Bioinformatics KMU Class

         for Department of Biomedical Science and Environmental Biology             

                                                                           

Teacher: Dr. Hsueh-Wei Chang          

   

     

    Email: changhw@kmu.edu.tw; 

    Tel: 07-3121101ext2691

  • Laboratory web link (實驗室網站);                                            

  • Other class page link: genomics

students' homework

*3*  作業要盡快交出, 1個x代表扣1分 [如果你有改正或補齊少寫的部份, 寄信給我  可以減少1個x]

*3*  黄老師2D程式可在E-learning下載; 童老師講義可在E-learning下載                                                                                 

 

update at 20111017  

1. class schedule

星期 起節次 迄節次 教室
1  1 4  CS207
12 月份 一 上課進度 講授者
02 09 [19]  An Overview of Bioinformatics  張學偉
02 09 [19]  Introduction to bioinformatics: Make your own homepage (frontpage; ftp)  張學偉
03 09 [26]  Introduction to Biological Database [NAR, Gene] TaxBrowser  張學偉
04 10 [03]  Sequence Analysis and Homology Search; NCBI-BLAST,  UCSC Genome Browser (ePCR; BLAT)  張學偉
04 10 [03] Biology WorkBench; Multiple sequence alignment  張學偉
06 10 [17]  Part I: Protein database I- Swissport; PDB; Swissmodel

 Part II: Protein database II- ExPASy; STRING Motif[ Pfam; Interpro; Prosite]

  張學偉
07 10 [24]

 Protein database II (2D-Electrophoresis, proteomics analysis) [Viewer_v502.exe] in elearning

  黃弘文
08 10 [31]  Protein-based Bioninformatics  黃斌
09 11 [07]  mid-term exam 　
10 11 [14]  Computational vaccinology [POPI2.0; POPISK]  童俊維
11 11 [21]  Evolutionary Computation  童俊維
12 11 [28]  Molecular docking  林盈廷
13 12 [05]  Evolutionary tree view for sequences - Mega  邱郁文
14 12 [12]  SNP I- Single Nucleotide Polymophysim; SNP500Cancer; [講義]  張學偉
15 12 [19]  SNP II-SNP-RFLPing; HapMap [SNP-RFLPing paper; user-guide to Hapmap] ; [講義]  張學偉
16 12 [26]

 student presentation- database/software I

  張學偉
17 01 [02]  student presentation- database/software II  張學偉
18 06 [13]  Final exam  張學偉

　

 Metabolomics I-KEGG pathway   [講義]; Metabolomics II- Reactome; String (protein-protein interacting network),Pathway Interaction Database, CGAP-Pathway [講義1; 講義2]

Protein database III (2D-電泳, 蛋白質體分析) (viewer_v502, Mass, Peptide-Mass)  Software for Protein Structure Visualization

　

2. Free software download

解壓縮檔軟體: Win_RAR; WinZIP 　 　
RasMolraswin Cn3D-4.1 [NCBI] 　 　
MDL Chime SP6 JavaWebStarter Genamics Expression 1.1  DNA and protein sequence analysis. 　

examples:

animation software (powerpoint; flash1; flash2; flash3)

prontpage insert flash--> to show flash in homepage[instruction;demo] (Many programs can insert and perform in this way.)  

KMU Web Server (www.kmu.edu.tw) 上 Counter CGI 的使用; 請注意: 使用時請將 try.dat 改成 "something.dat", 然後copy到 "記事本",再貼到frontpage的 HTML區即可.

on-line learning BLAST tutorial; BLAST Program Selection Guide; BLAST上課內容 Nucleotide-nucleotide BLAST (blastn); Protein-protein BLAST (blastp); Translated query vs. protein database (blastx); Protein query vs. translated database (tblastn); Translated query vs. translated database (tblastx). BLAST 2 SEQUENCES; materials for blast class: human P53 mRNA seq; Homo sapiens tumor protein p73 mRNA seq; secondary structure term: E= Extented; C = Coiled; H = Helix [terms for secondary structure of protein]

　

3. Useful links & tools.

Homo sapiens genome data and search tips [NCBI]

 NCBI logo   BioInformatics Glossary

 Basic html skill;

 Flash教學網站 1.完整Flash MX影片教學檔; 2.Flash MX 教學論壇; 3.Flash MX 動態網頁教學;  4. 基礎;進階;高階/港音發聲;

 NAR Database Issue Web Server Issue   NAR Database Issue    

 Update of Pedro's BioMolecular Research Tools (A Collection of WWW Links to Information and Services Useful to Molecular Biologists)

  swissmodel

　

4. Bioinformatics Journal list