Team:KU Leuven/Journal

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== Modeling ==
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'''01/07'''
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We installed '''Matlab''', took a look at some presentations about modeling. We are also investigating [http://www.mathworks.nl/products/simbiology/ SimBiology].
 
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'''02/07'''
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    <a href="https://2013.igem.org/Team:KU_Leuven/Journal" title="Team:KU_leuven">
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    <i class="livicon activeicon" data-name="calendar" data-color="white"></i></div>
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    <h3>Journals</h3>
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    </a>
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    <p>You are here!</p>
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We watched some [http://www.mathworks.nl/products/simbiology/webinars.html webinars about SimBiology]. In the afternoon we had an appointment with professor Bernaerts of the division of (bio)chemical procestechnology. It was very useful, as she gave some good ideas on how to get started. We will have to design a way of expressing the enzyme(s) in a cyclic manner. We could achieve this by expressing it during a short pulse, activated by the presence of a signal from other cells.
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    <a href="https://2013.igem.org/Team:KU_Leuven/Protocols">
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    <h3>Protocols</h3> </a>
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    <p>No magic involved - unfortunately</p>
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    <a href="https://2013.igem.org/Team:KU_Leuven/Safety">
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    <i class="livicon activeicon" data-name="biohazard" data-color="white"></i>
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    <h3>Safety</h3>
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    <p>Be careful!</p>
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'''03/07'''
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During the morning we brainstormed about some possible '''networks with oscillating behavior'''. We have to keep in mind that the colony has to be and stay '''synchronized'''. This could be achieved by a rapid (protein-protein interaction) feedback which is proportional to the phase difference.
 
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We had a meeting with the '''wetlab team''' and discussed our main focus for the upcoming weeks: figuring out an oscillating construct and simulating the behaviour of the methyl salicylate BioBrick.
 
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    <a href = "https://2013.igem.org/Team:KU_Leuven/Journal/Modelling">
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    <h3>Modelling</h3> </a>
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      <p align="justify">This summer, three dedicated male engineers spent a whole summer modelling our systems. <br/>However, without the help of a girl, Tina, this would have been a rather "nerdy" journal. Luckily, Tina was always there when the modelling team sought a balance between awful jokes and work efficiency. Nevertheless, without Sander's work tempo, Bert’s criticism and Tomas' factotum mind, the modelling would not have been as thorough as now.<br/>
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In this journal, you can read how they started modelling from scratch up to being modelling specialists, using Matlab, SimBiology, COBRA and even qPCR.</p>
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'''04/07'''
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    <a href = "https://2013.igem.org/Team:KU_Leuven/Journal/Ecology">
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    <h3><i>E. coligy</i></h3> </a>
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      <p align="justify">We worked together with two research groups, Biobest and pcfruit. Both offer a whole series of parasitoids and predators against aphids for the purpose of biological pest control and investigate the relationship between plant and aphid in search of a method to protect plants from this pest. Here, you can read more about the experiments Aurelie and Flore (Biobest) and Tina and Tomas (pcfruit) performed to test our model on aphids and ladybugs.</p>
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Bert and Sander are working on simulating the '''&Prime;Mortier Oscillator&Prime;''' in SimBiology.
 
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Tina and Tomas are modeling the network to produce methyl salicylate.
 
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:'''pchA''' and '''pchB''' catalyze the reactions from chorismate to isochorismate to salicylate.
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    <a href="https://2013.igem.org/Team:KU_Leuven/Journal/EBF/wetlab">
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    <h3>E-β-Farnesene</h3></a>
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      <p align="justify">Here we present the work on the <a href="Http://2013.igem.org/Team:KU Leuven/Project/Glucosemodel/EBF">EBF-biobrick</a>, a part of the glucose model, week by week. The contributors are Lukas and Su, which formed a very tight team that already started with lab work even during the exams in June. Lukas’ multitasking skills and Su’s precise work, combined with their cute smiles, made sure everyone regretted not being part of this team. <br/> You can read all about the extensive work the EBF guys have done in this part.</p>
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:'''BSMT1''' is the enzyme that catalyzes the reaction from salicylate to methyl salicylate.
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    <h3>Feed forward loop</h3> </a>
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      <p align="justify">Long team discussions and Bert’s persistence resulted this summer in a ‘proof of concept’ wetlab version of Bert Mortier’s oscillator, called the ‘feed forward loop’. <br/>
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Pieter and Sylvie were immediately up to form a subteam and started working in order to create a part of the <a href="https://2013.igem.org/Team:KU_Leuven/Project/Oscillator">oscillator</a>.<br/>
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In this part, you can read all about their big UP in the beginning, going to a down after a while and the eventual steady state with troubleshooting in the end.<br/>
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Nevertheless, this feed forward loop is only the beginning to create Bert’s oscillator.</p>
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Tomas and Sander are looking on how to use the '''[http://opencobra.sourceforge.net/openCOBRA/Welcome.html COBRA toolbox]''' for our purpose. We would need to check the constraints on reaction rates and add our new reactions.
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Bert made contact with professors Suykens of the [http://www.esat.kuleuven.be/scd/ department of electrical engineering] and professor Degrève of the division of (bio)chemical procestechnology in order to have an idea of how to analyse the MO, we apparently need '''[http://en.wikipedia.org/wiki/Bifurcation_theory bifurcation analysis]''', which Bert started looking up about.
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    <h3>Methyl Salicylate</h3> </a>
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      <p align="justify">The Methyl Salicylate team or ‘MeS boys’, in normal life called Robbert and Laurens, worked on the improvement of the methyl salicylate brick round the clock almost whole summer.  The journal can be found here. More information on the MeS biobrick can be found on <a href="https://2013.igem.org/Team:KU_Leuven/Project/Glucosemodel/MeS"> this page</a>.</p>
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'''05/07'''
 
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Tomas started the development of another oscillator, while Sander and Tina are looking deeper into metabolic network modeling.
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<a href="https://2013.igem.org/Team:KU_Leuven/Journal/MeS/qPCR">
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    <h3>qPCR</h3> </a>
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      <p align="justify">The modelling team also performed a qPCR, a new and appeasing way to characterise and to find data for our <a href="https://2013.igem.org/Team:KU_Leuven/Project/qPCR">computer model</a>. In this part, you can read how to properly manage with troubles and how to search for promising directions.</p>
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'''07/07'''
 
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We are in touch with professor Roose of the [http://wms.cs.kuleuven.be/groups/natw/index.html applied mathematics division], who suggested the use of '''[http://www.matcont.ugent.be/ MatCont]''' for the analysis of our oscillator.
 
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'''08/07'''
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We’re investigating the [http://pubs.acs.org/doi/abs/10.1021/sb300084h AutoBioCAD] software and looking for a better model to our quorum sensing system using PDEs.
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'''09/07'''
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We started investigation of literature of ecology. We chose our '''model species''' (aphid and crop). We’ll try to model aphid reproduction and the influence of bèta-farnesene and methylsalicylate on life cycle and movement. We’ll have to make an estimation of the damage/loss of crops due to a certain population of aphids.
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Bert added spatial heterogeneity in his Mortier Oscillator to see what happens on a population level.
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Latest revision as of 10:27, 3 January 2014

iGem

Secret garden

Congratulations! You've found our secret garden! Follow the instructions below and win a great prize at the World jamboree!


  • A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
  • For one of our models we had to do very extensive computations. To prevent our own computers from overheating and to keep the temperature in our iGEM room at a normal level, we used a supercomputer. Which centre maintains this supercomputer? (Dutch abbreviation)
  • We organised a symposium with a debate, some seminars and 2 iGEM project presentations. An iGEM team came all the way from the Netherlands to present their project. What is the name of their city?

Now put all of these in this URL:https://2013.igem.org/Team:KU_Leuven/(firstname)(abbreviation)(city), (loose the brackets and put everything in lowercase) and follow the very last instruction to get your special jamboree prize!

tree ladybugcartoon

Journals

You are here!

Protocols

No magic involved - unfortunately

Safety

Be careful!

Modelling

This summer, three dedicated male engineers spent a whole summer modelling our systems.
However, without the help of a girl, Tina, this would have been a rather "nerdy" journal. Luckily, Tina was always there when the modelling team sought a balance between awful jokes and work efficiency. Nevertheless, without Sander's work tempo, Bert’s criticism and Tomas' factotum mind, the modelling would not have been as thorough as now.
In this journal, you can read how they started modelling from scratch up to being modelling specialists, using Matlab, SimBiology, COBRA and even qPCR.

E. coligy

We worked together with two research groups, Biobest and pcfruit. Both offer a whole series of parasitoids and predators against aphids for the purpose of biological pest control and investigate the relationship between plant and aphid in search of a method to protect plants from this pest. Here, you can read more about the experiments Aurelie and Flore (Biobest) and Tina and Tomas (pcfruit) performed to test our model on aphids and ladybugs.

E-β-Farnesene

Here we present the work on the EBF-biobrick, a part of the glucose model, week by week. The contributors are Lukas and Su, which formed a very tight team that already started with lab work even during the exams in June. Lukas’ multitasking skills and Su’s precise work, combined with their cute smiles, made sure everyone regretted not being part of this team.
You can read all about the extensive work the EBF guys have done in this part.

Feed forward loop

Long team discussions and Bert’s persistence resulted this summer in a ‘proof of concept’ wetlab version of Bert Mortier’s oscillator, called the ‘feed forward loop’.
Pieter and Sylvie were immediately up to form a subteam and started working in order to create a part of the oscillator.
In this part, you can read all about their big UP in the beginning, going to a down after a while and the eventual steady state with troubleshooting in the end.
Nevertheless, this feed forward loop is only the beginning to create Bert’s oscillator.

Methyl Salicylate

The Methyl Salicylate team or ‘MeS boys’, in normal life called Robbert and Laurens, worked on the improvement of the methyl salicylate brick round the clock almost whole summer. The journal can be found here. More information on the MeS biobrick can be found on this page.

qPCR

The modelling team also performed a qPCR, a new and appeasing way to characterise and to find data for our computer model. In this part, you can read how to properly manage with troubles and how to search for promising directions.

Retrieved from "http://2013.igem.org/Team:KU_Leuven/Journal"