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From jchang@SMI.Stanford.EDU Tue Nov 13 04:02:05 2001 From: jchang@SMI.Stanford.EDU (Jeffrey Chang) Date: Mon, 12 Nov 2001 20:02:05 -0800 Subject: [BioPython] Fwd: O'Reilly Bioinformatics Technology Conference 011112 Message-ID: >Date: Mon, 12 Nov 2001 16:45:07 -0800 (PST) >From: "O'Reilly Conferences" >To: jchang@SMI.Stanford.EDU >Subject: O'Reilly Bioinformatics Technology Conference 011112 > >"Today, the desktop computer has become >an indispensable part of the biologist's >tool chest." -Lincoln D. Stein, Cold Spring >Harbor Laboratory > >---------------------------------------------- > A N N O U N C I N G > >Practical Tools For Innovation >O'Reilly Bioinformatics Technology Conference >Westin La Paloma Resort and Spa >January 28-31, 2002, Tucson, AZ >http://conferences.oreilly.com/biocon/ > >Platinum Sponsors > Sun Microsystems > Nature Publishing Group >---------------------------------------------- > >O'Reilly & Associates is pleased to announce its >first Bioinformatics Technology Conference, an event >exploring the engineering, software development, >and tool-building aspects of bioinformatics. This >conference will deliver knowledge from the >biotechnology innovators in the form of useful skills >you can take back to improve the way you do research. > >************************************************ >Register Now and Save $200 on conference registration >and $345 on tutorial fees - $545 total savings >ACT NOW - Offer ends December 7, 2001 >http://conferences.oreilly.com/biocon/ > >Early Bird registration also entitles you to a >free O'Reilly book - see registration for details. >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/register.html >************************************************ > >Read why O'Reilly founder and President Tim O'Reilly >thinks bioinformatics is the first technology revolution >of the 21st century, and why our conference is a >great opportunity to join others at the forefront >of discovery - >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/tim.html > > >Keynote Speakers--Our keynote speakers are leaders >in bioinformatics and work in the trenches where >innovation is born: > >Lincoln D. Stein, Cold Spring Harbor Laboratory >Ewan Birney, European Bioinformatics Institute >Gene Myers, Celera Genomics >Terry Gaasterland, Rockefeller University >James Ostell, National Center For Biotechnology Information > >For further details on our keynote, tutorial, and session >speakers, please visit >http://conferences.oreilly.com/biocon/ > > >Tutorials and Sessions >-In the Trenches Education, Getting the Job Done > >Our tutorials concentrate on the essentials, assuring a >solid foundation in successful computational biology. >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/tutorials.html > >The O'Reilly Bioinformatics Technology Conference >offers the hottest session topics, applications, and >tools - visit our website for details: >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/sessions.html > > >Conference Community Meetings >-Coming Together to Share and Develop >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/community.html > >The Gene Ontology Consortium (GO) will meet February 1st >through the 3rd at the Westin La Paloma, at the conclusion >of the conference. > >Bioinformatics.org will hold its annual meeting at the >O'Reilly Bioinformatics Technology Conference, including >a one-day technical track open to all registered attendees. > >The Open Bioinformatics Foundation (OBF) will exhibit and >host birds-of-a-feather (BOF) sessions for Bioperl developers, >new Bioperl users, and Biopython users & developers. > > >Related News > >Interview with Ewan Birney--O'Reilly Web editor Bruce >Stewart spoke with conference keynote Ewan Birney >about Bioperl, Ensembl, and the importance of open >source bioinformatics. >http://www.oreillynet.com/pub/a/network/2001/10/18/birney.html > >Read Why Biologists Want to Program Computers by >conference speaker James Tisdall >http://www.oreilly.com/news/perlbio_1001.html > >Bio Hackathon--For the first time, open source >bioinformatics developers will meet face-to-face in >an international "hackathon" - a hands on programming >event held in coordination with the conference. >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/community.html > > >The Venue >-Location, Location, Location > >Where else in January? The O'Reilly Bioinformatics >Technology Conference is in Tucson, Arizona, where >attendees have the opportunity to "get away" and >relax in this warm southwestern resort. >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/hotel.html > >See & Do > >Our conference planners have your family in mind. If >you are looking for a warm and adventure filled holiday >for your family while you attend the conference, here >are highlights of services and destinations your family >will enjoy. For more details visit our conference >See & Do page >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/see_do.html > >Just for Kids--The Westin La Paloma provides an >entertainment package, a children's lounge, and day care. >For additional child care services, the Children's Lounge >has names and phone numbers of local child care >professionals available on request. > >Your children will also enjoy the specially designed >"kids-only" pool at the Westin La Paloma. In addition, >youngsters at least three and a half feet tall can >enjoy the Slidewinder, Arizona's longest resort >water slide. > >Golf enthusiasts will enjoy testing out their >skills on Tucson's picturesque golf courses. The >celebrated 27-hole Jack Nicklaus signature course >is located at the Westin La Paloma Resort. > >Take a tour of Columbia University's Biosphere 2 Center, >one of the world's largest ecological laboratories. >The Biosphere 2, covering 3.15 acres, contains several >different biomes housing a rain forest, a million >gallon salt-water ocean, a coastal fog desert, >and four other wilderness ecosystems. > >The Mission San Xavier del Bac, established in the 17th >century by Spanish missionaries, is known as one of the >finest examples of mission architecture in the country. >It is called the "White Dove of the Desert" for its stark >contrast. > >The Arizona/Sonora Desert Museum--A renowned natural >history museum and zoo, features botanical gardens and desert >paths where you're sure to encounter a variety of >desert wildlife. > >The International Wildlife Museum--Highlighting over 400 >different kinds of mammals, insects and birds (some of >which are endangered or threatened) is a fascinating >museum to visit while in Tucson. > >If you are interested in sponsoring this conference please >email Andrew Calvo at andrewc@oreilly.com or call 707-827-7176. > >************************************************ >If you have not subscribed to this list but wish >to continue receiving email announcements about >the O'Reilly Bioinformatics Technology Conference, >please visit our opt-in conference email list >http://conferences.oreillynet.com/cs/bio2002/pub/w/17/maillist.html > >If do NOT want to receive email announcements >about The O'Reilly Bioinformatics Technology >Conference, please reply to this message with >REMOVE in the subject line, and you will not >receive future email notices. >************************************************ From kelleys@ucsu.colorado.edu Fri Nov 16 19:27:20 2001 From: kelleys@ucsu.colorado.edu (Scott T. Kelley) Date: Fri, 16 Nov 2001 11:27:20 -0800 Subject: [BioPython] writing clustalw alignment to file Message-ID: <001b01c16ed4$b816ab20$8a7e8a80@colorado.edu> I had a couple questions concerning Biopython I hope someone can help me answer. (I am using the Windows version BTW.) (1) I am trying to convert a clustalw alignment to a fasta alignment (pg. 38-39 of Cookbook). I can do this just like in the book, but then I want to write the fasta alignment to a file and I don't know how to do this. Also, I would really like to search through the fasta or clustalw file for particular sequence names (titles) so that I can retrieve the particular sequence but I do not know how this is done. For instance, I would like to find the following sequence from a file: >APE2174 ------------------------------------------------------------ --------------------------MVKGSQVKPSTTELLLKAVSAKAPSGD------- ---PIHQK---IGDLPFEKIVEIAIEKKPD--LLAKTLKAAVKTILGSARSIGVTVDGKD PKEVTRQVDEGVYDAVLAKYEEKWEEAEG (2) The other question has to do with parsing Genbank files. I can use the Genbank parser to retrieve exon and intron sequences just fine and I give a (partial) example of a function I wrote to do this below from the "mRNA" feature (very similar to the example in the cookbook). However, when I try to get the positions from the "gene" feature I run into problems. For example: gene 2..1021 /gene="HI0001" All I want is the positions of the gene and the gene name but I keep running into problems. Any feedback you could give me on these problems would be appreciated. Thanks! -Scott def get_introns(self, genbank_file_name): """Function parses a genbank file and finds all exonsequences""" # --- load a parser and iterator for our GenBank file gb_handle = open(genbank_file_name, "r") # -- a parser that will give you back SeqFeature objects feature_parser = GenBank.FeatureParser() iterator = GenBank.Iterator(gb_handle, feature_parser) # begin iterating through the file and getting GenBank records while 1: # get a SeqFeature object for the next GenBank record. When we run # out of records in the file, cur_entry will be None cur_entry = iterator.next() if cur_entry is None: break print "Writing intron entries for %s to file" % cur_entry.id # loop through all of the features for the entry for feature in cur_entry.features: # when we've got mRNA features, parse the info out of them if feature.type == "mRNA": # loop through all of the subfeatures and get the # individual exons all_exons = [] for sub_feature in feature.sub_features: # add the info about the exon, ignoring fuzzy locations all_exons.append((sub_feature.location.nofuzzy_start, sub_feature.location.nofuzzy_end)) ------------------- Scott T. Kelley, Ph.D. Campus Box 347 MCD Biology University of Colorado Boulder, CO 80309-0347 Phone: (303) 735-1808 Fax: (303) 492-7744 E-mail: Scott.Kelley@Colorado.edu From dag@sonsorol.org Mon Nov 26 00:57:02 2001 From: dag@sonsorol.org (chris dagdigian) Date: Sun, 25 Nov 2001 19:57:02 -0500 Subject: [BioPython] OBF members; 30% discount to the O'Reilly Bioinformatics Technology Conference Message-ID: <3C01935E.2070908@sonsorol.org> Apologies for the massive cross-post; O'Reilly has reached out to several groups including Bioinformatics.org and the Open Bioinformatics Foundation and is offering a flat 30% discount off their conference registration fee for all OBF "members". This is the conference that Ewan Birney is keynoting and where various OBF-affiliated people will be found talking, running tutorial sessions & hosting BOF gatherings. We are not endorsing this conference in any sort of formal way but knowing that some portion of our membership will be attending we wanted to spread the word regarding the discount far & wide. Lacking any sort of concrete information on who is an OBF "member" I have taken the liberty of assuming that anyone who is a subscriber on any of our discussion-oriented mailing lists meets the criteria. Hence this email. If you are planning on attending theconference you can use the code ("BIC02OPEN") to save 30% on your registration fee. Warning: some of you (students in particular) may qualify for discounts that are greater than this 30% offer - check the website to see if you can get a better deal. Regards, Chris The details: > O'Reilly & Associates has extended a 30% discount to Open > Bioinformatics Foundation members for the January 28, 2002, > O'Reilly Bioinformatics Technology Conference in Tucson, AZ. This > discount is good for any time from now until the conference > begins. To receive the discount, use this discount code when > registering - BIC02OPEN > http://conferences.oreillynet.com/cs/bio2002/pub/w/17/register.html > > NOTE - This discount cannot be used in combination with other > discounts. Check the O'Reilly Conference registration page for > discounts for students and academic instructors - > http://conferences.oreillynet.com/cs/bio2002/pub/w/17/register.html >