[[MonthCalendar2(destine,2005,5)]]
CategoryWebLogDestine
[[http://bioinfo.sarang.net/wiki/destine_2f2005_2d05?action=edit|페이지 고치기]]
----
== 2005-05-29 ==
으아.. 학기말이 되니 밀려오는 진도의 압박. 사실 눈앞의 일보다는 앞으로의 스케쥴을 보고 미리 좌절하는 것은 아닐까.

== 2005-05-27 ==
BioPython의 PDB classes 에는 2차 구조 정보가 없는 것 같아서 끼워 넣고 있음. (혹시 있나요?--;)
[[http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html|PDB Format Description Version 2.2]]
[[http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_42.html|HELIX Record Format]]
[[http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_44.html|SHEET Record Format]]
[[http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_45.html|TURN Record Fromat]]

== 2005-05-25 ==
[BioPythonTutorial/Appendix]
[[http://www.biolinux.org/clustalw.html|Clustalw Download]]
[[http://www.lecb.ncifcrf.gov/~toms/paper/primer/|Information Theory Primer]]
[PDBAnalyzer.py] Uploads:1C3W.pdb - Sample Data : PDB에서 CA의 좌표만 갖고 오는 Script

== 2005-05-18 ==
[[http://blanco.biomol.uci.edu/mpex/|Membrane Protein Explorer (MPEx)]], a tool for exploring the topology and other features of membrane proteins by means of  hydropathy plots using thermodynamic principles.

[[http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html|Membrane Proteins of Known 3D Structure]]

[[http://www.cbs.umn.edu/labs/jward/Databases.html|Several Membrane Proteins Libraries]] - the WARD Lab at the University of Minnesota 

[[http://aramemnon.botanik.uni-koeln.de/index.html|Arabidopsis, Oriza Sativa membrane protein database]]

 ''MembraneProtein 페이지에 정리하면 좋을듯하여, 조금 편집함'' --[yong27], 2005-05-18

=== 논문 ===
[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1694455&dopt=Abstract|Membrane protein folding and oligomerization: the two-stage model (Abstract)]]

[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFB-4F31R0W-4&_coverDate=04%2F22%2F2005&_alid=278218604&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5222&_sort=d&view=c&_acct=C000003998&_version=1&_urlVersion=0&_userid=30343&md5=00ad5dd21c4dccb56af98c272d982ff2|Prediction of the mutation-induced change in thermodynamic stabilities of membrane proteins from free energy simulations]] - SNU

[[http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja043621r|Determination of peptide oligomerization in lipid bilayers using 19F spin diffusion NMR.]]

[[http://www.jbc.org/cgi/content/full/280/9/7659|Role of the Degree of Oligomerization in the Structure and Function of Human Surfactant Protein A]]

=== Application ===
[[http://split.pmfst.hr/split/4/|Membrane Protein Secondary Structure Prediction Server]]

== 2005-05-16 ==
[[http://sos.bio.sunysb.edu/packingmoments/|Helix Packing and Helix Packing Moments in Membrane Proteins]]

[[http://bioinfo.csb.yale.edu/|Gerstein Lab]] - Bioinformatics

[[http://engelman.csb.yale.edu/|Engelman Lab]] - Membrane 

[[http://bioinfo.mbb.yale.edu/tmstat/|TMSTAT]]

FlyBase

== 2005-05-13 ==
http://www.genomesonline.org/ GenomesOnLineDatabase [GOLD]

[[http://www.pasteur.fr/recherche/unites/sis/formation/python/|Biopython Examples]]

[[http://au.expasy.org/spdbv/text/getlinux.htm|Swiss-PDB Viewer]]

[[http://fasta.bioch.virginia.edu/fasta_www/cgi/search_frm2.cgi|Compare Two Sequences with FASTA]]

== 2005-05-11 ==
[Phenocopy]

== 2005-05-08 ==
=== IE Automation 관련 사이트(정리 할 것) ===
http://vsbabu.org/mt/archives/2003/06/13/ie_automation.html
http://sourceforge.net/projects/samie

http://www.unix.org.ua/orelly/perl/learn32/appa_18.htm
http://www.codecomments.com/archive300-2004-11-317585.html

http://www.mozilla.org/projects/xpcom/ 
http://aspn.activestate.com/ASPN/Downloads/Komodo/PyXPCOM/

[[http://home.comcast.net/~furmana/SWIEAutomation.htm|IE Automation Tool]]
http://spaces.msn.com/members/grazilee/Blog/cns!1pWrYYHYycw0kHJlB7ROFqcA!604.entry
http://www.rubycentral.com/book/win32.html

=== PythonChallenge ===
http://www.pythonchallenge.com
6번 푸는 중. 

== 2005-05-06 ==
http://www.pythonchallenge.com 시작

urllib.urlopen 한 70개 정도 open 하면 항상 에러가 발생함. 우연인가? 아님 무슨 문제 일까?

=== os.walk 사용 예제 ===
This example displays the number of bytes taken by non-directory files in each directory under the starting directory, except that it doesn't look under any CVS subdirectory: 
{{{
import os
from os.path import join, getsize
for root, dirs, files in os.walk('python/Lib/email'):
    print root, "consumes",
    print sum([getsize(join(root, name)) for name in files]),
    print "bytes in", len(files), "non-directory files"
    if 'CVS' in dirs:
        dirs.remove('CVS')  # don't visit CVS directories
}}}

In the next example, walking the tree bottom up is essential: rmdir() doesn't allow deleting a directory before the directory is empty: 
{{{
import os
from os.path import join
# Delete everything reachable from the directory named in 'top'.
# CAUTION:  This is dangerous!  For example, if top == '/', it
# could delete all your disk files.
for root, dirs, files in os.walk(top, topdown=False):
    for name in files:
        os.remove(join(root, name))
    for name in dirs:
        os.rmdir(join(root, name))
}}}

특정 Directory 아래의 모든 파일 방문(?) 하기( os.walk 이용 )
{{{
import os
from os.path import join 

def visitfile(file):
	print 'visiting',file
	
def walktree(dir, callback):
	for root, dirs, files in os.walk(dir):
		for name in files:
			callback(join(root,name))

if __name__ == '__main__':
    walktree(sys.argv[1], visitfile)
}}}

=== SwissProt database ===
(for 문 사용)
{{{
from Bio.SwissProt import SProt

fh = open(argv[1])                       
sp = SProt.Iterator(fh, SProt.RecordParser())

for record in sp:
    print record.accessions
    print record.annotation_update
    print record.comments
    print record.created
    print record.cross_references
    print record.data_class
    print record.description
    print record.entry_name
    print record.features
    print record.gene_name
    print record.keywords
    print record.molecule_type
    print record.organelle
    print record.organism
    print record.organism_classification
    print record.references
    print record.seqinfo
    print record.sequence
    print record.sequence_length
    print record.sequence_update
    print record.taxonomy_id

    print "============================================================="
    print "============================================================="
fh.close()
}}}

== 2005-05-05 ==
[[http://biopython.org/pipermail/biopython-dev/|The Biopython-dev Archives]]

BioPython Tutorial에 있는 코드가 제대로 실행되지 않는다. 왜 그럴까.
http://www.expasy.ch/cgi-bin/get-sprot-raw.pl 가 동작 하지 않는걸까.
영어 'O'를 써야 되는데 숫자'0'을 쓰는 바람에 잘못된 id가 입력되었던 문제였음. --; 
{{{
from Bio.WWW import ExPASy
ids = ['O23729', 'O23730', 'O23731']
all_results = ''
for id in ids:
     results = ExPASy.get_sprot_raw(id)
     all_results = all_results + results.read()
}}}

[[http://www.pasteur.fr/recherche/unites/sis/formation/python/ch13.html|BioPython Parsers 설명]]

SwissProt data file 읽기
{{{
from Bio.SwissProt import SProt
from sys import *

fh = open(argv[1])                       
sp = SProt.Iterator(fh, SProt.RecordParser())

while 1:
    record = sp.next()
    if record is None:
        break
    print record.accessions
    print record.annotation_update
    print record.comments
    print record.created
    print record.cross_references
    print record.data_class
    print record.description
    print record.entry_name
    print record.features
    print record.gene_name
    print record.keywords
    print record.molecule_type
    print record.organelle
    print record.organism
    print record.organism_classification
    print record.references
    print record.seqinfo
    print record.sequence
    print record.sequence_length
    print record.sequence_update
    print record.taxonomy_id

    print "============================================================="
    print "============================================================="
fh.close()
}}}

 ''참고로, 최근의 [Iterator]들은 굳이 while문을 안써도 됨. for문으로 다 해결가능.''--[yong27], 2005-05-06
   ''ㅎㅎ 그렇네요.''

특정 Directory 아래의 모든 파일 방문(?) 하기
{{{
import os, sys
from stat import *

def walktree(dir, callback):
    '''recursively descend the directory rooted at dir,
       calling the callback function for each regular file'''

    for f in os.listdir(dir):
        pathname = '%s/%s' % (dir, f)
        mode = os.stat(pathname)[ST_MODE]
        if S_ISDIR(mode):
            # It's a directory, recurse into it
            walktree(pathname, callback)
        elif S_ISREG(mode):
            # It's a file, call the callback function
            callback(pathname)
        else:
            # Unknown file type, print a message
            print 'Skipping %s' % pathname

def visitfile(file):
    print 'visiting', file

if __name__ == '__main__':
    walktree(sys.argv[1], visitfile)
}}}
 ''os.walk를 쓰면 단방에'' :) --[yong27], 2005-05-06
  ''그렇네요. os.walk를 쓰면 코드 이해하기도 쉽고 쓰기도 편하네요.''

== 2005-05-04 ==
내일은 박찬호 경기 하는 날이구나.
BiologicalDatabase
YeastTwoHybrid

== 2005-05-02 ==
StandAloneBlast
-- DB 다운 받는데 넘 오래 걸리네.
[[http://www.biochem.ucl.ac.uk/bsm/valdarprograms/|Valdar Programs 설명]]
[[http://www.ebi.ac.uk/Thornton/software.html|Thornton software 모음]]
[[http://www.rubygarden.org/ruby?RealWorldRuby|RealWorldRuby - Ruby로 할 수 있는 여러가지 일들]]

== 2005-05-01 ==
[[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl|The Scorecons Server (tool)]]
[[http://www.well.ox.ac.uk/biostag/valdar_7jul2002.pdf|Scoring residue conservation (pdf)]]
----