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| | + | Had our weekly meeting. |
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| - | *Discussed Restriction Digest, PCR and gel electrophoresis. Showed photos of gels. | + | *This morning Fahd, Stefan, Mandy and I attended the Ethics workshop held by AIF. Team members from the U of L and U of A teams were there and we got a chance to meet them and talk about their projects. The first part of the workshop was led by Dr. Gregor Wolbring and Dr. Lori Sheremeta, and we discussed the importantce of ethical considerations in Synthetic Biology. Each team had previously been assigned a team from last year that did well in the Human Practices section of their project and we did research on what they had done. We shared these findings with the rest of the group, explaining what we felt they did well as well as what we felt they could improve on. After this, we shared some of our ideas about what ethical considerations would be important for our own projects. We gave the other teams feedback and talked about some of the issues. |
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| + | *This workshop really got us thinking about ethical issues and where we want to go with our project in particular. We also got a chance to spend some time getting to know other teams, which was a lot of fun. |
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| + | Ethics Workshop and Team presentations May 29th 2009 |
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| - | WIKI CODING HERE
| + | Today I attended the Ethics workshop which was organized by the Alberta Ingenuity Fund (Our Platinum Sponsor). |
| - | | + | The ethics workshop was held at our university on May 31st. It was an excellent opportunity for more members of our team to meet the members of both Alberta and Lethbridge teams. At the workshop, we were given valuable insight on the exploration of ethical issues with the help of Dr. Gregor Wolbring and Ms. Lori Sheremeta. Each team was able to introduce their respective projects, and the ethical issues surrounding each project were discussed. We were able to discuss the following elements and concerns regarding each project in: |
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| + | Economics |
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| - | WIKI CODING HERE
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| + | Ethics |
| - | JAMIE
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| - | WIKI CODING HERE
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| | + | Legality |
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| | + | and Social Issues. |
| | + | While discussing all three projects, we were able to come across similar themes in what we would want to explore. These themes included looking at biosafety and patenting of processes/genes. Teams were also able to help each other determine what critical points should be explored, and how such issues should be approached. Students were coached on exploring ethics as a comprehensive look at all issues, displaying both pros and cons. |
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| | + | In addition to our own projects, we also examined a number of successful teams from last year and analyzed what the requirements are for the ethics component of iGEM, and what could be explored further this year. The ethics workshop was valuable preparation in outlining exploration of ethics for each project, and the feedback gained from Dr. Wolbring, Ms. Sheremeta, and all of the students provided an excellent starting point. |
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| - | Descriptive Title of What You're Doing
| + | Result section for AHL signaling system model |
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| - | WIKI CODING HERE
| + | At the beginning of this week, we were able to make a nice animation from our simulation, using a built-in function called “manipulate”. Our simulation is quit powerful and we believe we can extract more information out of our model. As a result, we designed new ways of representing results, such as “Rule Charts” and “Rule Patterns”. Rule Charts are bar graphs that show the distributions of the rules throughout the simulation. Rule Pattern is an array plot that shows in each step what rule was applied to what membrane using different colors. I also had three meeting this week. The first meeting was with Lindsay members. The second meeting was with Dr. Jacob and Afshin discussing features of our model, and the last meeting was with iGEM people. |
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| - | Island in Second Life
| + | Sequencing Results Are Back! |
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| - | There was a team meeting, including presentation/progress report by the second life team. This week, the island has finished processing, but we do not have permission to build yet so our second life team continues to attempt to obtain a competent understanding of manipulating objects within the various public sandboxes, mainly from the Knights Bishop public group sandbox.
| + | Results came back for sequencing. The sequencing reaction with VF1 did not work. VF2 sequencing results indicated vector contamination. |
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| - | WIKI CODING HERE
| + | Today, we attended the ethics workshop with the other 2 Albertan teams. We discussed the E3LS of our respective projects, and learned a bit regarding things that we should explore more into, such as biosafety hazards and patenting/the issues with open source biology. As well, we examined past successful ethics explorations of other iGEM teams and discussed what made them successful, and what we felt was lacking/could be improved upon. |
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| - | Descriptive Title of What You're Doing
| + | Molecules! |
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| - | WIKI CODING HERE
| + | Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day. |
| | + | |
| | + | My first ever biobrick simulator molecules created today! A single device, comprising a constitutive promoter, RBS, GFP coding sequence, a Terminator, and an RNAP. Later I would switch from coding sequences to 'translational units', as they are becoming the new standard in the registry, and the biobrick simulator has yet to incorporate mRNA. |
| | + | |
| | + | RNAP's DNA binding function, and protein production, would not be implemented for a while yet. |
| | + | |
| | + | I had believed I would be able to manage most of the interactions in world by the 'collision' event. It fires when two objects collide, and provides information about them. Unfortunately, it doesn't provide the right information for an object made up of multiple linked objects/prims (aka primitives), so I would end up building a workaround. |
| | + | |
| | + | I had at this point realized the need to minimize the freefloating objects tendency to escape. The method I used was to continuously set the object's speed and rotation to zero, on a short timer inside the object, but this would turn out to be very glitchy, and would be improved as well. |
| | + | |
| | + | Spent some time grappling with just what functionality a 'promoter' has, and determined that the opposite of a repressable promoter wouldn't actually be an activatable promoter and vice versa... it would be a 'repressable terminator', or 'activatable terminator'. (Since the function of a promoter is to permit RNA polymerase to bind, the opposite of that is to cause RNAP to unbind.) |
| | + | |
| | + | An 'activatable terminator' very roughly correlates to the idea of an 'operator site', a repressor binding site removed from its promoter. I didn't believe there was any such thing as a 'repressable terminator' (a terminator that is functional by default, but can be disabled by the action of some protein?), until I stumbled across anti-terminators while doing unrelated research much later. The curious are encouraged to look up the proteins N Lambda and Q Lambda. |
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CAROL
Weekly Team Meeting
- Presented G protein cascade example that is built in Matlab.
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CHINMOYEE
iGEM Journal Club
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EMILY
Ethics Workshop with AIF
- This morning Fahd, Stefan, Mandy and I attended the Ethics workshop held by AIF. Team members from the U of L and U of A teams were there and we got a chance to meet them and talk about their projects. The first part of the workshop was led by Dr. Gregor Wolbring and Dr. Lori Sheremeta, and we discussed the importantce of ethical considerations in Synthetic Biology. Each team had previously been assigned a team from last year that did well in the Human Practices section of their project and we did research on what they had done. We shared these findings with the rest of the group, explaining what we felt they did well as well as what we felt they could improve on. After this, we shared some of our ideas about what ethical considerations would be important for our own projects. We gave the other teams feedback and talked about some of the issues.
- This workshop really got us thinking about ethical issues and where we want to go with our project in particular. We also got a chance to spend some time getting to know other teams, which was a lot of fun.
|
|
|
FAHD
Ethics Workshop and Team presentations May 29th 2009
Today I attended the Ethics workshop which was organized by the Alberta Ingenuity Fund (Our Platinum Sponsor).
The ethics workshop was held at our university on May 31st. It was an excellent opportunity for more members of our team to meet the members of both Alberta and Lethbridge teams. At the workshop, we were given valuable insight on the exploration of ethical issues with the help of Dr. Gregor Wolbring and Ms. Lori Sheremeta. Each team was able to introduce their respective projects, and the ethical issues surrounding each project were discussed. We were able to discuss the following elements and concerns regarding each project in:
Economics
Ethics
Environment
Legality
and Social Issues.
While discussing all three projects, we were able to come across similar themes in what we would want to explore. These themes included looking at biosafety and patenting of processes/genes. Teams were also able to help each other determine what critical points should be explored, and how such issues should be approached. Students were coached on exploring ethics as a comprehensive look at all issues, displaying both pros and cons.
In addition to our own projects, we also examined a number of successful teams from last year and analyzed what the requirements are for the ethics component of iGEM, and what could be explored further this year. The ethics workshop was valuable preparation in outlining exploration of ethics for each project, and the feedback gained from Dr. Wolbring, Ms. Sheremeta, and all of the students provided an excellent starting point.
|
|
|
IMAN
Result section for AHL signaling system model
At the beginning of this week, we were able to make a nice animation from our simulation, using a built-in function called “manipulate”. Our simulation is quit powerful and we believe we can extract more information out of our model. As a result, we designed new ways of representing results, such as “Rule Charts” and “Rule Patterns”. Rule Charts are bar graphs that show the distributions of the rules throughout the simulation. Rule Pattern is an array plot that shows in each step what rule was applied to what membrane using different colors. I also had three meeting this week. The first meeting was with Lindsay members. The second meeting was with Dr. Jacob and Afshin discussing features of our model, and the last meeting was with iGEM people.
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JAMIE
Sequencing Results Are Back!
Results came back for sequencing. The sequencing reaction with VF1 did not work. VF2 sequencing results indicated vector contamination.
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KEVIN
Modelling our AI-2 system into Symbiology
I have attempted to model the AI-2 system in nature using the Symbiology tool in Matlab.
Figure 1. Diagram of AI-2 Signalling system without the presence of AI-2 in nature.
Figure 2. Diagram of AI-2 Signalling system with the presence of AI-2 in nature.
No experiments were done.
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MANDY
Ethics Workshop
Today, we attended the ethics workshop with the other 2 Albertan teams. We discussed the E3LS of our respective projects, and learned a bit regarding things that we should explore more into, such as biosafety hazards and patenting/the issues with open source biology. As well, we examined past successful ethics explorations of other iGEM teams and discussed what made them successful, and what we felt was lacking/could be improved upon.
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PATRICK
Molecules!
Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.
My first ever biobrick simulator molecules created today! A single device, comprising a constitutive promoter, RBS, GFP coding sequence, a Terminator, and an RNAP. Later I would switch from coding sequences to 'translational units', as they are becoming the new standard in the registry, and the biobrick simulator has yet to incorporate mRNA.
RNAP's DNA binding function, and protein production, would not be implemented for a while yet.
I had believed I would be able to manage most of the interactions in world by the 'collision' event. It fires when two objects collide, and provides information about them. Unfortunately, it doesn't provide the right information for an object made up of multiple linked objects/prims (aka primitives), so I would end up building a workaround.
I had at this point realized the need to minimize the freefloating objects tendency to escape. The method I used was to continuously set the object's speed and rotation to zero, on a short timer inside the object, but this would turn out to be very glitchy, and would be improved as well.
Spent some time grappling with just what functionality a 'promoter' has, and determined that the opposite of a repressable promoter wouldn't actually be an activatable promoter and vice versa... it would be a 'repressable terminator', or 'activatable terminator'. (Since the function of a promoter is to permit RNA polymerase to bind, the opposite of that is to cause RNAP to unbind.)
An 'activatable terminator' very roughly correlates to the idea of an 'operator site', a repressor binding site removed from its promoter. I didn't believe there was any such thing as a 'repressable terminator' (a terminator that is functional by default, but can be disabled by the action of some protein?), until I stumbled across anti-terminators while doing unrelated research much later. The curious are encouraged to look up the proteins N Lambda and Q Lambda.
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PRIMA
Media and Marketing
I contacted the Calgary Sun, the Herald and searched up contact information for the Metro. I also followed up with several companies to discuss how iGEM Calgary's project may be beneficial to the company.
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STEFAN
We have an island!
This week we found our island but unfortunately we cannot build on it yet. I started creating some things for the lab portion of our island such as the pipette and beakers. All of us are working together to plan our island so as to make it fit into iGEM and help people get the most out of it. Also, I worked on finding a person to draw our logo, which is now done except for the color scheme.
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VICKI
Laboratory meeting update
On the modelling side, I prepared and presented a handout that embodied an introduction to basic principles of modelling. This included an overview and an outline of some different types of mathematical modelling.
On the lab end, I analysed a gel of the LuxPQ PCR and restriction digest results from yesterday, which showed that I amplified something that apparently isn't LuxPQ.
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