From jeff at bioinformatics.org Fri May 11 23:42:53 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sat, 12 May 2001 03:42:53 +0000 Subject: [BiO BB] trivia question Message-ID: <3AFCB13D.1EE96A41@bioinformatics.org> What was the first bioinformatics program to be licensed under the GNU GPL? (I don't know the answer.) Cheers. Jeff From balarji at rediffmail.com Wed May 16 13:01:17 2001 From: balarji at rediffmail.com (balaji r) Date: 16 May 2001 17:01:17 -0000 Subject: [BiO BB] nucleosome positioning Message-ID: <20010516170117.29597.qmail@mailweb23.rediffmail.com> Hi .., I want some help. Does any one know whether Nucleosomal DNA of Yeast, that is the 146 mer DNA that is bound to HISTONES is available on any database. I want these sequences, can anyone guide me from where these sequences be obtained or is there any program to extract these from the yeast genome. thank you.. Balaji Indian Institute of Science, Bangalore ******************************************************* It is some thing like the following which is in genbank - _______________________________________________________ The following is an example for chicken (Gallus gallus which is a 148 mer) X69506 G.gallus DNA sequence from nucleosome 1 tgaaaaagac aagttggggc aggaaatgat gtacttccga acttctttat cccctcatga 61 ctcacagctt catgacagat ttcatttaag taatatcctt tcaaaattca aagtctcctg 121 tactttcagt acaaaagaga cataacca _____________________________________________________ Chat with your friends as soon as they come online. Get Rediff Bol at http://bol.rediff.com From balarji at rediffmail.com Wed May 16 13:04:44 2001 From: balarji at rediffmail.com (balaji r) Date: 16 May 2001 17:04:44 -0000 Subject: [BiO BB] nucleosome DNA of Yeast Message-ID: <20010516170444.10703.qmail@mailweb3.rediffmail.com> Hi .., I want some help. Does any one know whether Nucleosomal DNA of Yeast, that is the 146 mer DNA that is bound to HISTONES is available on any database. I want these sequences, can anyone guide me from where these sequences be obtained or is there any program to extract these from the yeast genome. thank you.. Balaji Indian Institute of Science, Bangalore ******************************************************* It is some thing like the following which is in genbank - _______________________________________________________ The following is an example for chicken (Gallus gallus which is a 148 mer) X69506 G.gallus DNA sequence from nucleosome 1 tgaaaaagac aagttggggc aggaaatgat gtacttccga acttctttat cccctcatga 61 ctcacagctt catgacagat ttcatttaag taatatcctt tcaaaattca aagtctcctg 121 tactttcagt acaaaagaga cataacca _____________________________________________________ Chat with your friends as soon as they come online. Get Rediff Bol at http://bol.rediff.com From reillywu at yahoo.com Thu May 17 14:55:29 2001 From: reillywu at yahoo.com (Chunlei Wu) Date: Thu, 17 May 2001 11:55:29 -0700 (PDT) Subject: [BiO BB] Standford Bioinformatics courses Message-ID: <20010517185529.743.qmail@web4905.mail.yahoo.com> Hi, Is any person attending the online bioinformatics courses from Standford? How about it? Is it worth the tuition? Are there any more online courses available right now? Thanks CL __________________________________________________ Do You Yahoo!? Yahoo! Auctions - buy the things you want at great prices http://auctions.yahoo.com/ From jeff at bioinformatics.org Thu May 17 17:32:43 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 17 May 2001 21:32:43 +0000 Subject: [BiO BB] Standford Bioinformatics courses References: <20010517185529.743.qmail@web4905.mail.yahoo.com> Message-ID: <3B04437B.F89CF1AD@bioinformatics.org> Chunlei Wu wrote: > > Are there any more online courses available right > now? I heard that Exeter, UK has a Master's program in bioinformatics that can be earned remotely (via the Internet?). For more info, contact Dr. Andy Dalby at ardalby at ex.ac.uk Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jchang at SMI.Stanford.EDU Thu May 17 23:45:52 2001 From: jchang at SMI.Stanford.EDU (Jeffrey Chang) Date: Thu, 17 May 2001 20:45:52 -0700 Subject: [BiO BB] Standford Bioinformatics courses In-Reply-To: <20010517185529.743.qmail@web4905.mail.yahoo.com> Message-ID: Hello, Currently, I'm one of the TA's for Stanford's class BMI214 Representations and Algorithms in Computational Molecular Biology, which is one of the three for the certificate. I can't say whether it's worth the tuition (don't know how much it is). The course covers a wide range of bioinformatics work and is updated yearly to make sure that it's current. This year, it's roughly organized into sequence, structure, and then function analysis and algorithms. The syllabus is available online at the web site: http://smi-web.stanford.edu/projects/helix/bmi214/ Plus, you can look at the assignments using a guest login. As far as taking it online, about 20% of our students are distance learners. It's doable, but needs extra coordination because they receive handouts later, don't have as good access to the instructors, and miss out on the community of other students and learning together. Jeff > From: Chunlei Wu > Reply-To: bio_bulletin_board at bioinformatics.org > Date: Thu, 17 May 2001 11:55:29 -0700 (PDT) > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Standford Bioinformatics courses > > Hi, > Is any person attending the online bioinformatics > courses from Standford? How about it? Is it worth the > tuition? > Are there any more online courses available right > now? > > Thanks > > CL > > __________________________________________________ > Do You Yahoo!? > Yahoo! Auctions - buy the things you want at great prices > http://auctions.yahoo.com/ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From reillywu at yahoo.com Sat May 19 12:11:52 2001 From: reillywu at yahoo.com (Chunlei Wu) Date: Sat, 19 May 2001 09:11:52 -0700 (PDT) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #33 - 3 msgs In-Reply-To: <200105181600.MAA28013@www.bioinformatics.org> Message-ID: <20010519161152.21531.qmail@web4902.mail.yahoo.com> Thank you two, I have another questions: This course, "Computational Molecular Biology (BIOCHEM218/MIS231)", is presented every autumn quarter. And also can be took at other quarters. So if I register it this summer, it will be the repeat of last autumn's. I think it's better to register it at this autumn. It will be a new one. Am I right? Thank you CL __________________________________________________ Do You Yahoo!? Yahoo! Auctions - buy the things you want at great prices http://auctions.yahoo.com/ From clin at scimagix.com Mon May 21 16:42:46 2001 From: clin at scimagix.com (Chin Chin Lin) Date: Mon, 21 May 2001 13:42:46 -0700 Subject: [BiO BB] posting new discussion Message-ID: Scimagix is the leading provider of image informatics solutions for the pharmaceutical and biotechnology industries. We are currently looking for a number of people with a life sciences background for sales, marketing and development. Feel free to check out our website for more info: www.scimagix.com, or feel free to give me a call directly: 650-508-2115 From winhide at sanbi.ac.za Wed May 23 10:38:11 2001 From: winhide at sanbi.ac.za (Dr. Winston Hide) Date: Wed, 23 May 2001 16:38:11 +0200 (SAST) Subject: [BiO BB] Fw: [BiO BB] Standford Bioinformatics courses (fwd) Message-ID: The s* online training programme is to be announced shortly. Watch the Bionet announce board. Also ISMB2001. Win Winston Hide. South African National Bioinformatics Institute Private Bag X17 University of the Western Cape Bellville South Africa +27 21 959 3645 Fax +27 21 959 2512 www.sanbi.ac.za ---------- Forwarded message ---------- Date: Wed, 23 May 2001 16:19:16 +0200 From: Tania Broveak Hide To: Win Hide Subject: Fw: [BiO BB] Standford Bioinformatics courses Do you want to respond to this group aboutr the *alliance? T ----- Original Message ----- From: Chunlei Wu To: Sent: Thursday, May 17, 2001 8:55 PM Subject: [BiO BB] Standford Bioinformatics courses > Hi, > Is any person attending the online bioinformatics > courses from Standford? How about it? Is it worth the > tuition? > Are there any more online courses available right > now? > > Thanks > > CL > > __________________________________________________ > Do You Yahoo!? > Yahoo! Auctions - buy the things you want at great prices > http://auctions.yahoo.com/ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From jeff at bioinformatics.org Wed May 23 10:56:51 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 23 May 2001 14:56:51 +0000 Subject: [BiO BB] BiO BoF 2001: BRIE & OAP '01 Message-ID: <3B0BCFB3.F719F767@bioinformatics.org> You may have seen this on BiO News, but we'll make the announcement here as well... Bioinformatics.org is announcing its first annual "Birds of a Feather" (BiO BoF) meeting. Every year we will host a conference on a topic of interest to our community. This year, we will be co-hosting the BRIE & OAP '01 joint satellite conference on July 26, at ISMB'01, in Copenhagen, Denmark. The "Biological Research with Information Extraction" (BRIE) 2001 conference will cover text mining for biology, while the "Open-Access Publications" (OAP) 2001 conference will cover the publication obstacles to information retrieval and extraction. The joint conferences will require only one registration per person. A formal announcement with more details will follow shortly. If you're planning to attend, please note that the main ISMB'01 conference runs from July 21 to 25, and the satellite conferences are either before (as with BOSC'01) or after. BRIE & OAP '01 will be held on the day AFTER the main conference (on Thursday). There is a new website with more information: http://bioinformatics.org/bof/brie-oap-01/ Cheers. Jeff From viswap_rri at 123india.com Thu May 24 00:22:11 2001 From: viswap_rri at 123india.com (viswap_rri at 123india.com) Date: 23 May 2001 21:22:11 -0700 Subject: [BiO BB] free energy minimization routines!! Message-ID: <20010524042211.25790.cpmta@c009.snv.cp.net> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From lhaifeng at dso.org.sg Fri May 25 03:55:57 2001 From: lhaifeng at dso.org.sg (Liu Haifeng) Date: Fri, 25 May 2001 15:55:57 +0800 (SGT) Subject: [BiO BB] Downloading Human Sequence Data by Cytogenetic position In-Reply-To: <20010524042211.25790.cpmta@c009.snv.cp.net> References: <20010524042211.25790.cpmta@c009.snv.cp.net> Message-ID: <990777357.3b0e100dc3344@demerzel.dso.org.sg> Hi, Although the draft Human Genome has been published and there are a lot of database around now, I am still wandering where I can download some human data by chromosome cytogenetic position, such as the whole 12q23 including draft parts, rather than a whole chromosome. It seems that Genbank just contains such cytogenetic sequence data which have been finished sequencing. So could anybody help me? Thanks a lot! Regards, Haifeng From thomas at genome.cbs.dtu.dk Fri May 25 04:56:14 2001 From: thomas at genome.cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: Fri, 25 May 2001 10:56:14 +0200 (MDT) Subject: [BiO BB] Downloading Human Sequence Data by Cytogenetic position In-Reply-To: <990777357.3b0e100dc3344@demerzel.dso.org.sg> Message-ID: > Hi, > Although the draft Human Genome has been published and there are a lot of > database around now, I am still wandering where I can download some human data > by chromosome cytogenetic position, such as the whole 12q23 including draft > parts, rather than a whole chromosome. It seems that Genbank just contains > such cytogenetic sequence data which have been finished sequencing. > > So could anybody help me? Thanks a lot! > The best resource today is ensembl (www.ensembl.org) which includes cytogenetic mappings. good luck -thomas Sicheritz-Ponten Thomas, Ph.D CBS, Department of Biotechnology thomas at biopython.org The Technical University of Denmark CBS: +45 45 252489 Building 208, DK-2800 Lyngby Fax +45 45 931585 http://www.cbs.dtu.dk/thomas De Chelonian Mobile ... The Turtle Moves ... From cfjell at bcgsc.bc.ca Wed May 30 21:09:25 2001 From: cfjell at bcgsc.bc.ca (Chris Fjell) Date: Wed, 30 May 2001 18:09:25 -0700 Subject: [BiO BB] new physical mapping viewer released Message-ID: <3B1599C5.7050305@bcgsc.bc.ca> Hi, Subscribers might be interested in a new Java application/applet (iCE) for viewing genomic physical maps (clones, contigs, fingerprints, etc), go to: http://ice.bcgsc.bc.ca. Anyone interested in adapting the code or making their own installations of iCE should contact me. -- Chris Fjell Programmer/Analyst - Genome Sequence Center, BC Cancer Agency 600 W 10th Avenue, Vancouver BC V5Z 4E6 email: cfjell at bcgsc.bc.ca fax: (604) 877-6085 www: http://www.bcgsc.bc.ca From selonline at hotmail.com Thu May 31 01:25:39 2001 From: selonline at hotmail.com (selvi subramanian) Date: Thu, 31 May 2001 10:55:39 +0530 Subject: [BiO BB] Hi all Message-ID: An HTML attachment was scrubbed... URL: From goswami at archeanit.com Thu May 31 04:17:28 2001 From: goswami at archeanit.com (Satyakam Goswami) Date: Thu, 31 May 2001 13:47:28 +0530 (IST) Subject: [BiO BB] Hi all In-Reply-To: References: Message-ID: <1536.192.168.0.1.991297048.squirrel@mail.archeanit.net> Hello, You are most welcome , which part of INDIA are you from?, what exactly are you doin in the field of bioinformatics. S.Goswami > Hi all > am Selvi Subramanian from India. Basically am a molecular Biologist and > presently am working in the field of bioinformatics.  i hope to learn > something off these posts !regards > Selvi SubramanianGet Your Private, Free E-mail from MSN Hotmail at > http://www.hotmail.com. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Archean Infotech Victory Vihar,Himayatnagar Hyderabad 500029,www.archeanit.com Ph:3228666,6570704,3228674 Mobile:9849016667 From idoerg at cc.huji.ac.il Thu May 31 06:36:31 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Thu, 31 May 2001 13:36:31 +0300 (GMT+0300) Subject: [BiO BB] Determining gap penalties & bits Message-ID: Hi all, A question regarding scoring matrices follows: Is there some formal way to determine gap penalties for the Smith-Waterman algorithm given a log-odds scoring matrix? I know GCG/Wisconsin package does something, but I could not find any documentation on that. Also, how do I determine the best number of bits in which to represent my scoring matrix? That is, what are good values for N in the function: N*log(Pij/Pi*Pj) (log in base 2) which is a matrix entry? Pij: frequency of substitutions between amino-acid j and amino-acid i Pi,Pj: frequencies of amino-acids i and j, respectively. Any pointers to relevant literature? Thanx, Iddo -- Iddo Friedberg | Tel: +972-2-6758647 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From senthil at www.cdfd.org.in Thu May 31 21:48:23 2001 From: senthil at www.cdfd.org.in (Mr M senthil kumar) Date: Thu, 31 May 2001 18:48:23 -0700 (PDT) Subject: [BiO BB] Determining gap penalties & bits In-Reply-To: Message-ID: Hi Friedberg, I think Emboss has a program called water which does the Smith-Waterman algorithm. More can be found at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/water.html Hope this helps, Senthil Kumar M. -- X*********************************************X # Senthil Kumar M. # # Junior Research Fellow, # # Center for DNA fingerprinting & Diagnostics,# # ECIL Road, Hyderabad 500 076, India. # # email: senthil at www.cdfd.org.in # # senthil at operamail.com # X*********************************************X On Thu, 31 May 2001, Iddo Friedberg wrote: > Hi all, > > A question regarding scoring matrices follows: > > > Is there some formal way to determine gap penalties for the Smith-Waterman > algorithm given a log-odds scoring matrix? I know GCG/Wisconsin package > does something, but I could not find any documentation on that. Also, how > do I determine the best number of bits in which to represent my scoring > matrix? That is, what are good values for N in the function: > > N*log(Pij/Pi*Pj) (log in base 2) > > which is a matrix entry? > > Pij: frequency of substitutions between amino-acid j and amino-acid i > Pi,Pj: frequencies of amino-acids i and j, respectively. > > Any pointers to relevant literature? > > Thanx, > > Iddo > > -- > > Iddo Friedberg | Tel: +972-2-6758647 > Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 > The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il > POB 12272, Jerusalem 91120 | > Israel | > http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Dag.Ahren at mbioekol.lu.se Thu May 31 12:48:20 2001 From: Dag.Ahren at mbioekol.lu.se (=?Windows-1252?Q?Dag_Ahr=E9n?=) Date: Thu, 31 May 2001 18:48:20 +0200 Subject: [BiO BB] php in bioinformatics? Message-ID: <000a01c0e9f1$81f23c20$112eeb82@mbioekol.lu.se> Hi, I am a PhD student (soon to be finished) using PHP programming in bioinformatics. Does anybody of you use PHP in bioinformatics? Sincerely, Dag Ahren Dag Ahren Microbial Ecology Ecology Building 223 56 Lund Phone +46 46 222 37 58 Fax +46 46 222 41 58 -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas at cbs.dtu.dk Thu May 31 17:02:47 2001 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: 31 May 2001 23:02:47 +0200 Subject: [BiO BB] php in bioinformatics? In-Reply-To: Dag =?iso-8859-1?q?Ahr=E9n's?= message of "Thu, 31 May 2001 18:48:20 +0200" References: <000a01c0e9f1$81f23c20$112eeb82@mbioekol.lu.se> Message-ID: Dag Ahr?n writes: > Hi, > > I am a PhD student (soon to be finished) using PHP programming in > bioinformatics. Does anybody of you use PHP in bioinformatics? > > Sincerely, > > ? > > Dag Ahren Occasionally (rather not) - e.g. for http://bioinformatics.org/software/ c ya @ISMB01 -thomas -- Sicheritz-Ponten Thomas, Ph.D CBS, Department of Biotechnology thomas at biopython.org The Technical University of Denmark CBS: +45 45 252489 Building 208, DK-2800 Lyngby Fax +45 45 931585 http://www.cbs.dtu.dk/thomas De Chelonian Mobile ... The Turtle Moves ...