"
Team:Waterloo/Notebook
From 2008.igem.org
(→Freezer Management (BioMortar)) |
|||
| (13 intermediate revisions not shown) | |||
| Line 1: | Line 1: | ||
| - | {| style="color:#1b2c8a;background-color:# | + | {| style="color:#1b2c8a;background-color:#FBCC30;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center" |
!align="center"|[[Team:Waterloo|Home]] | !align="center"|[[Team:Waterloo|Home]] | ||
!align="center"|[[Team:Waterloo/Team|The Team]] | !align="center"|[[Team:Waterloo/Team|The Team]] | ||
| Line 8: | Line 8: | ||
!align="center"|[[Team:Waterloo/Sponsors|Sponsors]] | !align="center"|[[Team:Waterloo/Sponsors|Sponsors]] | ||
|} | |} | ||
| + | |||
| + | <br> | ||
| + | |||
| + | |||
==Notebook== | ==Notebook== | ||
| Line 17: | Line 21: | ||
<b>Notes:</b><br> | <b>Notes:</b><br> | ||
' denotes that the construct contains the ribosome binding site (RBS) and the coding region for that gene <br> | ' denotes that the construct contains the ribosome binding site (RBS) and the coding region for that gene <br> | ||
| - | " denotes that the construct | + | " denotes that the construct contains the ribosome binding site, coding region for that gene, and a transcriptional terminator (TT)<br> |
<b>Construction Stages </b><br> | <b>Construction Stages </b><br> | ||
| Line 34: | Line 38: | ||
2) TT (reverse) PR<br> | 2) TT (reverse) PR<br> | ||
| - | + | ==Daily Log== | |
| + | A log of our daily activities can be found on our [[Team:Waterloo/Notebook/Daily Log|Lab Calendar]]. | ||
| + | |||
| + | ==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 [[Team:Waterloo/Notebook/Oligos|oligos]] we've used, either as PCR primers or for other purposes. | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
==Protocols== | ==Protocols== | ||
The list of protocols used can be found on the [[Team:Waterloo/Notebook/Protocols|Protocols]] page. | The list of protocols used can be found on the [[Team:Waterloo/Notebook/Protocols|Protocols]] page. | ||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||
==Recipes== | ==Recipes== | ||
| - | + | Our recipes for making media can be found on the [[Team:Waterloo/Notebook/Recipes|Recipes]] page. | |
| - | + | ||
| - | + | ||
Latest revision as of 04:05, 30 October 2008
| Home | The Team | The Project | Parts Submitted to the Registry | Modeling | Notebook | Sponsors |
|---|
Contents |
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.
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 we've used, either as PCR primers or for other purposes.
Protocols
The list of protocols used can be found on the Protocols page.
Recipes
Our recipes for making media can be found on the Recipes page.
