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| + | |
| − | <div class="container">
| + | |
| − | <div class="center">
| + | |
| − | <div class="book-wrapper">
| + | |
| − | <div id="flipbook">
| + | |
| − | <div class="page"><div class="page-inner"><h1 class="middle"> iGEM Week 1 </h1>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 20th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 17:00 </h2>
| + | |
| − | <p> Josh had his training today and was introduced to lab techniques that the rest of the team had worked on during the previous week. These techniques included fire drills, safety techniques as well as use of the sterile hood. </p>
| + | |
| − | <p> The team got split into two groups
| + | |
| − | <ul> <li> Group 1 (Kristina, Ollie and Josh): Made streak plates of all the colonies needed for the Interlab study. These streak plates were left to incubate over the weekend. Alongside colony cultures, liquid cultures were also made. </li> </ul>
| + | |
| − | <ul> <li> Group 1 (Jake, Emilija, Ollie, Kristina, Kerry, Rupert and Lauren): Looked at research papers in order to obtain more scientific data for the experiment. We wrote up the agenda as well as the minutes from the meeting we had. We also planned out the rest of the week and began a plan for the Wiki. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 21st, 2016 </h1>
| + | |
| − | <h2> 09:00 - 11:00 </h2>
| + | |
| − | <p> <ul> <li> We sat down to discuss ideas for the Wiki theme as well as the layout. We came up with the idea for baseball themed cards for the team description. With regards to the color scheme and theme, we were inspired by old coke adverts and the whole "pop-art" theme. </li> </ul> </p>
| + | |
| − | <h2> 11:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> We had a lecture on how to use COMSOL and MATLAB by Dana Ofiteru. </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 13:30 </h2>
| + | |
| − | <p> <ul> <li> Checked the streak plates from yesterday. The team was then split into sub-groups to research about "Beyond the bench" ideas as well as the light bulb component of the breadboard. </li> </ul> </p>
| + | |
| − | <h2> 16:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Had a team Skype session with Edinburgh University and discussed the potential for collaboration. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 22nd, 2016 </h1>
| + | |
| − | <h2> 09:00 - 11:00 </h2>
| + | |
| − | <p> <ul> <li> Jake and Kristina: Analysed the InterLab Results. </li> </ul> </p>
| + | |
| − | <p> <ul> <li> Ollie and Josh: Researched papers on fuel cells and components for the light bulb. </li> </ul> </p>
| + | |
| − | <p> <ul> <li> Emilija and Lauren: Researched components for the light bulb and tried to construct some BioBricks on Benchling. </li> </ul> </p>
| + | |
| − | <p> <ul> <li> Kerry: Worked on the project description for the wiki. (Deadline: July 1st) </li> </ul> </p>
| + | |
| − | <h2> 11:00 - 11:30 </h2>
| + | |
| − | <p> <ul> <li> Ollie and Josh: Plated the Positive Control sample from the previous day in order to have enough of that sample for the team to repeat the interlab study. </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 15:00 </h2>
| + | |
| − | <p> <ul> <li> Everyone but Lauren and Emilija met with Professor Ian Head, Dr.Ed Milner and Paniz Izadi from the School of Civil Engineering and Geosciences to discuss microbial fuel cells. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | <p> <ul> <li> Lauren and Emilija met with our supervisors to discuss the Killer BioBrick </li> </ul> </p>
| + | |
| − | <h2> 15:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> We met with supervisors (See Agenda and Minutes for the 22nd June) </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 23rd, 2016 </h1>
| + | |
| − | <h2> 09:00 - 11:00 </h2>
| + | |
| − | <p> <ul> <li> We finalized the Killer BioBrick construct.</li> </ul> </p>
| + | |
| − | <h2> 11:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> We had a lecture on modelling by Anil Wipat.</li> </ul> </p>
| + | |
| − | <h2> 12:00 - 12:30 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time!</li> </ul> </p>
| + | |
| − | <h2> 12:30 - 14:00 </h2>
| + | |
| − | <p> <ul> <li> Continued our training in modelling BioBricks after having lunch. We were also introduced to RuleBender. </li> </ul> </p>
| + | |
| − | <h2> 14:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Attempted to model our Killer BioBrick using RuleBender. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 24th, 2016 </h1>
| + | |
| − | <h2> 09:30 - 10:30 </h2>
| + | |
| − | <p> <ul> <li> We had a late start due to the outcome of the EU Referendum. As a team bonding activity we all decided to go out for breakfast together before beginning work. </li> </ul> </p>
| + | |
| − | <h2> 10:30 - 11:00 </h2>
| + | |
| − | <p> <ul> <li> We all went to the library and double-checked our BioBrick design that we created using Benchling. Once we had agreed on the design we met up with Jem (one of our advisors) in order to verify that everything was ready to be sent off. </li> </ul> </p>
| + | |
| − | <h2> 11:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> Before lunch we went through all of the Action Points. We categorized them into groups based on what was completed and what still needed to be done. The tasks that needed to be done were assigned amongst the team. </li> </ul> </p>
| + | |
| − | <h2> 12:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> All the previously assigned tasks were carried out. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1 class="middle"> iGEM Week 2 </h1>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 27th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 13:00 </h2>
| + | |
| − | <p> <ul> <li> We visited FabLab in Sunderland. They offer 3D printing, laser printing as well as much more. We were able to tour the lab and get a better idea of what that company could offer us. We decided that the two areas which interested us were the 3D printing for our breadboard but also the formation of electrical circuits. </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 14:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time! </li> </ul> </p>
| + | |
| − | <h2> 14:00 - 15:00 </h2>
| + | |
| − | <p> <ul> <li> Meeting with Andrew Filby to be introduced and become accustomed to the concept of flow cytometry. </li> </ul> </p>
| + | |
| − | <h2> 15:00 - 16:00 </h2>
| + | |
| − | <p> <ul> <li> Obtained components for the fuel cell. Components included methylene blue, carbon electrode, cationic exchange membrane alongside other chemicals. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | <h2> 14:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Went through action points and planned what needed to be completed. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 28th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 10:00 </h2>
| + | |
| − | <p> <ul> <li> Made microbial fuel cell. See below for the microbial fuel cell protocol. </li> </ul> </p>
| + | |
| − | <h2> 10:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> Liquid cultures of our samples were made and then left in the fridge overnight to be ready for incubation tomorrow. </li> </ul> </p>
| + | |
| − | <h2> 12:00 - 13:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time! </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 17:00 </h2>
| + | |
| − | <p> We went to the library where we carried out a variety of tasks </p>
| + | |
| − | <p> <ul> <li> The breadboard design was made using TinkerCad software. We designed an approximation of the sizes of different components as well as how they would fit into the breadboard. </li> </ul> </p>
| + | |
| − | <p> <ul> <li> In the meantime the light-bulb construct was redesigned.</li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | <p> <ul> <li> The Team Wiki was looked at and altered. We tried to fix the Navigation Bar and get some information up</li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> June 30th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 11:00 </h2>
| + | |
| − | <p> <ul> <li> The InterLab study was discussed with Tom. We discussed the errors that were made (systematic and experimental). We ran through the steps of the protocol with him and explained what was done at each step. Then we discussed limitations as well as modifications for the experiment. </li> </ul> </p>
| + | |
| − | <h2> 11:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> The light-bulb design construct was run through with Jem. </li> </ul> </p>
| + | |
| − | <h2> 12:00 - 13:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time! </li> </ul> </p>
| + | |
| − | <p> <ul> <li> The team members who were going to Paris also went into town to buy essentials and exchange Euros. </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 15:00 </h2>
| + | |
| − | <p> <ul> <li> More cultures were grown up for another run of the InterLab study. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | <p> <ul> <li> IWBDA was booked and the Paris tickets were confirmed and picked up. </li> </ul> </p>
| + | |
| − | <h2> 15:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Started writing up the final versions of various protocols we were using (for the InterLab, for the microbial fuel cell,etc). </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 1st, 2016 </h1>
| + | |
| − | <h2> 12:00 - 21:00 </h2>
| + | |
| − | <p> <ul> <li> Half of the team travelled to Paris while the other half stayed back in Newcastle. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 2nd, 2016 </h1>
| + | |
| − | <h2> 09:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> Exhibition Stands in Paris. </li> </ul> </p>
| + | |
| − | <h2> 12:00 - 14:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch Break </li> </ul> </p>
| + | |
| − | <h2> 14:00 - 15:30 </h2>
| + | |
| − | <p> <ul> <li> Roundtable 1 - Synthetic Biology: Challenges and Risks
| + | |
| − | <ul><li> François Képès - Research Director at CNRS, founding director of the Epigenomics Project an iSSB </ul></li> <ul><li> Héloïse Muller - PhD at Institute Pasteur </ul></li> <ul><li> Andrew Tolonen - Leader of Tolonen group at the Genoscope-CEA </ul></li> <ul><li> Christophe Genisset - Security Officer at SGDSN (French Secretariat for Defence and National Security) </ul></li> <ul><li> Alexei Grinbaum - Researcher at LARSIM, the Philosophy of Science Group at CEA-Saclay </ul></li></li></ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | <h2> 15:30 - 16:00 </h2>
| + | |
| − | <p> <ul> <li> Coffee Break </li> </ul> </p>
| + | |
| − | <h2> 16:00 - 17:30 </h2>
| + | |
| − | <p> <ul> <li> Roundtable 2 - Synthetic Biology: A New Economic World <ul><li> Philippe Jais - Chief Executive and Scientific Officer at Eukarys </ul></li> <ul><li> Cyrille Pauthenier -President of Abolis Biotechnologies </ul></li> <ul><li> Samuel Juillot - CSO at Glowee (In absentia - sent a PhD student in his place) </ul></li> <ul><li> Michael Krel - CEO at Enobraq </ul></li> </li> </ul> </p>
| + | |
| − | <h2> 17:30 - 18:00 </h2>
| + | |
| − | <p> <ul> <li> Talk from Randy Rettberg about iGEM and its importance in the world </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 3rd, 2016 </h1>
| + | |
| − | <h2> 09:00 - 18:00 </h2>
| + | |
| − | <p> <ul> <li> Site-seeing around Paris </li> </ul> </p>
| + | |
| − | <h2> 18:00 - 02:10 </h2>
| + | |
| − | <p> <ul> <li> Travel back to Newcastle </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1 class="middle"> iGEM Week 3 </h1>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 4th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> COMSOL Training Day. The Multiphysics libraries were looked at and the sample projects were completed. Then using the sample as a guideline, we started trying to make a model for our experiment. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 5th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 13:00 </h2>
| + | |
| − | <p> <ul> <li> The InterLab study was run again. See below for the protocol. </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 14:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time! </li> </ul> </p>
| + | |
| − | <h2> 14:00 - 16:00 </h2>
| + | |
| − | <p> <ul> <li> COMSOL modelling continued. Errors came up with regards to Temperature Coupling so we were working on trying to solve the error. </li> </ul> </p>
| + | |
| − | <p> <ul> <li> In the meantime, the rest of the team was working on the Action Points and trying to complete what hadn't been done yet. </li> </ul> </p>
| + | |
| − | <h2> 16:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Attended a seminar entitled: "Synthetic Biology: Perspectives from artificial life" which was conducted by Professor Martin Hanczyc. His area of expertise revolved around microbial fuel cells and therefore his seminar was of great use. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | <p> <ul> <li> He seemed interested in our iGEM project which led to us Skyping him at a further date described later on. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 6th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 09:30 </h2>
| + | |
| − | <p> <ul> <li> Checked the plate reader in order to obtain the results from the InterLab. </li> </ul> </p>
| + | |
| − | <h2> 09:30 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> Results from the InterLab were processed and put into an Excel document. In the meantime, other members of the team were completing more of the Action Points which had not been done yet. </li> </ul> </p>
| + | |
| − | <h2> 12:00 - 13:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time! </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 14:00 </h2>
| + | |
| − | <p> <ul> <li> Skyped Chennai. We were able to exchange ideas and propose collaboration seen as they needed us to carry out some surveys in order for them to see how their project idea would be perceived in the UK and whether or not it would be accepted. </li> </ul> </p>
| + | |
| − | <h2> 14:00 - 15:00 </h2>
| + | |
| − | <p> <ul> <li> Planned and prepared for the afternoon meeting with our supervisors.</li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner">
| + | |
| − | <p> <ul> <li> We went over the agenda and made sure that we were fully ready for any questions which were going to be asked. </li> </ul> </p>
| + | |
| − | <h2> 15:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Had meeting with our supervisors. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 7th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> Started preparation for plasmids to be sent to DNA 2.0 </li> </ul> </p>
| + | |
| − | <h2> 12:00 - 13:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time! </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 14:30 </h2>
| + | |
| − | <p> <ul> <li> Continued preparing cultures for freezing and for the plasmids to be sent to DNA 2.0. </li> </ul> </p>
| + | |
| − | <h2> 14:30 - 15:30 </h2>
| + | |
| − | <p> <ul> <li> Ollie and Lauren filmed for the School of Biology </li> </ul> </p>
| + | |
| − | <h2> 15:30 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Went over and completed Action Points. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | <div class="page"><div class="page-inner"><h1> July 8th, 2016 </h1>
| + | |
| − | <h2> 09:00 - 12:00 </h2>
| + | |
| − | <p> <ul> <li> Mini-prepped plasmids to be sent to DNA 2.0 </li> </ul> </p>
| + | |
| − | <h2> 12:00 - 13:00 </h2>
| + | |
| − | <p> <ul> <li> Lunch break time! </li> </ul> </p>
| + | |
| − | <h2> 13:00 - 14:00 </h2>
| + | |
| − | <p> <ul> <li> Using spectrophotometry, we measured the absorbance values of the plasmids as well as their concentration and packaged up the sample chosen to be sent to DNA 2.0. </li> </ul> </p>
| + | |
| − | <h2> 14:00 - 16:00 </h2>
| + | |
| − | <p> <ul> <li> Went over and worked on Action Points </li> </ul> </p>
| + | |
| − | <h2> 16:00 - 17:00 </h2>
| + | |
| − | <p> <ul> <li> Meeting with Patrick Degenaar to discuss our experiment and potential limitations which it may have. </li> </ul> </p>
| + | |
| − | </div></div>
| + | |
| − | </div>
| + | |
| − | </div>
| + | |
| − | </div>
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| − | </div>
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| − | </div>
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| − | </div>
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| − | <hr>
| + | #right-menu |
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| + | <p>01/05/2016 Team Registration for iGEM deadline</p> |
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| + | <p>30/06/2016 InterLab Sign-up Deadline</p> |
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| + | <p>01/07/2016 Project Description Deadline</p> |
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| + | <p>02/07/2016 <a href="https://2016.igem.org/Team:Newcastle/Collaborations">European Teams Meet Up in Paris</a></p> |
| | + | <p>15/07/2016 About our Lab Form Deadline</p> |
| | + | <p>15/07/2016 About our Project Form Deadline</p> |
| | + | <p>28/07/2016 <a href="https://2016.igem.org/Team:Newcastle/Collaborations">Scottish Teams Meet Up in Edinburgh</a></p> |
| | + | <p>12/08/2016 Track Selection Deadline – Foundational Advance</p> |
| | + | <p>12/08/2016 <a href="https://igem.org/Team.cgi">Title and Abstract Deadline</a></p> |
| | + | <p>17/08/2016 – 18/08/2016 <a href="https://2016.igem.org/Team:Newcastle/Collaborations">UK Teams Meet Up in Westminster, London</a></p> |
| | + | <p>25/08/2016 <a href="https://2016.igem.org/Team:Newcastle/Collaborations">Edinburgh Undergraduate Team Visits Newcastle</a></p> |
| | + | <p>31/08/2016 Giant Jamboree Registration Deadline</p> |
| | + | <p>02/09/2016 <a href="https://2016.igem.org/Team:Newcastle/InterLab">InterLab Data Deadline</a></p> |
| | + | <p>09/09/2016 Team Rosters Deadline</p> |
| | + | <p>16/09/2016 <a href="https://2016.igem.org/Team:Newcastle/Notebook/Safety">Final Safety Form Deadline</a></p> |
| | + | <p>07/10/2016 Team Banners Deadline</p> |
| | + | <p>14/10/2016 <a href="https://igem.org/2016_Judging_Form?id=1895">Judging Form Deadline</a></p> |
| | + | <p>19/10/2016 Wiki Freeze</p> |
| | + | <p>21/10/2016 <a href="http://parts.igem.org/cgi/dna_transfer/batch_list.cgi?group_id=2361">Part Submission Deadline</a></p> |
| | + | <p>27/10/2016 – 31/10/2016 Giant Jamboree 2016 @ Hynes Convention Center, Boston, MA</p> |
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