Team:CBNU-Korea/Notebook/2
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Latest revision as of 03:51, 27 September 2012
NOTEBOOK
- Notebook
![](https://static.igem.org/mediawiki/2012/6/6e/CBK_overlay_001.png)
May - June
May. 1st – May 5th
Tuesday
■Meeting with instructors.
■Produced the flow chart of
project
(Build DB -> Presumption of essential genes &
essential function -> Analysis on the array of genes -> Implement
Designer.
Thursday
■Build DB of the genome which belong to Gamma.
■Grouped
essential genes depending on functions.
■Calculated
percentage of 15 species
Friday
■Planned to annotate by BLAST.
■Identify the essential
function using GO database only.
(Progress the plans at a
same time because of exclusive relationship between them)
■Analysis of the arrangement essential function -> Make a
Bio-Brick by each genes which exist rule.
----------------------------------------------------------
Divided CBNU-team into 3 team to work efficiently
■A : Bio-Brick SW team
■B : Minimal Genome Designer SW team
■C : Essential gene analyzing team.
----------------------------------------------------------
May. 20th – May. 27th
Monday - Friday
■studied for the every iGem team of previous year who won a medal.
June. 4th – June. 10th
Monday
■Found problems using Go DB.
Tuesday
■Found problems again using GO DB.
Thursday
■Opened Bio-Brick team & Re-organized the date of the conference.
Modified some of Go problems.
Friday
■Studied for the function of software team to specify the subject of SW that we are going to develop.
June. 11th – June. 17th
Monday
■Discussed to set the subject of SW.
modified GO
problems.
Tuesday
■Learned basic theory and selected topic through brainstorming.
Wednesday
■Learned Biobrick components : Learned Bio-brick components and found Bio-brick DB in iGem.
Thursday
■Studied how to use MySql Dump File of XML format provided from iGem.
Friday
■Studied what information to built and discussed how to use it.
June. 18th – June. 24th
Monday
■A : Studied the methods of Bio-brick synthetic and discussed the main function of SW.
Tuesday
■A : Announced the main function of SW & Had meeting and decision.
Wednesday
■A : Investigated the information of Prefix and Suffix.
Friday
■A : Studied restriction sites such as EcoRI, PstI, SpeI and XbaI.
■B : Completed GO problem and calculated percent and sampling
Sunday
■C : Sampled locus_tag & Complied the table of essential genes.
June. 25th – July. 1st
Monday
■A : Studied the function of synthetic between two kinds of Bio-bricks to use prefix, suffix and restriction sites.
■B : Studied the function of BLAST & Studied how to use BLAST
result of XML format for analysis.
Defined EG and EF.
Studied GO(Made a decision not to use GO because of complex of DB
design).
Studied DEG(Studied DEG which provide
experimentally presumed EG).
Began to analyze subset of
whole genome because of a the lack of time to analyze the group of
all the species.)
Studied PATRIC(Built DB)
June. 27th – June. 29th
Thuesday
■A : Specified program requirement & modified it through a conference.
■B : Drew a chart Selected by the three species of the 17 species
in the DEG. Ran BLAST through our own standard, and Annotated Synb
Code by the Best Hit Algorithm.
Number of Essential Gene
: 104.
Selected three species :
Caulobacter_crescentus_NA1000, Helicobacter_pylori_26695,
Streptococcus_sanguinis_SK36
Blast standards : Identity >
25%, |Length| < 5%, e-value < 0.05, bit-score > 200
Chart: made a table if each of gene exists in each of species or
not.
Wednesday
■A : Studied providing DB of Bio-brick by iGem.
Thursday
■A : GUI work (Study about specific running Brick, Made GUI)
■C : Made a decision how to catch a standard on array analysis. Wondered two hypotheses. The first is based on origin. The second is based on the genes that exist in every species.