

Environmental Sensor Networks: A revolution in the earth system science?
Hart, Martinez

Environmental Sensor Networks (ESNs) facilitate study of fundamental processes and development of hazard response systems. They have evolved into “intelligent” sensor networks that has a network of automatic sensor nodes and communications systems which communicate their data to Sensor Network Server (SNS) where the data can be integrated with other environmental datasets. ESNs will become a standard research tool for future Earth and Environmental Science.  

Big Picture Research

Lori has been doing a lot of the "big picture" research that provides some background on the "why" aspect of our project. If you want to follow along with what she is digging in to then dive right in!

Denton Stream Team Newscast
http://www.nbcdfw.com/news/green/Putting-North-Texas-Water-Quality-to-the-Test-139900243.html?_osource=Newsletter-Daily

Texas Stream Team site at Texas State University
http://txstreamteam.rivers.txstate.edu/

Texas Water Development Board for kids
http://www.twdb.state.tx.us/conservation/education/kids/

USGS Water Quality Data
http://water.usgs.gov/owq/data.html

Take Care of Texas for Teachers
http://www.takecareoftexas.org/teachers

One Planet, One Chance
http://inmotion.magnumphotos.com/essay/one-planet-one-chance


Nutrient removal from polluted stream water by artificial
aquatic food web system
Dawoon Jung Æ Ahnna Cho Æ Young-Gun Zo Æ
Æ Ahnna Cho Æ Young-Gun Zo Æ
Seung-Ik Choi Æ Tae-Seok Ahn
Æ Tae-Seok Ahn
http://www.springerlink.com/content/3r210447r062j63k/fulltext.pdf

Journal article:
Non -point source Pollution A distributed water quality modeling approach
http://www.sciencedirect.com/science/article/pii/S0043135400003365

Index for evaluating water quality in Streams
https://docs.google.com/viewer?a=v&pid=gmail&attid=0.1&thid=1382f4145b19d157&mt=application/pdf&url=https://mail.google.com/mail/?ui%3D2%26ik%3D4d9928d494%26view%3Datt%26th%3D1382f4145b19d157%26attid%3D0.1%26disp%3Dsafe%26realattid%3Df_h3yr5eom0%26zw&sig=AHIEtbTn62i5bh0jU1j9ZCNjqzYwTJKktQ

Here are some reference sites for scientific articles on water quality.  
http://water.sigmaxi.org/?page_id=39

http://www.sciencedirect.com/science

http://www.journals.elsevier.com/water-research/

Research

Below you will find links that will open a PDF copy of each of the papers I have pulled as part of my research on the project so far.





Challenges for Efficient Communication in Underwater Acoustic Sensor Networks


INSTRUMENTING THE WORLD WITH WIRELESS SENSOR NETWORKS




PSFQ: A Reliable Transport Protocol for Wireless Sensor Networks




Seaglider: A Long-Range Autonomous Underwater Vehicle for Oceanographic Research




Underwater Gliders for Ocean Research




VigilNet: An Integrated Sensor Network System for Energy-Efficient Surveillance


Wireless Sensor Networks for Habitat Monitoring



Monitoring water quality through a telematic sensor network and a fuzzy expert system


User Friendly Smart Home Infrastructure: BeeHouse



Environmental Wireless Sensor Networks



Environmental sensor networks in ecological research



Design of a Wireless Sensor Network for Long-term, In-Situ Monitoring of an Aqueous Environment



The Challenges of Building Scalable Mobile Underwater Wireless Sensor Networks for Aquatic Applications



Environmental Sensor Networks: A revolution in the earth system science?



An Efficient, Time-of-Flight-Based Underwater Acoustic Ranging System for Small Robotic Fish



SECURITY IN WIRELESS SENSOR NETWORKS



A Robust, Adaptive, Solar-Powered WSN Framework for Aquatic Environmental Monitoring











Wednesday, June 27, 2012

Week 3 Day 3

Today we focused on finishing the build for the table top artificial stream model. This involved a lot of time with all three of us running the Dremel and another trip to Lowe's. We started off with me finishing out the riffles. I learned from yesterday and made sure to wear my safety goggles.


I probably should have also worn a mask...


While I was working on that Lori was marking off the tubs and Joe was cutting them.





Once we had everything cut and ready we sanded down the edges and tried the PVC cement we got to bind things together. We ran into two problems during this process. First, the cement didn't create a good seal. We decided to fix that with JB WaterWeld and marine epoxy.



Second, the cardboard we had been using to elevate the tubs seemed unlikely to hold up the weight of the tubs with rocks and water so we cut down a sheet of 1/2" plywood to 1 foot sections and made platforms. Joe and Lori put their heads together to get the seals done.



We are going to let that set over night and then we will install the pump, add the rocks and fill it with water. I really hope it doesn't leak after all that work sealing it!


On a final note... here is a better picture one of the other groups took of me after getting iced with PVC dust... Enjoy!


Images from yesterday

Things got a little busy yesterday and I didn't get a chance to load all the pictures and video from what we got accomplished. Here is what you missed!

The aquarium with the probes.

Cutting the down spout into lengths.

Taking off the top of the down spout so it can be used as a riffle. 

A quick tour of the lab. 

Testing the sensor cluster and data sink. Not everything went according to plan...

Tuesday, June 26, 2012

Week 3 Day 2

Today is a down and dirty work day to get our table top model assembled. We started off by rounding up Jennifer (so she could pay) and heading to Lowe's to grab some stuff. The shopping expedition was tedious but necessary.





After we checked out we made some excellent choices on how to transport everything back to the lab.


Back in the lab we got everything laid out and set up my Dremel to start charging so we could cut the down spout to size for our riffles.



Everything was going pretty smoothly... until my Dremel refused to charge. Luckily Lori lives about 5 minutes away and she has one as well. Sadly, when she brought hers up the collar wouldn't release the burr bit so that was no good. We have my battery sitting in the charge with our fingers crossed, Lori is taking hers home to see if there is any tool in her house that can make the collar say uncle and we have Jennifer bringing up her Dremel for tomorrow to see if that works. At this point I'm seriously considering finding out if Makita or Dewalt makes something similar since Dremel has been such an epic fail.

With the absolute failure of our tools we switched gears and set up to start taking reading from our aquarium. The good news is the sensor cluster node has plenty of range to broadcast from the workshop lab to the computer lab. The down side is that the data is way off. We calibrated the spark probes and also took some low tech reading with test strips to get a base line for comparison. The dissolved oxygen probe worked great right off and so did the temperature probe. The pH probe was just plain wrong. The test strip indicated it was between 7.5 and 8. The spark, once it was calibrated, was reading about 8.3. That Atlas probe in our sensor cluster insists that the pH is 5.9. Seems unlikely... We have tried calibrating it several times to get it more in line with the other readings but it is being stubborn. Yixin is focused on that problem and is working towards a solution.



For any one who is curious, our minnows are doing great. They seem perfectly happy and really dig the probes.

This afternoon we are going to a seminar that focuses on ways to take what we are learning here and translating it to a useful format in our classrooms. Yay Lesson Plan Development with Dr. Thompson!

Monday, June 25, 2012

Week 3 Day 1

The day started off with a little hands on work. Sharon brought us some plants and minnows so it was time to get our hands wet and slap together an aquarium. The tank was cleaned and filled on Friday so that part was ready to roll. I treated the water first to reduce the transfer shock the fish were likely to experience and to prime the tank with helpful bacteria and micro-nutrients. Then I dumped in plants and some minnows. All of the plants are locally sourced, including one very cool carnivorous plant called bladderwort. The fish we chose are minnows because they are pretty hardy and the can gulp from the surface if the need to (which is likely since we will eventually start messing with dissolved oxygen...). Once every thing was in the tank Joe and I did some decorating by anchoring the plants.



 Once that was knocked out it sort of ended our hands on portion of the day. The next thing that happened was a quick status update for Dr. Thompson on where our project stands and where it is going. She was encouraged by our progress and gave us the green light to start acquiring parts to build our sensor clusters and data sink. We also got the go-ahead for to start hammering out our table top stream model. I'm excited about that because it means lots more hands-on build time this week. We will also begin collecting data very soon if we actually get all the parts soon. Yay! One thing that we did discuss as a minor issue is that there is a a strong desire by the group running the project to include streaming video as part of the sensor cluster. Every one agrees that it is a great  idea and we would all like to see it happen but that is really almost a separate project in and of itself because of the processing demands of streaming video. It is likely that will be extended into a group assignment for next year and part of our teams responsibility is to do some planning for that contingency and to create a possible parts list to tackle that project so that there are parts on hand. (Here's hoping we are invited back next year to finish that out!)

Status update complete, the whole group dove deep into literature. Lori is building skeleton descriptors for the research we have pulled so far to include in the literature review section of our paper. Joe has accumulated several dead trees worth of material that he is stitching together to form our introduction. I am data mining the research we have already pulled to both widen our net and to try to get at some of the primary research that underpins a lot of these papers.

Friday, June 22, 2012

Week 2 Day 5

Today is awesome. Yixin Gu is awesome. We now have a complete prototype that is fully functional. Here is some completely inaccurate code to express my feelings... (It's like a nerdy haiku.)



int Yixin = 1 gagillion;
int Zac = 3;
int YCode = 0;
int ZCode - 0;

Void Loop() {
ZacAttempt(Zac);

While (Yixin > Zac) {
   YCode ++;
   Yixin += Ycode;
   Serial.println("Yixin is responsible for fixing all the code.");
}

int ZacAttempt(Zac) {
   If (ZCode = true){
     Zac ++;
   }
}

There. Homage complete. The short version is that I hit a wall and my code was needlessly complex. Yixin was able to get something clean and quick out of the snarl and it works/looks great. "If I had more time I'd of made it shorter." definitely applies here. Here is the completed code for the three probes together.


#include <SoftwareSerial.h>                                                    //add the soft serial libray
#define rxpin 2                                                                //set the RX pin to pin 2
#define txpin 3                                                                //set the TX pin to pin 3

SoftwareSerial myserial(rxpin, txpin);                                         //enable the soft serial port
String inputstring = "";                                             //a string to hold incoming data from the PC
String sensorstring = "";                     //a string to hold the data from the Atlas Scientific product boolean input_stringcomplete = false;                      //have we received all the data from the PC boolean sensor_stringcomplete = false;       //have we received all the data from the Atlas 
                                                                  //Scientific product
  void setup(){                                                                //set up the hardware
     Serial.begin(38400);                            //set baud rate for the hardware serial port to 38400
     myserial.begin(38400);                           //set baud rate for software serial port to 38400
     inputstring.reserve(5);                          //set aside some bytes for receiving data from the PC
     sensorstring.reserve(30);   //set aside bytes for receiving data from Atlas Scientific product
     }      void serialEvent() {                                              //if the hardware serial port receives a char
               char inchar = (char)Serial.read();                               //get the char we just received
               inputstring += inchar;                                           //add it to the inputString
               if(inchar == '\r') {input_stringcomplete = true;}                //if the incoming character is                         
                                                                                         //a <CR>, set the flag
              }      void loop(){                                                                   //here we go....
       if (input_stringcomplete){                     //if a string from the PC has been recived in its entierty 
      myserial.print(inputstring);                           //send that string to the Atlas Scientific product
      inputstring = "";                                                        //clear the string:
      input_stringcomplete = false;                                            //reset the flage used to tell if we 
                                                                          //have recived a completed string from the PC
      } 
  while (myserial.available()) {                                   //while a char is holding in the serial buffer
         char inchar = (char)myserial.read();                                  //get the new char
         sensorstring += inchar;                                               //add it to the sensorString
         if (inchar == '\r') {sensor_stringcomplete = true;}                   //if the incoming character 
                                                                                                //is a <CR>, set the flag
         }

   if (sensor_stringcomplete){           //if a string from the Atlas Scientific product has been 
                                                      //received in its entirety
       Serial.print(sensorstring);             //use the hardware serial port to send that data to the PC
       sensorstring = "";                                                      //clear the string:
       sensor_stringcomplete = false;                                          //reset the flag used to tell if we 
                                                                                       //have received a completed string 
                                                                                       //from the Atlas Scientific product
      }}
Here is the user interface.

Code accomplished. That is not all, though. We also have a a working prototype of the probe cluster. Want to see? Of course you do.






Pretty impressive, right? Look at that soldering work. That's pretty intimidating. Here I am explaining what's going on with all this stuff.




After my spiel Dr. Fu came in and approved the sensor cluster and data sink assembly which means we are go for production. They are ordering all the parts to assemble five full sensor cluster nodes plus a data sink. I'm pretty excited about getting to roll this out so we can start collecting real data. Here is a picture of the meeting when Dr. Fu told every one we were doing a great job.


After the kudos we started talking about where we were headed and what our next steps are.



Now that we know our sensor network is functioning it is time to start collecting data. That will begin on Monday. We will begin collecting data under controlled conditions in the lab so we can compare the data our sensor suite gathers versus other commercially available solutions. Once we have a feel for how accurate it is under lab conditions we will move out to the field and cross our fingers. To test this sensor cluster in the lab we will eventually drop it into our table top model. Since that is not complete yet we need another option. That option is pretty simple... an aquarium. Joe and I cleaned one out and got it set to run so that we can drop in plants and minnows on Monday and start probing!




Parts List


If you have been following our parts lists then here is an updated one.

Classroom Model (List of what we’ll need for each of our classrooms):
Materials Needed:
A.           Project Supplies

  1. 4 Plastic tubs
  2. Plastic tubing
  3. epoxy
  4. ½ horse pump
  5. gravel
  6. water
  7. vinyl gutter
  8. 5 gallon bucket
  9. 10 ft White aluminum downspot- Gutter
B.     Water Testing
a. Water conditioner
b.   Sensors, probes or water quality kits which are used to measure: temperature, pH, dissolved oxygen (DO)
c.    water sample container



Teacher Model:


10 ft White aluminum downspot- Gutter: $6.47
http://www.lowes.com/pd_82573-205-4601100120_4294806370__?productId=1101827&Ns=p_product_qty_sales_dollar|1&pl=1&currentURL=%3FNs%3Dp_product_qty_sales_dollar%7C1&facetInfo=