2012 iGEM

CBNU-Korea

+ MENU

August

Aug. 1st - Aug. 5th

Wednesday

■B : Organized result and processes the we made until now for a reporting to instructors.

■C : Analyzed pattern of genome. Analyzed on calculating confidence interval(statistic word) had been failed.

Thursday

■A : Reviewed and modified errors in Bio-Brick synthesize. Implemented function of User-brick addition and deletion from DB.

■B : Had a meeting with instructors. Received research papers that is about providing reliability of the selecting standard of blast.
(Paper : Putative essential and core_essential
-genes in Mycopiasma enomes
-Yan Lin1 & Randy Ren Zhang2
-1Department of Physics, Tianjin University, Tianjun 300072, China 2Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit 48201, USA.)

Friday

■C : Performed T Test & Kruskal-Wallise Test(statistic word).
Calculated strand ratio on each section on 14 species.
Calculated T Value & P Value(statistic word).

Aug. 6th – Aug. 12th

Monday

■A : Implemented function of view in linear form.

■C : Set standard of location to each genome.

Monday

■C : Studied reliability testing on a blast standard. Selected 16 number of blast cut off standard. Planed to analyze with the standard.

Tuesday

■C : Builded DB of Salmonella.

Thursday

■A : Implemented function of view in circular form.

■B : Specified SW UI & divided the role of UI implementation.

■C : Analyzed the location on each genes in each genome.

Aug. 13th – Aug. 19th

Monday

■A : Reviewed and modified error on function of viewer.

■C : Analyzed the location of each genes and genome and organized.

Tuesday

■A : Discussed about whether to implement function of file saving as Sbol and Genbank format.

Thursday

■A : To improve portability between different software, started to implement function of file saving as a Genbank type.

■B : Developed SW UI.

■C : Analyzed location of genes in 17 species of DEG.

Friday

■B : Tried to draw ROC Curve a lot of times, need to study about it more.

Aug. 20th - Aug. 26th

Monday

■A : Implemented function of SBOL type saving : Reviewed and modified on function of file saving as SBOL and genbank type.

■B : Realized that ROC Curve(statistic word) is not a useful method to obtain a reliability of blast. Started to study for P Value(statistic word).

■C : Calculated the sample size to analyze genes.

Tuesday

■A : Reviewed in primary error in SW : Specified a failure occurred in developed SW.

■B : Realized that it is impossible to use P-Value(statistic word) so we decided to use reliability and accuracy.

■C : Sampled Streptococcus.

Wednesday

■B : Realized that there are a lot of genes in Streptococcus pneumoniae TIGR4 that are not annotated GI number in PATRIC DB. Discussed about this problem to find a way to analyze.

Thursday

■A : Modified primary error : Performed a modification on developed SW.

■B : Discussed how to use DB for SW. ⇨ Decided to connect server to use Synb DB in SW.
Calculated Reliability by comparing essential gene of Streptococcus pneumoniae TIGR4 with DEG and SynB DB.
TP : 120, FP : 96
FN : 102, TN: 1515
Sensitivity(%) : 54.05
Specificity(%) 94.04
Accuracy(%) 89.19

■C : Organized the way to analyze essential gene.

Aug. 24th – Aug. 31st

Friday – Friday

■B : Adjusted same algorithm for 82 species. (To consider a efficiency, divided 82 species into four groups)

Aug. 27th – Aug. 31st

Monday

■A : Additionally modified primary error : Failure that is occurred on circular form when a user put a mouse on it.

■C : Organized method of strand analysis

Tuesday

■A : Implemented additional function : Screen-shot function.

Thursday

■A : Implemented primary function of Biobrick Software.

■C : Analyzed strand on 51 species in 82 species.