iGEM 2008 — Team Waterloo

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# Team:Waterloo/Notebook

### From 2008.igem.org

| [Home](/Team%3AWaterloo "Team:Waterloo") | [The Team](/Team%3AWaterloo/Team "Team:Waterloo/Team") | [The Project](/Team%3AWaterloo/Project "Team:Waterloo/Project") | [Parts Submitted to the Registry](/Team%3AWaterloo/Parts "Team:Waterloo/Parts") | [Modeling](/Team%3AWaterloo/Modeling "Team:Waterloo/Modeling") | **Notebook** | [Sponsors](/Team%3AWaterloo/Sponsors "Team:Waterloo/Sponsors") |
| --- | --- | --- | --- | --- | --- | --- |

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| Contents   * [1 Notebook](#Notebook) * [2 Daily Log](#Daily_Log) * [3 Freezer Management (BioMortar)](#Freezer_Management_.28BioMortar.29) * [4 Oligos](#Oligos) * [5 Protocols](#Protocols) * [6 Recipes](#Recipes) |

## Notebook

This year we are using a [http://www.google.com/notebook/public/05889908560840673300/BDRepIgoQp4H14akj Google Notebook] to co-ordinate our lab activities among team members. This includes our day to day activities and our progress.

**Tentative Plans**

**Notes:**
' denotes that the construct contains the ribosome binding site (RBS) and the coding region for that gene
" denotes that the construct contains the ribosome binding site, coding region for that gene, and a transcriptional terminator (TT)

**Construction Stages**
1) Construction of CI"
2) Construction of Plac CI"
3) Ligate Plac (reverse) TT and Plac CI"

**CI Repression Test**
1) Construct Pconst CI?
2) Construct PR CI rfp"
3) Ligate above two constructs together (Pconst CI" PR CI rfp")
4) Test above repression by CI

**Synthesize**
1) Plac (reverse) TT
2) TT (reverse) PR

## Daily Log

A log of our daily activities can be found on our [Lab Calendar](/Team%3AWaterloo/Notebook/Daily_Log "Team:Waterloo/Notebook/Daily Log").

## Freezer Management (BioMortar)

Our freezer management was done using [http://igem.uwaterloo.ca/biomortar BioMortar]. BioMortar is an application written in-house for administration of BioBricks. It understands standard assembly and can gather information from the Parts Registry. BioMortar will also be capable of generating protocols for future projects.

Originally, we were keeping track of everything in spreadsheets, but this became burdensome quickly. BioMortar was supposed to be more than a simple freezer manager. It is specifically geared to iGEM and Standard Assembly so it keeps track of BioBrick part numbers and also knows that some parts are composite parts made of other parts. The advantage of this is that it can construct sequences for composite parts automatically. Although Standard Assembly makes it easy to ligate parts, it is fairly easy to reverse the enzymes accidentally. One of the goals of BioMortar was to generate prepared protocols with the enzymes filled in to prevent such errors. It also could do the math to calculate the quantities of solutions needed.

## Oligos

A list of all [oligos](/Team%3AWaterloo/Notebook/Oligos "Team:Waterloo/Notebook/Oligos") we've used, either as PCR primers or for other purposes.

## Protocols

The list of protocols used can be found on the [Protocols](/Team%3AWaterloo/Notebook/Protocols "Team:Waterloo/Notebook/Protocols") page.

## Recipes

Our recipes for making media can be found on the [Recipes](/Team%3AWaterloo/Notebook/Recipes "Team:Waterloo/Notebook/Recipes") page.

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