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hsiaoyi0504 / CMDM.md
Last active November 17, 2015 08:18
Some materials for beginners of CMDM lab (computational chemistry group)

##引言 用資訊方法去幫助新藥開發算是我們實驗室中這一組主要的目標,剛進入一個新的領域一定會有很多需要知道的背景知識,在這裡記錄了我自己學習歷程中,覺得對大家會有幫助的東西,歡迎有興趣的大家多多自行翻閱,補充,希望之後可以變成我們組的wiki這樣,也算是一種傳承吧ＸＤ

##Molecule File Format

  • 常用的大概就SDF,mol,mol2,SMILES,GROMACS,PDB
  • wiki有蠻完整的介紹

##Drug Discovery(新藥開發) ###Article

@hsiaoyi0504
hsiaoyi0504 / Eita-Bio 2015.md
Last active October 25, 2015 04:14
Recood of Eita-Bio 2015

#Eita-Bio 2015 http://www.eitc.org/eita/eita-venture-community/eita-venture-forum/year-2015/eita-bio-2015

A bioinformatics approach to the infection of Hepatitis C virus using human protein-protein interation data

  • Hepatitis C virus
  • PPI network
  • Network properties:Guimera, Roger, and Luis A. Nunes Amaral. "Functional cartography of complex metabolic networks." Nature 433.7028 (2005): 895-900.
  • KEGG pathway

Clinical-based indices for selection of single nucleotide polymorphisms in late-onset Alzheimer's disease

  • Dementia (失智症)
@hsiaoyi0504
hsiaoyi0504 / presentationRecord20151026.md
Last active October 26, 2015 12:23

#Characterizing gene regulation network via competitive endogenous RNAs (ceRNA) Record of content of the presentation of the research of "Characterizing gene regulation network via competitive endogenous RNAs"

  • UT San Antonio Health Science Center
  • TraceRNA
  • ceRNA network
  • Hepatoblastoma
  • MBDCAp-Seq
  • miRNAs regulate expression of up to 1/3 of the protein coding genes in human
  • Dysregulation of miRNAs is associated with oncogenesis, tumor progressionm and clinical patient survival
  • Exsiting approaches discovering ceRNA relationship
@hsiaoyi0504
hsiaoyi0504 / Fundaments of Biomedical Engineering.md
Last active November 16, 2015 17:57
Some collections of materials of Fundaments of Biomedical Engineering of NTU, 2015 Spring
@hsiaoyi0504
hsiaoyi0504 / introduction.md
Last active December 5, 2015 17:09
KNIME Development Guide for CMDM Lab

#KNIME Development Guide for CMDM Lab

蕭毅 | Nov, 2015

如果內容有誤，覺得有可以討論的地方，或者有想要放上來的東西

你可以用任何管道發訊息轟炸我，或用底下的 gist comment 留言。

我的e-mail: r04945027@ntu.edu.tw or hsiaoyi0504@gmail.com

@hsiaoyi0504
hsiaoyi0504 / GROMACS_resources.md
Created January 10, 2016 11:25
GROMACS_resources
@hsiaoyi0504
hsiaoyi0504 / ML_finale.md
Created January 13, 2016 04:07
  • Data analysis
  • Feature extracton
  • model learning
  • hypothese blenging
@hsiaoyi0504
hsiaoyi0504 / git_cheat_sheet.md
Last active February 17, 2016 12:09
My git cheat sheet

Pull remote branch to new local branch with same name

git fetch origin <branch_name>

git checkout <branch_name>

Delete a local branch

git branch -d <local_branch_name>

Remove a remote branch

@hsiaoyi0504
hsiaoyi0504 / windows_server.md
Created February 16, 2016 03:09
commands about windows server

Setting

sconfig

開機選單

bcdedit

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hsiaoyi0504 / RDKit_SMILES_failed_cases.txt
Last active December 16, 2016 18:08
Some SMILES failed parsed by RDKit
From ChEMBL
[Al+3].[PH6-3]
C1C[O-][Te+4][O-]1
CC12O[Te]34OC(C)(C1(C)O3)C2(C)O4
From ZINC
CC(=O)Nc1ccc(cc1)S(=O)(=O)N=N=N
COc1ccc(cc1)COC(=O)N=N=N
CCCC[C@@H](C(=O)OC)NC(=O)C=N=N