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Week 12: the 14^th-18^th of September

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-Writing and constructing wiki pages.
-Our sweaters and T-shirts arrived!

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-Cloning our biobricks by use of the plasmid backbone originating from the InterLab Measurement Study. As a result,the biobricks CheZ-GFP, LuxI-His, LuxR-E and Ag43-YFP were obtained!
-Assembling the biobrick CheZ-GFP behind a strong promoter and RBS in order to characterize this biobrick.
-Assembling a strong promoter with GFP in order to compare the fluorescence to our library of promoters generated during the InterLab Measurement Study. Unfortunately the strong promoter was not green which indicates that the ligation did not work.
-Performing the OHHL quantification method and the leucine quantification method.

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-Making new continuous model simulation videos simulating each part of the model separately.

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-Working further on our educational card game about synthetic biology.

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-Our wiki game is online!

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-Graphical design of our wiki
-Design of our poster

Week 11: the 7^th-11^th of September

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- On Monday, we had our ‘iGEM Symposium Day on Synthetic Biology, Cell Systems and Ethics in Biochemistry’

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- Constructing the BioBricks LuxI-His, RBS-LuxI-His and CheZ-GFP, RBS-CheZ-GFP by high fidelity tail-PCR, digestion and ligation in pSB1C3
- Transforming these BioBricks in E. cloni, testing colonies by PCR and preparing for sequencing. The high fidelity PCR and cloning of other potential BioBricks was repeated.
- Making our strains ΔtarΔtsr and ΔtarΔcheZ electrocompetent
- Checking our colonies containing the assembled gBlocks by restriction mapping showed the presence of the original pUC19 vector in our samples. Treating the assembled gBlocks with DpnI should circumvent this since DpnI only cuts the methylated DNA.
- Digesting with DpnI eliminated the original pUC19 and not a single colony grew on the control plate transformed with plasmid only. Analysing the positive colonies showed presence of pUC19.

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- Hybrid model: implementing periodic boundary conditions
- Hybrid model: incorporating the first draft of the internal model into hybrid model
- Attendeding MATLAB webinar: Optimizing and Accelerating your MATLAB Code

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- Preparing games and presentations for school visits
- Visiting schools to teach children about DNA and synthetic biology
- Analyzing the results of our survey

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- Writing texts for the Wiki
- Putting our 'Secret'-page online!

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- Working on the design of the sweaters

Week 10: the 31^thAugust-6^th of September

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- We have new sponsors: Gips Mineral, Genzyme and VWR!
- We kindly received gadgets from our sponsors to distribute in our goody bags for the Symposium
- Ordering our self-designed bacteria stickers

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- Miniprepping and analyzing the assembled gBlocks is showing the assembled plasmid, but also the presence of pUC19 used as template. Transformation of the gel-purified correct plasmid was done in E. Cloni
- In parallel, assembling LuxI with gBlocks 1+2+3 and gBlocks 5+6 with gBlocks 1+2+3 was conducted with colonies that did not contain any pUC. Analysis of the gel was not showing any sign of digestion.

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- Collaboration with Toulouse: diffusion in Comsol
- Implementation of cells algorithm for nearest neighbor search
- Optimization of the code
- Meeting with Dirk Roose
- Examining effects of different contributions to cell movement in hybrid mode

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- Making a presentation and writing the scenario for our symposium
- Arranging our symposium
- Working on an educational game about synthetic biology

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- Adapting the team page: our mentors and advisors are online!
- Adapting our website for mobiles
- Making a game for our secret page

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- Designing our iGEM banner
- Designing our sweaters
- Adapting buttons of the wiki
- Designing the bacterium stickers of our promoter and supervisor
- Designing funny pictures for the secret page

Week 8: the 17^th-21^th of August

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- We are in the track ‘New applications’
- Receiving offers for sweaters, stickers and tattoos
- Collaboration: Skype session with TU Delft
- Collaboration: Measuring pH of tap water and river water & sending samples to the iGEM team of York
- Collaboration: Interviewing people on the street for chewing-gum survey of the iGEM team of Aix-Marseille Université
- Translating our survey in French for further distribution in Wallonie.

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- Searching more information about lab safety
- Analyzing the results of the InterLab Measurement Study

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- Preparing electrocompetent cells
- Optimizing the tail PCR to make Biobricks
- Cloning the PCR products into pSB1C3, transforming the plasmids and screening of colonies to find the correct insert
- Transforming the devices for the Interlab Measurement Study
- Preparation of the standard curve based on fluorescein and measuring the fluorescence of the new devices
- Assembling the gBlocks using NEBuilder® HiFi DNA Assembly Master Mix and transforming the checked pcr products in electrocompetent E. cloni

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- Meeting with Tim Odenthal
- Optimization of hybrid model code
- Implementation of cell-cell interactions, including repulsion as well as attraction

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- Contacting keynote speakers for the Symposium
- Organizing symposium
- Mailing schools to give a playful course about synthetic biology
- Deciding on the rules for a nice card game about synthetic biology

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- Adapting pages
- Putting ‘Symposium’-page online

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- Making informative images for the Research-page
- Making buttons for the wiki
- Designing bacteria-stickers for use in schools and as gadgets
- Continuing with the design of our sweaters
- Designing funny images for our secret page on the wiki

Week 7: the 10^th-14^th of August

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- Our flyers and sponsor brochures arrived!
- Conducting a survey about synthetic biology interviewing people on the street
- Working on a team song

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- Making a protocol for leucine detection
- Researching lab safety

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- Switching from transformation of chemocompetent cells to electroporation due to low efficiency for the Interlab Measurement Study
- Checking the intactness of other genes in the tar-tap-cheRBYZ operon by PCR
- Ordering NEBuilder to repeat the failed Gibson Assembly
- Making three BioBricks starting from our gBlocks by tail PCR and restriction digestion
- Ordering materials for leucine and AHL detection

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- Finishing implementation of the hybrid model I in 2D, including ADI scheme for PDE part
- Extending hybrid model II to 2D
- Running hybrid model simulations
- Finishing report Simbiology
- Contacting Toulouse team for collaboration
- Contacting professors for possible collaboration

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- Brainstorming about educational games

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- Putting our ‘Newsfeed’ & ‘Research’-page online!
- Implementing an EasySwitch button and a Lightbox

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- Making informative images for the ‘Research’-page
- Starting the design of sweaters
- Photoshopping funny images for our secret page

Week 6: the 3^th-7^th of August

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- We received lab material kindly provided by KOLO Instruments - Paulussen Freddy
- Searching hotels in Bordeaux for the iGEM Meetup France 2015
- Ordering folders and brochures

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- Writing protocols for AHL detection
- Writing abstract about literature on Wiki

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- Confirming the double knock-outs and checking the intactness
- Performing a motility test to verify the phenotypical change of knocking out cheZ
- Assembling the gBlocks using the Gibson Assembly Method
- Transforming E. cloni with the BioBricks J23101, I12504, J23106 and J23117 to participate in the iGEM 2015 Measurement Interlab Study.

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- Writing a report about Simbiology
- Extending the Hybrid Model to 2D

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- Contacting potential keynote speakers for the symposium

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- Putting the History-page online

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- Making images for wiki-icons for subsections of the Newsfeed
- Making tattoo-images to use as gadgets

Week 5: the 27^th-31^th of July

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- Booking plane tickets to Boston
- Booking hotels Boston
- Two new companies are sponsoring: Eppendorf & LRD!

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- Preparing the protocol for plasmid assembly
- Making the protocol for leucine detection
- Making protocol for AHL detection
- Designing & ordering primers for the Gibson Assembly Method

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- Making double knock-out strains by P1 transduction
- Performing PCR and gel electrophoresis to confirm correct double knock-outs

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- Finishing the 2D models on a 100 by 100 grid

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- Contacting potential keynote speakers for the symposium
- Making a survey about public perception of synthetic biology
- Mailing the Bordeaux iGEM team for the France Meetup 2015

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- Putting the Modeling page online
- Adjusting the description of the project

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- Designing images for wiki team presentation
- Designing images for wiki icons for subsections of the Newsfeed
- Designing animations that represent our pattern forming bacteria

Week 4: the 20^th-24^th of July

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- Meeting the Toulouse iGEM team on 07/21/2015 at ESI (Expo Science International) in Brussels

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- Searching parameters necessary in mathematical model
- Designing and ordering the designed plasmid in gBlocks

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- Checking the removal of the kanamycin cassette in the Δtar strain and make a stock of our successful knockout
- Preparing phage P1 lysate to make the double knock-out strains

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- Simulating cell A and cell B in SymBiology
- Looking for usable constants
- Adapting the 2D continuous model

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- Inviting potential keynote speakers for the symposium

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- Adding the Team page

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- Making images for wiki team presentation
- Designing the flyer
- Making images of animals with new patterns for the wiki

Week 3: the 13^th-17^th of July

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- Constructing the plasmids
- Designing & ordering primers for controlling the knock-out proces
- Researching an alternative knock-out technique for double knockouts

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- Calculating the transformation efficiency of competent E. cloni cells
- Ordering 3 knock-out strains (Δtar, Δtsr and ΔcheZ) & preparing a stock
- Ordering Chromobacterium violaceum CV026 transposon mutant for usage in AHL detection & preparing a stock
- Removing the kanamycin resistance gene of the Δtar strain by transforming a plasmid with recombinase gene

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- Making and adapting the 1D hybrid and continuous model to the conditions of the wet lab
- Making a simple 2D continuous model
- Implementing biologically relevant parameters
- Making a 1D model with pdepe in Matlab
- Exploring symbiology
- Making a 2D model with the PDE toolbox in Matlab (not ready yet)

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- Preparing e-mail for symposium and contacting possible keynote speakers

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- Putting the description of our project online

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- Making images for the wiki

Week 2: the 6^th-10^th of July

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- Discussion with modeling team: which parameters do they need?
- Searching experiments for quantification of specific proteins, small molecules and amino acids
- Deciding on promoters of the plasmid
- Constructing the plasmids
- Making a working scheme (strategy)

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- Preparing LB agar medium
- Preparing competent cells (E. cloni) and testing their competency

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- Researching literature about hybrid models
- Further working on single cell agent-based model
- Implementing a simple one-dimensional hybrid model
- Exploring PDE Toolbox
- Working on an implicit continuous model
- Trying to simulate pattern formation of bacteria in COMSOL

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- First meeting about school projects
- Brainstorming about a symposium

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- Designing images and layout of wiki
- Designing images and brochure for sponsors

Week 1: the 1^st-3^th of July

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- Lab safety training
- Discussing tasks and practical arrangements (tickets Boston)
- Taking photos to use in the brochure, on the wiki and for social media
- Taking a tour through our high tech bio laboratory
- Meeting with potential sponsor

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- Searching for strains and BioBricks for our circuit

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- Setting up GitHub
- Constructing a simple single cell agent-based model
- Working on an explicit discretization of a continuous model