sudo apt-get install sbcl cl-quicklisp make gcc
cd /usr/share/cl-quicklisp
sbcl --load quicklisp.lisp
sudo su | |
apt-get install docker.io | |
cd | |
mkdir gentoo | |
cd gentoo | |
wget http://ftp.jaist.ac.jp/pub/Linux/Gentoo/releases/amd64/current-iso/stage3-amd64-20140403.tar.bz2 | |
tar jxpf stage3-amd64-20140403.tar.bz2 | |
tar -c . | docker.io import - gentoo | |
docker.io run -t -i gentoo /bin/bash |
emerge-webrsync | |
eselect news read new | |
emerge mirrorselect | |
mirrorselect -i -o >> /etc/portage/make.conf | |
mirrorselect -i -r -o >> /etc/portage/make.conf | |
emerge layman | |
echo "source /var/lib/layman/make.conf" >> /etc/portage/make.conf | |
layman -L | |
layman -a betagarden | |
CONFIG_PROTECT_MASK="/etc" emerge gentwoo --autounmask-write |
keymap.replaceKey( "Apps", "RWin" ) | |
keymap.replaceKey( "Space", "LCtrl" ) | |
keymap.replaceKey( "Caps", "Enter" ) | |
keymap.replaceKey( 28, "RAlt" ) | |
keymap.replaceKey( 29, "LShift" ) | |
keymap_global[ "O-LCtrl" ] = "Space" | |
keymap_global[ "S-LCtrl" ] = "S-Space" |
brew install hub lein | |
hub clone daviddpark/drugbank | |
cd drugbank | |
lein deps | |
lein repl |
~% java -Xmx4g -jar paxtools-4.2.1.jar toSbgn 18.0/data/biopax-level3.owl l3.sbgn | |
5363 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371. null | |
5364 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax- |
source("http://bioconductor.org/biocLite.R") | |
biocLite(c("genefilter", "ecoliLeucine")) | |
library("ecoliLeucine") | |
library("genefilter") | |
data("ecoliLeucine") | |
eset = rma(ecoliLeucine) | |
r = rowttests(eset, eset$strain) | |
write.csv(r, file="ttest.csv") |
eco:b4015 | |
eco:b2624 | |
eco:b1982 | |
eco:b0111 | |
eco:b0908 | |
eco:b4017 | |
eco:b0863 | |
eco:b0864 | |
eco:b3433 | |
eco:b0928 |
from paver.easy import * | |
from paver.git import pull | |
@task | |
def gp(): | |
current = path("./") | |
for lib_dir in current.dirs(): | |
pull(lib_dir) |
FROM ubuntu:14.04 | |
RUN apt-get update;apt-get install -y libglpk-dev libxml2-dev python-dev python-pip python-scipy wget swig | |
RUN wget http://downloads.sourceforge.net/project/sbml/libsbml/5.10.0/stable/libSBML-5.10.0-core-src.tar.gz | |
RUN tar xf libSBML-5.10.0-core-src.tar.gz | |
RUN cd libsbml-5.10.0/; ./configure --with-python; make; make install | |
RUN pip install cobra --pre |