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1 Biopython Python Yasushi MASUDA ymasuda at cubelab.com

jp/ def xpdlist(fname): f = open(fname, 'r') ret = [] for i in f.

2 Python Open-Bio BOF 2004 at GIW2004 (Perl Ruby ) 1990 C/C++ ( ) Python Home PyJUG (Japanese UG) def xpdlist(fname): f = open(fname, 'r') ret = [] for i in f.readlines(): si = i.strip() if len(si)>0: ret.append(si) return ret

3 Python (1/3) csv XML (csv,, xml) (formatter, re) zip/tar (os.path, zipfile, tarfile) HTTP FTP (urllib, ftplib)

4 Python (2/3) DB DBMS (PostgreSQL( PostgreSQL MySQL Oracle etc......) DB (Access, FileMaker) CGI (cgi, httpserver) XPAK (appeared in GIW2000, Python+PostgreSQL+Python Imaging Library)

(Python+ wxpython+vtk, not published) C (Numeric/numarray

5 Python (3/3) BL-SOM visualization (Python +Tk+ DDBJ ClastalX, not published) Spherical Som visualization (Python+ wxpython+vtk, not published) C (Numeric/numarray numarray) (PIL, matplotlib etc) GUI (Tkinter, PyQt, wxpython, etc.)

BioPython Jeffrey Chang, Andrew Dalke (Aug 1999) Biopython project http://www.biopython.

6 BioPython Jeffrey Chang, Andrew Dalke (Aug 1999) Biopython project The Biopython Project ( is a new open collaborative effort to develop freely available Python libraries and applications that address the needs of current and future work in bioinformatics, including sequence analysis, structural biology, pathways, expression data,, etc.

7 Biopython (1/2) CDD, ECell,, EMBL, Enzyme, FASTA, GenBank,, NCBI Geo, Gobase,, MASE, MetaTool, InterPro, Kabat,, KEGG, LocusLink,, NBRF/PIR, Affymetirx Cel,, NDB, PDB, Prosite,, Rebase, SAF, SwissProt,, etc.. Web NCBI (Entrez( Entrez,, BLAST, PubMed), Swiss-Prot, ExPASy BLAST, Clustalw,, EMBOSS, SVM etc...

8 Biopython (2/2) 0 UQ4NXT 54T SZK UZ4XAV 1 R68Y2I M39HFO EECG5U VM8F1S IV3NN8 2 N9VTBA 6ELXN7 MPO9Y4 Q Q6J1I 5X9G SJ GY9PXU 9HAG TP EIY7IM 3PBNQW Randomly generated Organism 3 CLHNRO ZPAJI3 O0CKIP K3ZK3L FJI45X W2VJAS ZFZ7EL QJ59TA Y8FTEI MDQH0N 4 62DL32 5DLOHN 5 1P1RBS 4RHMPM 5EJ805 6B9ZJF TPIWEF VT87Y0 VW 661T DF MF1J YVNOOD YK2XZB QZISI9 7VKXFQ CFVJA2 0ECQQR 6 DNSK0B Z A3F8B 7 EH9KP3 BS1IJK 1HBHJ1 KZ5B3S 8 5M591W 249M2S ZRA0SZ OUWQ7O VEOHC5 W T0O 6V Z 21G 1G MOEVPS W L57C8 GR8ETH VS6SRL 9RXE9K 9 J35AQ M 8KZ6U4 J6TWU1 XVT8OF 10 6IOO5T VF3MM6 ZMOYMJ NB21C9 LOPC2G R3DG B6 O8RFUJ NLJK4R B5EHV0 ERIM5R 6TRIEZ DAY5UM 7M5VLZ N5ZDJ8 QX9OT5 11 AAC4MY BUAJGA HE9J8D T4SMDH XL62PV EPBWVJ JHQ81D 1W A26W4D EPDH GHY7TY 8KF62S QJEV1P 12 GA, HMM, k-means, k k-k NN, naive Bayes,, ANN, pairwise alignment, SVD Cromosome,, Pathway SQL DB BioSQL: Biopython DB

9 Open-Bio BOF 2004 at GIW2004 ( )

http://www.biopython.org www.biopython.org/ : biopython@biopython.org : biopython-dev@biopython.

10 : biopython@biopython.org : biopython-dev@biopython.org ( )

11 Biopython Biopython Biopython!!!

12 (1/2) from Bio.WWW import NCBI # NCBI res = NCBI.query('Search', 'PubMed', term='biopython',doptcmdl='summary') # of = open('outfile.html', 'wb') of.write(res.read()) of.close() # import webbrowser webbrowser.open('outfile.html')

13 (2/2) Open-Bio BOF 2004 at GIW2004 from Bio.PubMed import Dictionary, search_for # PubMed entries = search_for('catechin synthesis') print entries from Bio.Medline import RecordParser # Medline recparser = RecordParser() # 10 3 # rdict = Dictionary(delay=3.0, parser=recparser) for e in entries[:10]: record = rdict[e] print record.authors, record.title, record.source [' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ',... ' ', ' ', ' ', '229857', ' ', ' '] ['Saito A', 'Doi Y', 'Tanaka A', 'Matsuura N', 'Ubukata M', 'Nakajima N'] Systematic synthesis of four epicatechin series procyanidin trimers and their inhibitory activity on the Maillard reaction and antioxidant activity. Bioorg Med Chem 2004 Sep 15;12(18): ['Ihara N', 'Kurisawa M', 'Chung JE', 'Uyama H', 'Kobayashi S'] Enzymatic synthesis of a catechin conjugate of polyhedral oligomeric...

14 Acknowledgements and Copyrights Open-Bio BOF 2004 at GIW2004 Microsoft OfficeOnline (ymasuda at ethercube.com) Copyright Notice Copyright Yasushi Masuda, 2004 All Rights Reserved Permission to use, copy, modify, and distribute this product for any purpose and without fee is hereby granted, provided that above copyright notice and this permission notice is attached with every copies or distributions. Disclaimer Yasushi Masuda (the author hereafter) disclaims all warranties with regard to this product, including all implied warranties of merchantability and fitness, in no event the author shall be liable for any special, indirect or consequential damages or any damages whatsoever resulting from loss of use, data or profits, whatever in an action pf contract, negligence or other tortious action, arising out of or in connection with the use or derivation of this product. The author makes any warranty, express or implied, or assumes any liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately-owned rights. Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the author. The views and opinions of authors expressed herein do not necessarily state or reflect those of the author, and shall not be used for advertising or product endorsement purposes. PDF

ScanFront300/300P セットアップガイド

ScanFront300/300P セットアップガイド libtiff Copyright (c) 1988-1996 Sam Leffler Copyright (c) 1991-1996 Silicon Graphics, Inc. Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby