From benjaminelsy at hotmail.com Sat Dec 1 03:41:35 2001 From: benjaminelsy at hotmail.com (Elsy Benjamin) Date: Sat, 1 Dec 2001 14:11:35 +0530 Subject: [BiO BB] Software for Proteomics Message-ID: Hello Board Members, I would like to know the different areas of proteomics where the techniques and result predictions can be automated using current advances in bioinformatics. Any idea about the working of deemed software or a link for the popular existing software in the field of proteomics will be highly appreciated. Thanks in advance.. Benjamin E. -------------- next part -------------- An HTML attachment was scrubbed... URL: From NorthstarNews at northstaragents.com Sat Dec 1 16:59:09 2001 From: NorthstarNews at northstaragents.com (NorthstarAgents.com) Date: Sat, 1 Dec 2001 16:59:09 -0500 Subject: [BiO BB] Life science companies looking for Bioinformatics/Cheminformatics professionals Message-ID: Attention Bioinformatics/Cheminformatics Professional: I am writing to inform you that top life science companies are now subscribing to our resume subscription database and are looking for bioinformatics and cheminformatics professionals. NorthstarAgents.com is the first and only online recruitment network that exclusively serves the bioinformatics and cheminformatics industries. When your resume is posted on NorthstarAgents.com you can expect the following benefits: * More hiring managers/recruiters will receive your resume * Bioinformatics and cheminformatics job postings with leading companies * Breaking news on new products and tools * Advice on creating a resume and tips for interviewing * A bioinformatics/cheminformatics forum to share ideas with your peers Best of all, NorthstarAgents.com is absolutely FREE for bioinformatics and cheminformatics professionals. NorthstarAgents.com serves all bioinformatics and cheminformatics professionals (scientists, programmers, sales, marketing, executives) so feel free to pass this information along to your colleagues. In the meantime, don't hesitate to call us if you have questions. What to do next? Follow these steps and you will be in a position where top life science companies can contact you about job openings: * STEP 1 - Visit www.northstaragents.com website and create an account * STEP 2 - Create your online resume profile; takes between 10-20 min. * STEP 3 - Relax! Life science companies are now contacting candidates Don't miss out on having top life science companies view your online resume. Visit www.NorthStarAgents.com today and FIND YOUR FUTURE. Sincerely, Randall S. Rogers Chief Executive Officer NorthstarAgents.com rrogers at northstaragents.com (877)765-7832 From ngadewal at yahoo.com Mon Dec 3 04:04:48 2001 From: ngadewal at yahoo.com (nikhil gadewal) Date: Mon, 3 Dec 2001 01:04:48 -0800 (PST) Subject: [BiO BB] Pattern & Motif Message-ID: <20011203090448.83232.qmail@web9505.mail.yahoo.com> hi members, WHAT IS A DIFFERENCE BETWEEEN 'PATTERN' AND 'MOTIFS'? thank you in advance. NIKHIL ===== NIKHIL. S. GADEWAL * HOME ADDRESS * # 22, subhshree apts, Bioinformatics center, * near vijan hospital, Cancer Research Institute, * college road, Parel, Mumbai-12. * nashik-422005 cri3 at soochak.ncst.ernet.in * Phone no. 0253-580490 Phone no. 4123803 etx. 242 * __________________________________________________ Do You Yahoo!? Buy the perfect holiday gifts at Yahoo! Shopping. http://shopping.yahoo.com From ngadewal at yahoo.com Mon Dec 3 06:29:39 2001 From: ngadewal at yahoo.com (nikhil gadewal) Date: Mon, 3 Dec 2001 03:29:39 -0800 (PST) Subject: [BiO BB] expression profile In-Reply-To: <3C038B79.A0ECFA2F@bioinfo.weizmann.ac.il> Message-ID: <20011203112939.33432.qmail@web9506.mail.yahoo.com> HI www.informatics.jax.org/searches/gxdindex_form.shtml http://bodymap.ims.u-tokoyo.ac.jp/ ABove sites are for mouse exp data. NIKHIL --- Dana Gerber wrote: > Hi, > > Where can I find a expression profile of specific > gene from c.elegans, > mouse and E.coli. > I need any information about their lethality, tissue > specific > expression, condition specific expression. It's > unknown gene that don't > have any information in central database such as > WormDB, AceDB, EcoCyc > and others. > > > Thanks a lot, > all best, > > Dana > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== NIKHIL. S. GADEWAL * HOME ADDRESS * # 22, subhshree apts, Bioinformatics center, * near vijan hospital, Cancer Research Institute, * college road, Parel, Mumbai-12. * nashik-422005 cri3 at soochak.ncst.ernet.in * Phone no. 0253-580490 Phone no. 4123803 etx. 242 * __________________________________________________ Do You Yahoo!? Buy the perfect holiday gifts at Yahoo! Shopping. http://shopping.yahoo.com From jeff at bioinformatics.org Mon Dec 3 12:06:17 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 03 Dec 2001 12:06:17 -0500 Subject: [BiO BB] ANNOUNCE: BioMail at Bioinformatics.Org Message-ID: <3C0BB109.D1C263A0@bioinformatics.org> ANNOUNCING BIOMAIL @ BIOINFORMATICS.ORG We are pleased to announce that BioMail 0.70 is now up and running at Bioinformatics.Org. For information about what BioMail does and why you should use it, see the description below. The URL is http://www.bioinformatics.org/biomail BioMail is a small web-based application for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is written to automate searching for recent scientific papers in the PubMed Medline database. BioMail is free and will stay free. What does BioMail do? Periodically BioMail does a user-customized Medline search and sends all matching articles recently added to Medline to the users' e-mail address. HTML-formatted e-mails generated by BioMail can be used to view selected references in medline format (compatible with most reference manager programs). Why is BioMail helpful? If you use Medline, it may be hard to remember when you did your last search. Often you must scan titles you have already seen to be certain you didn't miss an important reference. BioMail will perform routine searches for you. This program alerts users to all new papers in their fields automatically. It also helps the user to 'refine' search patterns once and for all. There is no need to wonder: 'What was that great search pattern I used last Saturday?'. All patterns are safe in the database and can be accessed, tuned, or deleted any time. From pooja_jain25 at hotmail.com Mon Dec 3 23:27:05 2001 From: pooja_jain25 at hotmail.com (Pooja Jain) Date: Tue, 4 Dec 2001 09:57:05 +0530 Subject: [BiO BB] Pattern & Motif References: <20011203090448.83232.qmail@web9505.mail.yahoo.com> Message-ID: Hello Nikhil, When discussing sequence homology we use terms as "patterns", "motifs" and "similarity". These are broad and vague terms, it is enough to think about concepts like patterns of behavior or musical motifs. When we use these terms for sequences, we use them in a given context and a restricted sense. Typically, a PROSITE pattern which is a special sequence pattern that makes sense only in the context of the PROSITE database and the software that can be used to search it. In other terms, there is a proper mathematical definition of patterns used in PROSITE and in the search software. If we keep this in mind we will not be disturbed by the fact that some workers call the PROSITE patterns as "motifs" - they refer to the same thing. So, in conclusion we can say that the "Patterns" and "Motifs" are the interchangeable terms used to define certain region of proteins which has a characteristic sequence (amino acid) and usually associated with a particular function. Hope this helps!! Pooja ----- Original Message ----- From: "nikhil gadewal" To: Sent: Monday, December 03, 2001 2:34 PM Subject: [BiO BB] Pattern & Motif > hi members, > > WHAT IS A DIFFERENCE BETWEEEN 'PATTERN' AND > 'MOTIFS'? > > thank you in advance. > NIKHIL > > ===== > NIKHIL. S. GADEWAL * HOME ADDRESS > * # 22, subhshree apts, > Bioinformatics center, * near vijan hospital, > Cancer Research Institute, * college road, > Parel, Mumbai-12. * nashik-422005 > cri3 at soochak.ncst.ernet.in * Phone no. 0253-580490 > Phone no. 4123803 etx. 242 * > > __________________________________________________ > Do You Yahoo!? > Buy the perfect holiday gifts at Yahoo! Shopping. > http://shopping.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From kiran_ayyagari at yahoo.com Tue Dec 4 05:33:46 2001 From: kiran_ayyagari at yahoo.com (Ayyagari Kiran) Date: Tue, 4 Dec 2001 02:33:46 -0800 (PST) Subject: [BiO BB] pattern & Motif (A.S.Kiran) In-Reply-To: <200112031700.MAA23626@www.bioinformatics.org> Message-ID: <20011204103346.41961.qmail@web11904.mail.yahoo.com> Hi Nikhil, Hope this summary would clear your doubt. A pattern represents any type of sub-sequence that fits the regular expression defined( For instance, C-X(2,4)-[DE] is a sequence pattern matching any sequence containing a sub-string starting with C, followed by between two and four arbitrary symbols, followed by either a D or an E. This pattern is an example of a deterministic pattern.likewise there are probabilistic patterns(Profile HMMs) Sequence and structure patterns can be used for characterising protein families which are defined to be sets of functionally or structurally related proteins Motifs are short patterns that repeat quite often within a given set of protein sequences,(with some variations) and usually serve some important functional role from a biochemical viewpoint representing information conserved during the process of evolution.. A motif may typically contain information regarding the tertiary structures of the proteins and other biological information, whereas, a pattern occurs more of a statistical presence than a biological one. On a general basis a pattern can be defined as a motif, if it is conserved strongly within a given set of sequences. It is also important to note that all motifs are patterns but, not all patterns are motifs. A.S.Kiran Bioinformatician __________________________________________________ Do You Yahoo!? Buy the perfect holiday gifts at Yahoo! Shopping. http://shopping.yahoo.com From crasmen at magic.fr Tue Dec 4 06:04:10 2001 From: crasmen at magic.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Tue, 4 Dec 2001 12:04:10 +0100 Subject: [BiO BB] Pattern & Motif In-Reply-To: References: <20011203090448.83232.qmail@web9505.mail.yahoo.com> Message-ID: At 9:57 +0530 4/12/01, Pooja Jain wrote: >So, in conclusion we can say that the "Patterns" and "Motifs" are the >interchangeable terms used to define certain region of proteins which has a >characteristic sequence (amino acid) and usually associated with a >particular function. BTW, the French translation of "pattern" is "motif". Corentin From jeff at bioinformatics.org Tue Dec 4 12:49:56 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 04 Dec 2001 12:49:56 -0500 Subject: [BiO BB] Early Registration for Annual Meeting Ends Friday Message-ID: <3C0D0CC4.6A6E63EA@bioinformatics.org> Greetings. I thought I'd post this reminder, in case you didn't see it on BiO News. When registering for the O'Reilly Bioinformatics Technology Conference and the Annual Meeting of Bioinformatics.Org, use the registration code BIC02ORG for 30% off of the industry (no discounts) price. But after Friday, December 7, all of the prices will go up. Conference homepage: http://conferences.oreilly.com/biocon/ Registration page: http://conferences.oreillynet.com/cs/bio2002/pub/w/17/register.html 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 youhg at email.uc.edu Tue Dec 4 17:01:19 2001 From: youhg at email.uc.edu (H. You) Date: Tue, 04 Dec 2001 17:01:19 -0500 Subject: [BiO BB] Short peptide alignment search Message-ID: <5.1.0.14.2.20011204164741.00a77388@email.uc.edu> Hi, I have a short peptide (~ 5 - 8 amino acids). I used BLAST (actually the tblastn) to search the alignment in the "nr" database. The expect value was set at 10000 and word size is 2. The matrix used is PAM30. I usually get either no matches or more than a hundred matches. It is real time consuming to go through all the matches. In textbooks or tutorials, protein alignment with long sequence is usually discussed. My question is what is the strategy to conduct an alignment search with a protein of short sequence. I hope that I can get some help from veterans in this field. Thanks. Hong From benjaminelsy at hotmail.com Wed Dec 5 00:11:46 2001 From: benjaminelsy at hotmail.com (Elsy Benjamin) Date: Wed, 5 Dec 2001 10:41:46 +0530 Subject: [BiO BB] Fw: Software for Proteomics Message-ID: ----- Original Message ----- From: Elsy Benjamin To: bio_bulletin_board at bioinformatics.org Sent: Saturday, December 01, 2001 2:11 PM Subject: Software for Proteomics Hello Board Members, I would like to know the different areas of proteomics where the techniques and result predictions can be automated using current advances in bioinformatics. Any idea about the working of deemed software or a link for the popular existing software in the field of proteomics will be highly appreciated. Thanks in advance.. Benjamin E. -------------- next part -------------- An HTML attachment was scrubbed... URL: From danag at bioinformatics.weizmann.ac.il Wed Dec 5 04:11:47 2001 From: danag at bioinformatics.weizmann.ac.il (Dana Gerber) Date: Wed, 05 Dec 2001 11:11:47 +0200 Subject: [BiO BB] Short peptide alignment search References: <5.1.0.14.2.20011204164741.00a77388@email.uc.edu> Message-ID: <3C0DE4CD.BCDA3016@bioinfo.weizmann.ac.il> Hong hi, Try to restrict your search to SWISS PROT database. Also i suggest you to search in Blocks database bioinformatics.weizmann.ac.il/blocks "H. You" wrote: > Hi, > > I have a short peptide (~ 5 - 8 amino acids). I used BLAST (actually the > tblastn) to search the alignment in the "nr" database. The expect value > was set at 10000 and word size is 2. The matrix used is PAM30. I usually > get either no matches or more than a hundred matches. It is real time > consuming to go through all the matches. In textbooks or tutorials, > protein alignment with long sequence is usually discussed. My question is > what is the strategy to conduct an alignment search with a protein > of short sequence. I hope that I can get some help from veterans in this > field. > > Thanks. > > Hong > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From btiwari at molbiol.ox.ac.uk Wed Dec 5 05:17:24 2001 From: btiwari at molbiol.ox.ac.uk (Bela Tiwari) Date: Wed, 5 Dec 2001 10:17:24 +0000 (GMT) Subject: [BiO BB] Short peptide alignment search In-Reply-To: <5.1.0.14.2.20011204164741.00a77388@email.uc.edu> Message-ID: >I have a short peptide (~ 5 - 8 amino acids). I used BLAST (actually the >tblastn) to search the alignment in the "nr" database. The expect value >was set at 10000 and word size is 2. The matrix used is PAM30. I usually >get either no matches or more than a hundred matches. It is real time >consuming to go through all the matches. In textbooks or tutorials, >protein alignment with long sequence is usually discussed. My question is >what is the strategy to conduct an alignment search with a protein >of short sequence. Hello, We have a web page that has a couple of hints on searching with short sequences, although its not complete! (I will be taking notes on any advice sent in answer to your question...) The page is at: http://www.molbiol.ox.ac.uk/databases/dbsearching/shortsearch.htm On that page, there is also a link to info at the NCBI about using blast to search with short sequences: http://www.ncbi.nlm.nih.gov/BLAST/blast_FAQs.html#Short Good luck. Bela .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- Dr. Bela Tiwari Bioinformatics Officer OU Bioinformatics Centre South Parks Road, 01865 (2)75507 Oxford OX1 3RE http://www.molbiol.ox.ac.uk .-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- From kavithabekkari at yahoo.com Wed Dec 5 06:02:20 2001 From: kavithabekkari at yahoo.com (Kavitha Reddy) Date: Wed, 5 Dec 2001 03:02:20 -0800 (PST) Subject: [BiO BB] Request Message-ID: <20011205110220.38504.qmail@web14510.mail.yahoo.com> Dear sir, I would like to participate in all the addressed questions to the subscribers.Please i request to send me the details of subscribing. kavitha bekkari __________________________________________________ Do You Yahoo!? Buy the perfect holiday gifts at Yahoo! Shopping. http://shopping.yahoo.com From thriotus at yahoo.com Wed Dec 5 06:51:23 2001 From: thriotus at yahoo.com (nabula easter) Date: Wed, 5 Dec 2001 03:51:23 -0800 (PST) Subject: [BiO BB] Short peptide alignment search In-Reply-To: <5.1.0.14.2.20011204164741.00a77388@email.uc.edu> Message-ID: <20011205115123.39636.qmail@web21003.mail.yahoo.com> Use dbEST and then trace best EST hits to protein coding regions of proteins either using unigene or by manual inspection. hope this will work! SP __________________________________________________ Do You Yahoo!? Buy the perfect holiday gifts at Yahoo! Shopping. http://shopping.yahoo.com From jeff at bioinformatics.org Wed Dec 5 11:45:16 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 05 Dec 2001 11:45:16 -0500 Subject: [BiO BB] Fw: Software for Proteomics References: Message-ID: <3C0E4F1C.22B4F9B8@bioinformatics.org> Benjamin, Does the automation software have to be specifically for proteomics? There are several systems being developed for the automation of data processing in bioinformatics: OpenBSA ISYS Piper http://bioinformatics.org/piper/ Systems Biology Workbench http://bioinformatics.org/sbw/ You can find the first 2 by searching Google. There are some systems for visualization (really data processing) which may suit your needs as well: Khoros http://www.khoros.com/products/products.html OpenDX http://www.research.ibm.com/dx/ http://www.opendx.org/ AVS http://www.avs.com/software/soft_t/avsxps.html Cheers. Jeff > I would like to know the different areas of proteomics where > the techniques and result predictions can be automated using > current advances in bioinformatics. Any idea about the > working of deemed software or a link for the popular existing > software in the field of proteomics will be highly appreciated. -- 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 Joel.Dudley at DevelopOnline.com Wed Dec 5 11:54:05 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 5 Dec 2001 09:54:05 -0700 Subject: [BiO BB] custom blast server Message-ID: Hello All, I am creating a biological database for an application that I am working on. The database contains cDNA and AA sequences among other things. My application needs to perform a BLAST search on sequences in my database only. I would like to create my own custom BLAST server that performs BLAST searches on my PostgreSQL database. I planned on writing my own threading BLAST server in Java but I was wondering if anyone know of some tools, Classes, or libraries that would perform a BLAST on sequences in a PostgreSQL DB. Any language is welcome. If there is something close that is open-source I could modify the source to make it work I guess. Thanks. - Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From idoerg at cc.huji.ac.il Wed Dec 5 12:20:57 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Wed, 5 Dec 2001 19:20:57 +0200 (GMT+0200) Subject: [BiO BB] custom blast server In-Reply-To: Message-ID: Hi Joel, I do not know the answer to your specific question. However, I am a bit curious as to why you would like to run BLAST vs. an SQL database. You can easily convert any data you may have to a flat format fasta file, and then use NCBI tools formatdb to create the format which BLAST recognizes. A table which translates from your FFFF to the SQL key fields can correlate between the two, in case you have more than just sequence information in your SQL database. This is not a criticism of your choice of methods, I was just wondering what is the application demand that makes you want to take the trouble. I have toyed with the idea of doing something similar myself, but I always caved in and resorted to the method above. But hey, if you write up such a thing, that would be really cool! Yours, Iddo On Wed, 5 Dec 2001, Joel Dudley wrote: : Hello All, : I am creating a biological database for an application that I am working : on. The database contains cDNA and AA sequences among other things. My : application needs to perform a BLAST search on sequences in my database : only. I would like to create my own custom BLAST server that performs BLAST : searches on my PostgreSQL database. I planned on writing my own threading : BLAST server in Java but I was wondering if anyone know of some tools, : Classes, or libraries that would perform a BLAST onsequences in a : PostgreSQL DB. Any language is welcome. If there is something close that is : open-source I could modify the source to make it work I guess. Thanks. : : - Joel : -- Iddo Friedberg | Tel: +972-2-6757374 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 Joel.Dudley at DevelopOnline.com Wed Dec 5 12:37:21 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 5 Dec 2001 10:37:21 -0700 Subject: [BiO BB] custom blast server Message-ID: Well, Here is the deal. I am assuming that you suggest that I dump all my sequences, format them, and use the BLAST executable provided by NCBI, right? I thought about that too. However, The application is going to make a BLAST request over the internet and the BLAST server needs to thread (so we can handle many concurrent connections) and return the BLAST results to the application when the search is complete. I could make a wrapper type server in Perl, but I think that is a bad idea. I would like to have something cleaner. Ideally I would like to have a Threading server that handles BLAST requests via XML RPC or something like that and integrates better with my application. Am I making any sense here? - Joel -----Original Message----- From: Iddo Friedberg [mailto:idoerg at cc.huji.ac.il] Sent: Wednesday, December 05, 2001 10:21 AM To: 'bio_bulletin_board at bioinformatics.org' Cc: Joel Dudley Subject: Re: [BiO BB] custom blast server Hi Joel, I do not know the answer to your specific question. However, I am a bit curious as to why you would like to run BLAST vs. an SQL database. You can easily convert any data you may have to a flat format fasta file, and then use NCBI tools formatdb to create the format which BLAST recognizes. A table which translates from your FFFF to the SQL key fields can correlate between the two, in case you have more than just sequence information in your SQL database. This is not a criticism of your choice of methods, I was just wondering what is the application demand that makes you want to take the trouble. I have toyed with the idea of doing something similar myself, but I always caved in and resorted to the method above. But hey, if you write up such a thing, that would be really cool! Yours, Iddo On Wed, 5 Dec 2001, Joel Dudley wrote: : Hello All, : I am creating a biological database for an application that I am working : on. The database contains cDNA and AA sequences among other things. My : application needs to perform a BLAST search on sequences in my database : only. I would like to create my own custom BLAST server that performs BLAST : searches on my PostgreSQL database. I planned on writing my own threading : BLAST server in Java but I was wondering if anyone know of some tools, : Classes, or libraries that would perform a BLAST onsequences in a : PostgreSQL DB. Any language is welcome. If there is something close that is : open-source I could modify the source to make it work I guess. Thanks. : : - Joel : -- Iddo Friedberg | Tel: +972-2-6757374 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/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchang at smi.stanford.edu Wed Dec 5 13:10:10 2001 From: jchang at smi.stanford.edu (Jeffrey Chang) Date: Wed, 5 Dec 2001 10:10:10 -0800 Subject: [BiO BB] custom blast server In-Reply-To: References: Message-ID: <20011205101010.A1971@krusty.stanford.edu> On Wed, Dec 05, 2001 at 10:37:21AM -0700, Joel Dudley wrote: > Well, > Here is the deal. I am assuming that you suggest that I dump all my > sequences, format them, and use the BLAST executable provided by NCBI, > right? I thought about that too. However, The application is going to make a > BLAST request over the internet and the BLAST server needs to thread (so we > can handle many concurrent connections) and return the BLAST results to the > application when the search is complete. I could make a wrapper type server > in Perl, but I think that is a bad idea. I would like to have something > cleaner. Ideally I would like to have a Threading server that handles BLAST > requests via XML RPC or something like that and integrates better with my > application. Am I making any sense here? > > - Joel Honestly, no. From the best I can figure out, you have an application and a BLAST server that are running on separate machines across the internet. You want the BLAST server to be able to handle multiple requests concurrently, and you have a relational database of sequences that you want to BLAST against. The standard way to do this is to run BLAST over HTTP, and fork an instance of the executable for every run. You'll get less performance than a persistant multi-threaded one, but I don't think that's how NCBI BLAST is written. And anyway, the bottleneck is going to be the database searches, not the process forking. I think Iddo asked a good question, and I'm also wondering about the requirement to be run off the SQL database. I'm not sure what that has to do with threading and XML RPC. Jeff From biologynext at yahoo.com Thu Dec 6 01:18:47 2001 From: biologynext at yahoo.com (Bio Next) Date: Wed, 5 Dec 2001 22:18:47 -0800 (PST) Subject: [BiO BB] Request In-Reply-To: <20011205110220.38504.qmail@web14510.mail.yahoo.com> Message-ID: <20011206061847.33144.qmail@web21107.mail.yahoo.com> Looks like you are already subscribed. May be you would like to take a look at: http://www.gweep.ca/~edmonds/usenet/ml-etiquette.html Have a nice day! -Tom. --- Kavitha Reddy wrote: > Dear sir, > > I would like to participate in all the addressed > questions to the subscribers.Please i request to send > me the details of subscribing. > > kavitha bekkari > __________________________________________________ Do You Yahoo!? Send your FREE holiday greetings online! http://greetings.yahoo.com From Joel.Dudley at DevelopOnline.com Thu Dec 6 11:21:42 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Thu, 6 Dec 2001 09:21:42 -0700 Subject: [BiO BB] custom blast server Message-ID: Well I have no problems using the NCBI BLAST, but does it run as a HTTP service out of the box? or do I need to wrap it on some server code? my main problem is that I am not interested in returning high scoring sequences, rather I need to get another value associateed to the high scoring sequences and return a file. That is where arrangement is custom. - Joel ----------------------------------- Honestly, no. From the best I can figure out, you have an application and a BLAST server that are running on separate machines across the internet. You want the BLAST server to be able to handle multiple requests concurrently, and you have a relational database of sequences that you want to BLAST against. The standard way to do this is to run BLAST over HTTP, and fork an instance of the executable for every run. You'll get less performance than a persistant multi-threaded one, but I don't think that's how NCBI BLAST is written. And anyway, the bottleneck is going to be the database searches, not the process forking. I think Iddo asked a good question, and I'm also wondering about the requirement to be run off the SQL database. I'm not sure what that has to do with threading and XML RPC. Jeff _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From tvavouri at hotmail.com Fri Dec 7 10:33:57 2001 From: tvavouri at hotmail.com (Tanya Vavouri) Date: Fri, 07 Dec 2001 15:33:57 +0000 Subject: [BiO BB] help ! Message-ID: Help ! I have a very simple problem that I'm trying to solve using Perl...but I've spent quite a bit of time thinking about it and I have only come up with a very slow solution (too slow!). I'm sure that there must be a fast and easy solution to this problem so if you have any ideas please let me know. The problem is : I have sequences in groups that may overlap and I am trying to get all the groups that overlap together. So, lets say that every sequence is represented by a letter and I have groups such as: Group 1 : A B C Group 2 : D E F K Group 3 : G H A Group 4 : L M H R S So, I want to write a program to give me only 2 "super" groups from the above, ie Supergroup I : A B C G H L M R S Supergroup II : D E F K Any ideas would be very VERY welcome ! Thanks in advance, Tanya _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From ames at alpha.ces.cwru.edu Fri Dec 7 12:15:50 2001 From: ames at alpha.ces.cwru.edu (jeffames) Date: Fri, 7 Dec 2001 12:15:50 -0500 (EST) Subject: [BiO BB] help ! In-Reply-To: Message-ID: On Fri, 7 Dec 2001, Tanya Vavouri wrote: > The problem is : I have sequences in groups that may overlap and I am trying > to get all the groups that overlap together. I'm not sure this would be fast, but.... Create some ordering for the elements of the group (e.g., A = 1, B = 2, ...). Then convert each group into a binary string representing the membership of the group. So your first group, A B C, becomes 1110000... (to the end of your alphabet). Then the main algorithm would be something like this: (pseudocode) loop: for each group i for each group j > i if (binarystring[i] & binarysring[j]) { join(i, j) goto loop } and the join function would just be something like binarystring[newgroup] = binarystring[i] | binarystring[j], then delete the ith and jth groups. This assumes you have a finite alphabet, and that the number of members per group won't be extremely smaller than the alphabet size. It might be faster to record that i and j should be joined, but keep processing the loops instead of doing the joining right away and having to restart the loops. From rick at bioinformatics.org Fri Dec 7 13:15:19 2001 From: rick at bioinformatics.org (Rick Ree) Date: 07 Dec 2001 10:15:19 -0800 Subject: [BiO BB] help ! In-Reply-To: References: Message-ID: <1007748919.30166.0.camel@loco.ucdavis.edu> The following python code is an implementation of the algorithm you're looking for: def add_component(components, c): nc = len(components) i = 0 for comp in components: if intersects(comp, c): components[i] = combine(comp, c) if i == nc - 1: return components components[i:] = add_component(components[i+1:], comp) i += 1 if i == nc: components.append(c) return components Here, 'components' is a list of 'supergroups', i.e. lists of objects (whatever you're grouping), and 'c' is a list you want to add to it. This function calls 'intersects(a, b)' which should return true if list a and list b overlap, and 'combine(a, b)' which should return the union of list a and list b. E.g.: supergroups = [] # empty list for group in groups_to_combine: supergroups = add_component(supergroups, group) On Fri, 2001-12-07 at 07:33, Tanya Vavouri wrote: > Help ! > > I have a very simple problem that I'm trying to solve using Perl...but I've > spent quite a bit of time thinking about it and I have only come up with a > very slow solution (too slow!). I'm sure that there must be a fast and easy > solution to this problem so if you have any ideas please let me know. > > The problem is : I have sequences in groups that may overlap and I am trying > to get all the groups that overlap together. So, lets say that every > sequence is represented by a letter and I have groups such as: > > Group 1 : A B C > Group 2 : D E F K > Group 3 : G H A > Group 4 : L M H R S > > So, I want to write a program to give me only 2 "super" groups from the > above, ie > > Supergroup I : A B C G H L M R S > Supergroup II : D E F K > > Any ideas would be very VERY welcome ! > > Thanks in advance, > Tanya > > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From naka at nethere.com Fri Dec 7 23:31:49 2001 From: naka at nethere.com (M----->) Date: Fri, 07 Dec 2001 20:31:49 -0800 Subject: [BiO BB] Re:Auto-Separation of FASTA from rest of text References: <200112051700.MAA30400@www.bioinformatics.org> Message-ID: <3C1197B5.52C106CC@nethere.com> Today in a Bioinformatics session we looked up a protein cross-species, then we cut and pasted 12 inididual sequences into the tree builder. Aren't there servers where one can go in one (or two) steps from 1) Specifying protein 2) Viewing tree of species with indicators as to age and degree of relation (i.e. more or less related to initial sequence..? Does FASTA have an indicator when the end of the sequence is reached, so that a parser can ignore remaining non-amino-acid text ? Mike Tenner San Diego From whatifwhatnext at on.aibn.com Sun Dec 9 06:00:03 2001 From: whatifwhatnext at on.aibn.com (Howard Oliver) Date: Sun, 9 Dec 2001 06:00:03 -0500 Subject: [BiO BB] Innovative funding methods In-Reply-To: Message-ID: Hi: Wanted to see if anyone has come across particularly innovative methodologies for funding Bioinformatics start-ups. We are working with a particularly good technology that has "legs". Wanted to see if there are any new ideas out there beyond the normal VC (ok I'll say it) Bull Sh_t. Howard From bmbpo at bmb.leeds.ac.uk Sun Dec 9 12:47:05 2001 From: bmbpo at bmb.leeds.ac.uk (Peter Oledzki) Date: Sun, 9 Dec 2001 17:47:05 -0000 Subject: [BiO BB] Bioinformatics SME's Message-ID: <200112091733.MAA03733@www.bioinformatics.org> I'm writing a review on Bioinformatics SME's (small-medium enterprises)and was wondering if anyone out there has material on such a subject ie examples of small bioinformatics companies, how easy it is to set up, competitiveness and sucess rates.... etc etc you get the idea. Any help would be much appreciated. Thank you Pete Oledzki From whatifwhatnext at on.aibn.com Sun Dec 9 10:00:28 2001 From: whatifwhatnext at on.aibn.com (Howard Oliver) Date: Sun, 9 Dec 2001 10:00:28 -0500 Subject: [BiO BB] Bioinformatics SME's In-Reply-To: <200112091733.MAA03733@www.bioinformatics.org> Message-ID: Hi Peter Im very interested in the subject as well would be happy to exchange ideas with you. Regards Howard Oliver Principal What If What Next (TM) Consulting holiver at whatifwhatnext.com Tel: 416-638-8582 Mobile: 416-432-2764 www.whatifwhatnext.com -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Peter Oledzki Sent: Sunday, December 09, 2001 12:47 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Bioinformatics SME's I'm writing a review on Bioinformatics SME's (small-medium enterprises)and was wondering if anyone out there has material on such a subject ie examples of small bioinformatics companies, how easy it is to set up, competitiveness and sucess rates.... etc etc you get the idea. Any help would be much appreciated. Thank you Pete Oledzki _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: Howard Oliver (E-mail).vcf Type: text/x-vcard Size: 530 bytes Desc: not available URL: From fanfuhao at yahoo.com.cn Sat Dec 8 00:02:41 2001 From: fanfuhao at yahoo.com.cn (FRANK Fan) Date: Sat, 8 Dec 2001 13:02:41 +0800 Subject: [BiO BB] (no subject) Message-ID: <007a01c1810b$e3c13d00$01739ad3@fuhaofan> -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Thu Dec 13 13:29:34 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 13 Dec 2001 13:29:34 -0500 Subject: [BiO BB] Bio-IT World Magazine Message-ID: <3C18F38E.50F13586@bioinformatics.org> Greetings. Last week, Debbie Walsh from BioIT World contacted us at Bioinformatics.Org and said that BiO members can get **FREE** charter ("first on board") subscriptions to their new print magazine, Bio-IT World: "strategic IT applications for life science professionals". A paid subscription would cost $199 in the US. This is for 12 issues, and there is no obligation to renew. BiO members, please use this URL to subscribe: http://www.omeda.com/cgi-win/biw.cgi?+WD1BRG NOTE: BIOINFORMATICS.ORG IS NON-PROFIT AS RECEIVES NO PAYMENT FOR ANYTHING POSTED ANYWHERE. WHAT WE POST IS CONSIDERED OF GENERAL INTEREST AND USE TO THE MEMBERSHIP. 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 balarji at rediffmail.com Fri Dec 21 09:25:27 2001 From: balarji at rediffmail.com (balaji r) Date: 21 Dec 2001 14:25:27 -0000 Subject: [BiO BB] Bioinformatics SME's Message-ID: <20011221142527.12978.qmail@mailweb24.rediffmail.com> Hi Peter Im interested in the SME's as well would try to give some suggestions. balaji > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > Behalf Of Peter > Oledzki > Sent: Sunday, December 09, 2001 12:47 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Bioinformatics SME's > > > I'm writing a review on Bioinformatics SME's > (small-medium > enterprises)and was wondering if anyone out there has > material on such a > subject ie examples of small bioinformatics companies, > how easy it is to > set up, competitiveness and sucess rates.... etc etc > you get the idea. > Any help would be much appreciated. > Thank you > Pete Oledzki > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board From whatifwhatnext at on.aibn.com Fri Dec 21 09:51:38 2001 From: whatifwhatnext at on.aibn.com (Howard Oliver) Date: Fri, 21 Dec 2001 09:51:38 -0500 Subject: [BiO BB] Bioinformatics SME's In-Reply-To: <20011221142527.12978.qmail@mailweb24.rediffmail.com> Message-ID: HI All: I had a thought. What if we collectively, using this board created a check list for BI SME's? I propose to start with something simple: (SWOT- Broad Analysis) Strengths Weaknesses Opportunities Threats (PEST - Drivers) Political Economic Societal Technological We can see how it goes from there. I'd be willing to post our results on my website and edit it if that is cool with everybody. Hey something to do while drinking holiday punch! Happy Holidays: Howard Oliver Principal What If What Next (TM) Consulting holiver at whatifwhatnext.com Tel: 416-638-8582 Mobile: 416-432-2764 www.whatifwhatnext.com -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of balaji r Sent: Friday, December 21, 2001 9:25 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Bioinformatics SME's Hi Peter Im interested in the SME's as well would try to give some suggestions. balaji > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org]On > Behalf Of Peter > Oledzki > Sent: Sunday, December 09, 2001 12:47 PM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Bioinformatics SME's > > > I'm writing a review on Bioinformatics SME's > (small-medium > enterprises)and was wondering if anyone out there has > material on such a > subject ie examples of small bioinformatics companies, > how easy it is to > set up, competitiveness and sucess rates.... etc etc > you get the idea. > Any help would be much appreciated. > Thank you > Pete Oledzki > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_- > board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: Howard Oliver (E-mail).vcf Type: text/x-vcard Size: 530 bytes Desc: not available URL: From jfreeman at variagenics.com Fri Dec 21 15:15:11 2001 From: jfreeman at variagenics.com (jfreeman) Date: Fri, 21 Dec 2001 15:15:11 -0500 Subject: [BiO BB] Bio-IT World Magazine References: <3C18F38E.50F13586@bioinformatics.org> Message-ID: <3C23984F.2AC4B37B@variagenics.com> Hi Jeff, Is there a link to the bioinformatics journal from your front page? Could there be? I was trying to get an article for a colleague and tried to find a link on your page, I think it would help. See you soon, Jim "J.W. Bizzaro" wrote: > > Greetings. > > Last week, Debbie Walsh from BioIT World contacted us at Bioinformatics.Org > and said that BiO members can get **FREE** charter ("first on board") > subscriptions to their new print magazine, Bio-IT World: "strategic IT > applications for life science professionals". A paid subscription would > cost $199 in the US. This is for 12 issues, and there is no obligation to > renew. > > BiO members, please use this URL to subscribe: > > http://www.omeda.com/cgi-win/biw.cgi?+WD1BRG > > NOTE: BIOINFORMATICS.ORG IS NON-PROFIT AS RECEIVES NO PAYMENT FOR ANYTHING > POSTED ANYWHERE. WHAT WE POST IS CONSIDERED OF GENERAL INTEREST AND USE TO > THE MEMBERSHIP. > > 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 > -- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jeff at bioinformatics.org Fri Dec 21 16:16:44 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 21 Dec 2001 16:16:44 -0500 Subject: [BiO BB] Bio-IT World Magazine References: <3C18F38E.50F13586@bioinformatics.org> <3C23984F.2AC4B37B@variagenics.com> Message-ID: <3C23A6BC.2FDE8F86@bioinformatics.org> jfreeman wrote: > > Is there a link to the bioinformatics journal from your front page? > Could there be? I was trying to get an article for a colleague and tried > to find a link on your page, I think it would help. Hi Jim. Are you talking about Bio-IT World or the journal Bioinformatics? Bio-IT Worls didn't send us a link to the magazine's homepage, and I couldn't find it elsewhere on the server. I don't think the magazine is in print yet, so maybe they simply don't have one. There's just the subscription page: http://www.omeda.com/cgi-win/biw.cgi?+WD1BRG You could try contacting Deborah Walsh . 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 Deborah_Walsh at idg.com Fri Dec 21 16:21:09 2001 From: Deborah_Walsh at idg.com (Deborah_Walsh at idg.com) Date: Fri, 21 Dec 2001 16:21:09 -0500 Subject: [BiO BB] Bio-IT World Magazine Message-ID: <88256B29.0075D7AF.00@gcsmtp2.idg.com> we don't have much of a website yet (just info about the upcoming Conference & Expo) but the address is http://www.bioitworld.com Debbie Walsh Circulation Director BioIT World P.O. Box 9010 500 Old Connecticut Path Framingham, MA 01701 (508)628-4809 dwalsh at idg.com |--------+-------------------------> | | "J.W. Bizzaro" | | | | | | | | | 12/21/2001 | | | 04:16 PM | | | Please respond | | | to | | | bio_bulletin_bo| | | ard | | | | |--------+-------------------------> >----------------------------------------------------------------------------| | | | To: bio_bulletin_board at bioinformatics.org | | cc: (bcc: Deborah Walsh/IDGCOMM/IDG) | | Subject: Re: [BiO BB] Bio-IT World Magazine | >----------------------------------------------------------------------------| jfreeman wrote: > > Is there a link to the bioinformatics journal from your front page? > Could there be? I was trying to get an article for a colleague and tried > to find a link on your page, I think it would help. Hi Jim. Are you talking about Bio-IT World or the journal Bioinformatics? Bio-IT Worls didn't send us a link to the magazine's homepage, and I couldn't find it elsewhere on the server. I don't think the magazine is in print yet, so maybe they simply don't have one. There's just the subscription page: http://www.omeda.com/cgi-win/biw.cgi?+WD1BRG You could try contacting Deborah Walsh . 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 -- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From gabeeichler at yahoo.com Sun Dec 23 23:34:43 2001 From: gabeeichler at yahoo.com (Gabriel Eichler) Date: Sun, 23 Dec 2001 23:34:43 -0500 Subject: [BiO BB] Graduate Programs In Bioinformatics Message-ID: <003701c18c34$502737a0$6401a8c0@brain> I recently completed a computer science degree from the University of Pennsylvania and I am currently applying to graduate schools in Bioinformatics. I was wondering if people could comment on the different programs in the United States and perhaps compare some of the major differences or highlights between them Thank you, Gabriel Eichler -------------- next part -------------- An HTML attachment was scrubbed... URL: From clarisca at cwpanama.net Tue Dec 25 14:05:09 2001 From: clarisca at cwpanama.net (Claris Castillo T) Date: Tue, 25 Dec 2001 14:05:09 -0500 Subject: [BiO BB] I want to set up a simple Biocluster for a project proposal. BioSoftware suggetion? Message-ID: Hi, we want to set up a biocluster for a demo but we are dummies and we would like to hear any suggestion to use a biosoftware very simple (this is our first step) to run on a Boewulf Cluster of a minimun number of computers. We would like to implement the most simple system as our first step in the project. Thanks in advance, Claris Claris Castillo T. Technology Development Engineer Centauri Technologies Corporation email: clarisca at cwpanama.net tel (507) 2138367 mobile: (507) 6175992 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pooja_jain25 at hotmail.com Wed Dec 26 06:17:53 2001 From: pooja_jain25 at hotmail.com (Pooja Jain) Date: Wed, 26 Dec 2001 16:47:53 +0530 Subject: [BiO BB] Pathway Bioinformatics References: Message-ID: Hello all, Does anybody in this group is working on Pathway bioinformatics? Could someone please suggest me the basic algorithms followed for protein interaction analysis? Thanks. Pooja -------------- next part -------------- An HTML attachment was scrubbed... URL: From roumieu at genops.com Wed Dec 26 13:06:14 2001 From: roumieu at genops.com (jordan) Date: Wed, 26 Dec 2001 10:06:14 -0800 Subject: [BiO BB] RE: biocluster software Message-ID: <003501c18e38$02aba280$7efab440@bc.hsia.telus.net> Dear Claris, You could try http://www.genops.com/download/default.htm to download Ngene, an integrated sequence analysis platform that takes advantage of a Linux cluster. Once the trial version is downloaded and installed you would default to a 64-node cluster in Korea. The website indicates current functions including distributed BLAST, parallel HMMer, databases and more. The software is modular and can be customized depending to your need. Jordan Roumieu Genops Bioinformatics Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From srab2001 at yahoo.com Thu Dec 27 12:46:40 2001 From: srab2001 at yahoo.com (srab2001 at yahoo.com) Date: Thu, 27 Dec 2001 12:46:40 -0500 Subject: [BiO BB] looking for people Message-ID: <00c901c18efe$71131d40$a42f1718@hwrd1.md.home.com> I am looking for people interested in researching a bioinformatics startup opportunity. Let me know if you have an interest in this up&coming field. thanks stuart srab2001 at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From franciswyeung at yahoo.com Thu Dec 27 15:44:57 2001 From: franciswyeung at yahoo.com (Francis Yeung) Date: Thu, 27 Dec 2001 12:44:57 -0800 (PST) Subject: [BiO BB] looking for people In-Reply-To: <00c901c18efe$71131d40$a42f1718@hwrd1.md.home.com> Message-ID: <20011227204457.99833.qmail@web14305.mail.yahoo.com> Stuart, What do you mean by "in researching..." ? Are you in VC business ? There are opportunities in hardware/software/ASIC as well as "methods/algorithms". Do you have any specific in mind. Regards. Francis --- srab2001 at yahoo.com wrote: > I am looking for people interested in researching a > bioinformatics startup opportunity. Let me know if > you have an interest in this up&coming field. > > thanks > > stuart > srab2001 at yahoo.com > __________________________________________________ Do You Yahoo!? Send your FREE holiday greetings online! http://greetings.yahoo.com From Sameer_Mohta at satyam.com Thu Dec 27 22:39:52 2001 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Fri, 28 Dec 2001 09:09:52 +0530 Subject: [BiO BB] looking for people Message-ID: <877B003B6F03D511A22E00B0D078E7A8542A5F@hst.satyam.com> what exactly you mean to say. i didn't get your point. can you please give more detail ? -----Original Message----- From: srab2001 at yahoo.com [mailto:srab2001 at yahoo.com] Sent: Thursday, December 27, 2001 11:17 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] looking for people I am looking for people interested in researching a bioinformatics startup opportunity. Let me know if you have an interest in this up&coming field. thanks stuart srab2001 at yahoo.com ************************************************************************** This email (including any attachments) is intended for the sole use of the intended recipient/s and may contain material that is CONFIDENTIAL AND PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or distribution or forwarding of any or all of the contents in this message is STRICTLY PROHIBITED. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. ************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From infogenix at libero.it Fri Dec 28 03:25:08 2001 From: infogenix at libero.it (Roberto Gozzetti) Date: Fri, 28 Dec 2001 09:25:08 +0100 Subject: [BiO BB] (no subject) Message-ID: <004701c18f79$2a23f960$1400a8c0@spidernet.it> ok -------------- next part -------------- An HTML attachment was scrubbed... URL: From avinash_abhyankar at hotmail.com Sat Dec 29 13:04:59 2001 From: avinash_abhyankar at hotmail.com (Avinash Abhyankar) Date: Sat, 29 Dec 2001 18:04:59 +0000 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #160 - 4 msgs Message-ID: I am Dr. Avinash Abhyankar. Have completed MBBS and MD in Microbiology, also a short course in Bioinformatics at IIT, Bombay. I am interested in research in bioinformatics. Could you tell me more about what opportunities I have. Thanks. Dr. Avinash Abhyankar. >From: bio_bulletin_board-admin at bioinformatics.org >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: BiO_Bulletin_Board digest, Vol 1 #160 - 4 msgs >Date: Fri, 28 Dec 2001 12:00:04 -0500 > > >Send BiO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > >To subscribe or unsubscribe via the web, visit > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board >or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org >You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > >When replying, please edit your Subject line so it is more specific than >"Re: Contents of BiO_Bulletin_Board digest...") > > >Today's Topics: > > 1. looking for people (srab2001 at yahoo.com) > 2. Re: looking for people (Francis Yeung) > 3. RE: looking for people (Sameer_Mohta) > 4. (no subject) (Roberto Gozzetti) > >--__--__-- > >Message: 1 >From: srab2001 at yahoo.com >To: >Subject: [BiO BB] looking for people >Date: Thu, 27 Dec 2001 12:46:40 -0500 >boundary="----=_NextPart_000_00C6_01C18ED4.87BFF600" >Reply-To: bio_bulletin_board at bioinformatics.org > >This is a multi-part message in MIME format. > >------=_NextPart_000_00C6_01C18ED4.87BFF600 >Content-Type: text/plain; > charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > >I am looking for people interested in researching a bioinformatics = >startup opportunity. Let me know if you have an interest in this = >up&coming field. > >thanks > >stuart >srab2001 at yahoo.com > >------=_NextPart_000_00C6_01C18ED4.87BFF600 >Content-Type: text/html; > charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > > > >http-equiv=3DContent-Type> > > > > >
I am looking for people interested in = >researching a=20 >bioinformatics startup opportunity.  Let me know if you have an = >interest in=20 >this up&coming field.
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href=3D"mailto:srab2001 at yahoo.com">srab2001 at yahoo.com
ODY> > >------=_NextPart_000_00C6_01C18ED4.87BFF600-- > > >_________________________________________________________ >Do You Yahoo!? >Get your free @yahoo.com address at http://mail.yahoo.com > > >--__--__-- > >Message: 2 >Date: Thu, 27 Dec 2001 12:44:57 -0800 (PST) >From: Francis Yeung >Subject: Re: [BiO BB] looking for people >To: bio_bulletin_board at bioinformatics.org >Reply-To: bio_bulletin_board at bioinformatics.org > >Stuart, > >What do you mean by "in researching..." ? Are you in >VC business ? > >There are opportunities in hardware/software/ASIC as >well as "methods/algorithms". Do you have any specific >in mind. > >Regards. > >Francis > > >--- srab2001 at yahoo.com wrote: > > I am looking for people interested in researching a > > bioinformatics startup opportunity. Let me know if > > you have an interest in this up&coming field. > > > > thanks > > > > stuart > > srab2001 at yahoo.com > > > > >__________________________________________________ >Do You Yahoo!? >Send your FREE holiday greetings online! >http://greetings.yahoo.com > >--__--__-- > >Message: 3 >From: Sameer_Mohta >To: "'bio_bulletin_board at bioinformatics.org'" > >Subject: RE: [BiO BB] looking for people >Date: Fri, 28 Dec 2001 09:09:52 +0530 >boundary="------------InterScan_NT_MIME_Boundary" >Reply-To: bio_bulletin_board at bioinformatics.org > >This message is in MIME format. Since your mail reader does not understand >this format, some or all of this message may not be legible. > >--------------InterScan_NT_MIME_Boundary >Content-Type: multipart/alternative; > boundary="----_=_NextPart_001_01C18F51.4ED920A0" > >------_=_NextPart_001_01C18F51.4ED920A0 >Content-Type: text/plain; > charset="iso-8859-1" > >what exactly you mean to say. i didn't get your point. >can you please give more detail ? > >-----Original Message----- >From: srab2001 at yahoo.com [mailto:srab2001 at yahoo.com] >Sent: Thursday, December 27, 2001 11:17 PM >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] looking for people > > >I am looking for people interested in researching a bioinformatics startup >opportunity. Let me know if you have an interest in this up&coming field. > >thanks > >stuart >srab2001 at yahoo.com > >************************************************************************** >This email (including any attachments) is intended for the sole use of the >intended recipient/s and may contain material that is CONFIDENTIAL AND >PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or >distribution or forwarding of any or all of the contents in this message is >STRICTLY PROHIBITED. If you are not the intended recipient, please contact >the sender by email and delete all copies; your cooperation in this regard >is appreciated. >************************************************************************** > >------_=_NextPart_001_01C18F51.4ED920A0 >Content-Type: text/html; > charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > > > >charset=3Diso-8859-1"> > > > > > > >
class=3D406204203-20102001>what=20 >exactly you mean to say. i didn't get your point.
>
class=3D406204203-20102001>can=20 >you please give more detail ?
>
>
face=3DTahoma=20 > size=3D2>-----Original Message-----
From: = >srab2001 at yahoo.com=20 > [mailto:srab2001 at yahoo.com]
Sent: Thursday, December 27, = >2001 11:17=20 > PM
To: = >bio_bulletin_board at bioinformatics.org
Subject: [BiO=20 > BB] looking for people

>
I am looking for people interested = >in researching=20 > a bioinformatics startup opportunity.  Let me know if you have = >an=20 > interest in this up&coming field.
>
 
>
thanks
>
 
>
stuart
>
= >href=3D"mailto:srab2001 at yahoo.com">srab2001 at yahoo.com
BLOCKQUOTE> > >

FACE=3D"Arial">*********************************************************= >*****************

> >

This email (including any attachments) = >is intended for the sole use of the intended recipient/s and may = >contain material that is CONFIDENTIAL AND PRIVATE COMPANY INFORMATION. = >Any review or reliance by others or copying or distribution or = >forwarding of any or all of the contents in this message is STRICTLY = >PROHIBITED. If you are not the intended recipient, please contact the = >sender by email and delete all copies; your cooperation in this regard = >is appreciated.

> >

FACE=3D"Arial">*********************************************************= >*****************

> >------_=_NextPart_001_01C18F51.4ED920A0-- > >--------------InterScan_NT_MIME_Boundary-- > >--__--__-- > >Message: 4 >Reply-To: "Roberto Gozzetti" >From: "Roberto Gozzetti" >To: >Subject: [BiO BB] (no subject) >Date: Fri, 28 Dec 2001 09:25:08 +0100 >Organization: infogenix >boundary="----=_NextPart_000_0044_01C18F81.8AFD6520" >Reply-To: bio_bulletin_board at bioinformatics.org > >This is a multi-part message in MIME format. > >------=_NextPart_000_0044_01C18F81.8AFD6520 >Content-Type: text/plain; > charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > >ok > >------=_NextPart_000_0044_01C18F81.8AFD6520 >Content-Type: text/html; > charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > > > >charset=3Diso-8859-1"> > > > > >
ok
> >------=_NextPart_000_0044_01C18F81.8AFD6520-- > > > > >--__--__-- > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >--__--__---- > >End of BiO_Bulletin_Board Digest _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From bioinfo at biosystemsconsulting.com Sat Dec 29 16:40:31 2001 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Sat, 29 Dec 2001 16:40:31 -0500 Subject: [BiO BB] I want to set up a simple Biocluster for a project proposal. BioSoftware suggetion? In-Reply-To: Message-ID: <000201c190b1$73e78b50$01fea8c0@biosys> You might want to check out bioIT World in March. Mark -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Claris Castillo T Sent: Tuesday, December 25, 2001 2:05 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] I want to set up a simple Biocluster for a project proposal. BioSoftware suggetion? Hi, we want to set up a biocluster for a demo but we are dummies and we would like to hear any suggestion to use a biosoftware very simple (this is our first step) to run on a Boewulf Cluster of a minimun number of computers. We would like to implement the most simple system as our first step in the project. Thanks in advance, Claris Claris Castillo T. Technology Development Engineer Centauri Technologies Corporation email: clarisca at cwpanama.net tel (507) 2138367 mobile: (507) 6175992 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Greg at tekadence.net Sun Dec 30 12:15:21 2001 From: Greg at tekadence.net (Greg Deocampo) Date: Sun, 30 Dec 2001 12:15:21 -0500 Subject: [BiO BB] looking for people In-Reply-To: <20011227204457.99833.qmail@web14305.mail.yahoo.com> Message-ID: Hello Francis, I am currently applying a software technology I've developed for automated application assembly from distributed components and "database processing" -- a kind of ".NET for bioinformatics"-- to the development of personal curative vaccines. I would love to correspond about the opportunities you think exist in terms of hardware/software/ASIC as well as in methods and algorithms. My personal background is in applied mathematics, software engineering, molecular immunology and technology startups. I am not a VC but I know some (human, nice ones) and am a serial entrepreneur. Best regards, Greg /* /* Greg Deocampo <> CEO /* Tekadence Incorporated /* 1600 Main Street <> Second Floor /* Venice, CA 90291 /* 310 577 1396 /* /* "Biology is digital." - Matt Ridley, Genome /* -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Francis Yeung Sent: Thursday, December 27, 2001 3:45 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] looking for people Stuart, What do you mean by "in researching..." ? Are you in VC business ? There are opportunities in hardware/software/ASIC as well as "methods/algorithms". Do you have any specific in mind. Regards. Francis --- srab2001 at yahoo.com wrote: > I am looking for people interested in researching a > bioinformatics startup opportunity. Let me know if > you have an interest in this up&coming field. > > thanks > > stuart > srab2001 at yahoo.com > __________________________________________________ Do You Yahoo!? Send your FREE holiday greetings online! http://greetings.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Greg at tekadence.net Sun Dec 30 12:40:12 2001 From: Greg at tekadence.net (Greg Deocampo) Date: Sun, 30 Dec 2001 12:40:12 -0500 Subject: [BiO BB] Graduate Programs In Bioinformatics In-Reply-To: <003701c18c34$502737a0$6401a8c0@brain> Message-ID: Congratulations on your CS degree. This link may be helpful to you: http://www.hgmp.mrc.ac.uk/GenomeWeb/docs-bioinf-course-info.html It seems to me that there are three broad areas of study: 1) information technology for bioinformatics, 2) computer science for bioinformatics, 3) predictive biosimulations. 1) seems to be about how to use existing products ie Oracle 9 to manage bohunkin' (that's a technical term: HUGE) databases for sequencing etc projects 2) seems to be about what's the best algortihm or method for figgerin' where the protein needle is in this sequence haystack 3) to me is where it all comes together. i confess to physics envy: how do we use all this data to predict disease and successful therapy? I'm a fan of what these people are doing and how they are doing it: http://www.cse.ucsc.edu/research/compbio/ This guy, http://www.cse.ucsc.edu/~kent/, in addition to having godlike cognitive abilities and a saint-like philosophy regarding credit and sharing his work, would probably spare you an email to give you good advice based on what you have specifically done, what you think you want to do, and what the community as a whole needs done. Please let me know if you might be interested in project-based opporuntities during your academic interphase. Best regards! Greg Deocampo - CEO, Applied Biocomputing Incorporated aka Tekadence Incorporated. 323 252 3863 2175 Hercules Drive, Los Angeles, CA 90046 -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Gabriel Eichler Sent: Sunday, December 23, 2001 11:35 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Graduate Programs In Bioinformatics I recently completed a computer science degree from the University of Pennsylvania and I am currently applying to graduate schools in Bioinformatics. I was wondering if people could comment on the different programs in the United States and perhaps compare some of the major differences or highlights between them Thank you, Gabriel Eichler -------------- next part -------------- An HTML attachment was scrubbed... URL: