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CAROL
Descriptive Title of Heading
WIKI CODING HERE
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CHINMOYEE
Research : how does the Stochastic simulation for Simbiology work ?
The Stochastic simulation works with Gillespie's Algorithm . There is more than one version of Gillespie's algorithm : Direct Method , ()
Direct Method :
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EMILY
Gradient BBK Amplification of TOPO Trial Three
- See protocol on June 6th 2009
- PCR Products were visualized on a 1% agarose gel with 1.0 kb Generuler DNA Ladder.
- See gel photo below.
- Lanes 1-9 contain LuxOD47E in pCR2.1-TOPO vector, lane 10 is a (clean!) negative control.
- Analysis: Because the negative control lane is clean (no bands) indicating that there is no contaiminatioin of my products, we will move on to movinh my gene of interest (LuxOD47E) from the pCR2.1-TOPO vector into the Biobrick psBA1C3 vector.
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FAHD
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IMAN
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JAMIE
Descriptive Title of What You're Doing
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JEREMY
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KATIE
Keeping the Lab Clean
There is a problem faced was clutter within the PCR machine’s personal inventory where avatar will be given permission to drop the material required for PCR. However, this means they will also have permission to drop whatever else they want into it. I will attempt to solve this problem by creating a cleaning script, which will store all of the items in the inventory in a list and each item in the list can then be compared to the objects that are required within the machine including the scripts.
My other goals this week are:
1) Help create a gel electrophoresis simulation and restriction digest station
2) Build physical representations of the objects that are required to be dropped into the PCR machine, which will most likely be rezzed from different sites around the lab or island
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KEVIN
Modelling
Editing of AI-2 signalling system model on symbiology. No experiments were performed
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MANDY
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PATRICK
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PRIMA
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STEFAN
Descriptive Title of What You're Doing
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VICKI
Construction of LuxOD47A BBk into psB1AC3
- Antarctic phosphatase treatment
- Purpose: to prevent to formation of a phospodiester bond between ccdB and psB1AC3
- Protocol: The vector (psB1AC3 + ccdB) tubes were treated in accordance with the Antarctic phosphatase protocol on the protocol page.
- Ligation of LuxOD47A BBk to psB1AC3
- Purpose: to ligate the insert to the vector in BioBrick form (so that all of the BioBrick sites are preserved).
- Protocol: the tubes were treated in accordance with the Ligation protocol on the protocol page.
Transformation of LuxOD47A BBk on psB1AC3 into competent TOP 10 cells
Purpose: The constructs are in a water solution, where they will be stable for about 2 weeks. If they are in competent cells with natural DNA repair mechanisms, they will be stable for much longer. To accommodate this, the constructs need to be inserted into competent cells.
Protocol: The transformation was conducted in accordance with the transformation protocol on the protocol page. pBluescript was also transformed into a set of cells to act as a positive control. We’re using an AC-resistant vector, so any bacteria that are properly transformed with some non-ccdB gene on the AC plasmid will survive. pBluescript does not afford AC resistance, so cells transformed with that will die. We already tested the plates to ensure that the antibiotic works, so there’s no need for a negative control.
Once the transformation occurred, plates were made of the transformed cells so that distinct colonies could grow, in accordance with the culture plate protocol on the protocol page.
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