2012 iGEM

CBNU-Korea

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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.

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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.

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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.