Team:TU-Munich/Results/Implementation

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Implementation of a Plant Biofilter

How does a biofilter look like? To face this question we considered the requirements for a moss filter and took a look at existing solutions.
We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a symbiosis between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our Advisory Board) on biological process engineering for Physcomitrella patens. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter.
Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The tube reactor mainly consists of glass tubes in which the plant is grown. The open pond model is a meander-shaped pond or slowly floating stream.

Closed tube reactor

Figure 9: tube reactor

File:TUM13 moss tube turning.gif

Figure 10: moss turning

The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.

The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values.

This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.

Open filter on felt base

Figure 11: open pond

Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.

The open pond implementation can be used as the last step of a wastewater treatment plant. Even though the contact surface between moss and water might not be as big as in the tube reactor, an implementation with membrane bound effectors is still thinkable. Using membrane bound effectors has the advantage that an emission of effectors into the clean water can be avoided almost entirely. Yet a secretion of effectors to the water may accomplish the biodegradation more effectively.

Our swimming remediation raft

Figure 12: Rendering of our remediation rafts in front of the MIT

Figure 13: 3D-print of our remediation raft

At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense. The tube reactor guarantees a big contact surface between water and moss which is an asset to the filter properties, but the carbon dioxide exchange is a major problem due to the lack of water-air through mix. To manage big scale filtering on an appropriate area it's inevitable to stack the tubes. That makes extra lighting necessary. The open pond model brings along a smaller water-moss surface, therefore the filter properties may suffer and a wider area is needed. As opposed to the tube reactor the costs are lower and there are no air exchange problems to face.

Slightly we return to the question how a biofilter could look like. It has to be a solution that can be implemented in any scale. The costs must be kept as low as possible. Additionally the energy consumption and maintenance must be kept to a absolute minimum to make it universally usable.

Figure 14: Blueprint for our remediation raft

Such a solution has to be engineered cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.

Our answer to that is the remediation raft.
It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers. The light weight and handy size make it mobile and and transportable and a higher quantity of rafts can easily arranged to a honeycombed structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.

Shopping for the remediation raft

**Table 1**: Shopping list for our Arduino-Project
Component	Quantity	Source	Price in € (per piece)	Price in € (sum)
PVC-tubes 1,5 m, ⌀ 75mm	3	Hardware Store	4,69	14,07
One-eight bend (45°)	3	Hardware Store	1,09	3,27
Bend (67°)	3	Hardware Store	1,09	3,27
Fleece	1,3 m²	Hardware Store	3,99 (per m²)	5,19
Clamps	3	Hardware Store	2,30	6,90
Carbon rod	1 (1,25 m)	Hardware Store	4,75	4,75
Round eyelets	3	Hardware Store	0,34	1,01
Total				38,44

Images from our trip to the construction center

Monitoring by an Arduino Microcontroller

Introduction

Figure 21: Arduino Uno, released in September 2010

One advantage of our raft is that it works quite autonomic. Once the moss is installed it filters until it's "saturated", assumed that the environmental parameters fit and a proper living space is provided. The main goal of our measurement device is to monitor these environmental parameters in real time. Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited. Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans. So our aim was to engineer a low cost and low energy solution, that maintain the filters autonomy.

Figure 22: Idea for a measuring device

This is where Arduino comes into play. Arduino is a platform that is based on one microcontroller which is attached to a circuit board. Its convenient handling and easy programming, the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for multidisciplinary applications. Among its many fans it already enjoys cult status. We first used the Arduino Uno. It is the most commonly used board. The first revision was released in September 2010. Designed for beginners, it gave us an easy start into the handling, since none of us had any experience working with microcontrollers. Most libraries already worked out of the box and all shields and sensors we ordered came with an example code. But the Arduino Uno came to it's limits, when we tried to get a display, WiFi and several sensors working.

Therefore we ordered the Arduino Due, which is the most powerful Arduino board at the moment. It has 16 times more flash memory (code storage) than the Arduino Uno and its clock runs 5 times faster. Instead of 2KB SRAM there are 96KB. At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).

We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A temperature and a light sensor collect weather data and a water sensor attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface. For testing purposes we even attached a display to the microcontroller. All collected data are sent via WiFi and stored at a server's MySQL database in real time. Alternatively the data can also be sent via GSM if there is no WiFi hotspot close by. All data can then easily be displayed.

File:TUM13 How It Works Flowmodel.gif

Figure 23: How it works

The controller can easily be extended by other sensors, such as a color sensor to monitor the moss's health or a potential die off, a pH-Sensor or even a webcam.

Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a tutorial how to set up an Arduino Due with some basic functions.

Figure 24: components

**Table 2**: Shopping list for our Arduino-Project
Component	Quantity	Source	Price	Figure
Arduino Due microcontroller	1	[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]	46.41 €	Fig. 1 A
Arduino WIFI Shield	1	sparkfun	63.58 €	Fig. 1 B
Watterott mega msd-shield	1	[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]	19.49 €	Fig. 1 C
Display MI0283QT-9	1	[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]	36.00 €	Fig. 1 D
Light sensor TSL2561	1	[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]	7.74 €	Fig. 1 E
Temperature sensor DS18B20	1	[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]	8.80 €	Fig. 1 G
Water sensor	1	[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]	2.90 €	Fig. 1 H
Lithium-Battery	1	[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]	16.35 €
Stackable Headers	3	[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]	5.37 €
Linking wires and resistors			1.00 €
Photo-diodes	3
			207.64 €	280.77 $

Server site

To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then save.php stores them in a MySQL database. The data can be viewed by visiting index.php, which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time real.php periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.

How could it look installed in a river?

New York PARALLEL NETWORKS

In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the fixation of carbon dioxide, food production and local recreation without hindering the renewable energy generation, furthermore the transportation of passengers and goods. As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the "great structural flexibility and expandability of the triangular floating pods". We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.

Commercially available rafts called "Kampen"

Figure 30: Commercially available rafts

During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.

Swimming remediation raft in action

References:

http://bvt.blt.kit.edu/ KIT Homepage about Institute of bioprocess Engineering

http://op-n.net/filter/work/PARALLEL-NETWORKS Op.N Op.N Homepage

http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ www.bustler.net, Thursday, August 04, 2011 Article: ONE PRIZE: Water as the 6th Borough - Winners Announced;

http://www.bestmann-green-systems.de/ BGS Ingenieurbiologie und -ökologie GmbH BGS Homepage

@@ Line 8: / Line 8: @@
 ==Implementation of a Plant Biofilter==
 How does a '''biofilter''' look like?
-To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''. We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the Institute of bioprocess engineering in Karlsruhe. So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. Although his institute mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.
+To face this question we considered the '''requirements''' for a moss filter and took a look at '''existing solutions'''.<br>
+We talked to Prof. Dr.-Ing. Clemens Posten, who is head of the [http://bvt.blt.kit.edu/ Institute of bioprocess engineering] at the Karlsruhe Institute of Technology (KIT). So we were shown the institutes's bioreactors and Prof. Posten gave us an idea how a '''symbiosis''' between plant and technology can look like. In the past his group worked on a collaboration project with Prof. Dr. Reski (see our [https://2013.igem.org/Team:TU-Munich/HumanPractice/Interviews Advisory Board]) on biological process engineering for ''Physcomitrella patens''. Throughout this discussion we figured out several important parameters we will have to control and possible problems we might have to solve in order to successfully implement our PhyscoFilter. <br>
+Although his institute at the moment mainly works with algae, two solutions became apparent as sensible. The '''tube reactor''' mainly consists of glass tubes in which the plant is grown. The '''open pond''' model is a meander-shaped pond or slowly floating stream.
-----
 <html>
 <div class="box-center">
 <ul class="bxgallery">
-     <li><img src="https://static.igem.org/mediawiki/2013/8/80/TUM13_Postenvisit1.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/8/80/TUM13_Postenvisit1.jpg/350px-TUM13_Postenvisit1.jpg" alt="Figure 1"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/7/75/TUM13_Postenvisit2.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b9/TUM13_Postenvisit3.jpg/350px-TUM13_Postenvisit3.jpg" alt="Figure 2" /></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/b/b9/TUM13_Postenvisit3.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/1/16/TUM13_Postenvisit5.jpg/350px-TUM13_Postenvisit5.jpg" alt="Figure 3" /></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/4/43/TUM13_Postenvisit4.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/7/75/TUM13_Postenvisit2.jpg/350px-TUM13_Postenvisit2.jpg"  alt="Figure 4"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/1/16/TUM13_Postenvisit5.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/4/43/TUM13_Postenvisit4.jpg/350px-TUM13_Postenvisit4.jpg"  alt="Figure 5"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/c/cb/TUM13_Postenvisit6.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/c/cb/TUM13_Postenvisit6.jpg/350px-TUM13_Postenvisit6.jpg"  alt="Figure 6"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/7/70/TUM13_Postenvisit7.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/7/70/TUM13_Postenvisit7.jpg/350px-TUM13_Postenvisit7.jpg"  alt="Figure 7"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/d/de/TUM13_Postenvisit8.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/d/de/TUM13_Postenvisit8.jpg/350px-TUM13_Postenvisit8.jpg"  alt="Figure 8"/></li>
 </ul>
 </div>
 </html>
+<div class="box-left" style="height: 1650px;">
+===Closed tube reactor===
+[[File:TUM13 Tube_reactor.png|thumb|center|420px|'''Figure 9''': tube reactor]]
+[[File:TUM13_moss_tube_turning.gif|thumb|center|420px|'''Figure 10''': moss turning]]
+The flat disposal of the polyurethane tube guarantees a maximum of incoming light. It consists of one tube with the length of 15m arranged in a spiral shape. A meander shape wasn't possible, because the tube's bending radius is limited. The tube has an inner diameter of 4mm and an outer diameter of 6mm. It is fixated on a wooden board with hot glue.
+The idea behind that solution was to grow the moss on a big textile fiber inside the tube or on the tube wall. In this manner many parameters are set and degradation experiments could return significant values.
+This "bioreactor" is an ideal solution to clean highly contaminated water within a closed system. The big area of contact between the moss and the water enables the use of membrane bound effectors. Compared to the open pond and Remediation Raft implementation, the ratio of contact surface and water volume is relatively high. Therefore a secretion of effectors into the water is not needed.
-<html>
-<div class="box-center">
-<ul class="bxgallery">
-    <li><img src="https://static.igem.org/mediawiki/2013/8/80/TUM13_Postenvisit1.jpg" /></li>
-</ul>
 </div>
-</html>
-[[File:TUM13 Pod_assembly_1.png|thumb|center|220px| Figure 3:]]
+<div class="box-right" style="height: 1650px;">
-[[File:TUM13 Pod_assembly_2.png|thumb|center|220px| Figure 3:]]
-[[File:TUM13 Pod_assembly_3.png|thumb|center|220px| Figure 3:]]
-[[File:TUM13 Pod_assembly_4.png|thumb|center|220px| Figure 3:]]
-[[File:TUM13 Pod_assembly_5.png|thumb|center|220px| Figure 3:]]
-[[File:TUM13 Pod_assembly_6.png|thumb|center|220px| Figure 3:]]
-[[File:TUM13 Pod_assembly_7.png|thumb|center|220px| Figure 3:]]
-[[File:TUM13 Pod_assembly_8.png|thumb|center|220px| Figure 3:]]
-----
+===Open filter on felt base===
-<div class="box-left">
+[[File:TUM13 Open_pond.png|thumb|center|420px|'''Figure 11''': open pond]]
-===Closed tube reactor===
+Our open pond model consists of meander shaped perspex and two threads to adjust the pond's pitch. Therefore different flow speeds can be implemented. The floor of our open pond is lined with agar to grow the moss on. The pond's lid can be taken off to remove the moss.
-[[File:TUM13 Tube_reactor.png|thumb|center|420px| Figure 3:]]
-left
-</div>
+The open pond implementation can be used as the last step of a wastewater treatment plant. Even though the contact surface between moss and water might not be as big as in the tube reactor, an implementation with membrane bound effectors is still thinkable. Using membrane bound effectors has the advantage that an emission of effectors into the clean water can be avoided almost entirely. Yet a secretion of effectors to the water may accomplish the biodegradation more effectively.
-<div class="box-right">
-===Open filter on felt base===
-[[File:TUM13 Open_pond.png|thumb|center|420px| Figure 3:]]
-right
 </div>
-<br><br>
+==Our swimming remediation raft==
+[[File:TUM13_RenderingMIT.jpg|aft.png|thumb|right|910px|'''Figure 12''': Rendering of our remediation rafts in front of the MIT]]
-==Our swimming PhyscoFilter Prototype pod==
-[[File:TUM13 Blueprint_for_pod.png|thumb|right|420px| Figure 3:]]
-<br><br>
+[[File:Raft.png|thumb|right|420px|'''Figure 13''': 3D-print of our remediation raft]]
 At least there are problems both reactor types don't solve. In both cases upscaling involves a great deal of expense.
@@ Line 77: / Line 58: @@
 Slightly we return to the question how a '''biofilter''' could look like.
 It has to be a solution that can be implemented in '''any scale'''. The '''costs''' must be kept as low as possible. Additionally the '''energy consumption''' and '''maintenance''' must be kept to a absolute minimum to make it universally usable.
+[[File:TUM13_Blueprint_for_pod.png|thumb|right|420px| '''Figure 14''': Blueprint for our remediation raft]]
 Such a solution has to be '''engineered''' cleverly. Robust to environmental influences, expendable, modular and handy, even when in use. It must provide an ideal environment for the moss to grow and set off an alert if such a setting is no longer provided.
-Our answer to that is the '''PhyscoFilter pod'''. <br>
+Our answer to that is the '''remediation raft'''. <br>
-It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the pod raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers.
+It consists of a triangular shaped tube in which a felt cloth is stretched. As a float, the raft raises and falls with the water level, so the cloth is always kept on the water surface. Our experiments showed that felt is a very good matrix for the moss to grow on and its roots maintain stable on the fibers.
-The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of pods can easily arranged to a '''honeycombed''' structure. That makes pods are very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.
+The light weight and handy size make it '''mobile''' and and transportable and a higher quantity of rafts can easily arranged to a '''honeycombed''' structure. That makes remediation rafts very applicable at any location. In ponds, lakes and rivers; any scale is thinkable.
+===Shopping for the remediation raft===
-===Shopping for the pod===
 {|cellspacing="0" border="1"
-|+ Table 1: Shopping list for our Arduino-Project
+|+ '''Table 1''': Shopping list for our Arduino-Project
 !Component
 !Quantity
 !Source
-!Price
+!Price in € (per piece)
-!Figure
+!Price in € (sum)
 |-
-|Tubes
+|PVC-tubes 1,5 m, ⌀ 75mm
-|3
+| align=right | 3
-|Building center
+|Hardware Store
-|
+| align=right | 4,69
-|
+| align=right | 14,07
+|-
+|One-eight bend (45°)
+| align=right | 3
+|Hardware Store
+| align=right | 1,09
+| align=right | 3,27
+|-
+|Bend (67°)
+| align=right | 3
+|Hardware Store
+| align=right | 1,09
+| align=right | 3,27
+|-
+|Fleece
+| align=right | 1,3 m<sup>2</sup>
+|Hardware Store
+| align=right | 3,99 (per m<sup>2</sup>)
+| align=right | 5,19
+|-
+|Clamps
+| align=right | 3
+|Hardware Store
+| align=right | 2,30
+| align=right | 6,90
+|-
+|Carbon rod
+| align=right | 1 (1,25 m)
+|Hardware Store
+| align=right | 4,75
+| align=right | 4,75
+|-
+|Round eyelets
+| align=right | 3
+|Hardware Store
+| align=right | 0,34
+| align=right | 1,01
 |-
-|Connectors
+|'''Total'''
-|6
-|Building center
 |
-|
-|-
-|Felt base
-|xx m<sub>3</sub>
-|Building center
 |
 |
+| align=right | '''38,44'''
 |-
-|}<br>
+|}
+===Images from our trip to the construction center===
 <html>
+<div class="box-center">
 <ul class="bxgallery">
-     <li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/f/f8/TUM13_Foto_Kampen_1.jpg/350px-TUM13_Foto_Kampen_1.jpg" alt="Figure 15"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/d/d9/TUM13_Foto_Kampen_2.jpg/350px-TUM13_Foto_Kampen_2.jpg" alt="Figure 16"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/3/3c/TUM13_Foto_Kampen_3.jpg/350px-TUM13_Foto_Kampen_3.jpg" alt="Figure 17"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/9/96/TUM13_Foto_Kampen_4.jpg/350px-TUM13_Foto_Kampen_4.jpg" alt="Figure 18"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/b/b3/TUM13_Foto_Kampen_5.jpg/350px-TUM13_Foto_Kampen_5.jpg" alt="Figure 19"/></li>
-     <li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" /></li>
+     <li><img src="https://static.igem.org/mediawiki/2013/thumb/3/38/TUM13_Foto_Kampen_6.jpg/350px-TUM13_Foto_Kampen_6.jpg" alt="Figure 20"/></li>
 </ul>
+</div>
 </html>
-<br><br>
+==Monitoring by an Arduino Microcontroller==
-==Automatic monitoring of moss on a swimming pod by an Arduino Microcontroller==
 ===Introduction===
-[[File:TUM13_measuring_device.png|thumb|left|400px|Figure x: Idea for a measuring device]]
+[[File:Arduino_Uno.png|thumb|left|300px|'''Figure 21''': Arduino Uno, released in September 2010]]
-One advantage of our pod is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that
+One advantage of our raft is that it works quite '''autonomic'''. Once the moss is installed it filters until it's "saturated", assumed that
 the environmental parameters fit and a proper living space is provided.
 The main goal of our measurement device is to '''monitor''' these environmental parameters in real time.
-Since the filter's the costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.
+Since the filter's costs should be kept as low as possible, the usage of ordinary lab measurement tools is limited.
 Looking one step ahead it is conceivable to use a moss-filter in order to clean ponds or streams etc. Places that are not continuously supervised by humans.
 So our aim was to engineer a '''low cost and low energy solution''', that maintain the filters autonomy.
-[[File:Arduino_Uno.png|thumb|right|250px|Fig A: Arduino Uno, released in September 2010]]
+[[File:TUM13_measuring_device.png|thumb|right|200px|'''Figure 22''': Idea for a measuring device]]
 This is where '''Arduino''' comes into play.
-We installed an Arduino on one edge of our pod in order to monitor the setting.
 Arduino is a platform that is based on one '''microcontroller''' which is attached to a circuit board. Its convenient handling and easy programming,
 the lots of available hardware and the great community support make it one of the most popular prototyping platforms these days, especially for
@@ Line 151: / Line 164: @@
 At least there are a lot more free pins that can be used for sensors etc, and still its costs don't exceed 50€ (~60$).
-[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|Gruppenfoto]]
+We installed a solar powered Arduino on one edge of our remediation raft in order to monitor the setting. A '''temperature''' and a '''light sensor''' collect weather data and a '''water sensor''' attached to the side of the raft registers, if the raft's tubes take on water and whether it lowers its height on the surface.
+For testing purposes we even attached a '''display''' to the microcontroller. All collected data are sent via '''WiFi''' and stored at a '''server's MySQL database in real time'''. Alternatively the data can also be sent via '''GSM''' if there is no WiFi hotspot close by. All data can then easily be displayed.
+[[File:TUM13_How_It_Works_Flowmodel.gif|thumb|left|600px|'''Figure 23''': How it works]]
+The controller can easily be extended by other sensors, such as a '''color sensor''' to monitor the moss's health or a potential die off, a '''pH-Sensor''' or even a '''webcam'''.
+Concerning the low costs, the unlimited capabilities and the handiness we highly recommend the use of the Arduino as measuring device. We have created a [https://2013.igem.org/Team:TU-Munich/Results/How_To#Setting_up_a_basic_Arduino_measuring_device '''tutorial'''] how to set up an Arduino Due with some basic functions.
+[[File:TUM13_Arduinokomponenten.png|thumb|right|350px|'''Figure 24''': components]]
 {|cellspacing="0" border="1"
-|+ Table 1: Shopping list for our Arduino-Project
+|+ '''Table 2''': Shopping list for our Arduino-Project
 !Component
 !Quantity
@@ Line 163: / Line 184: @@
 |Arduino Due microcontroller
 |1
-|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 Source]
+|[http://www.watterott.com/de/Arduino-Due?xfb7d6=d868f3f07c538128ec6013c6d984b089 watterott]
 |46.41 €
 |Fig. 1 A
@@ Line 169: / Line 190: @@
 |Arduino WIFI Shield
 |1
-|[https://www.sparkfun.com/products/11287 Source]
+|[https://www.sparkfun.com/products/11287 sparkfun]
 |63.58 €
 |Fig. 1 B
@@ Line 175: / Line 196: @@
 |Watterott mega msd-shield
 |1
-|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield Source]
+|[http://www.watterott.com/de/Arduino-Mega-mSD-Shield watterott]
 |19.49 €
 |Fig. 1 C
@@ Line 181: / Line 202: @@
 |Display MI0283QT-9
 |1
-|[http://www.watterott.com/de/MI0283QT-2-Adapter Source]
+|[http://www.watterott.com/de/MI0283QT-2-Adapter watterott]
 |36.00 €
 |Fig. 1 D
@@ Line 187: / Line 208: @@
 |Light sensor TSL2561
 |1
-|[http://www.watterott.com/de/TSL2561-Lichtsensor Source]
+|[http://www.watterott.com/de/TSL2561-Lichtsensor watterott]
 |7.74 €
 |Fig. 1 E
@@ Line 193: / Line 214: @@
 |Temperature sensor DS18B20
 |1
-|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html Source]
+|[http://www.exp-tech.de/Sensoren/Sparkfun-Temperature-Sensor---Waterproof--DS18B20-.html exp-tech]
 |8.80 €
-|Fig. 1 F
+|Fig. 1 G
 |-
 |Water sensor
 |1
-|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html Source]
+|[http://www.exp-tech.de/Sensoren/Seeedstudio-Grove---Water-Sensor.html exp-tech]
 |2.90 €
-|Fig. 1 G
+|Fig. 1 H
 |-
 |Lithium-Battery
 |1
-|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery Source]
+|[http://www.amazon.com/s/ref=nb_sb_noss_1/176-6668907-5443152?url=search-alias%3Daps&field-keywords=lithium%20battery&sprefix=lithi%2Caps&rh=i%3Aaps%2Ck%3Alithium%20battery amazon]
 |16.35 €
 |
@@ Line 211: / Line 232: @@
 |Stackable Headers
 |3
-|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html Source]
+|[http://www.exp-tech.de/Zubehoer/Steckverbinder/Arduino-Stackable-Header-Kit.html exp-tech]
 |5.37 €
 |
@@ Line 231: / Line 252: @@
 |
 |207.64 €
-|
+|280.77 $
-|}<br>
+|}
-===part description===
+=== Server site ===
-====Arduino Due====
+To store the sensor data the Arduino connects to a web server via WLAN. The sensor measurements are encoded as GET parameters and sent to the server in a HTTP request, then [[Team:TU-Munich/TUM13_save.ph|save.php]] stores them in a MySQL database. The data can be viewed by visiting [[Team:TU-Munich/TUM13_index.ph|index.php]], which accesses the MySQL database and plots the sensor data in a graph. To view new data sets in real time [[Team:TU-Munich/TUM13_real.ph|real.php]] periodically requests new data from the server by using AJAX. An example of this setup can be viewed at http://igem.wzw.tum.de/arduino.
-[[File:Arduino_Due.jpg|thumb|right|250px|Fig 1 A: Arduino Due, released in October 2012]]
-The Arduino Due is the most powerful Arduino board. It's underlying 32bit-processor is the Atmel SAM3X8E.
-Contrary to the other boards which run at 5V, a power supply of 3.3V is sufficiant.
-Data:
-Mhz	CPU Clock
-	KBytes of SRAM.
-	KBytes of Flash memory.
-	Digital I/O Pins
-	Analog Input Pins
-	(DAC)Analog Outputs Pins
-====Arduino WiFi Shield====
-[[File:Arduino_WiFi.png|thumb|right|250px|Fig 1 B: Arduino WiFi, released in August 2012]]
-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.
-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
-.3V
-V
-====Watterott mega msd-shield====
-[[File:Arduino_Mega_MSD.JPG|thumb|right|250px|Fig 1 C: 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 won't 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 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 have 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.
-'''Pin usage:'''
- Pin  4	SS for SD card
- Pin  6	SS for the touch of the touch display
- Pin  7 (25)SS for the LCD (Workarround of the double usage of pin 7 by the WIFI Shield)
- 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 50	SPI MISO
- Pin 51	SPI MOSI
- Pin 52	SPI SCK
-     gnd
-.3V
-====Display MI0283QT-9====
-[[File:Arduino_MI0283.jpg|thumb|right|250px|Fig 1 D: 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====
-[[File:Arduino_Tsl2561.png|thumb|right|150px|Fig 1 E: TSL2561]]
-[[File:Arduino_Tsl2561_Curve.png|thumb|right|150px|Fig 1 E1: TSL2561 Absorption Curve]]
-The light sensor is a small, so called, breakout board. It is usually connected by wires instead of directly plugged to the Arduino.
-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
-.3V
-====Temperature sensor DS18B20====
-[[File:Arduino_Tempsen.jpg|thumb|right|250px|Fig 1 F: DS18B20 ]]
-The temperature sensor is embedded into a water proof cable. It is addressed via a One-Wire 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.
-Similar to the I²C (TwoWire) bus, you only have to get the One-Wire interface working once. After that, you can easily set up One-Wire more 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====
-[[File:Arduino_Watersensor.jpg|thumb|right|250px|Water sensor Fig 1 G]]
-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 A7	Water sensor
-     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===
-*Breadboard
-*Soldering bolt
-*Solder
-===Assembly===
-[[File:Arduino_Pinout.png|right|x400px|Arduino Due pinout diagram ]]
-Keep everything clear during your assembly. If you have different colored linking cables, always try to use the same color code.
-For example: brown cable for 3.3V etc. Troubleshooting can get nasty.
-<br><br>
 ==How could it look installed in a river?==
+===New York PARALLEL NETWORKS===
+<html>
+<div class="box-center">
+<ul class="bxgallery">
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/e/ea/TUM13_parallel_networks1.png/350px-TUM13_parallel_networks1.png" alt="Figure 25: embedding the PhyscoFilter pod"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/a/ac/TUM13_parallel_networks2.png/350px-TUM13_parallel_networks2.png" alt="Figure 26"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9f/TUM13_parallel_networks3.png/350px-TUM13_parallel_networks3.png" alt="Figure 27"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/1/12/TUM13_parallel_networks4.png/350px-TUM13_parallel_networks4.png" alt="Figure 28"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/0/02/TUM13_parallel_networks5.png/350px-TUM13_parallel_networks5.png" alt="Figure 29"/></li>
+</ul>
+</div>
+</html>
-===NY parallel networks===
+In a design competition that focuses on New York and its waterways in 2011, we found an impressive proposal working on New York's Upper Bay. Re-imagining recreational space, public transportation, local industry, and native environment, the [http://op-n.net/filter/work/PARALLEL-NETWORKS NY PARALLEL NETWORKS] project considered using swimming triangles as versatile platform for various purposes. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the Canadians Ali Fard and Ghazal Jafari. These triangles, so called pods, fulfill different tasks such as the '''fixation of carbon dioxide''', '''food production''' and '''local recreation''' without hindering the '''renewable energy generation''', furthermore the '''transportation''' of passengers and goods.
-[[File:TUM13_Architecture1.png|thumb|right|400px|Fig x: ‘Water as the 6th Borough’ Design Competition for NYC
+As we were amazed finding such a great sustainable concept, we didn't hesitate to get in touch with Op.N (Ali Fard and Ghazal Jafari). We asked for their permission for mentioning their work on our page, and they gave us a nice and fast feedback affirming the '''"great structural flexibility and expandability of the triangular floating pods"'''.
-]]
+We believe that this design is feasible and that an additional PhyscoFilter pod could extend this design. Using the rafts close to big cities doesn't bring along the problems other solutions have to face. Most cities use just a fraction of their water surface, leaving much space that could easily be made use of. At this point the the PARALLEL NETWORKS concept establishes. The raft's great flexibility also enable a short time of usage, simply changing their location if they get in the way of other schemes, avoiding greater costs.
-In the Desing competition for NYC of the year 2011 we found an impressive proposal how a river could be used to meed all the requirements of an urban population by insalling swimming triangles. The winning contribution for the [http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough] was designed by the canadians Ali Fard and Ghazal Jafari which was called  [[File:TUM13_NY_PARALLEL_NETWORKS.PDF NY pralllel networks]].  These triangles, so called pods fulfill different tasks such as the fixation of carbon dioxide, food production and local recreation without hindering the renewable energy generation and transporatation of passengers and goods. We believe that this design could become realized and that an additional sort of swimming pod with a PhyscoFilter could complete this desing.
-===The Pods utelized in this proposal===
+===Commercially available rafts called "Kampen"===
-[[File:TUM13_Architecture2.png|thumb|left|400px|Fig x: Types of swimming pods
+[[File:TUM13_Schwimmkampen.png|thumb|right|400px|'''Figure 30''': Commercially available rafts]]
-]]
+During the search for a possibility to build remediation rafts for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company that developed and provides products for the revegetation of rivers and wetlands. The company has its head office in Tangstedt, Pinneberg (BW) and is specialized in engineering on biological tasks. It is one of the leading manufacturer for individual solutions that must harmonize with the environments natural development.
-===Commercially availible pods called "Kampen"===
+==Swimming remediation raft in action==
-[[File:TUM13_Schwimmkampen.png|thumb|right|400px|Fig x: Commercially availible swimming pods]]
+<html>
-In the search for a possibility to built swimming pods for our moss filter we found [http://www.bestmann-green-systems.de BGS Ingenieurbiologie und -ökologie GmbH] which is a German company which developed and provids solutions for the revegeation of rivers and wetlands.
+<div class="box-center">
+<ul class="bxgallery">
-===Our own swimming pod for the implementation of our PhyscoFilter===
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/6/6e/TUM13_Foto_Arduino_1.png/350px-TUM13_Foto_Arduino_1.png" alt="Figure 31"/></li>
-[[File:TUM13_Our_swimming_pod.png|thumb|left|400px|Fig x: Our swimming pod in action]]
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/6/68/TUM13_Our_swimming_pod.png/350px-TUM13_Our_swimming_pod.png" alt="Figure 32"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/9/9a/TUM13_Foto_Arduino_4.png/350px-TUM13_Foto_Arduino_4.png" alt="Figure 33"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/0/09/TUM13_Foto_Arduino_2.png/350px-TUM13_Foto_Arduino_2.png" alt="Figure 34"/></li>
-==Swimming PhyscoFilter Pod in action==
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/5/53/TUM13_Foto_Arduino_9.png/350px-TUM13_Foto_Arduino_9.png" alt="Figure 35"/></li>
+    <li><img src="https://static.igem.org/mediawiki/2013/thumb/6/60/TUM13_Foto_Arduino_6.png/350px-TUM13_Foto_Arduino_6.png" alt="Figure 36"/></li>
-<br>
+<li><img src="https://static.igem.org/mediawiki/2013/9/99/TUM13_arduino_light_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 37"/></a></li>
+<li><img src="https://static.igem.org/mediawiki/2013/0/00/TUM13_arduino_temperature_curve.png" alt="<a href='http://igem.wzw.tum.de/arduino/'>Figure 38</a>"/></li>
+</ul>
+</div>
+</html>
 ==References:==
-<!-- Kopiervorlagen -->
-[[http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984]]
-#[[http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984]] Edens, L., Bom, I., Ledeboer, A. M., Maat, J., Toonen, M. Y., Visser, C., and Verrips, C. T. (1984). Synthesis and processing of the plant protein thaumatin in yeast. ''Cell'', 37(2):629–33.
 <!-- Ab hier richtige Referenzen einfügen -->
+[[http://bvt.blt.kit.edu/ KIT]] Homepage about Institute of bioprocess Engineering
-[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ ONE PRIZE: Water as the 6th Borough - Winners Announced; Posted on http://www.bustler.net Thursday, August 04, 2011]]
+[[http://op-n.net/filter/work/PARALLEL-NETWORKS Op.N]] Op.N Homepage
-#
+[[http://www.bustler.net/index.php/article/one_prize_water_as_the_6th_borough_-_winners_announced/ www.bustler.net, Thursday, August 04, 2011]] Article: ONE PRIZE: Water as the 6th Borough - Winners Announced;
+[[http://www.bestmann-green-systems.de/ BGS Ingenieurbiologie und -ökologie GmbH]] BGS Homepage
 <!-- Ende des Inhalts -->