Kozo Nishida kozo2

Windows 7 (64bit)上でE-Cell4のPython拡張をビルドする

E-Cell4はwin32ブランチをチェックアウトして用いる. 必要なら各自Gitをインストールして使う: https://github.com/ecell/ecell4

以下がビルドに利用したもの:

import libsbml
document = libsbml.readSBML('BMID000000140222.xml')

model = document.getModel()

f = open('hoge.txt', 'w')

the authors do not cite the origin of the gene expression dataset they use in their example.
as far as I can tell, there is no tutorial provided with KEGGscape. At a minimum, the authors should provide instructions for opening a KGML file and loading a dataset.

	~/src/iron-maiden-cl$ make
	gcc -shared -o iron-maiden.so -fPIC iron-maiden.c
	sbcl --eval '(progn (ql:quickload :clx) (ql:quickload :cl-ppcre) (quit))'
	This is SBCL 1.1.14.debian, an implementation of ANSI Common Lisp.
	More information about SBCL is available at <http://www.sbcl.org/>.

	SBCL is free software, provided as is, with absolutely no warranty.
	It is mostly in the public domain; some portions are provided under
	BSD-style licenses. See the CREDITS and COPYING files in the
	distribution for more information.

	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")

	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

	import re
	import libsbml

	reader = libsbml.SBMLReader()
	doc = reader.readSBMLFromFile('BMID000000140222.xml')
	model = doc.getModel()

	hoge = 0
	for i in range(0, model.getNumReactions()):
	if len(re.findall(r'REACTOME:', model.getReaction(i).getNotesString())) > 0:

	In file included from ../ecell4/epdp/EGFRDSimulator.hpp:44:
	../ecell4/epdp/GreensFunction3DRadInf.hpp:22:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
	static const Real TOLERANCE = 1e-8;
	^ ~~~~
	../ecell4/epdp/GreensFunction3DRadInf.hpp:26:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
	static const Real THETA_TOLERANCE = 1e-5;
	^ ~~~~
	../ecell4/epdp/GreensFunction3DRadInf.hpp:28:23: warning: in-class initializer for static data member of type 'const Real' (aka 'const double') is a GNU extension [-Wgnu-static-float-init]
	static const Real MIN_T = 1e-12;
	^ ~~~~~