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Team:CBNU-Korea/Notebook/4
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| + | href="https://2012.igem.org/Team:CBNU-Korea/Notebook">- March, | ||
| + | April</a></li> | ||
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| + | href="https://2012.igem.org/Team:CBNU-Korea/Notebook/2">- May, | ||
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| + | href="https://2012.igem.org/Team:CBNU-Korea/Notebook/3">- July</a></li> | ||
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Latest revision as of 03:52, 27 September 2012
NOTEBOOK
- Notebook
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.
