Team:TU-Munich/Results/How To

From 2013.igem.org

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Revision as of 23:52, 28 October 2013

Our Tutorials

During our iGEM summer we have acquired many skills which are useful for iGEMers and for every synthetic biologist. In order to spread this knowledge we created some tutorials. We hope that these tutorials enable future iGEM teams to present their project in a more colorful fashion.

Wiki Tips & Tricks

Below is a list of iGEM wiki related tips and tutorials for future teams.

Picture viewer

Maybe you have not noticed it yet, but if you clicked any of the pictures on our wiki, you were not redirected to the ugly wiki page of the file. Instead a nice picture viewer opened and after you closed it, you did not have to go back to the site you saw the picture on. To get the same effect on your wiki follow the steps listed below:

Get the files!
We modified the original slimbox 2 viewer to work with the wiki and to not exceed the browser viewport, so it is recommended to use our versions, which can be found at Team:TU-Munich/TUM13_slimbox2.css and Team:TU-Munich/TUM13_slimbox2.js.
Embed the files in your wiki!
The two files mentioned above and [http://jquery.com/ jQuery] have to be embedded on all the pages that should use the picture viewer.
Include the autoload code block!
A bit of JavaScript code that attaches the viewer to the right pictures needs to be executed on all the pages that use it. This code attaches the picture viewer to all images on the page which are embedded with the [[File:xxx.png|thumb|caption]] wiki code and it adds the corresponding caption to the viewer.

$(document).ready(function(){
	$("div.thumbinner > a img").slimbox({/* Put custom options here */}, function(el) {
		url = el.src;
		if (url.indexOf('thumb') != -1) {
			url = url.substring(0, url.lastIndexOf('/'));
			url = url.replace('/thumb/', '/');
		}
		description = $(el).parents("div.thumbinner").children("div.thumbcaption").text();
		return [url, description];
	}, function(el) {
		return (this == el);
	});
});

Test it!
Below is an example picture, click on it to see what the picture viewer looks like.

Figure 1: The logo of our project.

Slideshow

To create a good looking slideshow just follow the instructions below:

Get the files!
You can get the Stylesheet and Javascript for the slideshow either from [http://bxslider.com/ bxSlider] or from our wiki: Team:TU-Munich/TUM13_bxslider.css and Team:TU-Munich/TUM13_bxslider.js.

Embed the files in your wiki!
The two files mentioned above and [http://jquery.com/ jQuery] have to be embedded on all the pages that should use the slideshow.

Include the initializing code block!
A bit of JavaScript code that activates the slideshow needs to be executed on all the pages that use it. This code changes all unordered lists of the class bxslider into slideshows.

$(document).ready(function(){
	$('.bxslider').bxSlider({
		responsive: false,
		auto: true,
		autoHover: true
	});
});

Add the slideshow to the page!
To add a slideshow just put the pictures you want to include in an unordered list like shown below:

<html>
<ul class="bxslider">
	<li><img src="https://static.igem.org/mediawiki/2013/9/97/TUM13_slider_team1.jpg" /></li>
	<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_team2.jpg" /></li>
	<li><img src="https://static.igem.org/mediawiki/2013/3/30/TUM13_slider_moos.jpg" /></li>
	<li><img src="https://static.igem.org/mediawiki/2013/6/66/TUM13_slider_kampen.jpg" /></li>
</ul>
</html>

Test it!
Below is an example of the slideshow.

Generation of Rotating Protein Structures

Animated gifs of rotating protein structures have been used for some time in the iGEM competition. Here we present an easy to reproduce tutorial for iGEMers which are interested in similar images.

If there is no PDB file available for your protein of interest, you can use a homology search to find the most homologous structure. A good homology search tool is [http://toolkit.tuebingen.mpg.de/hhpred HHpred].
The entry for the best matching structure was used for the figure. If it is only a homologous structure please cite this together with the homology when presenting the resulting image.
You can save the PDB file of the homologous structure on your computer.
If you do not have [http://www.pymol.org/ PyMol] (freeware) installed on your computer download and install it.
Start PyMol software and open the PDB file by clicking File -> Open.
The following approach was adapted from a PyMol tutorial http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html Wong.
The following commands were entered into the command line:

PyMOL> orient PyMOL> hide everything, all PyMOL> show cartoon, all PyMol> bg_color white click> Settings>Rendering>Shadows>Occlusion PyMOL> color purple, ss h; color yellow, ss s; color green, ss "" PyMOL> show surface, all PyMOL> set transparency, 0.75 PyMOL> set surface_quality, 1 (command will prolongue the process significantly, you may skip it) PyMOL> set ray_trace_frames=1 (command will prolongue the process significantly, you may skip it) PyMOL> mset 1 x180 PyMOL> util.mroll 1,180 PyMOL> mpng frame

Afterwards the *.png files were automatically converted to *.tif files using [http://www.xnview.com/de/xnconvert/ XnConvert].
The program [http://www.animake.de/gif-animation.htm Animake] was used to generate the annimated gifs.
- The Animake software was started
- A new working folder was generated (File -> New) and the *.tif files were imported (Edit -> Import_from_file)
- The background was set to white (Animation -> Settings)
- The range of colors was set to 256 (Edit -> Select_all and Edit -> Change_Color)
- The size of the file has to be reduced in order to be able to upload it on the iGEM wiki. This can be done by clicking Edit -> Change_size. We suggest a size of 320x240 px or even smaller if the resulting gif becomes to big.
- Finally the animated gif can be saved in the program format (.abp) and as gif (File -> Save_as)
- If you have problems to upload the file on the iGEM server you may try a reduced size (e.g. 300x225 px)

This is how your protein of interest could look like:

File:TUM13 Annimated test.gif

Figure 2: Protein

Setting up a basic Arduino measuring device

Introduction

File:TUM13 Arduino Assembly Animation.gif

Figure 3: Assembly Order

Since the Arduino Due was released in autumn 2012, this is the first iGEM year this very powerful device can be used. We found it a useful supervising tool for short and long-term experiments. It can be used in as well as outside the lab. The improvements that were made from Uno to Due are considerable.

It is capable of handling many things at once, such as a WiFi shield, a display, a SD-Card and multiple sensors. At this point the Uno did not match up any longer.

To establish the usage of Arduino in iGEM even more we want to share our experiences and help you building up a basic device that can collect and view sensor data on its display and upload them to a server.

Part Description

Arduino Due

The Arduino Due is the most powerful Arduino board. Its underlying 32bit-processor is the Atmel SAM3X8E. Contrary to the other boards which run at 5V, a power supply of 3.3V is sufficient. It was released in October 2012.

Data:

 84 Mhz	CPU Clock
 96 	KBytes of SRAM.
512 	KBytes of Flash memory. 
 54 	Digital I/O Pins
 12 	Analog Input Pins
  2 	(DAC)Analog Outputs Pins

Arduino WiFi Shield

The Arduino WiFi Shield is an attachable shield that provides Wireless LAN 802.11b/g to the Arduino. It scans and connects to networks and opens TCP and UDP sockets for data transfer. It also supports WEP and WPA2 encryption. It was released in August 2012. The WiFi Shield is fully supported by the Arduino Due and Arduino supplies a suitable stock WiFi library. There is also an on-board SD-card socket to store received data. As the SD-card is accessible separately, it can also be used as a storage for any data generated by the Arduino. The SD-card socket is also supported by a stock library. The communication between Arduino Due and the WiFi Shield runs via an SPI/ICSP interface.

Pin usage:

Pin  4	SS for SD card (Slave Select)
Pin  7	Handshake between Arduino and WiFi Shield
Pin 10	SS for WiFi
Pin 74	SPI MISO (Master in, Slave out)
Pin 75	SPI MOSI (Master out, Slave in)
Pin 76	SPI SCK  (Serial clock)
    gnd
    3.3V
    5V

Watterott Mega MSD-Shield

The Mega MSD-Shield was designed by Watterott and consists of a couple of components. The components are one real time clock, one SD-card socket (we will not use), a small battery and a socket for a touch display. To get it ready to run, the shield must be assembled. The stackable headers and the clock's quartz must be soldered to the board and the battery must be inserted. Unluckily the Mega MSD-Shield and therefore also the MI0283QT-9 touch display don't come with a working library for the Arduino Due. The existing library only supports all boards up to the Arduino Uno. Therefore all libraries had to be rewritten. The touch display and the SD-card slot communicate with the Arduino Due via SPI/ICSP. The real time clock transmits its data via I²C.

Pin usage:

Pin  4	SS for SD card
Pin  6	SS for the touch of the touch display
Pin  8	reset LCD
Pin  9	LCD LED
Pin 20	RTC (real time clock) 	I²C	SDA (Serial Data Line)
Pin 21	RTC  			I²C	SCL (Serial Clock)
Pin 25 SS (7) for the LCD (Workarround of the double usage of pin 7 by the WIFI Shield)
Pin 50	SPI MISO
Pin 51	SPI MOSI
Pin 52	SPI SCK
    gnd
    3.3V

Display MI0283QT-9

The MI0283QT-9 is a multicolor touch display. It comes already attached to a board, where only the pin headers are left to be soldered. Once assembled it can easily be plugged into the Mega MSD-Shield. It has an on-board touch controller (TI ADS7846). The display size is 2.83"(43.2 x 57.6mm) with a resolution of 240x320. It supports 262k colors. The pin usage is already considered in the Mega MSD-Shield description.

Light Sensor TSL2561

The light sensor is a small, so called, breakout board. It is usually connected by wires instead of directly plugged into the Arduino's headers. The light sensor has two photo diodes on-board that measure visible and infrared light. Similar to the RTC, the TSL2561 is addressed via I²C. Once you get the I²C library working on your Arduino Due working it takes only little effort to integrate additional I²C devices. Just very few lines of the library have to be rewritten here. The photo diodes can be addressed separately or both at one. Their output is already converted to Lux.

Pin usage:

Pin 20	TSL2561		 	I²C	SDA (Serial Data Line)
Pin 21	TSL2561			I²C	SCL (Serial Clock)
    gnd
    3.3V

Temperature Sensor DS18B20

The temperature sensor is embedded into a water proof cable. It is addressed via a OneWire interface. The provided data are digital raw data, which need to be converted into degree Celsius. Information about the conversion are given by the manufacturer. Similar to the I²C (TwoWire) bus, you only have to get the OneWire interface working once. After that, you can easily set up more OneWire devices. Again, just very few lines of the library have to be rewritten.

Pin usage:

Pin 14 	One-Wire DS18B20 (pin was randomly chosen)
Pin gnd
Pin 3.3V

Water Sensor

Setting up the water sensor is very easy. If and how much water the sensor registered can be measured via an analog pin.

pin usage:

Pin A5	Water sensor
    gnd
    3.3V

Tools

Breadboard
Soldering bolt
Solder

Assembly

Keep everything clear during your assembly. If you have different colored linking cables, always try to use the same color code (e.g. red cable for 3.3V etc.) otherwise troubleshooting can get nasty.

All steps you need to follow building up your own Arduino measuring device are explained below in the slide show and the image descriptions.

File:TUM13 Arduino in action.gif

Figure 33: Arduino in action

For more explaining photos visit our photo gallery. On the left you see the Arduino as it boots up, connects to a WiFi hotspot and collects data.

Code

We strongly recommend the usage of Microsoft Visual Studio with the "visual micro" plugin. Microsoft Intellisense helps you a lot, when you are unfamiliar with the manufacturer provided libraries (automatic code completion). In order to compile the code properly you need the latest beta version of [http://arduino.cc/en/Main/Software Arduino's software]. In the visual micro settings, choose the path to the Arduino IDE on your hard drive, also disable "Upload using programmer". In the settings of the Arduino IDE, select "use external software".

Now you are ready to start programming. Below we share our code, feel free to use, edit and play around with it! But wait first you need our libraries! They're exclusively fitted to the Arduino Due, mostly based on the existing manufacturer's libraries for the Arduino Uno.

Assuming you followed our tutorial until here. Once you adapted the code to your WiFi and server settings and uploaded it to the Arduino it does the following:

it starts up and the screen turns from black to white
if you have pressed the screen, the calibration process starts
it searches for networks and displays the total number of found networks on its screen
it displays the first six WiFi stations that were found
it tries to connect to the WiFi station you have set
if a connection was established it shows the Arduino's IP address and the SSID (name) of the WiFi it is connected to
then it idles until you you press the screen
after you pressed the screen it jumps to the "loop"-section of the code
it continuously runs and displays:
1. the current time
2. the temperature
3. the measured infrared and broadband light
4. the measured values of the photodiodes
5. the coordinates of the point you pressed on the screen
it builds up a connection to a server, calling a PHP script, passing on the collected data

#include "SPI.h" // SPI library (stock)
#include "Wire.h" // TwoWire library (stock) sda-scl
#include "DS1307.h" // Real time clock library (original library, slightly rewritten to fit the Due)
#include "MI0283QT9.h" // LCD library (quite much had to be rewritten). Pins were changed, usage of Software SPI... quite a mess but it works great
#include "ADS7846.h" // Touch controller (same story as at the lcd library)
#include "Adafruit_TSL2561.h" // light sensor library (had to be rewritten in some parts to fit the Due) functions were added to correct the lux-output that wasn't always correct with the stock library
#include "OneWire.h" // OneWire (I don't know, but I guess it's the stock library)
#include "avr/dtostrf.h" // optional library to workaround some compatibility problems with the Due
#include "math.h" // standard C-maths library
#include "SD.h" // SD reader (stock)
#include "WiFi.h" // (stock)
#include "time.h" // standard C-time library

DS1307 *rtc; // real time clock
MI0283QT9 *lcd;
ADS7846 *tscr; // the "touch" of the touchscreen
OneWire *tempsen;
Adafruit_TSL2561 *lightsen;
WiFiClient *client;
boolean lastConnected, firstrun=1;
char c;

uint8_t sea; // current value of seconds
uint16_t counter=0,valueCounter[3]; // vlauecounter 0:Water 1:Temp 2:Light/IR
float valueWater=0, valueTemp=0, valueLight=0, valueLightIR=0; // these are the sensor values that are avaredged over each time interval between the sending processes
uint32_t valueTime=0;

void initDisplay() // initialize the lcd display
{
	lcd->led(100); // lights on 100%
	lcd->setOrientation(180); // flip screen orientation to 180° (optional)
	lcd->clear(COLOR_WHITE);
	tscr->service();
	if(tscr->getPressure()>5) // Calibration on pressure
	{
		tscr->doCalibration(lcd);
	}
	lcd->printClear();
}

void initLightSen() // initialize the light sensor
{
	lightsen->setIntegrationTime(TSL2561_INTEGRATIONTIME_101MS);
	lightsen->enableAutoGain(true);	
	lightsen->begin();
}

void initWiFi() // initialize the WIFI
{
	char buf[64];
	uint8_t nonet;
	IPAddress ip;
	nonet=WiFi.scanNetworks();
	sprintf(buf,"Number of Networks: %2i",nonet); // Output of up to 6 networks in your range + display
	lcd->drawText(10,15,buf,1,COLOR_BLACK,COLOR_WHITE); // All display outputs need to be written into a String or char-array before they can be passed to the lcd controller
	sprintf(buf,WiFi.SSID(0));
	lcd->drawText(10,30,buf,1,COLOR_BLACK,COLOR_WHITE);
	sprintf(buf,WiFi.SSID(1));
	lcd->drawText(10,45,buf,1,COLOR_BLACK,COLOR_WHITE);
	sprintf(buf,WiFi.SSID(2));
	lcd->drawText(10,60,buf,1,COLOR_BLACK,COLOR_WHITE);
	sprintf(buf,WiFi.SSID(3));
	lcd->drawText(10,75,buf,1,COLOR_BLACK,COLOR_WHITE);
	sprintf(buf,WiFi.SSID(4));
	lcd->drawText(10,90,buf,1,COLOR_BLACK,COLOR_WHITE);

	WiFi.begin("YOURWIFI","YOURPASSWORD"); // Connection to a WIFI (feel free to change these settings)
	strcpy(buf,WiFi.SSID());
	lcd->drawText(10,120,buf,1,COLOR_BLACK,COLOR_WHITE); // Output of the SSID (WIFI name) if the WiFi Shield was connected successfully
	ip=WiFi.localIP();
	sprintf(buf,"%3i.%3i.%3i.%3i",ip[0],ip[1],ip[2],ip[3]); // Show the Arduino's IP address
	lcd->drawText(10,135,buf,1,COLOR_BLACK,COLOR_WHITE);
	while(tscr->getPressure()==0) // Idle until the touchscreen is pressed to continue
	{
		delay(20);
		tscr->service();
	}
	lcd->clear(COLOR_WHITE);
}

void initPhoto() // Initialize the photodiodes
{
	analogReadResolution(12); // Set the reading resolution and the pinmode
	pinMode(A0,INPUT);
	pinMode(A1,INPUT);
	pinMode(A1,INPUT);
}

void updateSenTemp(){ // get current temperature data
  byte data[12]; // array the incoming values should be stored to
  byte addr[8] = {0x28,0x1D,0xF1,0xB0,0x04,0x00,0x00,0x6B}; // OneWire temperature sensor address
  
	tempsen->reset(); // build up a connection and request data
	tempsen->select(addr);
	tempsen->write(0x44,1);
	tempsen->depower();
	tempsen->reset();
	tempsen->select(addr);
	tempsen->write(0xBE);
 
	for(byte z = 0; z < 9; z++) data[z] = tempsen->read(); // read out the return and store it byte per byte to the array
 
	unsigned int raw = (data[1] << 8) | data[0];
	char buf[20],temp[8];
	dtostrf(((float)raw / 16.0)-1.5,4,2,temp);// conversion of the raw data into degrees Celsius
	valueTemp=(float)((valueCounter[1]*valueTemp)+((float)raw / 16.0)-1.5)/(float)(valueCounter[1]+1); // Take the current temperature into account for the avaredged value
	valueCounter[1]++;
	strcat(temp,"C  ");
	sprintf(buf, "temperature: "); // Display output
	strcat(buf,temp);
	lcd->drawText(10, 90, buf, 1, COLOR_BLACK, COLOR_WHITE);
}

void updateSenLight() // get current light values
{
	char buf[32];
	uint16_t lsbroadband,lsinfrared; // definition
	lightsen->getLuminosity(&lsbroadband,&lsinfrared); // the full function is implemented in the library
	lsbroadband=((float)lsbroadband*lightsen->getMultiplier());
	lsinfrared=((float)lsinfrared*lightsen->getMultiplier()); // getMultipier is a function I added. I believe the developers just missed something out in their lib
	sprintf(buf, "complete:  %5i lux ",lsbroadband);
	lcd->drawText(10, 60, buf, 1, COLOR_BLACK, COLOR_WHITE); // Display output
	sprintf(buf, "infrared:  %5i lux ",lsinfrared);
	lcd->drawText(10, 75, buf, 1, COLOR_BLACK, COLOR_WHITE);
	valueLight=(((float)valueCounter[2]*valueLight)+(float)lsbroadband)/(float)(valueCounter[2]+1.0); // Calculate the avaredged values
	valueLightIR=(((float)valueCounter[2]*valueLightIR)+(float)lsinfrared)/(float)(valueCounter[2]+1.0);
	valueCounter[2]++;
}

void updateSenWater() // get current water values
{
	char buf[20],wtr[7];
	float water = (0.0009765625*(float)analogRead(A5)); // The water sensor doesn't really work lineary. Here is my approximation for correction.
	water = 1.0-water;
	water = -pow(water,7.0);
	water = pow(2.0,water);
	water = 200.0*(1-water);
	if(water>0)
		dtostrf(water,4,2,wtr);
	else
	{
		sprintf(wtr,"0.0");
		water=0.0;
	}
	valueWater=((valueCounter[0]*valueWater)+water)/(valueCounter[0]+1); // avaredged value
	valueCounter[0]++;
	sprintf(buf,"Wasser: "); // Display output
	strcat(buf,wtr);
	strcat(buf,"  ");
	lcd->drawText(10, 105, buf, 1, COLOR_BLACK, COLOR_WHITE);
}

void updateTouch() // Register if someone touched the display
{
	uint16_t pos;
	char buf[7];
	tscr->service(); // some kind of flush-function. Gets the touchpads current state.
	pos=tscr->getX();
	sprintf(buf,"X=%04i",pos);
	lcd->drawText(10,30,buf,1,COLOR_BLACK,COLOR_WHITE); // Display the x and y touch position
	pos=tscr->getY();
	sprintf(buf,"Y=%04i",pos);
	lcd->drawText(10,45,buf,1,COLOR_BLACK,COLOR_WHITE);
	tscr->service();
}

void updateRTC() // update the time from the clock
{
	uint8_t se,mi,ho,da,mo;
	uint16_t yr;
	uint32_t unixtime;
	rtc->get(&se,&mi,&ho,&da,&mo,&yr);
	if(sea!=se) // Only refresh the values on the display if they changed (when the seconds value has changed since the last call)
	{
		char buf[24];
		sprintf(buf,"%02i:%02i:%02i %02i.%02i:%04i",ho,mi,se,da,mo,yr);
		lcd->drawText(10,15,buf,1,COLOR_BLACK,COLOR_WHITE);
		sea=se;
	}
	struct tm t; // Calculate the unixtime from year, month and so on
	time_t t_of_day;
	t.tm_year=yr-1900;
	t.tm_mon=mo-1;
	t.tm_mday=da;
	t.tm_hour=ho;
	t.tm_min=mi;
	t.tm_sec=se;
	t_of_day = mktime(&t); 
	valueTime=t_of_day; // pass the unixtime to the global variable
}

void updatePhoto(){ // update the photosensors (just an analogue readout)
	char buf[5];
	sprintf(buf,"%04i",analogRead(A0));
	lcd->drawText(10,120,buf,1,COLOR_BLACK,COLOR_WHITE); // Display output
	sprintf(buf,"%04i",analogRead(A1));
	lcd->drawText(10,135,buf,1,COLOR_BLACK,COLOR_WHITE);
	sprintf(buf,"%04i",analogRead(A2));
	lcd->drawText(10,150,buf,1,COLOR_BLACK,COLOR_WHITE);
}

void WifiDatasend(){
	char key[] = "YOURKEY",url[] = "http://igem.yourwebsite.com/save.php"; // key and url to your php-save-script (feel free to change)
	if(firstrun)
	{
		delay(1000); // fix, because there are no good values on the first run
		firstrun=0;
		return;
	}
	if (client->connect("igem.yourwebsite.com", 80)) // build up a conntection to the server on port 80 (feel free to change)
	{
		Serial.println("Connected, Sending Data...");
		client->println("GET " + String(url) + "?key=" + String(key) + "&water="+String(valueWater,3) + "&temp="+String(valueTemp,3) + "&light1="+String(valueLight,3) + "&light2="+String(valueLightIR,3) +"&time="+String(valueTime));
		Serial.println("GET " + String(url) + "?key=" + String(key) + "&water="+String(valueWater,3) + "&temp="+String(valueTemp,3) + "&light1="+String(valueLight,3) + "&light2="+String(valueLightIR,3) +"&time="+String(valueTime));
		client->println("Connection: close");
		Serial.println("Connection: close");
	}
	else
	{
		Serial.println("***** CONNECTION FAILED *****");
	}
	for(int i=0;i<3;i++)
		valueCounter[i]=0; // Reset all counters and values for the avaredging process
	valueWater=0.0;
	valueTemp=0.0;
	valueLight=0.0;
	valueLightIR=0.0;
}

void WifiDataReceive()
{
	int i=0;
	while (client->connected() && i++<200)              // Read out the servers response and pass it to the Serial output (needs connection to a PC)
	{
		if(client->available())
		{
			while (client->available())
			{
				char response = client->read();	
				Serial.print(response);
			}
			i=200;
		}
		else
			delay(1);
	}
	if(i==200)
		Serial.println();
}

// Here are the main functions that are called by the arduino.
// All devices had to be defined as pointers and initialized in the setup function due to compiler issues with the Arduino Due.
// The usage of the Arduino Due isn't quite established and the arduino software has still some room for improvement here.
// Setup is called once at the startup and at each reset
// All called functions are commented and explained in detail above ;)

void setup()
{
	lightsen = new Adafruit_TSL2561(TSL2561_ADDR_FLOAT,12345);
	lcd = new MI0283QT9();
	rtc = new DS1307();
	tscr = new ADS7846();
	tempsen = new OneWire(14);
	client = new WiFiClient();
	pinMode(A5,INPUT); // Pin A5 is an analogue input

	lastConnected = false;
	Serial.begin(9600);

	SD.begin(4);
	rtc->start();
	lcd->init();
	tscr->init();
	initDisplay();
	initLightSen();
	initPhoto();
	initWiFi();
}


// The if(counter%xx==0) code functions as some kind of process handler. Some functions should be called more often than others.
// at each run there is a delay of 1ms and a value of '1' is added to the counter. Most of the functions hardly take any time.
// But some are quite time-consuming.
// The % operator is the modulo. At counter%7==0 the function is called every 7th run.
// For example the functions WifiDatasend and -Receive, which don't have to be called that often. They are executed every 1000th/5000th time.

void loop()
{
	if(counter%29==0)	updateRTC();
	if(counter%7==0)	updateTouch();
	if(counter%503==0)	updateSenTemp();
	if(counter%197==0)  {updateSenLight();updatePhoto();};
	if(counter%457==0)	updateSenWater();
	if(counter%5000==0)	WifiDatasend();
	if(counter%1000==1)	WifiDataReceive();
	if(counter%5000==4300) // Around 700 ms before the data will be sent the Arduino breaks up the old connection to the server
	{
		client->stop();
		Serial.println("Done.");
		client->flush();
	}
	counter++;
	delay(1);
}

Libraries

Since it's not possible uploading files of the type file.h or file.cpp, we zipped our libraries, named the suffix .zip.txt and uploaded THEM to the wiki. To unzip the libraries simply remove the .txt. We're very sorry but it was simply to much code to locate it as text on our pages. Unzip the archive into your ./arduino/libraries folder.

The data generated by the Arduino was stored on a web server. For this purpose the Arduino sends the data sets in a GET request to the server, where a PHP script (save.php) stores them in a MySQL database. To view the data, another PHP script(index.php) retrieves the data from the MySQL database and plotted as a chart by utilising the JavaScript chart library [http://nvd3.org/ NVD3]. To view the data from our Arduino visit [http://igem.wzw.tum.de/arduino/].

Please also visit our GitHub repo.

Arduino photo gallery

/>

References

The 2D Graphic of the Arduino Due was taken from a open source software called "fritzing"

@@ Line 115: / Line 115: @@
 [[File:TUM13_Arduino_Assembly_Animation.gif|thumb|left|400px|'''Figure 3:''' Assembly Order]]
-Since the Arduino Due was released in autumn 2012, this is the first IGEM-year this '''very powerful''' device can be used. We found it a useful '''supervising tool''' for short- and long-time experiments. It can be used in as well as outside the lab. The improvements that were made from Uno to Due are considerable.
+Since the Arduino Due was released in autumn 2012, this is the first iGEM year this '''very powerful''' device can be used. We found it a useful '''supervising tool''' for short and long-term experiments. It can be used in as well as outside the lab. The improvements that were made from Uno to Due are considerable.
-It is capable of handling many things at once, such as a WiFi Shield, a Display, a SD-Card and multiple Sensors.
+It is capable of handling many things at once, such as a WiFi shield, a display, a SD-Card and multiple sensors.
-At this point the Uno didn't match up any longer.
+At this point the Uno did not match up any longer.
-To establish the usage of Arduino in IGEM even more we'd like to share our experiences and help you building up a '''basic device''' that can '''collect''' and '''view sensor data''' on its '''display''' and '''upload''' them to a server.
+To establish the usage of Arduino in iGEM even more we want to share our experiences and help you building up a '''basic device''' that can '''collect''' and '''view sensor data''' on its '''display''' and '''upload''' them to a server.
 ===Part Description===
@@ Line 132: / Line 132: @@
          <li><img src="https://static.igem.org/mediawiki/2013/9/99/Arduino_Tsl2561.png" alt="Figure 8: TSL2561 light sensor" /></li>
          <li><img src="https://static.igem.org/mediawiki/2013/a/a5/Arduino_Tsl2561_Curve.png" alt="Figure 9: TSL2561 absorption curve" /></li>
-         <li><img src="https://static.igem.org/mediawiki/2013/3/3d/Arduino_Watersensor.png" alt="Figure 10: water sensor" /></li>
+         <li><img src="https://static.igem.org/mediawiki/2013/3/3d/Arduino_Watersensor.png" alt="Figure 10: Water sensor" /></li>
 </ul>
 </div>
@@ Line 138: / Line 138: @@
 ====Arduino Due====
-The Arduino Due is the most powerful Arduino board. It's underlying 32bit-processor is the Atmel SAM3X8E.
+The Arduino Due is the most powerful Arduino board. Its underlying 32bit-processor is the Atmel SAM3X8E.
-Contrary to the other boards which run at 5V, a power supply of 3.3V is sufficiant.
+Contrary to the other boards which run at 5V, a power supply of 3.3V is sufficient.
 It was released in October 2012.
-Data:
+'''Data:'''
 Mhz	CPU Clock
@@ Line 155: / Line 155: @@
 The Arduino WiFi Shield is an attachable shield that provides Wireless LAN 802.11b/g to the Arduino.
 It scans and connects to networks and opens TCP and UDP sockets for data transfer. It also supports WEP and WPA2 encryption. It was released in August 2012.
-The WiFi Shield is fully supported by the Arduino Due and Arduino supplies a suitable stock WiFi-library.
+The WiFi Shield is fully supported by the Arduino Due and Arduino supplies a suitable stock WiFi library.
 There is also an on-board SD-card socket to store received data.
 As the SD-card is accessible separately, it can also be used as a storage for any data generated by the Arduino.
@@ Line 171: / Line 171: @@
 V
-====Watterott mega msd-shield====
+====Watterott Mega MSD-Shield====
-The mega msd-shield was designed by Watterott and consists of a couple of components.
+The Mega MSD-Shield was designed by Watterott and consists of a couple of components.
-The components are one real time clock, one SD-card socket (we won't use), a small battery and a socket for a touch display.
+The components are one real time clock, one SD-card socket (we will not use), a small battery and a socket for a touch display.
 To get it ready to run, the shield must be assembled. The stackable headers and the clock's quartz must be soldered to the board and the battery must be inserted.
-Unluckily the mega msd-shield and therefore also the MI0283QT-9 touch display don't come with a working library for the Arduino Due. The existing library only supports all boards up to the Arduino Uno.
+Unluckily the Mega MSD-Shield and therefore also the MI0283QT-9 touch display don't come with a working library for the Arduino Due. The existing library only supports all boards up to the Arduino Uno.
-Therefore all libraries have to be rewritten.
+Therefore all libraries had to be rewritten.
-The touch display and the SD-card-slot communicate with the Arduino Due via SPI/ICSP. The real time clock transmit its data via I²C.
+The touch display and the SD-card slot communicate with the Arduino Due via SPI/ICSP. The real time clock transmits its data via I²C.
 '''Pin usage:'''
@@ Line 197: / Line 197: @@
 The MI0283QT-9 is a multicolor touch display. It comes already attached to a board, where only the pin headers are left to be soldered.
-Once assembled it can easily be plugged into the mega msd-shield. It has an on-board touch controller (TI ADS7846).
+Once assembled it can easily be plugged into the Mega MSD-Shield. It has an on-board touch controller (TI ADS7846).
 The display size is 2.83"(43.2 x 57.6mm) with a resolution of 240x320. It supports 262k colors.
-The pin usage is already considered in the mega msd-shield description.
+The pin usage is already considered in the Mega MSD-Shield description.
-====Light sensor TSL2561====
+====Light Sensor TSL2561====
 The light sensor is a small, so called, breakout board. It is usually connected by wires instead of directly plugged into the Arduino's headers.
-The light sensor has two photo-diodes on-board that measure visible and infrared light. Similar to the RTC, the TSL2561 is addressed via I²C.
+The light sensor has two photo diodes on-board that measure visible and infrared light. Similar to the RTC, the TSL2561 is addressed via I²C.
 Once you get the I²C library working on your Arduino Due working it takes only little effort to integrate additional I²C devices.
 Just very few lines of the library have to be rewritten here.
-The photo-diodes can be addressed separately or both at one. Their output is already converted to Lux.
+The photo diodes can be addressed separately or both at one. Their output is already converted to Lux.
-'''pin usage:'''
+'''Pin usage:'''
   Pin 20	TSL2561		 	I²C	SDA (Serial Data Line)
@@ Line 216: / Line 216: @@
 .3V
-====Temperature sensor DS18B20====
+====Temperature Sensor DS18B20====
-The temperature sensor is embedded into a water proof cable. It is addressed via a One-Wire interface.
+The temperature sensor is embedded into a water proof cable. It is addressed via a OneWire interface.
-The provided data are digital raw data, which need to be converted into degrees Celsius. Information about the conversion are given by the manufacturer.
+The provided data are digital raw data, which need to be converted into degree Celsius. Information about the conversion are given by the manufacturer.
-Similar to the I²C (TwoWire) bus, you only have to get the One-Wire interface working once. After that, you can easily set up more One-Wire devices.
+Similar to the I²C (TwoWire) bus, you only have to get the OneWire interface working once. After that, you can easily set up more OneWire devices.
 Again, just very few lines of the library have to be rewritten.
-'''pin usage:'''
+'''Pin usage:'''
   Pin 14 	One-Wire DS18B20 (pin was randomly chosen)
@@ Line 229: / Line 229: @@
   Pin 3.3V
-====Water sensor====
+====Water Sensor====
 Setting up the water sensor is very easy. If and how much water the sensor registered can be measured via an analog pin.
@@ Line 238: / Line 238: @@
       gnd
 .3V
-====Photo-diodes====
-We disassembled a broken "Biorad 550"-photometer and recovered a halogen lamp, a small number of wavelength filters,
-three of eight photo-diodes and their fitting Resistors.
 ===Tools===
@@ Line 252: / Line 247: @@
-Keep everything clear during your assembly. If you have different colored linking cables, always try to use the same color code.
+Keep everything clear during your assembly. If you have different colored linking cables, always try to use the same color code (e.g. red cable for 3.3V etc.) otherwise troubleshooting can get nasty.
-For example: red cable for 3.3V etc. Troubleshooting can get nasty.
 All '''steps''' you need to follow building up your own Arduino measuring device are '''explained below''' in the '''slide show''' and the image descriptions.
@@ Line 261: / Line 255: @@
 <ul class="bxgallery">
 <li><img src="
-https://static.igem.org/mediawiki/2013/thumb/d/d7/TUM13_Arduiono_Assembly_1.png/350px-TUM13_Arduiono_Assembly_1.png" alt="Figure 11: place your Arduino Due on your desk"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/d/d7/TUM13_Arduiono_Assembly_1.png/350px-TUM13_Arduiono_Assembly_1.png" alt="Figure 11: Place your Arduino Due on your desk"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/c/c4/TUM13_Arduiono_Assembly_2.png/350px-TUM13_Arduiono_Assembly_2.png" alt="Figure 12: connect ground and 3.3V to two different lines of you breadboard"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/c/c4/TUM13_Arduiono_Assembly_2.png/350px-TUM13_Arduiono_Assembly_2.png" alt="Figure 12: Connect ground and 3.3V to two different lines of you breadboard"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/2/21/TUM13_Arduiono_Assembly_3.png/350px-TUM13_Arduiono_Assembly_3.png" alt="Figure 13: connect the light sensor's ground and the 3.3V line"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/2/21/TUM13_Arduiono_Assembly_3.png/350px-TUM13_Arduiono_Assembly_3.png" alt="Figure 13: Connect the light sensor's ground and the 3.3V line"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/9/9b/TUM13_Arduiono_Assembly_4.png/350px-TUM13_Arduiono_Assembly_4.png" alt="Figure 14: connect the sda line of your light sensor to pin 20 and scl to pin 21"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/9/9b/TUM13_Arduiono_Assembly_4.png/350px-TUM13_Arduiono_Assembly_4.png" alt="Figure 14: Connect the sda line of your light sensor to pin 20 and scl to pin 21"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/9/9c/TUM13_Arduiono_Assembly_5.png/350px-TUM13_Arduiono_Assembly_5.png" alt="Figure 15: connect the temperature sensor's ground and the 3.3V line"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/9/9c/TUM13_Arduiono_Assembly_5.png/350px-TUM13_Arduiono_Assembly_5.png" alt="Figure 15: Connect the temperature sensor's ground and the 3.3V line"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Arduiono_Assembly_6.png/350px-TUM13_Arduiono_Assembly_6.png" alt="Figure 16: connect the signal line of your temp sensor via the breadbroad to pin 14" /></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Arduiono_Assembly_6.png/350px-TUM13_Arduiono_Assembly_6.png" alt="Figure 16: Connect the signal line of your temp sensor via the breadbroad to pin 14" /></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/8/83/TUM13_Arduiono_Assembly_7.png/350px-TUM13_Arduiono_Assembly_7.png" alt="Figure 17: place a ~50kOhm resistor between the 3.3V line and the temps sensor's signal line on your breadboard" /></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/8/83/TUM13_Arduiono_Assembly_7.png/350px-TUM13_Arduiono_Assembly_7.png" alt="Figure 17: Place a ~50kOhm resistor between the 3.3V line and the temps sensor's signal line on your breadboard" /></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/b/b0/TUM13_Arduiono_Assembly_8.png/350px-TUM13_Arduiono_Assembly_8.png" alt="Figure 18: connect the water sensor to the ground and 3.3V line"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/b/b0/TUM13_Arduiono_Assembly_8.png/350px-TUM13_Arduiono_Assembly_8.png" alt="Figure 18: Connect the water sensor to the ground and 3.3V line"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/e/e4/TUM13_Arduiono_Assembly_9.png/350px-TUM13_Arduiono_Assembly_9.png" alt="Figure 19: connect the signal line of your water sensor to pin A5"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/e/e4/TUM13_Arduiono_Assembly_9.png/350px-TUM13_Arduiono_Assembly_9.png" alt="Figure 19: Connect the signal line of your water sensor to pin A5"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/8/86/TUM13_Arduiono_Assembly_10.png/350px-TUM13_Arduiono_Assembly_10.png" alt="Figure 20: voila! You are done with the basic connection of your three sensors. The next steps explain how to connect the WiFi shield, the msd shield and the display. You can connect all the sensors to the shield's and header's pins the same way, you connected them to the Arduino Due"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/8/86/TUM13_Arduiono_Assembly_10.png/350px-TUM13_Arduiono_Assembly_10.png" alt="Figure 20: Voila! You are done with the basic connection of your three sensors. The next steps explain how to connect the WiFi shield, the msd shield and the display. You can connect all the sensors to the shield's and header's pins the same way, you connected them to the Arduino Due"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_11.png/350px-TUM13_Arduiono_Assembly_11.png" alt="Figure 21: first solder a short copper cable to the msd shield, connecting its pin 25 to pin 7"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_11.png/350px-TUM13_Arduiono_Assembly_11.png" alt="Figure 21: First solder a short copper cable to the msd shield, connecting its pin 25 to pin 7"/></li><li><img src="
 https://static.igem.org/mediawiki/2013/thumb/1/18/TUM13_Arduiono_Assembly_12.png/350px-TUM13_Arduiono_Assembly_12.png" alt="Figure 22: Then bend pin 7 and pin 4, so they don't connect to the WiFi shield's pins. Pin 4 would be a double usage of the msd shield's and the wifi shield's sd card. Pin 7 (lcd slave select) interferes with the wifi handshake pin"/></li><li><img src="
 https://static.igem.org/mediawiki/2013/thumb/9/99/TUM13_Arduiono_Assembly_13.png/350px-TUM13_Arduiono_Assembly_13.png" alt="Figure 23: This is just an explanation of how the shield's sub-devices are connected. A deeper understanding of the following diagrams goes along with a deeper understanding of the program's source code and the additional libraries. All shields are of course connected to the Arduino Due's ground and 3.3V line"/></li><li><img src="
 https://static.igem.org/mediawiki/2013/thumb/e/e8/TUM13_Arduiono_Assembly_14.png/350px-TUM13_Arduiono_Assembly_14.png" alt="Figure 24: The yellow link shows the spi interface between Arduino Due and the WiFi shield"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Arduiono_Assembly_15.png/350px-TUM13_Arduiono_Assembly_15.png" alt="Figure 25: the thinner yellow lines are the WiFi handshake and the wifi slave select connections"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Arduiono_Assembly_15.png/350px-TUM13_Arduiono_Assembly_15.png" alt="Figure 25: The thinner yellow lines are the WiFi handshake and the wifi slave select connections"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_16.png/350px-TUM13_Arduiono_Assembly_16.png" alt="Figure 26: the blue link is the sd reader's slave select"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/d/d0/TUM13_Arduiono_Assembly_16.png/350px-TUM13_Arduiono_Assembly_16.png" alt="Figure 26: The blue link is the sd reader's slave select"/></li><li><img src="
 https://static.igem.org/mediawiki/2013/thumb/6/6d/TUM13_Arduiono_Assembly_17.png/350px-TUM13_Arduiono_Assembly_17.png"
-alt="Figure 27: the green link represents the connection to the real time clock"/></li><li><img src="
+alt="Figure 27: The green link represents the connection to the real time clock"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Arduiono_Assembly_18.png/350px-TUM13_Arduiono_Assembly_18.png" alt="Figure 28: the pink link represents the spi interface between the msd shield and the Arduino Due, required for the communication with the lcd and its touch functions (pins 50, 51 and pin 52)"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Arduiono_Assembly_18.png/350px-TUM13_Arduiono_Assembly_18.png" alt="Figure 28: The pink link represents the spi interface between the msd shield and the Arduino Due, required for the communication with the lcd and its touch functions (pins 50, 51 and pin 52)"/></li><li><img src="
-https://static.igem.org/mediawiki/2013/thumb/4/4b/TUM13_Arduiono_Assembly_19.png/350px-TUM13_Arduiono_Assembly_19.png" alt="Figure 29:
+https://static.igem.org/mediawiki/2013/thumb/4/4b/TUM13_Arduiono_Assembly_19.png/350px-TUM13_Arduiono_Assembly_19.png" alt="Figure 29: Lcd slave select, lcd reset and lcd LED"/></li><li><img src="
-lcd slave select, lcd reset and lcd LED"/></li><li><img src="
+https://static.igem.org/mediawiki/2013/thumb/f/fd/TUM13_Arduiono_Assembly_20.png/350px-TUM13_Arduiono_Assembly_20.png" alt="Figure 30: Lcd's touch slave select"/></li>
-https://static.igem.org/mediawiki/2013/thumb/f/fd/TUM13_Arduiono_Assembly_20.png/350px-TUM13_Arduiono_Assembly_20.png" alt="Figure 30: lcd's touch slave select"/></li>
 <li><img src="https://static.igem.org/mediawiki/2013/thumb/5/5c/TUM13_Arduiono_Assembly_21.png/350px-TUM13_Arduiono_Assembly_21.png" alt="Figure 31: the power supply can be established with a 9V block battery"/></li>
-<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ef/TUM13_Arduiono_Assembly_22.png/350px-TUM13_Arduiono_Assembly_22.png" alt="Figure 32: at last: an overview"/></li>
+<li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ef/TUM13_Arduiono_Assembly_22.png/350px-TUM13_Arduiono_Assembly_22.png" alt="Figure 32: At last: an overview"/></li>
 </ul>
@@ Line 290: / Line 283: @@
 </html>
 [[File:TUM13_Arduino_in_action.gif|thumb|500px|left|'''Figure 33:''' Arduino in action]]
-For more explaining photos visit our [[#Arduino_photo_gallery|photo gallary]]. On the left you see the Arduino as it boots up, connects to a WiFi hotspot and collects current data.
+For more explaining photos visit our [[#Arduino_photo_gallery|photo gallery]]. On the left you see the Arduino as it boots up, connects to a WiFi hotspot and collects data.
 ===Code===
@@ Line 296: / Line 289: @@
 We strongly recommend the usage of '''Microsoft Visual Studio''' with the '''"visual micro"''' plugin. Microsoft Intellisense helps you a lot, when you are unfamiliar with the manufacturer provided libraries (automatic code completion). In order to compile the code properly you need the latest beta version of [http://arduino.cc/en/Main/Software Arduino's software]. In the visual micro settings, choose the path to the Arduino IDE on your hard drive, also disable "Upload using programmer". In the settings of the Arduino IDE, select "use external software".
-Now you are ready to start programming. We'd like to share our code. Feel free to use, edit and play around with it!
+Now you are ready to start programming. Below we share our code, feel free to use, edit and play around with it!
 But '''wait''' first you need our '''[[#Libraries|libraries]]'''! They're exclusively '''fitted''' to the Arduino Due, mostly based on the existing manufacturer's libraries for the Arduino Uno.
-Assumed you followed our tutorial until here.
+Assuming you followed our tutorial until here.
 Once you adapted the code to your WiFi and server settings and uploaded it to the Arduino it does the following:
 #it starts up and the '''screen''' turns from black to white
 #if you have pressed the screen, the calibration process starts
 #it '''searches for networks''' and displays the total number of found networks on its screen
-#it displays up the first six '''WiFi stations''' that were found
+#it displays the first six '''WiFi stations''' that were found
 #it tries to '''connect''' to the WiFi station you have set
 #if a connection was established it shows the '''Arduino's IP address''' and the SSID (name) of the WiFi it is connected to
 #then it idles until you you press the screen
-#after you pressed the screen it humps to the '''"loop"-section''' of the code
+#after you pressed the screen it jumps to the '''"loop"-section''' of the code
 #it continuously runs and displays:
 ##the current '''time'''
@@ Line 315: / Line 308: @@
 ##the measured values of the '''photodiodes'''
 ##the '''coordinates''' of the point you '''pressed''' on the screen
-#it builds up a '''connection to a server, calling a php script, passing on the collected data'''
+#it builds up a '''connection to a server, calling a PHP script, passing on the collected data'''
   <nowiki>

Team:TU-Munich/Results/How To

From 2013.igem.org

Revision as of 23:52, 28 October 2013

Our Tutorials

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Slideshow

Generation of Rotating Protein Structures

Setting up a basic Arduino measuring device

Introduction

Part Description

Arduino Due

Arduino WiFi Shield

Watterott Mega MSD-Shield

Display MI0283QT-9

Light Sensor TSL2561

Temperature Sensor DS18B20

Water Sensor

Tools

Assembly

Code

Libraries

Arduino photo gallery

References

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