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Kozo Nishida kozo2

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kozo2 / pathviewPVT.R
Last active September 17, 2015 05:50
library(pathview)
library(stringr)
dopathview <- function(csvfilepath, pathwayid) {
df <- read.csv(csvfilepath)
keggdf <- df[!is.na(df$kegg), ]
cpdlist <- str_split(keggdf$kegg, "\\|")
log2list <- c()
for (i in 1:length(cpdlist)) {
@kozo2
kozo2 / PIERO-path.rq
Created September 17, 2015 05:59
SELECT DISTINCT ?o3
WHERE {
kegg:C00267 ?p1 ?rp1 .
?rp1 rdf:type kegg:rpair .
?rp1 ?p3 ?o3 .
?o3 rdf:type kegg:compound .
}
@kozo2
kozo2 / openmpi.md
Created September 25, 2015 11:02
keep for openmpi environment

packages

  • openmpi-bin
  • mpic++
  • libmlx4-1

config

/etc/security/limits.conf

* soft memlock unlimited
@kozo2
kozo2 / kof2015-lod.md
Created September 28, 2015 11:48
kof2015

title

Linked Open Data(LOD)とデータアグリゲーション

一覧、パンフレット印刷用の紹介文（100文字）

WEBページに公開される内容（画像などを使って出来るだけ詳細に書いてください）投稿後に再編集が可能です。

@kozo2
kozo2 / gist:25a41b5f193246d77b6f
Last active July 15, 2023 09:25
We couldn’t find that file to show.
@kozo2
kozo2 / a.md
Last active July 15, 2023 18:28
tomato
@kozo2
kozo2 / cyviz-workflow.md
Last active October 31, 2015 00:49

  1. 列名CPD1-name、CPD2-nameはCPDnameに置換 (これだけエクセルフォーマットの変更をお願いします)

  2. toolbarから "Import Network From File" iconをクリック (ネットワークの構築と、edgeへの属性情報の追加)

  3. "TableS2-rev.xlsx" を指定

  4. "Source Interaction" は "Column1 (CPD1)" に、"Interaction Type" は "Default Interaction" のままに、"Target Interaction" は "Column4 (CPD2)" に

  5. "Preview" 枠で "Reaction" 列から最後列 までクリックし "Enable" の状態にする (これでedge tableにこれらの列の情報が追加されます)

  6. menubarから "Layout -> yFiles Layouts -> Hierarchic" をクリック (レイアウト)

  7. toolbarから "Import Table From File" iconをクリック (nodeへの属性情報の追加)

@kozo2
kozo2 / pythoncyc.py
Created November 12, 2015 08:24
import pythoncyc as cyc
orgids = cyc.all_orgids()
eco = cyc.PGDB(orgids[1])
eco.all_pathways()
@kozo2
kozo2 / pathways.csv
Created November 16, 2015 12:53
We can make this file beautiful and searchable if this error is corrected: No commas found in this CSV file in line 0.
00710
00190
00010
01200
@kozo2
kozo2 / ecell4.rb
Last active December 1, 2015 10:26
linuxbrew formula for ecell4
# additional prerequisites for ubuntu
# apt-get install python-setuptools python-dev
# additional prerequisties for centos7
# linuxbrew does NOT figure out gcc and g++ in centos. you need to symlink with
# ln -s `which gcc` `brew --prefix`/bin/gcc-4.8
# ln -s `which g++` `brew --prefix`/bin/g++-4.8
# yum install python-setuptools python-devel
class Ecell4 < Formula