From mgruenb at gmx.net Fri Aug 1 07:04:55 2003 From: mgruenb at gmx.net (mgruenb at gmx.net) Date: Fri, 1 Aug 2003 13:04:55 +0200 (MEST) Subject: [BiO BB] bad signature from steletch@biomedicale.univ-paris5.fr Message-ID: <21944.1059735895@www50.gmx.net> Hello Dimitri, you could add the following two lines to your gpg.conf: keyserver wwwkeys.pgp.net keyserver-options auto-key-retrieve The first line specifies the key server and the second line says to check keys on the keyserver automatically. You could also type this on the command line. See gpg -h for info. Best regards, Michael. On Thu, 2003-07-31 at 22:52, Dmitri I GOULIAEV wrote: > Hi! > > ,---[ output ]--- > | [-- PGP output follows (current time: Thu Jul 31 16:24:08 2003) --] > | gpg: Signature made Thu Jul 31 15:50:08 2003 CDT using DSA key ID F44CAE88 > | gpg: BAD signature from "Teletch\xc3\xa9a St\xc3\xa9phane (perso) " > | [-- End of PGP output --] > `---[ ]--- > > I would like to ask others on this list: has anyone the same problem as I do (I mean -- "BAD signature")? Or I should look closer to my gpg configuration file? > > Thanks for any tips. > > > Best regards, -- COMPUTERBILD 15/03: Premium-e-mail-Dienste im Test -------------------------------------------------- 1. GMX TopMail - Platz 1 und Testsieger! 2. GMX ProMail - Platz 2 und Preis-Qualit?tssieger! 3. Arcor - 4. web.de - 5. T-Online - 6. freenet.de - 7. daybyday - 8. e-Post From umudiga at unity.ncsu.edu Fri Aug 1 12:47:48 2003 From: umudiga at unity.ncsu.edu (Usharani Mudiganti) Date: Fri, 01 Aug 2003 11:47:48 -500 Subject: [BiO BB] drosophila affymetrix data analysis Message-ID: <200308011547.h71Flnj5000708@uni05mr.unity.ncsu.edu> Hi, When I go to the locuslink number given in affymetrix "complete entries", I see three different sequences (protein) starting with AAF or NP_ or NM_. Dont' know which one to believe. And also, need suggestions about getting useful functional data from the protein sequences. Can anyone help? Any pointers are greatly appreciated. thank you "Have a nice day" Usharani Mudiganti Graduate Student, Molecular & Structural Biochemistry NCSU,Raleigh,NC,USA. From mgollery at unr.edu Fri Aug 1 18:59:49 2003 From: mgollery at unr.edu (Martin Gollery) Date: Fri, 1 Aug 2003 15:59:49 -0700 Subject: [BiO BB] GRAVY index program anyone? In-Reply-To: <3F298B68.4060200@burnham.org> References: <3F298B68.4060200@burnham.org> Message-ID: <1059778789.3f2af0e513ed1@webmail.unr.edu> Hi Iddo, I have a Perl script that might help you, although I am not familiar with the GRAVY terminology. It uses kyte/doolittle hydropathy numbers, and gives a number of useful values- would you like to have a look at it? Marty calculates Quoting Iddo Friedberg : > Hi, > > Does anybody have a program which calculates a sequence's Grand average > of hydropathicity (GRAVY)? > > TIA, > > ./I > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 New phone number! 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From dig at bioinformatics.org Sat Aug 2 05:23:43 2003 From: dig at bioinformatics.org (Dmitri I GOULIAEV) Date: Sat, 2 Aug 2003 04:23:43 -0500 Subject: [BiO BB] bad signature from steletch@biomedicale.univ-paris5.fr In-Reply-To: <21944.1059735895@www50.gmx.net>; from mgruenb@gmx.net on Fri, Aug 01, 2003 at 01:04:55PM +0200 References: <21944.1059735895@www50.gmx.net> Message-ID: <20030802042343.I21368@lifebook> Hi, Michael ! On Fri, Aug 01, 2003 at 01:04:55PM +0200, mgruenb at gmx.net wrote: > you could add the following two lines to your gpg.conf: > keyserver wwwkeys.pgp.net > keyserver-options auto-key-retrieve They are already there. What seems to be a problem is that I can easily verify the signature from other people (I should say, my MUA correctly verifies most of messages), but not from Stefane and few other people. So, I try to understand why it fails sometimes (famous Russian question: Whose fault?). > The first line specifies the key server and the second line says to > check keys on the keyserver automatically. You could also type this on > the command line. See gpg -h for info. Thanks for the information. "BAD signature" signifies that both content and signature information are available, but are not corresponding one to another. So, I guess that the verification failure is due to the fact that both the identity and the content contain non-ascii characters. I just wanted to know if my configuration (mutt-1.2.5.1i + gnupg-1.2.1) is somewhat erroneous. Apparently, it is the case. Regards, -- DIG (Dmitri I GOULIAEV) http://www.bioinformatics.org/~dig/ 1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 From mgruenb at gmx.net Sat Aug 2 07:14:36 2003 From: mgruenb at gmx.net (Michael Gruenberger) Date: 02 Aug 2003 11:14:36 +0000 Subject: [BiO BB] bad signature from steletch@biomedicale.univ-paris5.fr In-Reply-To: <20030802042343.I21368@lifebook> References: <21944.1059735895@www50.gmx.net> <20030802042343.I21368@lifebook> Message-ID: <1059822876.4408.4.camel@vogel> Sorry Dimitri, I misunderstood you there. Have you tried checking Stefane's signature on the command line (gpg --recv-keys --keyserver wwwkeys.pgp.net keyid). That might bring you a step closer to find out 'whose fault it is' :-) Btw, Stefane's signature verify's on my machine. Michael. On Sat, 2003-08-02 at 09:23, Dmitri I GOULIAEV wrote: > Hi, Michael ! > > On Fri, Aug 01, 2003 at 01:04:55PM +0200, mgruenb at gmx.net wrote: > > > you could add the following two lines to your gpg.conf: > > keyserver wwwkeys.pgp.net > > keyserver-options auto-key-retrieve > > They are already there. > > What seems to be a problem is that I can easily verify the signature from other people (I should say, my MUA correctly verifies most of messages), but not from Stefane and few other people. So, I try to understand why it fails sometimes (famous Russian question: Whose fault?). > > > The first line specifies the key server and the second line says to > > check keys on the keyserver automatically. You could also type this on > > the command line. See gpg -h for info. > > Thanks for the information. > > "BAD signature" signifies that both content and signature information are available, but are not corresponding one to another. So, I guess that the verification failure is due to the fact that both the identity and the content contain non-ascii characters. > > I just wanted to know if my configuration (mutt-1.2.5.1i + gnupg-1.2.1) is somewhat erroneous. > Apparently, it is the case. > > > Regards, -- Michael Gruenberger Computer Officer, University of Cambridge Developer, Pathbase, http://www.pathbase.net PGP-Public Key ID: 278E1DFF -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From lxyiwc at yahoo.com Sat Aug 2 12:33:38 2003 From: lxyiwc at yahoo.com (l x yi) Date: Sat, 2 Aug 2003 09:33:38 -0700 (PDT) Subject: [BiO BB] re: protein profile question Message-ID: <20030802163338.19620.qmail@web21207.mail.yahoo.com> Thanks to all who has reponded to my previous email. I do appreciate your help. Lily --------------------------------- Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.chaudhuri at bham.ac.uk Sat Aug 2 15:18:21 2003 From: r.chaudhuri at bham.ac.uk (Chaudhuri, Roy) Date: Sat, 2 Aug 2003 20:18:21 +0100 Subject: [BiO BB] GRAVY index program anyone? Message-ID: <2967754783C6E34C94243EAC0D161368C03BD4@med-ex1.bham.ac.uk> > Does anybody have a program which calculates a sequence's Grand average > of hydropathicity (GRAVY)? Try CodonW (available from http://www.molbiol.ox.ac.uk/cu/). It will calculate gravy scores, as well as aromaticity and all manner of codon usage indices. Roy. ------------------------------------------ Dr. Roy Chaudhuri University of Birmingham, UK Developer of coliBASE- an online database for E.coli comparative genomics http://colibase.bham.ac.uk From ammar at 1ummah.org Sun Aug 3 00:13:25 2003 From: ammar at 1ummah.org (A. Abbas Naqvi) Date: Sat, 2 Aug 2003 23:13:25 -0500 (CDT) Subject: [BiO BB] Job market Message-ID: <2611.24.47.128.225.1059884005.squirrel@www.1ummah.org> Hi, I am a CS major right now but im really thinking of changing t Bioinformatics. How is it work-wise? Hard? And job wise.. whats salary, where are jobs available, etc. thanks Ammar From hustlf at cs.cmu.edu Sun Aug 3 17:27:06 2003 From: hustlf at cs.cmu.edu (Li Fan) Date: Sun, 03 Aug 2003 17:27:06 -0400 Subject: [BiO BB] gene regulatory network reconstruction and pathway finding from the micro-array data References: <2611.24.47.128.225.1059884005.squirrel@www.1ummah.org> Message-ID: <3F2D7E2A.ED54BB86@cs.cmu.edu> Hi, I am a graduate student in CS dept. I am dointg some work in learning gene regulatory network from the micro-array data. On major problem I am facing is that it is very hard to evaluate the results. For example, I have runned experiments on 6211 yeast genes and my experimental results suggest that gene YBR231C is "directly " connected with YAR014C YBR261C YBR237W YBR215W YBL111C YER138C YBR169C YAR073W YBL064C YBR022W YCR093W YBR025C YDR180W YCR040W YGL130W YBR213W YBR160W (sorted according to descending probability score) However, it is hard to judge to what extent the program has succeeded. I know Nir Friedman has done a fundamental experiment http://www.cs.huji.ac.il/labs/compbio/expression/. But it is still difficult to give a direct comparisan because Friedman's experiment is only on the 800 cell cycle genes, not on the all 6000 genes. Further more, only few edges are listed with comments from biologists in that paper. So could somebody give me some suggestions about the benchmark which can be used to evaluate the success of the bayes network structure learning algorithm(which is used to learn the genetic structure)? Thanks a lot Fan Li From dmb at mrc-dunn.cam.ac.uk Mon Aug 4 06:59:33 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 04 Aug 2003 11:59:33 +0100 Subject: [BiO BB] Peer-to-peer Computing is Good Business (GRIDtoday) Message-ID: <3F2E3C95.1060608@mrc-dunn.cam.ac.uk> I thought people may be interested in this article, for subscription to 'GRIDtoday' see the last lines of this email. Dan. -------- Original Message -------- Subject: 740062 Intel 08.04.03 Date: Mon, 4 Aug 2003 03:26:11 -0700 (PDT) From: Grid Today To: dmb at mrc-dunn.cam.ac.uk Intel 08.04.03 GRIDtoday ====================================================================== Peer-to-peer Computing is Good Business Leave it to a teenager to change the world of computing. The hobby project that became Napster sparked a revolution in computing that has made "Peer-to- Peer" the buzzword of the new Millennium. As it turns out, the buzz goes well beyond kids sharing music. Now businesses are looking for opportunities to take advantage of this latest industry trend. Peer-to-peer applications have wide-ranging business applications beyond the MP3-sharing utility that made it a household name. In fact, peer-to-peer is at the center of the next computing revolution and will fundamentally change the face of the Internet. According to Cheryl Currid, president of Currid & Company, an emerging technology research firm, every IT manager should explore peer-to-peer computing. At last fall's Intel Developer Forum, Currid proclaimed every organization has a need for the benefits of peer-to-peer technology. In the enterprise, peer-to-peer computing offers companies a cost-efficient way of sharing computing resources, improving network performance, and increasing overall productivity. Its uses are varied, including everything from collaboration and file sharing, to distributed computing and edge services. Unlocking the power of peer-to-peer computing can help grow your company's bottom line by reducing infrastructure costs and improving employee productivity. What is peer-to-peer? Peer-to-peer computing isn't exactly new. As many as 30 years ago, companies were working on architectures that would now be labeled peer-to-peer. But today, several factors have lit a fire under the peer-to-peer movement: inexpensive computing power, bandwidth, and storage. Put simply, peer-to-peer computing is the sharing of computer resources and services by direct exchange between systems. These resources and services include the exchange of information, processing cycles, cache storage, and disk storage for files. Peer-to-peer computing takes advantage of existing desktop computing power and networking connectivity, allowing economical clients to leverage their collective power to benefit the entire enterprise. In a peer-to-peer architecture, computers that have traditionally been used solely as clients communicate directly among themselves and can act as both clients and servers, assuming whatever role is most efficient for the network. This reduces the load on servers and allows them to perform specialized services (such as mail-list generation, billing, etc.) more effectively. At the same time, peer-to-peer computing can reduce the need for IT organizations to grow parts of its infrastructure in order to support certain services, such as backup storage. Ultimately, peer-to-peer technology is yet another tool for bringing innovative solutions to complex network dilemmas. "Peer-to-peer is really the opportunity to use the Internet for its real, underlying architecture--an ad hoc, resilient, worldwide network of resources, all being able to directly communicate and interact with each other," says Pat Gelsinger, Vice President and Chief Technology Officer, Intel(TM) Architecture Group. "To a great degree, we're restoring the Internet to what it was built for." Peer-to-Peer at Work In the enterprise, peer-to-peer is about more than just the universal file-sharing model popularized by Napster. Business applications for peer-to-peer computing fall into a handful of scenarios. Collaboration. Peer-to-peer computing empowers individuals and teams to create and administer real-time and off-line collaboration areas in a variety of ways, whether administered, unadministered, across the Internet, or behind the firewall. Peer-to-peer collaboration tools also mean that teams have access to the freshest data. Collaboration increases productivity by decreasing the time for multiple reviews by project participants and allows teams in different geographic areas to work together. As with file sharing, it can decrease network traffic by eliminating e-mail and decreases server storage needs by storing the project locally. Edge services. It's exactly what you think: Akamai for the enterprise. Peer-to-peer computing can help businesses deliver services and capabilities more efficiently across diverse geographic boundaries. In essence, edge services move data closer to the point at which it is actually consumed acting as a network caching mechanism. For example, a company with sites in multiple continents needs to provide the same standard training across multiple continents using the Web. Instead of streaming the database for the training session on one central server located at the main site, the company can store the video on local clients, which act essentially as local database servers. This speeds up the session because the streaming happens over the local LAN instead of the WAN. It also utilizes existing storage space, thereby saving money by eliminating the need for local storage on servers. Distributed computing and resources. Peer-to-peer computing can help businesses with large-scale computer processing needs. Using a network of computers, peer-to-peer technology can use idle CPU MIPS and disk space, allowing businesses to distribute large computational jobs across multiple computers. In addition, results can be shared directly between participating peers. The combined power of previously untapped computational resources can easily surpass the normal available power of an enterprise system without distributed computing. The results are faster completion times and lower cost because the technology takes advantage of power available on client systems. Intelligent agents. Peer-to-peer computing also allows computing networks to dynamically work together using intelligent agents. Agents reside on peer computers and communicate various kinds of information back and forth. Agents may also initiate tasks on behalf of other peer systems. For instance, Intelligent agents can be used to prioritize tasks on a network, change traffic flow, search for files locally or determine anomalous behavior and stop it before it effects the network, such as a virus. Intel and Peer-to-Peer Intel believes peer-to-peer computing and all its potential applications represent a shift in how the PC infrastructure will be used. Peer-to-peer technology is in a position to revolutionize computing environments. Recognizing that the basic building block--clients PCs, network infrastructure, and the enabling servers--remain the same; Intel is working with the computer industry to create solutions that will unlock the potential of peer-to-peer computing. Processors such as the Intel&174; Pentium(TM) 4 processor mean more power for clients to handle still unimagined peer-to-peer tasks and shoulder more of the enterprise workload. Although peer-to-peer computing will revolutionize the way businesses use and interact with the network, some work has yet to be completed. Standards and manageability will be a key part of peer-to-peer acceptance. Intel is working with independent software vendors on peer-to-peer solutions, while at the same time contributing to the efforts of the Peer-to-Peer Working Group, an industry consortium devoted to the advancement of infrastructure standards for peer-to- peer computing. Providing Peer-to-Peer Solutions Peer-to-peer solutions are being offered today by many solutions providers, including Groove Networks, Entropia, Distributed Science, McAfee AsAP, and Consilient. Collaboration: Groove is Internet communications software that allows people to make direct connections for real-time interaction. It exploits peer-to-peer computing for collaboration, enabling instant messaging, live voice, file sharing, free-form drawing, and other ways of working together. Edge Services: At McAfee AsAP, they've introduced a new peer-to-peer technology called Rumor*, which permits users to share anti-virus and firewall configuration updates with one another. McAfee AsAP's VirusScan* ASaP and PC FireWall* ASaP agents work through proxy servers and firewalls where the Rumor technology broadcasts configuration updates throughout the network. Distributed Resource Computing: Entropia and Distributed Science are two companies that have assembled global computing grids with thousands of Internet PCs around the world. Today, these networks are being used to test web site Quality of Service levels, from the end-users perspective. Response times are tracked for sample transactions that are launched from heterogeneous PCs, ISPs, and geographical locations. Intelligent Agents: Consilient allows businesses to create intelligent agents that carry out business processes. The intelligent agents advance a business process by moving control and data directly between peer clients via personalized user interfaces. The technology can be used to automate business processes like procurement or other collaborative tasks. These are just a few examples of peer-to-peer computing at work. Businesses that take advantage of such technologies stand to benefit from more efficient use of human and IT resources. The world is still in the early stages of the peer-to-peer revolution. Over the coming months, Intel will deliver the latest updates on standards, articles describing new solutions, and case studies of companies successfully using peer-to-peer technology for a competitive advantage. Register for the Intel Business Computing newsletter to receive updates on this and other emerging technologies. We also encourage you to visit the sites of the companies referenced in this article for more information about peer-to-peer solutions. **************************************************************************** GRIDtoday has released all copyright restrictions for this item. Please feel free to distribute this article to your friends and colleagues. For a subscription, send e-mail to freegridtoday at gridtoday.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From tania at egenetics.com Mon Aug 4 16:18:44 2003 From: tania at egenetics.com (Tania Broveak Hide) Date: Mon, 4 Aug 2003 13:18:44 -0700 Subject: [BiO BB] Job market References: <2611.24.47.128.225.1059884005.squirrel@www.1ummah.org> Message-ID: <01fd01c35ac5$9ca015a0$7202a8c0@boing> Apologies in advance for being so blunt, but... "How hard is the work?" and "How much do I get paid?" are not usually questions that endear you to potential employers. Usually, CS grads that we employ are attracted by things like: - the challenging problem - the up-to-date technology that is employed - the thought of contributing to the greater good Regards, Tania Hide employer of bioinformatics programmers ----- Original Message ----- From: "A. Abbas Naqvi" To: Sent: Saturday, August 02, 2003 9:13 PM Subject: [BiO BB] Job market > Hi, > > I am a CS major right now but im really thinking of changing t > Bioinformatics. How is it work-wise? Hard? And job wise.. whats salary, > where are jobs available, etc. thanks > > Ammar > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From hz5 at njit.edu Mon Aug 4 10:15:06 2003 From: hz5 at njit.edu (hz5 at njit.edu) Date: Mon, 04 Aug 2003 10:15:06 -0400 (EDT) Subject: [BiO BB] drosophila affymetrix data analysis In-Reply-To: <200308011547.h71Flnj5000708@uni05mr.unity.ncsu.edu> References: <200308011547.h71Flnj5000708@uni05mr.unity.ncsu.edu> Message-ID: <1060006506.3f2e6a6ad9539@webmail.njit.edu> NP is for protein, I believe it stands for Natural Protein. NM is mRNA, I believe it stands for Natural Mrna. AAF is wierd, GenBank number formate is one letter and 5 number or 2 letter plus 6 number, like U69127 or AA002200. Others are XP or XM, these are referenced protein and mRNA seq, generated by insilico approach. I don't really know which to trust, but if you need protein sequence, you definitly won't use NM_, whereas is you need mRNA sequence, you definitley don't need NP_. I think it is depending on you research project. NCBI has FAQs and other education materials about these topic, hehe! Good luck! haibo //cheers Quoting Usharani Mudiganti : > Hi, > When I go to the locuslink number given in affymetrix "complete > entries", I see three different sequences (protein) starting with AAF or > NP_ or NM_. Dont' know which one to believe. > And also, need suggestions about getting useful functional data from the > protein sequences. Can anyone help? > > Any pointers are greatly appreciated. > thank you > > > > "Have a nice day" > Usharani Mudiganti > Graduate Student, > Molecular & Structural Biochemistry > NCSU,Raleigh,NC,USA. > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ========================================================= Haibo Zhang, PhD student Computational Biology, NJIT & Rutgers University Center for Applied Genomics, PHRI http://afs13.njit.edu/~hz5 From zfu at cs.ucr.edu Mon Aug 4 21:16:44 2003 From: zfu at cs.ucr.edu (Zheng Fu) Date: Mon, 4 Aug 2003 18:16:44 -0700 (PDT) Subject: [BiO BB] Tools for Genome rearrangement? Message-ID: Hi guys, Is there any tools for analyze genome rearrangement? I mean sorting one genome's sequences to another one bye reversals.Thank you very much. Carol -- Love & Peace Http://www.cs.ucr.edu/~zfu From jgagnon at rsvs.ulaval.ca Tue Aug 5 11:55:45 2003 From: jgagnon at rsvs.ulaval.ca (Jules Gagnon) Date: 05 Aug 2003 11:55:45 -0400 Subject: [BiO BB] Tools for Genome rearrangement? In-Reply-To: References: Message-ID: <1060098945.4109.5.camel@evolution.rsvs.ulaval.ca> There are many, but the one I find easier to use is GRIMM : http://www-cse.ucsd.edu/groups/bioinformatics/GRIMM/index.html You can also check http://www.math.tau.ac.il/~rshamir/GR/ On Mon, 2003-08-04 at 21:16, Zheng Fu wrote: > Hi guys, > > Is there any tools for analyze genome rearrangement? I mean sorting one > genome's sequences to another one bye reversals.Thank you very much. > > Carol -- Jules Gagnon -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part URL: From zfu at cs.ucr.edu Tue Aug 5 12:44:06 2003 From: zfu at cs.ucr.edu (Zheng Fu) Date: Tue, 5 Aug 2003 09:44:06 -0700 (PDT) Subject: [BiO BB] Tools for Genome rearrangement? In-Reply-To: <1060098945.4109.5.camel@evolution.rsvs.ulaval.ca> Message-ID: Thank you so much. On 5 Aug 2003, Jules Gagnon wrote: > There are many, but the one I find easier to use is GRIMM : > http://www-cse.ucsd.edu/groups/bioinformatics/GRIMM/index.html > > You can also check http://www.math.tau.ac.il/~rshamir/GR/ > > > On Mon, 2003-08-04 at 21:16, Zheng Fu wrote: > > Hi guys, > > > > Is there any tools for analyze genome rearrangement? I mean sorting one > > genome's sequences to another one bye reversals.Thank you very much. > > > > Carol > -- Love & Peace Http://www.cs.ucr.edu/~zfu From rdhayes at chem.ucla.edu Tue Aug 5 20:35:23 2003 From: rdhayes at chem.ucla.edu (Richard D. Hayes) Date: Wed, 6 Aug 2003 00:35:23 -0000 Subject: [BiO BB] Proteomics Visualization? Message-ID: <200308060035.h760ZNAE026256@carbon.chem.ucla.edu> Hi. I'm working in a proteomics/mass spectroscopy lab, and we're looking for a simple way to assemble 2D gel images, spot locations, the mass spec data and protein IDs into a nice clear presentation. Obviously, we could go with a full-scale LIMS for this sort of thing, but the big professional packages (from Biorad, for example) have currently been deemed overkill and too expensive for the simple visualizations that we need. We're looking for a more midrange approach. Does anyone on this list have suggestions for this? Existing APIs and that sort of thing are really what I'm looking for, as I have enough computer experience to customize, build an interface, etc. Also, does anyone have experience the the ExPASy Melanie suite? Any guidance is appreciated. Regards, Richard D. Hayes Graduate Student Department of Chemistry and Biochemistry University of California, Los Angeles From sravan_111 at rediffmail.com Thu Aug 7 05:35:26 2003 From: sravan_111 at rediffmail.com (sravan sravan) Date: 7 Aug 2003 09:35:26 -0000 Subject: [BiO BB] (no subject) Message-ID: <20030807093526.10220.qmail@webmail9.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From zfu at cs.ucr.edu Thu Aug 7 13:38:09 2003 From: zfu at cs.ucr.edu (Zheng Fu) Date: Thu, 7 Aug 2003 10:38:09 -0700 (PDT) Subject: [BiO BB] About clustering genes to gene family In-Reply-To: Message-ID: Hi everyone, Does anyone know how to clustering genes to a gene family based on the sequence alignments. For two genes, we can define a threshold to seperate the homolog and non-homolog. But for three or more genes,how to define the homologs?(Such as Gene A and Gene B has high alignment score, A and C also has high sore, but B and C doesn't have high socre, can we say ABC are homologs? Thank you. Carol -- From mgollery at unr.edu Thu Aug 7 14:44:03 2003 From: mgollery at unr.edu (Martin Gollery) Date: Thu, 7 Aug 2003 11:44:03 -0700 Subject: [BiO BB] About clustering genes to gene family In-Reply-To: References: Message-ID: <1060281843.3f329df3c4ef5@webmail.unr.edu> Hi Carol, Take a look at the D2_cluster program by Hide, Burke, and Davidson. I don't recall the journal. The program is available free from Biotique for academics. Marty Quoting Zheng Fu : > Hi everyone, > > Does anyone know how to clustering genes to a gene family based on the > sequence alignments. > For two genes, we can define a threshold to seperate the homolog and > non-homolog. But for three or more genes,how to define the homologs?(Such > as Gene A and Gene B has high alignment score, A and C also has high sore, > but B and C doesn't have high socre, can we say ABC are homologs? > > Thank you. > > Carol > > -- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director of Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 New phone number! 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From dmb at mrc-dunn.cam.ac.uk Thu Aug 7 14:57:19 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 07 Aug 2003 19:57:19 +0100 Subject: [BiO BB] About clustering genes to gene family References: Message-ID: <3F32A10F.3040005@mrc-dunn.cam.ac.uk> What you describe can occur for 2 good reasons... You are forming a 'complex cluster', created by *multiple domain* proteins... A has domains in common with B, B has domains in common with C. A and C have no domains in common, and hence no homology. I.e. A: |------W------/-----X-----| B: |------x-----/-----Y-------| C: |------y-------/--------hello mum!------| OR A and C are too distantly related for sequence searches to uncover their true homology. However, sequence B is *intermediate* to A and C, having homology to both... B / \ / \ / \ A C NB: Sequence similarity is not a metric, as it does not obey triangular equality. (I think it is metric at high levels of similarity though?) In this case you have used the transitive nature of sequence similarity to uncover distant homology via an intermediate sequence. Jong Park and Sarah Techimann worked on both these ideas, and has created a family clustering package called GENEFAMMER, Specifically DIVCLUS breaks up complex clusters into domain families. Transitivity is implemented (kinda) in psiblast / hmm models, all three of which are used in PFAM, so you might want to look there for your families. Or you could insist your allignments cover 90% of the shortest sequence, and then cluster using single linkage. Dan. Zheng Fu wrote: >Hi everyone, > >Does anyone know how to clustering genes to a gene family based on the >sequence alignments. >For two genes, we can define a threshold to seperate the homolog and >non-homolog. But for three or more genes,how to define the homologs?(Such >as Gene A and Gene B has high alignment score, A and C also has high sore, >but B and C doesn't have high socre, can we say ABC are homologs? > >Thank you. > >Carol > > > From Joel.Dudley at asu.edu Thu Aug 7 13:47:45 2003 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Thu, 07 Aug 2003 10:47:45 -0700 Subject: [BiO BB] About clustering genes to gene family Message-ID: <9EAE2E44897BC749ACB3A62683B2C8D112FBC2@ex4.asurite.ad.asu.edu> Carol, This site may provide some useful information for you: http://pbil.univ-lyon1.fr/databases/hovergen.html Joel Dudley Faculty Research Associate Arizona State University Center for Evolutionary and Functional Genomics http://lsweb.la.asu.edu/skumar/ -----Original Message----- From: Zheng Fu [mailto:zfu at cs.ucr.edu] Sent: Thursday, August 07, 2003 10:38 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] About clustering genes to gene family Hi everyone, Does anyone know how to clustering genes to a gene family based on the sequence alignments. For two genes, we can define a threshold to seperate the homolog and non-homolog. But for three or more genes,how to define the homologs?(Such as Gene A and Gene B has high alignment score, A and C also has high sore, but B and C doesn't have high socre, can we say ABC are homologs? Thank you. Carol -- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From operon at www.bioinformatics.org Thu Aug 7 15:44:07 2003 From: operon at www.bioinformatics.org (Marcos Oliveira de Carvalho) Date: Thu, 7 Aug 2003 15:44:07 -0400 (EDT) Subject: [BiO BB] About clustering genes to gene family In-Reply-To: Message-ID: Hi Carol, I use TribeMCL software with good results. Here is the URL -> http://www.ebi.ac.uk/research/cgg/tribe/ And here is the abstract of the paper about TribeMCL: TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases, proteins in the same protein familywill have similar functional properties. TribeMCL uses a novel clustering method (Markov Clustering or MCL) which solves problems which normally hinder protein sequence clustering. These problems include: multi-domain proteins, peptide fragments and proteins which possess domains which are very widespread (promiscuous domains). The efficiency of the method makes it applicable to the clustering of very large datasets. We routinely use the algorithm to cluster datasets as large as 500,000 peptides. Cheers Marcos On Thu, 7 Aug 2003, Zheng Fu wrote: > Hi everyone, > > Does anyone know how to clustering genes to a gene family based on the > sequence alignments. > For two genes, we can define a threshold to seperate the homolog and > non-homolog. But for three or more genes,how to define the homologs?(Such > as Gene A and Gene B has high alignment score, A and C also has high sore, > but B and C doesn't have high socre, can we say ABC are homologs? > > Thank you. > > Carol > > -- Marcos Oliveira de Carvalho operon at bioinformatics.org From dmb at mrc-dunn.cam.ac.uk Fri Aug 8 07:02:06 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 08 Aug 2003 12:02:06 +0100 Subject: [BiO BB] About clustering genes to gene family References: Message-ID: <3F33832E.8070503@mrc-dunn.cam.ac.uk> This method uses an all against all blast comparison as input to the clustering. Can you really do that 'routinely' with 500,000 sequences without dedicated hardware? I guess once you have your initial 'pairs DB' you can then add new sequences in without much work, and I guess the actuall clustering is the 'efficient' part of the method. The handling of multidomain proteins is interesting, but I don't really see how it differs from demanding a certain length of allignment within the family. Although the technique is mathmatically clean, it is a bit hazy when it comes to the multi domain issue. I.e. if we have protein 1 with domains ABC, what happens to protein 2 with domains AB? What happens to the 'families' of type 1 and 2 in this strategy? I love the extension of pairwise similarity to group similarity using the network of blast hits - that is really nice, but the biological significance of the r factor (number of clusters) is not investigated, which is a shame. Anyone heard of BAG for domain decomposition from such a network? Thanks for the info, Dan. Marcos Oliveira de Carvalho wrote: >Hi Carol, >I use TribeMCL software with good results. > >Here is the URL -> http://www.ebi.ac.uk/research/cgg/tribe/ > >And here is the abstract of the paper about TribeMCL: > >TribeMCL is a method for clustering proteins into related groups, which >are termed 'protein families'. This clustering is achieved by analysing >similarity patterns between proteins in a given dataset, and using these >patterns to assign proteins into related groups. In many cases, proteins >in the same protein familywill have similar functional properties. >TribeMCL uses a novel clustering method (Markov Clustering or MCL) which >solves problems which normally hinder protein sequence clustering. These >problems include: multi-domain proteins, peptide fragments and proteins >which possess domains which are very widespread (promiscuous domains). The >efficiency of the method makes it applicable to the clustering of very >large datasets. We routinely use the algorithm to cluster datasets as >large as 500,000 peptides. > >Cheers >Marcos > >On Thu, 7 Aug 2003, Zheng Fu wrote: > > > >>Hi everyone, >> >>Does anyone know how to clustering genes to a gene family based on the >>sequence alignments. >>For two genes, we can define a threshold to seperate the homolog and >>non-homolog. But for three or more genes,how to define the homologs?(Such >>as Gene A and Gene B has high alignment score, A and C also has high sore, >>but B and C doesn't have high socre, can we say ABC are homologs? >> >>Thank you. >> >>Carol >> >> >> >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zfu at cs.ucr.edu Fri Aug 8 13:10:27 2003 From: zfu at cs.ucr.edu (Zheng Fu) Date: Fri, 8 Aug 2003 10:10:27 -0700 (PDT) Subject: [BiO BB] About clustering genes to gene family In-Reply-To: <3F32A10F.3040005@mrc-dunn.cam.ac.uk> Message-ID: How to differentiate the fist case(complex cluster) and the second(distantly related with homolog). And where can I find the information about GENEFAMMER? Thank you. On Thu, 7 Aug 2003, Dan Bolser wrote: > What you describe can occur for 2 good reasons... > > You are forming a 'complex cluster', created by *multiple domain* > proteins... > > A has domains in common with B, > B has domains in common with C. > > A and C have no domains in common, and hence no homology. > > I.e. > > A: |------W------/-----X-----| > B: |------x-----/-----Y-------| > C: |------y-------/--------hello > mum!------| > > OR > > A and C are too distantly related for sequence searches to uncover their > true homology. However, sequence B is *intermediate* to A and C, > having homology to both... > > B > / \ > / \ > / \ > A C > > NB: Sequence similarity is not a metric, as it does not obey triangular > equality. > (I think it is metric at high levels of similarity though?) > > In this case you have used the transitive nature of sequence similarity > to uncover > distant homology via an intermediate sequence. > > Jong Park and Sarah Techimann worked on both these ideas, and has > created a > family clustering package called GENEFAMMER, Specifically DIVCLUS breaks up > complex clusters into domain families. Transitivity is implemented > (kinda) in psiblast / > hmm models, all three of which are used in PFAM, so you might want to > look there > for your families. > > Or you could insist your allignments cover 90% of the shortest sequence, > and then > cluster using single linkage. > > Dan. > > > Zheng Fu wrote: > > >Hi everyone, > > > >Does anyone know how to clustering genes to a gene family based on the > >sequence alignments. > >For two genes, we can define a threshold to seperate the homolog and > >non-homolog. But for three or more genes,how to define the homologs?(Such > >as Gene A and Gene B has high alignment score, A and C also has high sore, > >but B and C doesn't have high socre, can we say ABC are homologs? > > > >Thank you. > > > >Carol > > > > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Love & Peace Http://www.cs.ucr.edu/~zfu From dmb at mrc-dunn.cam.ac.uk Fri Aug 8 13:23:53 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 08 Aug 2003 18:23:53 +0100 Subject: [BiO BB] About clustering genes to gene family References: Message-ID: <3F33DCA9.3040506@mrc-dunn.cam.ac.uk> Zheng Fu wrote: >How to differentiate the fist case(complex cluster) and the >second(distantly related with homolog). > > You have to look at the alignments ... second case would look like... --------------------------A--------------------------------- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ---------------------------B--------------------------------- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ----------------------------C-------------------------------- And first case would be... A: |------W------/-----X-----| ||||||||||||| B: |------x-----/-----Y-------| |||||||||||| C: |------y-------/--------hello mum!------| >And where can I find the information about GENEFAMMER? > > Bioinformatics 1998 14: 144-150 >Thank you. > > :) Dan. > >On Thu, 7 Aug 2003, Dan Bolser wrote: > > > >>What you describe can occur for 2 good reasons... >> >>You are forming a 'complex cluster', created by *multiple domain* >>proteins... >> >>A has domains in common with B, >>B has domains in common with C. >> >>A and C have no domains in common, and hence no homology. >> >>I.e. >> >>A: |------W------/-----X-----| >>B: |------x-----/-----Y-------| >>C: |------y-------/--------hello >>mum!------| >> >>OR >> >>A and C are too distantly related for sequence searches to uncover their >>true homology. However, sequence B is *intermediate* to A and C, >>having homology to both... >> >> B >> / \ >> / \ >> / \ >> A C >> >>NB: Sequence similarity is not a metric, as it does not obey triangular >>equality. >>(I think it is metric at high levels of similarity though?) >> >>In this case you have used the transitive nature of sequence similarity >>to uncover >>distant homology via an intermediate sequence. >> >>Jong Park and Sarah Techimann worked on both these ideas, and has >>created a >>family clustering package called GENEFAMMER, Specifically DIVCLUS breaks up >>complex clusters into domain families. Transitivity is implemented >>(kinda) in psiblast / >>hmm models, all three of which are used in PFAM, so you might want to >>look there >>for your families. >> >>Or you could insist your allignments cover 90% of the shortest sequence, >>and then >>cluster using single linkage. >> >>Dan. >> >> >>Zheng Fu wrote: >> >> >> >>>Hi everyone, >>> >>>Does anyone know how to clustering genes to a gene family based on the >>>sequence alignments. >>>For two genes, we can define a threshold to seperate the homolog and >>>non-homolog. But for three or more genes,how to define the homologs?(Such >>>as Gene A and Gene B has high alignment score, A and C also has high sore, >>>but B and C doesn't have high socre, can we say ABC are homologs? >>> >>>Thank you. >>> >>>Carol >>> >>> >>> >>> >>> >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From isakti at hathway.com Wed Aug 13 03:05:05 2003 From: isakti at hathway.com (Suresh Swaminathan) Date: Wed, 13 Aug 2003 12:35:05 +0530 Subject: [BiO BB] Re: [Biodevelopers] visualization tools References: Message-ID: <024101c3616b$199e1010$0a01a8c0@isakti> Dear Zheng Fu, We have a Visualization software called Gene Picker, which is a proof of consept. Gene Picker is a web based tool that is developed to display Genetic Information in an easy to use graphical format. The objective is to enable the scientist to access Genetic information archived in a back end database through a graphical representation. This would enable the scientist to quickly seek and retrieve data useful to the research he is conducting. The basic search is done using a standard querying format of entering the text string into the search field and the relevant gene / intron is retrieved. The retrieved sequence is a text string of varying length and comprises the four nucleotides. Gene Picker is web based and is developed on open source platform. The main feature of Gene Picker is that it can be customized to a specific representation requirement of the Scientist. The application is scalable in that it can handle a huge volume of data and represent each retrieved sequence graphically and enable the end user to view all the annotations and enter annotations of their own. In a typical commercial deployment, more powerful search engines would be used to access data from multiple public and proprietary databases. If you would be interested , we could send you more details on Gene Picker and also give you a secured Login and password ,which you could browse through the application and get the feel of it. Looking forward to here from you, Warm Regards, Suresh Swaminathan Sakti Group NY ----- Original Message ----- From: "Zheng Fu" To: Sent: Tuesday, August 12, 2003 5:28 AM Subject: [Biodevelopers] visualization tools > Hello everyone, > > Does anyone knows any visualization tool for visualize the gene position? > Thank you so much. > > -- > Love & Peace > > > _______________________________________________ > Biodevelopers mailing list > Biodevelopers at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biodevelopers From landman at scalableinformatics.com Fri Aug 15 11:50:19 2003 From: landman at scalableinformatics.com (Joseph Landman) Date: 15 Aug 2003 11:50:19 -0400 Subject: [BiO BB] Fwd: Discontiguous MegaBLAST Message-ID: <1060962618.3264.0.camel@protein.scalableinformatics.com> -----Forwarded Message----- Date: 15 Aug 2003 10:56:28 -0400 Now available on the NCBI BLAST web pages is a new type of nucleotide search called Discontiguous MegaBLAST (http://www.ncbi.nlm.nih.gov/blast/discontiguous.html). Like MegaBLAST, this service uses a greedy algorithm and concatenates queries to save time scanning the databases. But instead of using exact matches to database sequences for initial hits, it finds matches to a discontiguous template made from the query. This results in fewer initial words but more statistically significant alignments. This makes Discontiguous MegaBLAST good for comparison of divergent sequences, especially from different organisms, which have alignments with low degree of identity but perhaps encode similar proteins. Discontiguous MegaBLAST can be found on the main NCBI BLAST web page at http://www.ncbi.nlm.nih.gov/BLAST/ It is also included in the WWW BLAST server located at (ftp://ftp.ncbi.nih.gov/blast/server). Discontiguous MegaBLAST searches can also be done using Standalone BLAST. To do this, you can specify in the megablast binary, template length option, with the -t parameter and the Template Type with parameter -N. The word size (-W) must also be set to 11 or 12 for Discontiguous MegaBLAST seaches. For any questions please contact blast-help at ncbi.nlm.nih.gov. -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From bioinfoset at lycos.com Sat Aug 16 03:18:41 2003 From: bioinfoset at lycos.com (S ET) Date: Sat, 16 Aug 2003 14:18:41 +0700 Subject: [BiO BB] interpret kyte doolittle plot and aliphatic index Message-ID: dear friends, i have two simple questions for u guy but hard questions for me. 1) how to interpret the kyte doolittle hydrophatic plot? how to determain where's the transmembrane region? what the figure indicates? 2) what is aliphatic index? what the figure indicates? what is the figure of each range? i've been searching the internet for this, but i can't find teh info that answer the question directly. somemore, i don't understand what most of the page tryign to explain. they lead me to no where. hoping for u guys help. thanks for yr time. regards, danni malaysia ____________________________________________________________ Get advanced SPAM filtering on Webmail or POP Mail ... Get Lycos Mail! http://login.mail.lycos.com/r/referral?aid=27005 From dmb at mrc-dunn.cam.ac.uk Sun Aug 17 15:22:59 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sun, 17 Aug 2003 20:22:59 +0100 (BST) Subject: [BiO BB] Can this be set up here? [Fwd: RE: [blast-help] filtering?] Message-ID: <33186.80.1.204.96.1061148179.squirrel@www.mrc-dunn.cam.ac.uk> Could the below be maintained (by me) at bioinformatics.org ? I would be willing to do this either here or at source forge, but I don't want to duplicate an existing forum. Cheers, Dan. -------- Original Message -------- Subject: RE: [blast-help] filtering? From: "Cooper, Peter (NIH/NLM/NCBI)" Date: Sat, August 16, 2003 2:18 pm To: "'Dan Bolser'" Cc: "'blast-help at ncbi.nlm.nih.gov'" Hello, ...[snip] Thanks for your suggestion about the mailing list. We would not be interested in maintaining it though. We're paid to answer questions about BLAST, dumb or otherwise. We don't have a searchable archive of blast-help questions. We can't provide this becuase of privacy issues. Peter ---------------------- Peter Cooper, Ph.D. NCBI / NLM Building 38A, 3S310 8600 Rockville Pike Bethesda, MD 20894 p: 301.435.5951 -----Original Message----- From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] Sent: Thursday, August 14, 2003 5:53 AM To: blast-help at ncbi.nlm.nih.gov Subject: [blast-help] filtering? Hello, what filtering params are sugessted for a database / database comparison? Could you set up a mailing list on source forge to stop dumb questions like this? I would be happy to do it. Where are messages to blast-help archived? Thanks for a answer to any of the above. From jeff at bioinformatics.org Mon Aug 18 07:32:29 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 18 Aug 2003 07:32:29 -0400 Subject: [BiO BB] Can this be set up here? [Fwd: RE: [blast-help] filtering?] References: <33186.80.1.204.96.1061148179.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <3F40B94D.1080107@bioinformatics.org> Hi Dan. Sure, we can set up a mailing list. But, what precisely will be the topic of the forum? Filtering? Databases? Cheers. Jeff Dan Bolser wrote: > Could the below be maintained (by me) at bioinformatics.org ? > > I would be willing to do this either here or at source forge, > but I don't want to duplicate an existing forum. > > Cheers, > Dan. > > -------- Original Message -------- > Subject: RE: [blast-help] filtering? > From: "Cooper, Peter (NIH/NLM/NCBI)" > Date: Sat, August 16, 2003 2:18 pm > To: "'Dan Bolser'" > Cc: "'blast-help at ncbi.nlm.nih.gov'" > > Hello, > > ...[snip] > > Thanks for your suggestion about the mailing list. We would not be interested in > maintaining it though. We're paid to answer questions about BLAST, dumb or > otherwise. > > We don't have a searchable archive of blast-help questions. We can't provide this > becuase of privacy issues. > > Peter > ---------------------- > Peter Cooper, Ph.D. > NCBI / NLM > Building 38A, 3S310 > 8600 Rockville Pike > Bethesda, MD 20894 > p: 301.435.5951 > > -----Original Message----- > From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] > Sent: Thursday, August 14, 2003 5:53 AM > To: blast-help at ncbi.nlm.nih.gov > Subject: [blast-help] filtering? > > > > Hello, what filtering params are sugessted for a database / database comparison? > > Could you set up a mailing list on source forge to stop dumb questions like this? > > I would be happy to do it. > > Where are messages to blast-help archived? > > Thanks for a answer to any of the above. > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- J.W. Bizzaro jeff at bioinformatics.org President, 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 dmb at mrc-dunn.cam.ac.uk Mon Aug 18 11:33:34 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 18 Aug 2003 16:33:34 +0100 (BST) Subject: [BiO BB] Can this be set up here? [Fwd: RE: [blast-help] filtering?] In-Reply-To: <3F40B94D.1080107@bioinformatics.org> Message-ID: I was thinking just blast-suite questions or ncbi-toolbox questions, but perhaps a more general topic (sequence searching?) would be more appropriate. This way we cover both sequence databases and filtering, as well as sequence searching strategies from basic algorithms to advanced protocols. Let me know what you think, Dan. On Mon, 18 Aug 2003, J.W. Bizzaro wrote: > Hi Dan. > > Sure, we can set up a mailing list. But, what precisely will be the > topic of the forum? Filtering? Databases? > > Cheers. > Jeff > > > Dan Bolser wrote: > > Could the below be maintained (by me) at bioinformatics.org ? > > > > I would be willing to do this either here or at source forge, > > but I don't want to duplicate an existing forum. > > > > Cheers, > > Dan. > > > > -------- Original Message -------- > > Subject: RE: [blast-help] filtering? > > From: "Cooper, Peter (NIH/NLM/NCBI)" > > Date: Sat, August 16, 2003 2:18 pm > > To: "'Dan Bolser'" > > Cc: "'blast-help at ncbi.nlm.nih.gov'" > > > > Hello, > > > > ...[snip] > > > > Thanks for your suggestion about the mailing list. We would not be interested in > > maintaining it though. We're paid to answer questions about BLAST, dumb or > > otherwise. > > > > We don't have a searchable archive of blast-help questions. We can't provide this > > becuase of privacy issues. > > > > Peter > > ---------------------- > > Peter Cooper, Ph.D. > > NCBI / NLM > > Building 38A, 3S310 > > 8600 Rockville Pike > > Bethesda, MD 20894 > > p: 301.435.5951 > > > > -----Original Message----- > > From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] > > Sent: Thursday, August 14, 2003 5:53 AM > > To: blast-help at ncbi.nlm.nih.gov > > Subject: [blast-help] filtering? > > > > > > > > Hello, what filtering params are sugessted for a database / database comparison? > > > > Could you set up a mailing list on source forge to stop dumb questions like this? > > > > I would be happy to do it. > > > > Where are messages to blast-help archived? > > > > Thanks for a answer to any of the above. > > > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From francis at bioinformatics.ubc.ca Mon Aug 18 12:06:28 2003 From: francis at bioinformatics.ubc.ca (Francis Ouellette) Date: Mon, 18 Aug 2003 09:06:28 -0700 Subject: [BiO BB] Can this be set up here? [Fwd: RE: [blast-help]filtering?] References: Message-ID: <3F40F984.3BFB4BF2@bioinformatics.ubc.ca> NCBI runs a couple of lists already which target these things: http://www.ncbi.nlm.nih.gov/mailman/listinfo/cpp and http://www.ncbi.nlm.nih.gov/mailman/listinfo/cpp-announce I think they are probably what you are looking for. cheers, f. -- BF Francis Ouellette http://bioinformatics.ubc.ca/ouellette Dan Bolser wrote: > > I was thinking just blast-suite questions > or ncbi-toolbox questions, but perhaps > a more general topic (sequence searching?) > would be more appropriate. > > This way we cover both sequence databases > and filtering, as well as sequence searching > strategies from basic algorithms to advanced > protocols. > > Let me know what you think, > Dan. > > On Mon, 18 Aug 2003, J.W. Bizzaro wrote: > > > Hi Dan. > > > > Sure, we can set up a mailing list. But, what precisely will be the > > topic of the forum? Filtering? Databases? > > > > Cheers. > > Jeff > > > > > > Dan Bolser wrote: > > > Could the below be maintained (by me) at bioinformatics.org ? > > > > > > I would be willing to do this either here or at source forge, > > > but I don't want to duplicate an existing forum. > > > > > > Cheers, > > > Dan. > > > > > > -------- Original Message -------- > > > Subject: RE: [blast-help] filtering? > > > From: "Cooper, Peter (NIH/NLM/NCBI)" > > > Date: Sat, August 16, 2003 2:18 pm > > > To: "'Dan Bolser'" > > > Cc: "'blast-help at ncbi.nlm.nih.gov'" > > > > > > Hello, > > > > > > ...[snip] > > > > > > Thanks for your suggestion about the mailing list. We would not be interested in > > > maintaining it though. We're paid to answer questions about BLAST, dumb or > > > otherwise. > > > > > > We don't have a searchable archive of blast-help questions. We can't provide this > > > becuase of privacy issues. > > > > > > Peter > > > ---------------------- > > > Peter Cooper, Ph.D. > > > NCBI / NLM > > > Building 38A, 3S310 > > > 8600 Rockville Pike > > > Bethesda, MD 20894 > > > p: 301.435.5951 > > > > > > -----Original Message----- > > > From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] > > > Sent: Thursday, August 14, 2003 5:53 AM > > > To: blast-help at ncbi.nlm.nih.gov > > > Subject: [blast-help] filtering? > > > > > > > > > > > > Hello, what filtering params are sugessted for a database / database comparison? > > > > > > Could you set up a mailing list on source forge to stop dumb questions like this? > > > > > > I would be happy to do it. > > > > > > Where are messages to blast-help archived? > > > > > > Thanks for a answer to any of the above. > > > > > > > > > > > > _______________________________________________ > > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Mon Aug 18 12:41:36 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 18 Aug 2003 17:41:36 +0100 (BST) Subject: [BiO BB] Can this be set up here? [Fwd: RE: [blast-help]filtering?] In-Reply-To: <3F40F984.3BFB4BF2@bioinformatics.ubc.ca> Message-ID: These look like good places for ncbi tookit questions, but they look a bit tekie for basic questions about sequence searching. I am looking for a place where people can discuss parameters, protocols and results of sequences searching. On Mon, 18 Aug 2003, Francis Ouellette wrote: > > NCBI runs a couple of lists already which target these things: > > > http://www.ncbi.nlm.nih.gov/mailman/listinfo/cpp > > and > > http://www.ncbi.nlm.nih.gov/mailman/listinfo/cpp-announce > > I think they are probably what you are looking for. > > cheers, > > f. > > > From francis at bioinformatics.ubc.ca Mon Aug 18 13:09:53 2003 From: francis at bioinformatics.ubc.ca (Francis Ouellette) Date: Mon, 18 Aug 2003 10:09:53 -0700 Subject: [BiO BB] Can this be set up here? [Fwd: RE: [blast-help]filtering?] References: Message-ID: <3F410861.BFCBFD7D@bioinformatics.ubc.ca> > I am looking for a place where people > can discuss parameters, protocols and > results of sequences searching. I don't think there is a place for this, although historically those queries probably went to bionet software, or bionet genbank (neither of which is really ideal, except maybe bionet software). see: http://www.bio.net http://www.bio.net/archives.html http://www.bio.net/hypermail/bio-software/ http://www.bio.net/hypermail/genbankb/ (that being said, for your blast questions, I would look at the latest O'Reilley book called: BLAST! http://www.oreilly.com/catalog/blast/ cheers, f. disclaimer: I am not associated with that book, if anything, it competes with a chapter in our book :-) -- BF Francis Ouellette http://bioinformatics.ubc.ca/ouellette Dan Bolser wrote: > > These look like good places for ncbi tookit > questions, but they look a bit tekie for > basic questions about sequence searching. > > I am looking for a place where people > can discuss parameters, protocols and > results of sequences searching. > > On Mon, 18 Aug 2003, Francis Ouellette wrote: > > > > > NCBI runs a couple of lists already which target these things: > > > > > > http://www.ncbi.nlm.nih.gov/mailman/listinfo/cpp > > > > and > > > > http://www.ncbi.nlm.nih.gov/mailman/listinfo/cpp-announce > > > > I think they are probably what you are looking for. > > > > cheers, > > > > f. > > > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Eitan.Rubin at weizmann.ac.il Thu Aug 21 02:11:13 2003 From: Eitan.Rubin at weizmann.ac.il (Eitan Rubin) Date: Thu, 21 Aug 2003 08:11:13 +0200 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #496 - 4 msgs References: <20030818160116.02ABDD25D2@www.bioinformatics.org> Message-ID: <002901c367ab$0743d3a0$0101c80a@weizmannnhc4zn> Hi, Regarding the Blast mailing list. Who would answer all the questions? NCBI's people are *payed* for that - we're not. Eitan > -------- Original Message -------- > Subject: RE: [blast-help] filtering? > From: "Cooper, Peter (NIH/NLM/NCBI)" > Date: Sat, August 16, 2003 2:18 pm > To: "'Dan Bolser'" > Cc: "'blast-help at ncbi.nlm.nih.gov'" > > Hello, > > ....[snip] > > Thanks for your suggestion about the mailing list. We would not be interested in > maintaining it though. We're paid to answer questions about BLAST, dumb or > otherwise. > > We don't have a searchable archive of blast-help questions. We can't provide this > becuase of privacy issues. > > Peter > ---------------------- > Peter Cooper, Ph.D. > NCBI / NLM > Building 38A, 3S310 > 8600 Rockville Pike > Bethesda, MD 20894 > p: 301.435.5951 > > -----Original Message----- > From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] > Sent: Thursday, August 14, 2003 5:53 AM > To: blast-help at ncbi.nlm.nih.gov > Subject: [blast-help] filtering? > > > > Hello, what filtering params are sugessted for a database / database comparison? > > Could you set up a mailing list on source forge to stop dumb questions like this? > > I would be happy to do it. > > Where are messages to blast-help archived? > > Thanks for a answer to any of the above. > From dmb at mrc-dunn.cam.ac.uk Tue Aug 19 05:29:35 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 19 Aug 2003 10:29:35 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #496 - 4 msgs In-Reply-To: <002901c367ab$0743d3a0$0101c80a@weizmannnhc4zn> Message-ID: Yup, but in all honesty I have found that they either are not interested, not capable or too buisy to answer my questions. Compared to pdb-l the speed/quality of response is bad. Dumb questions to pdb-l get answered by the hordes of willing subscribers, and advanced questions get the attention of the experts lurking on the mailing list. I have rarely had a question go unanswered, and the quality of the answer is usually very high. Goes to show the power of open source over corperate solutions if you ask me. If the mailing list worked well (i.e. became popular) the team at the ncbi would be out of a job. I would like to point out how grateful I am for the help they have provided me, however, it just dosn't compare to help from 'people in the same boat'. Dan. On Thu, 21 Aug 2003, Eitan Rubin wrote: > Hi, > > Regarding the Blast mailing list. Who would answer all the questions? > NCBI's people are *payed* for that - we're not. > > Eitan > > > -------- Original Message -------- > > Subject: RE: [blast-help] filtering? > > From: "Cooper, Peter (NIH/NLM/NCBI)" > > Date: Sat, August 16, 2003 2:18 pm > > To: "'Dan Bolser'" > > Cc: "'blast-help at ncbi.nlm.nih.gov'" > > > > Hello, > > > > ....[snip] > > > > Thanks for your suggestion about the mailing list. We would not be > interested in > > maintaining it though. We're paid to answer questions about BLAST, dumb or > > otherwise. > > > > We don't have a searchable archive of blast-help questions. We can't > provide this > > becuase of privacy issues. > > > > Peter > > ---------------------- > > Peter Cooper, Ph.D. > > NCBI / NLM > > Building 38A, 3S310 > > 8600 Rockville Pike > > Bethesda, MD 20894 > > p: 301.435.5951 > > > > -----Original Message----- > > From: Dan Bolser [mailto:dmb at mrc-dunn.cam.ac.uk] > > Sent: Thursday, August 14, 2003 5:53 AM > > To: blast-help at ncbi.nlm.nih.gov > > Subject: [blast-help] filtering? > > > > > > > > Hello, what filtering params are sugessted for a database / database > comparison? > > > > Could you set up a mailing list on source forge to stop dumb questions > like this? > > > > I would be happy to do it. > > > > Where are messages to blast-help archived? > > > > Thanks for a answer to any of the above. > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dig at bioinformatics.org Tue Aug 19 10:23:51 2003 From: dig at bioinformatics.org (Dmitri I GOULIAEV) Date: Tue, 19 Aug 2003 09:23:51 -0500 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #496 - 4 msgs In-Reply-To: <002901c367ab$0743d3a0$0101c80a@weizmannnhc4zn>; from Eitan.Rubin@weizmann.ac.il on Thu, Aug 21, 2003 at 08:11:13AM +0200 References: <20030818160116.02ABDD25D2@www.bioinformatics.org> <002901c367ab$0743d3a0$0101c80a@weizmannnhc4zn> Message-ID: <20030819092351.D17266@lifebook> Hi, Eitan Rubin ! On Thu, Aug 21, 2003 at 08:11:13AM +0200, Eitan Rubin wrote: > Regarding the Blast mailing list. Who would answer all the questions? > NCBI's people are *payed* for that - we're not. You weren't payed for answering Dan's question, were you? P.S. Thanks for top-quoting. Regards, -- DIG (Dmitri I GOULIAEV) http://www.bioinformatics.org/~dig/ 1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 From dmb at mrc-dunn.cam.ac.uk Tue Aug 19 10:09:18 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 19 Aug 2003 15:09:18 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #496 - 4 msgs In-Reply-To: <20030819092351.D17266@lifebook> References: <20030818160116.02ABDD25D2@www.bioinformatics.org> <002901c367ab$0743d3a0$0101c80a@weizmannnhc4zn> <20030819092351.D17266@lifebook> Message-ID: <36879.193.60.81.207.1061302158.squirrel@www.mrc-dunn.cam.ac.uk> Dmitri I GOULIAEV said: > Hi, Eitan Rubin ! > > On Thu, Aug 21, 2003 at 08:11:13AM +0200, Eitan Rubin wrote: > >> Regarding the Blast mailing list. Who would answer all the questions? >> NCBI's people are *payed* for that - we're not. > > You weren't payed for answering Dan's question, were you? > > > P.S. Thanks for top-quoting. One other thing I just thought of, the blast-help at ncbi dosn't archive pre answered questions, so you cant find answers using google where perhaps you would if they were archived. How can you turn a mailing list archive into an FAQ automatically? Cheers, > > Regards, > > -- > DIG (Dmitri I GOULIAEV) http://www.bioinformatics.org/~dig/ 1024D/63A6C649: > 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From johannes.huesing at uni-essen.de Wed Aug 20 03:53:18 2003 From: johannes.huesing at uni-essen.de (=?iso-8859-1?Q?Johannes_H=FCsing?=) Date: Wed, 20 Aug 2003 09:53:18 +0200 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #496 - 4 msgs In-Reply-To: <36879.193.60.81.207.1061302158.squirrel@www.mrc-dunn.cam.ac.uk>; from dmb@mrc-dunn.cam.ac.uk on Tue, Aug 19, 2003 at 03:09:18PM +0100 References: <20030818160116.02ABDD25D2@www.bioinformatics.org> <002901c367ab$0743d3a0$0101c80a@weizmannnhc4zn> <20030819092351.D17266@lifebook> <36879.193.60.81.207.1061302158.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <20030820095318.A42860@spi.power.uni-essen.de> On Tue, Aug 19, 2003 at 03:09:18PM +0100, Dan Bolser wrote: [...] > > How can you turn a mailing list archive into an FAQ automatically? > My guess is that this can be done by the same text parser and generator that automatically converts your lab log to a manuscript ready for publication :-) SCNR Johannes From dmb at mrc-dunn.cam.ac.uk Wed Aug 20 07:38:50 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 20 Aug 2003 12:38:50 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #496 - 4 msgs In-Reply-To: <20030820095318.A42860@spi.power.uni-essen.de> Message-ID: You mean I should use an NNN? On Wed, 20 Aug 2003, [iso-8859-1] Johannes H?sing wrote: > On Tue, Aug 19, 2003 at 03:09:18PM +0100, Dan Bolser wrote: > [...] > > > > How can you turn a mailing list archive into an FAQ automatically? > > > > My guess is that this can be done by the same text parser and > generator that automatically converts your lab log to a manuscript > ready for publication :-) > > SCNR > > > Johannes > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From j.d.tucker at vla.defra.gsi.gov.uk Thu Aug 21 05:03:45 2003 From: j.d.tucker at vla.defra.gsi.gov.uk (Tucker, James) Date: Thu, 21 Aug 2003 10:03:45 +0100 Subject: [BiO BB] Phylogenetics Message-ID: <104FE795DA19D411A71A0008C733F76404A43A49@vla6> Hi all, We have a sequence that encompasses two genes. When drawing up a tree from these sequences for several sub species of the same genus- we end up with a tree that does not reflect the results we would anticipate (from our current knowledge of the species, through RFLP, classical techniques, PCR RFLP etc). The genes are both outer membrane protein - the problem seems to lie in the fact that the genes are highly similar (85%) they can be in any order, there may be duplication of one or other gene and the other gene is not present. One possible solution we can think of for this is to build a tree based upon weighting: Either on secondary structure or gene expression. Does anyone know of any software that we would be able to carry this out with or alternative approaches. Obviously we don't want to ignore these events as they are obviously significant - we just want to be able to take them into account proportionally. Regards James James Tucker Brucella Research Group Department of Bacterial Diseases VLA Weybridge Woodham Lane New Haw Addlestone Surrey KT15 3NB Tel: ++44(0)1932 357227 Fax: ++44(0)1932 357873 mailto:j.d.tucker at vla.defra.gsi.gov.uk Veterinary Laboratories Agency (VLA) This email and any attachments is intended for the named recipient only. Its unauthorised use, disclosure, storage or copying is not permitted. If you have received it in error, please destroy all copies and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within VLA systems we can accept no responsibility once it has left our systems. Communications on VLA's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes. From sravan at www.cdfd.org.in Thu Aug 21 15:15:05 2003 From: sravan at www.cdfd.org.in (P Sravan Kumar. PAsst) Date: Thu, 21 Aug 2003 12:15:05 -0700 Subject: [BiO BB] (no subject) Message-ID: Hello all, I have a query: When we are running psipred the program takes the file of a sequence as input , run and give result ; Ex: x.seq--> x.horiz,x.ss,x.ss2,x.blast: (3 iterations of PSIBLAST/PSIPRED V) : 3 seconds: Actually I want to run psipred on a set of sequences loaded in a file at a time one by one.(Here the sequences will be in a file and should be read one by one.) Please provide me with a solution regarding the query and suggest me possible ways which will complete the task in a little time. May be at the rate of 1 or min for 50 sequences. A quick reply if possible is appreciated. Thank you all, Yours sincerely, sravan. ======================== P. Sravana Kumar c/o Dr. Shekhar C. Mande, Laboratory of Structural Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam 500 076, Hyderabad, India. Ph: Lab: Direct: 040-27171442 General: 040-27151344-1400 e-mail: sravan at www.cdfd.org.in ========================= From dmb at mrc-dunn.cam.ac.uk Fri Aug 22 11:55:53 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 22 Aug 2003 16:55:53 +0100 (BST) Subject: [BiO BB] (no subject) sequence searching mailing list? In-Reply-To: References: Message-ID: <34100.213.107.104.52.1061567753.squirrel@www.mrc-dunn.cam.ac.uk> Sorry for not answering the question, but I was wondering what the next step for the sequence search mailing list should be? Should I start a project and use the mailing list? Cheers, dan. P Sravan Kumar. PAsst said: > Hello all, > I have a query: > When we are running psipred the program takes the file of a > sequence as input , run and give result ; > Ex: x.seq--> x.horiz,x.ss,x.ss2,x.blast: (3 iterations of PSIBLAST/PSIPRED V) : 3 > seconds: > Actually I want to run psipred on a set of sequences loaded in a file at a time > one by one.(Here the sequences will be in a file and should be read one by one.) > Please provide me with a solution regarding the query and suggest me possible ways > which will complete the task in a little time. May be at the rate of 1 or min for > 50 sequences. > A quick reply if possible is appreciated. > Thank you all, > Yours sincerely, > sravan. > > ======================== > P. Sravana Kumar > c/o Dr. Shekhar C. Mande, > Laboratory of Structural Biology, > Center for DNA Fingerprinting and Diagnostics, > ECIL Road, > Nacharam 500 076, > Hyderabad, > India. > > Ph: Lab: Direct: 040-27171442 > General: 040-27151344-1400 > e-mail: sravan at www.cdfd.org.in > ========================= > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From wmueller at gbf.de Sun Aug 24 01:53:37 2003 From: wmueller at gbf.de (=?ISO-8859-1?Q?Werner_M=FCller?=) Date: Sun, 24 Aug 2003 07:53:37 +0200 Subject: [BiO BB] dnaplot binaries Message-ID: <4E14D604-D5F7-11D7-B504-000393D611C8@gbf.de> http://www.dnaplot.de:8080/werner/Folder.2003-05-10.5451/ mfg Werner Mueller -------------- next part -------------- A non-text attachment was scrubbed... Name: werner.vcf Type: text/directory Size: 500 bytes Desc: not available URL: From editor at phyloinformatics.org Tue Aug 26 08:02:12 2003 From: editor at phyloinformatics.org (Dennis DeGreve) Date: Tue, 26 Aug 2003 14:02:12 +0200 Subject: [BiO BB] Phyloinformatics: a new journal Message-ID: <2048CAC5-D7BD-11D7-9928-00039345483C@phyloinformatics.org> Phyloinformatics: call for papers / editors wanted - Phyloinformatics.org Phyloinformatics is a new, non-profit, international, peer reviewed, open access journal dedicated to publishing high quality papers on the use of informatics in taxonomy. Taxonomist often need to manage fairly large amounts of data for which elegant solutions are needed. And the inference of phylogeny itself is impossible without the use of computers and optimized algorithms. To help this emerging field of taxonomy grow, we have started Phyloinformatics. Phyloinformatics is not a regular journal: it's only available online and it's open access. Phyloinformatics offers all published papers as a free PDF download, there are no subscription or login procedures for readers and no page charges for authors. But open access means more than just free: our authors remain the copyright holders of their work. Being an online journal has lots of advantages: papers can be published very fast and are available to anyone with a computer and internet connection. CALL FOR PAPERS Phyloinformatics is just starting now and we are looking for high quality manuscripts in one of the following two categories: - Papers Describing new research developments in computational taxonomy, for example: new evolutionary models, algorithms, software involving new methods, taxonomic databases, proposals for new file formats and network information services, and their impact on taxonomy. - Application Notes Short descriptions about new software or new algorithm implementations, databases and network services. The software or data should be available online as free- or donationware. We are planning to publish our first articles before the end of 2003. Visit our site for more information on manuscript submission EDITORS WANTED We are looking for senior taxonomists with experience in the field of phylogenetic analysis and/or taxonomic databases who would like to join the editorial board. Just send an e-mail to editor at phyloinformatics.org The editorial board will be announced on our website soon. Apologies for any cross-postings. Sincerely, Dennis DeGreve Editor Phyloinformatics editor at phyloinformatics.org http://phyloinformatics.org From yyjia at pmail.ntu.edu.sg Tue Aug 26 09:29:59 2003 From: yyjia at pmail.ntu.edu.sg (#JIA YIYU#) Date: Tue, 26 Aug 2003 21:29:59 +0800 Subject: [BiO BB] FW: virtual conference summary: please forward Message-ID: <052033A55521254893A4E2041957E1D01AB1C6@mail03.student.main.ntu.edu.sg> -----Original Message----- From: Willy Valdivia Granda [mailto:willy.valdivia at NDSU.NODAK.EDU] Sent: Tuesday, August 26, 2003 11:32 AM To: VIRTCON-REAL at LISTSERV.NODAK.EDU Subject: virtual conference summary: please forward **************************************************************************** *********************** Third Virtual Conference on Genomics and Bioinformatics. Sharing Knowledge with the World September 16-19, 2003. No registration fees to Participate http://www.ndsu.nodak.edu/virtual-genomics/conference_2003.htm **************************************************************************** *********************** Advances in sequence analysis, transcriptional profiling, protein structural elucidation and other genomic techniques are producing an overwhelming accumulation of data and the shift in the way biological research is conducted. As new disciplines are integrated, the "Virtual Conferences on Genomics and Bioinformatics" provides an advanced collaborative environment for the exchange and discussion of innovations related to the post-genomic era. The Goals of the Virtual Conferences on Genomics and Bioinformatics are: *Transcend geographical and economical barriers for the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. *Address the benefits and limitations of the newest developments in post-genomic technologies. *Explore the social and ethical implications of genomic and bioinformatic research. *Establish new ways to introduce the high school community to today's multidisciplinary science. **************************************************************************** ********************** TOPICS OF THE 2003 VIRTUAL CONFERENCE http://www.ndsu.nodak.edu/virtual-genomics/program_2003.htm **************************************************************************** ********************** **Computational Chemistry and Structural Genomics. Kim Baldrigde, San Diego Supercomputer Center. USA Nathan Baker, Washington University in St. Louis School of Medicine. USA Jim Briggs, University of Houston. USA Jan Jensen, University of Iowa. USA Julie Mitchell, University of Wisconsin, Madison. USA **Complex Biological Systems: George M. Church, Harvard Medical School & MIT Health Sciences & Technology. USA Toni Kazic, University of Missouri Columbia. USA Eberhard Voit, Medical University of South Carolina. USA Deanne Taylor. Serono Reproductive Biology. USA Andreas Wagner, University of New Mexico. USA Yaneer Bar-Yam, New England Complex Systems Institute. USA **RNA-interference: Michael T. McManus, Center for Cancer Research. Massachusetts Institute of Technology, USA Ali Shilatifard, Saint Louis University Cancer Center, USA **Genomics of Infectious Diseases: Larry Simpson Howard Hughes Medical Institute/UCLA. USA Jose Stoute, US Army Medical Research Command. USA John H Adams, Center for Tropical Disease Research & Training. University of Notre Dame. USA **Bioinformatics and Grid Computing Natalia Maltsev, Argonne National Laboratory. USA Douglas L. Brutlag, Stanford University. USA Carole Goble, University of Manchester. United Kingdom Elia Stupka, Temasek Life Sciences Laboratory. Singapore Akihiko Konagaya, RIKEN Genomic Sciences Center. Japan David Sankoff, Department of Mathematics and Statistics. University of Ottawa. Canada Mark Wilkinson, Illuminae Media. Canada **Transcriptional Analysis: Bruce Aronow, Cincinnati Childrens Hospital Medical Center. USA Kristy Meyers, Spotfire. USA Eric Blalock, University of Kentucky. USA **Bioethics and Intellectual Property Rights Protection: Dennis Fernandez, Fernandez and Associates LLP. USA **************************************************************************** **************** Register to participate http://www.ndsu.nodak.edu/DCE/virtcon/conferenceRegistration2.htm From sravan at www.cdfd.org.in Mon Aug 25 15:25:41 2003 From: sravan at www.cdfd.org.in (P Sravan Kumar. PAsst) Date: Mon, 25 Aug 2003 12:25:41 -0700 Subject: [BiO BB] (no subject) Message-ID: Hello all, I have a query regarding sequence alignment. I constructed HMM profiles for a set of msas(multiple sequence alignments) individually.These are called my hosts.But I have .hmm files for only 400 msas out of 1000. I collected blosum series of matrices also. If I have to do sequence alignment using hmm profiles as basic substitution matrices, how can I do ? options 1: - use of only blosum for all - use of .hmms for those they are available and blosums for thouse .hmms are not available. I want to take the suggestions from you all regarding the options and also and possible matrices for sequence alignments. I appreciate your early response, as it will allow me to move littlebit quicker in my work. Thank you all, sravan. ======================== P. Sravana Kumar c/o Dr. Shekhar C. Mande, Laboratory of Structural Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam 500 076, Hyderabad, India. Ph: Lab: Direct: 040-27171442 General: 040-27151344-1400 e-mail: sravan at www.cdfd.org.in ========================= From rashi.bahadur at ciionline.org Tue Aug 26 02:14:14 2003 From: rashi.bahadur at ciionline.org (Rashi bahadur) Date: Tue, 26 Aug 2003 11:44:14 +0530 Subject: [BiO BB] Companies Message-ID: We are doing a report with DIT. It is regarding Manpower Forecasting in Bioinformatics in India. Could you please give me a list of Companies in Bioinformatics in India. Rashi Bahadur Confederation of Indian Industry 23, Institutional Area, Lodi Road New Delhi 110033 Tel: 011- 24629994-7 (extn 366) Fax 011-24601298/24626149 From tfiedler at rsmas.miami.edu Tue Aug 26 13:06:03 2003 From: tfiedler at rsmas.miami.edu (Tristan J. Fiedler) Date: Tue, 26 Aug 2003 13:06:03 -0400 (EDT) Subject: [BiO BB] perl scripting assistance In-Reply-To: <20030826160138.22F22D2447@www.bioinformatics.org> References: <20030826160138.22F22D2447@www.bioinformatics.org> Message-ID: <51738.129.171.101.25.1061917563.squirrel@domino.rsmas.miami.edu> Are any bulletin boards / discussion groups available for obtaining tips in scripting with perl? Thank you. -- Tristan J. Fiedler, Ph.D. Postdoctoral Research Fellow NIEHS Marine & Freshwater Biomedical Sciences Center Rosenstiel School of Marine & Atmospheric Sciences University of Miami tfiedler at rsmas.miami.edu t.fiedler at umiami.edu (alias) 305-361-4626 From landman at scalableinformatics.com Tue Aug 26 21:06:11 2003 From: landman at scalableinformatics.com (Joseph Landman) Date: 26 Aug 2003 21:06:11 -0400 Subject: [BiO BB] perl scripting assistance In-Reply-To: <51738.129.171.101.25.1061917563.squirrel@domino.rsmas.miami.edu> References: <20030826160138.22F22D2447@www.bioinformatics.org> <51738.129.171.101.25.1061917563.squirrel@domino.rsmas.miami.edu> Message-ID: <1061946370.2948.40.camel@protein.scalableinformatics.com> Try the biodevelopers group on bioinformatics.org ... On Tue, 2003-08-26 at 13:06, Tristan J. Fiedler wrote: > Are any bulletin boards / discussion groups available for obtaining tips > in scripting with perl? > > Thank you. -- Joseph Landman, Ph.D Scalable Informatics LLC email: landman at scalableinformatics.com web: http://scalableinformatics.com phone: +1 734 612 4615 From maria.mirto at unile.it Wed Aug 27 14:19:24 2003 From: maria.mirto at unile.it (Maria Mirto) Date: Wed, 27 Aug 2003 20:19:24 +0200 Subject: [BiO BB] Call for Papers: ITCC2004 Message-ID: <1062008364.3f4cf62c7d48a@wm.unile.it> Dear all, please find attached the Call For Papers for: 5th IEEE International Conference on Information Technology: Coding and Computing (ITCC2004) - Special Session on Methodologies, Technologies and Applications in distributed and Grid systems. Las Vegas, Nevada 5-7 April 2004 http://datadog.unile.it/itcc2004/cfp.htm http://www.itcc.info/ sponsored by IEEE Computer Society This Conference Track aims at offering a forum of discussion where young researchers and PhD students could present their research activities, either at an early or mature phase. Best regards, Maria Mirto. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Maria Mirto, CACT/ISUFI (Center for Advanced Computing Technology) Engineering Faculty, Department of Innovation Engineering University of Lecce, Via per Monteroni, 73100 Lecce, Italy phone: +39-0832-297304, fax: +39-0832-297279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We apologize if you receive multiple copies of this email. -------------------------------------------------------------------------------- Special Session on Methodologies, Technologies and Applications in distributed and Grid systems. ITCC 2004: IEEE International Conference on Information Technology: Coding and Computing Sponsored by the IEEE Computer Society April 5-7, 2004 The Orleans, Las Vegas, Nevada -------------------------------------------------------------------------------- Call for Papers http://datadog.unile.it/itcc2004/cfp.htm http://www.itcc.info ***************** Computational Grids, initially used for the sharing of distributed computation resources in scientific applications, start to be used in different application domains offering basic services for application definition and execution in heterogeneous distributed systems. In health systems, the Grid offers the power and ubiquity needed to the acquisition of biomedical data, processing and delivering of biomedical images (CT, MRI, PET, SPECT, etc) located in different hospitals, within a wide area. So, the Grid acts as a Collaborative Working Environment: doctors often want to aggregate not only medical data, but also human expertise and might want colleague around the world to visualize the examinations in the same way and at the same time so that the group can discuss the diagnosis in real time. The Grid offers a dynamic infrastructure for retrieving and on-demand processing of remote sensing data, for instance, retrieving of SAR metadata related to terabyte of SAR data, starting on-demand processing on raw data, starting on-demand post-processing on focalized data and creating a complex application composing simple tasks. For atmospheric and climate modeling, a Grid offers tools for simulate and forecasting meteorological phenomena, simulate emission and dispersion of pollutants for air quality studies and simulate complex phenomena about the impact of global climate changes. Grid Computing techniques can be used in the motor industry, reducing the optimization process time for improvement of diesel engine emission performance using, for instance, micro-genetic algorithms for engine chamber geometry optimization and Kiva3 code to calculate chamber geometry fitness. In the computer aided medicine, the Grid technologies can be used in the surgical simulations (including virtual environment and haptic interface). Interesting research areas involve the detection, in the virtual environment, of the contact points between artery walls and medical instruments, studies to generate, by means of the haptic interface, the force feedback associated to the interaction in the virtual environment and describe the physical behaviour of the organs considered as deformable tissues. Finally, bioinformatic applications call for the ability to read large datasets (e.g. protein databases) and to create new datasets (e.g. mass spectrometry proteomic data). They can require the ability to change (updating) existing datasets; consequently a Data Grid, i.e. a distributed infrastructure for storing large datasets, is needed. In the bioinformatic field, a Data Grid could reveal useful to build Electronic Patient Record systems (EPRs) for the management of patient information (data, metadata and images), to support data replication, allowing the integration and sharing of biological databases and, generally, for the developement of efficient bioinformatics (in particular proteomic) applications. The main goal of the Conference Track is to discuss well-known and emerging data-intensive applications in the context of distributed systems and Grid systems, and to analyze technologies and methodologies useful to develop such applications in such environments. In particular, this Conference Track aims at offering a forum of discussion where young researchers and PhD students could present their research activities, either at an early or mature phase. Topics include, but are not limited to: Data intensive applications in distributed and Grid systems: - Grid for biomedical imaging; - Grid for remote sensing and GIS application; - Grid for Atmospheric and Climate Modeling; - Grid for motor industry (diesel engine simulation); - Grid for surgery simulations; - Bioinformatic for: o Biomedical Imaging; o Proteomics and genomics; o Electronic Patient Records; o Medical images, data and metadata management; o Image Recognition, Processing and Analysis. Technologies and methodologies in distributed and grid-based applications: - Grid technologies (Grid portals, Web & Grid services, portlets); - Grid Information and Monitoring services and related (OO,Relational,XML) data models; - Grid Security; - Grid Workload and Data management services; - Grid Resource management; - Parallel and Distributed application (cluster and grid based); - Simulation and Applications of Modeling. IMPORTANT DATES October 17, 2003 Paper Due November 14, 2003 Author Notification December 19, 2003 Camera-Ready Copy Note: The Proceedings will be published by IEEE Computer Society. A special issue of an international journal is being planned consisting of selected papers from this conference. Authors of selected papers will be invited to submit an extended version for the journal. SUBMISSION DETAILS Papers should be original and contain contributions of theoretical or experimental nature. Interested authors should send a 5-page paper ( IEEE Proceedings format http://computer.org/cspress/instruct.htm ), including 5 keywords, before the 17nd October 2003 deadline, to the Special Session chair: Maria Mirto, CACT/ISUFI (Center for Advanced Computing Technology), c/o Engineering Faculty, Department of Innovation Engineering, University of Lecce, Via per Monteroni, 73100 Lecce, Italy, Voice: +39-0832-297304, Fax: +39-0832-297279, Email: maria.mirto at unile.it Electronic submission (PostScript or PDF) is strongly encouraged. From david.richardson at stud.man.ac.uk Wed Aug 27 15:06:39 2003 From: david.richardson at stud.man.ac.uk (David Richardson) Date: Wed, 27 Aug 2003 20:06:39 +0100 Subject: [BiO BB] perl scripting assistance In-Reply-To: <20030827160110.D4A9AD242F@www.bioinformatics.org> Message-ID: > -----Original Message----- > Are any bulletin boards / discussion groups available for obtaining tips > in scripting with perl? > > Thank you. You might want to try www.perlmonks.org. Hope that helps. Regards, Dave Richardson --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.512 / Virus Database: 309 - Release Date: 19/08/03 From Ttlusa at aol.com Wed Aug 27 15:40:47 2003 From: Ttlusa at aol.com (Ttlusa at aol.com) Date: Wed, 27 Aug 2003 15:40:47 -0400 Subject: [BiO BB] perl scripting assistance Message-ID: <3EF57657.3E476A2C.00055F61@aol.com> Anybody in Boston area might be interested in attending this conference? I participated last time at the end of July and was very successful, we had over 150 people from biotech and large pharma. Also, great opportunity to find employment. For registration, contact bw at studentvision.org Best regards, Mark J. Bergander TTL Clinical (www.ttlclinical.com) Dear friends, On behalf of the Nobel Pauling Committee, we invite you to participate ( a talk, a smart pitch, a booth or a sponsor) in the Nobel Pauling Biotech Symposium on September 28-29, 2003 at MIT Faculty Club. We have confirmed speakers from Amgen, Genentech, Biogen and Serono and other companies and Institution. Please see the biographies of some of our confirmed speakers Symposium Speakers. The topic of the panel discussion will be " Academia vs. Industry" for new drug discovery. Buffet dim sum food will be available throughout the proceedings (3 pm to 10 pm). Our 1st and 2nd Pauling Biotech Symposia on June 11 and July 30 were very successful. July 30, 2003 Nobel Pauling Biotech meeting: Biotech vs. Big Pharma Click for details June 11, 2003 Nobel Pauling Biotech Meeting: Cytokine Genomics RNAi Click for details This Symposium is by invitation only and pre-registration is necessary. Hope you can come! Best Regards Nobel Pauling Staffs Cycles King PhD & Canyon Smith MD From junding at yahoo.com Wed Aug 27 16:27:56 2003 From: junding at yahoo.com (Jun Ding) Date: Wed, 27 Aug 2003 13:27:56 -0700 (PDT) Subject: [BiO BB] perl scripting assistance In-Reply-To: <51738.129.171.101.25.1061917563.squirrel@domino.rsmas.miami.edu> Message-ID: <20030827202756.9534.qmail@web11606.mail.yahoo.com> http://www.omnitalk.com/download/f022203.zip --- "Tristan J. Fiedler" wrote: > Are any bulletin boards / discussion groups > available for obtaining tips > in scripting with perl? > > Thank you. > -- > Tristan J. Fiedler, Ph.D. > Postdoctoral Research Fellow > NIEHS Marine & Freshwater Biomedical Sciences Center > Rosenstiel School of Marine & Atmospheric Sciences > University of Miami > > tfiedler at rsmas.miami.edu > t.fiedler at umiami.edu (alias) > 305-361-4626 > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From zfu at cs.ucr.edu Wed Aug 27 20:02:35 2003 From: zfu at cs.ucr.edu (Zheng Fu) Date: Wed, 27 Aug 2003 17:02:35 -0700 (PDT) Subject: [BiO BB] How to identify homolog genes? Message-ID: Hello, I have a question about homolog genes. Given two gene sequences,how can I decide if they are homologs. I first used blastP to get the alignment of these two sequences. But those scores are based on some local alignment. They seem not so reliable. Is there any other criterion for this problem? Thank you very much. Best regards, Carol -- Love & Peace From jeff at bioinformatics.org Thu Aug 28 18:42:55 2003 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 28 Aug 2003 18:42:55 -0400 Subject: [BiO BB] Looking for suggestions on where to hold next meeting Message-ID: <3F4E856F.3050703@bioinformatics.org> Greetings. Bioinformatics.Org is looking to hold its 4th Annual Meeting (4AM) in 2004. The last 3 meetings took place as follows: 2001: ISMB, Copenhagen, Denmark 2002: O'Reilly Biocon, Tucson, Arizona 2003: O'Reilly Biocon, San Diego, California Note that O'Reilly won't be holding a bioinformatics conference in 2004. Some of the other conferences that come to mind include... - ISMB/ECCB 2004 (Scotland): http://www.iscb.org/ismbeccb2004/ - Bio-IT World 2004 (Boston): http://www.bioitworldexpo.com/ - IEEE/CSB 2004 (Stanford?): http://conferences.computer.org/bioinformatics/index.html Of course, there's also PSB and RECOMB: - PSB 2004 (Hawaii): http://psb.stanford.edu/ - RECOMB 2004 (San Diego): http://recomb04.sdsc.edu/ (The Westin-Horton seems to be a popular hotel) What other places would be good to hold our meeting? Should we consider Open Source and Linux conferences? Please suggest places that **YOU** would actually go to. Please don't say, "Go to this conference in Syberia", when you know that you wouldn't go. 2AM and 3AM had good attendance. Our track talks got between 50 and 100 attendees. We would like to match or improve upon that for 4AM. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org President, 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 idoerg at burnham.org Thu Aug 28 19:08:05 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 28 Aug 2003 16:08:05 -0700 Subject: [BiO BB] Looking for suggestions on where to hold next meeting In-Reply-To: <3F4E856F.3050703@bioinformatics.org> References: <3F4E856F.3050703@bioinformatics.org> Message-ID: <3F4E8B55.90209@burnham.org> I think ISMB is the best choice, given that the BOSC crowd there are: 1) Motivated to hear about open-source projects & 2) A captive audience :) RECOMB & PSB are smaller, and do not have a "critical mass" of people interested in joining in on open-source projects per-se. I don't know about the crowd IEEE or Bio-IT meetings. best, Iddo J.W. Bizzaro wrote: > Greetings. > > Bioinformatics.Org is looking to hold its 4th Annual Meeting (4AM) in > 2004. The last 3 meetings took place as follows: > > 2001: ISMB, Copenhagen, Denmark > 2002: O'Reilly Biocon, Tucson, Arizona > 2003: O'Reilly Biocon, San Diego, California > > Note that O'Reilly won't be holding a bioinformatics conference in 2004. > > Some of the other conferences that come to mind include... > > - ISMB/ECCB 2004 (Scotland): http://www.iscb.org/ismbeccb2004/ > > - Bio-IT World 2004 (Boston): http://www.bioitworldexpo.com/ > > - IEEE/CSB 2004 (Stanford?): > http://conferences.computer.org/bioinformatics/index.html > > Of course, there's also PSB and RECOMB: > > - PSB 2004 (Hawaii): http://psb.stanford.edu/ > > - RECOMB 2004 (San Diego): http://recomb04.sdsc.edu/ (The Westin-Horton > seems to be a popular hotel) > > What other places would be good to hold our meeting? Should we consider > Open Source and Linux conferences? Please suggest places that **YOU** > would actually go to. Please don't say, "Go to this conference in > Syberia", when you know that you wouldn't go. > > 2AM and 3AM had good attendance. Our track talks got between 50 and 100 > attendees. We would like to match or improve upon that for 4AM. > > Cheers. > Jeff -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From dmb at mrc-dunn.cam.ac.uk Fri Aug 29 11:39:39 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 29 Aug 2003 16:39:39 +0100 (BST) Subject: [BiO BB] Sequence searching Questions... In-Reply-To: <20030820095318.A42860@spi.power.uni-essen.de> Message-ID: Following the example set by the pdb-l and the fantastic information resource it provides (both for and by the community it serves), a new mailing list has been created: The Sequence Search Mailing List (ssml), http://bioinformatics.org/mailman/listinfo/ssml-general This new list aims to be the place for all your general sequence searching questions (for example those not specifically related to protein structural data). For example, questions regarding all aspects of biological sequence searching and the analysis of homology; sequence resources searching algorithms searhcing resources accuracy protocols etc... So if you have quesions related to sequence searching but were too afraid to ask (the structure community), or if you are an expert willing to offer your time to the community, or perhaps just curious, then this is the place for you (so tell your friends!). To subscribe, follow the above link! From bioinfo at biosystemsconsulting.com Fri Aug 29 12:18:19 2003 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Fri, 29 Aug 2003 12:18:19 -0400 Subject: [BiO BB] Bioinformatics Projects In-Reply-To: <2284046.1058817225742.JavaMail.nobody@wamui04.slb.atl.earthlink.net> Message-ID: <003901c36e49$29e09d40$1efea8c0@raptor> David, My group is actively working to produce a free open source software system for high-throughput sequence data management and bioinformatics research which is composed of separable but interoperable modules which may be distributed among a number of computers. The software principally resides under Linux/UNIX (Solaris), but its primary interface is a web application accessible through a browser on any platform. We currently have several modules working and have many more in the planning stages. If your interested please feel free to contact me directly at mark_burke at ncsu.edu or visit our website at www.alkahest.org. Mark -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of David Ballard Sent: Monday, July 21, 2003 4:54 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Bioinformatics Projects Hello all, I'm a current grad student in CS and am interested in learning more about bioinformatics - I have a biopsych/neuroscience background. I've looked through the projects on bioinformatics.org and sent some emails, but none seem to have much activity. Anyone with ideas on how I could get involved? Thank you, David _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Eitan.Rubin at weizmann.ac.il Sun Aug 31 09:24:11 2003 From: Eitan.Rubin at weizmann.ac.il (Eitan Rubin) Date: Sun, 31 Aug 2003 16:24:11 +0300 Subject: [BiO BB] Re: Looking for suggestions on where to hold next meeting In-Reply-To: <20030829160117.04F39D2862@www.bioinformatics.org> Message-ID: <688D51A7-DBB6-11D7-974B-003065C02E54@weizmann.ac.il> I vote for Boston. Eitan From Ttlusa at aol.com Sun Aug 31 23:32:38 2003 From: Ttlusa at aol.com (Ttlusa at aol.com) Date: Sun, 31 Aug 2003 23:32:38 EDT Subject: [BiO BB] Re: Looking for suggestions on where to hold next meeting Message-ID: <1f1.efe98a4.2c8417d6@aol.com> Me to (Boston) Mark -------------- next part -------------- An HTML attachment was scrubbed... URL: