From joel.mossong at crp-sante.lu Wed Aug 1 12:02:22 2001 From: joel.mossong at crp-sante.lu (Joel Mossong) Date: Wed, 01 Aug 2001 18:02:22 +0200 Subject: [BiO BB] Job: bioinformatics in Luxembourg Message-ID: <1.5.4.32.20010801160222.018bc644@pop3.restena.lu> The Centre de Recherche Public-Sant? in Luxembourg is a dynamic and rapidly growing research institute of international acclaim in the medical and life sciences. Within the program of the "Fonds National de la Recherche of Luxembourg" the CRP-Sant? offers a post-doctoral position in Bioinformatics. The applicant will be a key member of a large interdisciplinary project, which focuses on setting up a functional genomics core facility. He/she will work on problems in biostatistics (analysis of gene expression patterns and genomic micro-array data) and biological systems (modelling and simulation of cellular networks and regulatory processes). His/her role is to provide core programming, algorithm development and statistical analysis. Applicants are required to have a PhD in bioinformatics / biostatistics / statistics backed with a certain level of experience in biology. The ideal applicant will have comprehensive knowledge of the UNIX environment and programming languages as well as the interpersonal skills necessary to succeed within a multi-disciplinary team. The post is funded for 30 months, but is renewable subject to review. To receive more information or to apply (by sending your CV), please contact: Dr Evelyne Friederich LABORATOIRE DE BIOLOGIE MOL?CULAIRE, D'ANALYSE G?NIQUE ET DE MOD?LISATION Centre de Recherche Public-Sant? 18, rue Dicks L-1417 Luxembourg T?l. : 00 352 45 32 13 33 Fax. : 00 352 45 32 19 E-mail: Evelyne.Friederich at crp-sante.lu ========================================================================= Dr Jo?l Mossong, CRESIS, CRP-Sant?, 18 rue Dicks, L-1417 Luxembourg. Tel: +352 45 32 13 40 Fax: +352 45 32 19 Email: joel.mossong at crp-sante.lu ========================================================================= From jeff at bioinformatics.org Wed Aug 1 18:50:49 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 01 Aug 2001 18:50:49 -0400 Subject: [BiO BB] [Fwd: Position Announcement] Message-ID: <3B6887C9.ED815124@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: "Tom Abt" Subject: Position Announcement Date: Thu, 12 Jul 2001 10:44:49 -0700 Size: 7968 URL: From jeff at bioinformatics.org Thu Aug 2 14:49:32 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 02 Aug 2001 14:49:32 -0400 Subject: [BiO BB] Integrating Bioinformatics & Cheminformatics Message-ID: <3B69A0BC.7BC5CB72@bioinformatics.org> >From LaurieAnne Plax: Integrating Bioinformatics & Cheminformatics, November 14&15, 2001, LaCosta Resort and Spa, San Diego area, CA. Visit www.iqpc.com/NA-1673-01/bioinformatics Bioinformatics.org members can receive the academic rate by mentioning BF66. Jeff From mam at ist.unige.it Fri Aug 3 02:46:17 2001 From: mam at ist.unige.it (Assunta Manniello) Date: Fri, 03 Aug 2001 08:46:17 +0200 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #63 - 1 msg In-Reply-To: <20010718061435.76009.qmail@web8005.mail.in.yahoo.com> References: <200107161600.MAA10048@www.bioinformatics.org> Message-ID: <5.0.2.1.1.20010803084530.00a97160@ist.unige.it> I'm sorry to inform you that the NETTAB Abstracts's Book now are sold out, because there was a great request to our invitation. Best regards >Hi, > >I would be thankful to you if you can send me the >Abstracts' Book of the NETTAB >workshop to the following address. >Thank you in advance. > >Warm Regards, > >Kiran Kumar.C >DSQ Biotech Ltd, >43, Bellary Road, >Hebbal, Bangalore >India- 560024 > >____________________________________________________________ >Do You Yahoo!? >For regular News updates go to http://in.news.yahoo.com > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board Maria Assunta Manniello, PhD Biotechnology Department National Cancer Research Institute - Genova c/o Advanced Biotechnology Centre Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-289, Fax: +39-010-5737-295 E-mail: mam at ist.unige.it From mam at ist.unige.it Fri Aug 3 02:50:22 2001 From: mam at ist.unige.it (Assunta Manniello) Date: Fri, 03 Aug 2001 08:50:22 +0200 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #63 - 1 msg In-Reply-To: <20010718061435.76009.qmail@web8005.mail.in.yahoo.com> References: <200107161600.MAA10048@www.bioinformatics.org> Message-ID: <5.0.2.1.1.20010803084822.00a9be00@ist.unige.it> I'm sorry to inform you that the NETTAB Abstracts's Book now are sold out, because there was a great request to our invitation. Best regards >Hi, > >I would be thankful to you if you can send me the >Abstracts' Book of the NETTAB >workshop to the following address. >Thank you in advance. > >Warm Regards, > >Kiran Kumar.C >DSQ Biotech Ltd, >43, Bellary Road, >Hebbal, Bangalore >India- 560024 > >____________________________________________________________ >Do You Yahoo!? >For regular News updates go to http://in.news.yahoo.com > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board Maria Assunta Manniello, PhD Biotechnology Department National Cancer Research Institute - Genova c/o Advanced Biotechnology Centre Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-289, Fax: +39-010-5737-295 E-mail: mam at ist.unige.it From tabt at benchinternational.com Fri Aug 3 15:03:50 2001 From: tabt at benchinternational.com (Tom Abt) Date: Fri, 3 Aug 2001 12:03:50 -0700 Subject: [BiO BB] Position Announcement Message-ID: <00af01c11c4f$0827ba60$6b00a8c0@benchinternational.com> Senior Scientist, BioInformatics, Drug Safety Evaluation Northeast Pharma A major multinational pharmaceutical company, headquartered in the Northeast, has retained Bench International exclusively to identify an exceptional individual to lead the bioinformatics function within the Company's Global Drug Safety Evaluation organization. The Company recently has committed significant investment in emerging technologies dedicated to Drug Safety in order to make better, earlier decisions about which molecules should move forward in Development. Such technologies include proteomics, genomics, imaging and advanced pathology methods, which are used to generate fundamental data from assays performed in a wide range of systems including, cell-based assays, animal studies and clinical trials. The role of this position will be to work across multidisciplinary teams, including Drug Safety, Clinical Research and Drug Discovery, to develop and implement systems and applications for annotating and for visualization and mining of complex data sets obtained from the application of such technologies in the laboratory and the clinic. Additionally, the incumbent will have responsibility to integrate such data with conventional toxicology and clinical safety information and to develop new databases of molecular toxicology information. The incumbent will have a significant role in interoperation of information gained from these analyses and in guiding the company to apply such results appropriately to drug development decisions. The qualified individual will have a PhD, or equivalent, in life sciences or pharmaceutical chemistry with an emphasis on computational biology or bioinformatics. Experience in toxicology or other pre-clinical sciences will be a benefit. A substantial track record of achievement as evidenced by significant publication in peer-reviewed journals is highly desirable. The incumbent will have substantial experience in the use, development and applications of relational databases and querying, data mining and visualization tools as well associated programming languages (e.g., Perl, UNIX, JAVA, HTML). The successful candidate will have strong interpersonal, management and communications skills, as well as the ability and experience to work effectively within complex, matrixed teams and will be adaptable to changing needs and priorities. If you would like any additional information regarding this position or know of someone who might be appropriate for it, please contact me by return e-mail cgiffin at benchinternational.com or by telephone at (310) 854-9900. Very truly yours, J. Christopher Giffin Vice President Bench International, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: From siddroy at indiatimes.com Thu Aug 16 07:27:08 2001 From: siddroy at indiatimes.com (siddroy) Date: Thu, 16 Aug 2001 16:57:08 +0530 Subject: [BiO BB] career prospects for me!!1 Message-ID: <200108161120.QAA15300@WS0005.indiatimes.com> respected sir, i am a bit restless right now , becoz i have just done my m.sc. in genetics and plan to undergo training in bioinformatics or also take up a job in the same, please sir guide me up!! thanking you siddhartha roy Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM and Audio-Books from http://www.planetmonline.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Fri Aug 17 07:42:19 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 17 Aug 2001 07:42:19 -0400 Subject: [BiO BB] career prospects for me!!1 References: <200108161120.QAA15300@WS0005.indiatimes.com> Message-ID: <3B7D031B.3980AA17@bioinformatics.org> We'd suggest to anyone wanting to know what bioinformatics is, how to get an education, and/or how to get a job, that they read our FAQ: http://bioinformatics.org/faq/ It's now very extensive, thanks to the hard work of Damian Counsell. More specific questions, those not covered by the FAQ, would be great for this mailing list. Cheers. Jeff siddroy wrote: > > i am a bit restless right now , becoz i have just done my m.sc. in genetics > and plan to undergo training in bioinformatics or also take up a job in the > same, -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Fri Aug 17 07:48:28 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 17 Aug 2001 07:48:28 -0400 Subject: [BiO BB] IRC Channel Message-ID: <3B7D048C.2CC0F118@bioinformatics.org> Greetings. Until we get our own IRC server set up, we (BiO members) can use the following server and channel: irc.openprojects.net #bioinformatics Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From pilli50 at idirect.com Fri Aug 17 14:15:11 2001 From: pilli50 at idirect.com (Louis) Date: Fri, 17 Aug 2001 14:15:11 -0400 Subject: [BiO BB] If you are interested in Bioinformatics jobs.. Message-ID: http://www.exxcalibur.net specializes in Bioinformatics and other Bio Positions. From reillywu at yahoo.com Tue Aug 21 07:07:16 2001 From: reillywu at yahoo.com (Chunlei Wu) Date: Tue, 21 Aug 2001 04:07:16 -0700 (PDT) Subject: [BiO BB] Is there a database available including all non-repetitive sequences of human genome Message-ID: <20010821110716.3204.qmail@web4905.mail.yahoo.com> As title. I know the repetitive sequences in human genome can be masked by RepMasker. Did someone mask the entire human genome and make available the human genome sequnences without repetitive sequences? Thanks Newgene __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From thomas at cbs.dtu.dk Tue Aug 21 07:25:43 2001 From: thomas at cbs.dtu.dk (Thomas Sicheritz-Ponten) Date: 21 Aug 2001 13:25:43 +0200 Subject: [BiO BB] Is there a database available including all non-repetitive sequences of human genome In-Reply-To: Chunlei Wu's message of "Tue, 21 Aug 2001 04:07:16 -0700 (PDT)" References: <20010821110716.3204.qmail@web4905.mail.yahoo.com> Message-ID: Chunlei Wu writes: > As title. > I know the repetitive sequences in human genome can be > masked by > RepMasker. Did someone mask the entire human genome > and make available > the human genome sequnences without repetitive > sequences? > Check what ensembl provides: www.ensembl.org Maybe you can find a description about how ftp://ftp.ensembl.org/pub/current/data/fasta/dna/ensembl-1.1.0_masked_golden_path.gz has been masked. good luck -thomas -- Sicheritz-Ponten Thomas, Ph.D CBS, Department of Biotechnology thomas at biopython.org The Technical University of Denmark CBS: +45 45 252489 Building 208, DK-2800 Lyngby Fax +45 45 931585 http://www.cbs.dtu.dk/thomas De Chelonian Mobile ... The Turtle Moves ... From Joel.Dudley at DevelopOnline.com Tue Aug 21 19:11:10 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Tue, 21 Aug 2001 16:11:10 -0700 Subject: [BiO BB] open source ideas Message-ID: Hello, I have the greatest urge to create free, open-source applications for biological research, but as I scan the lists of available software it seems like it has all been done (Which I know is FAR from the truth). What kind of open-source software would be useful to the bioinformatics community? All ideas and opinions welcome. - Joel From jeff at bioinformatics.org Tue Aug 21 20:24:05 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 21 Aug 2001 20:24:05 -0400 Subject: [BiO BB] open source ideas References: Message-ID: <3B82FBA5.CA0FB9A3@bioinformatics.org> Joel Dudley wrote: > > I have the greatest urge to create free, open-source applications for > biological research, but as I scan the lists of available software it seems > like it has all been done If you're referring to projects list at BiO, most are just getting started or are under development. I wouldn't say they're "done" ;-) You may want to consider joining one of the projects, whatever interests you. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From bioinfo at biosystemsconsulting.com Tue Aug 21 23:27:02 2001 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Tue, 21 Aug 2001 23:27:02 -0400 Subject: [BiO BB] open source ideas In-Reply-To: Message-ID: Hello, How about starting with a windows application that allows easy compilation of EST Sequences for submission. It could have a "interrogator" function which allows the user to fill out all of the necessary fields then it annotates each EST sequence file either with the existing file name or some other format (for example a lab code and a number, the number could change while the lab code did not). T hen the program could move all the annotated files into one large file and add the final headers. The saved file could then be emailed to ESTDB. I doubt the program would take a huge amount of time to write and debug, but I bet it would save the average researcher (and the PERL programmer) time by allowing the average scientist to use a windows application to compile his or her own data. My two sense, Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Joel Dudley Sent: Tuesday, August 21, 2001 7:11 PM To: 'bio_bulletin_board at bioinformatics.org' Subject: [BiO BB] open source ideas Hello, I have the greatest urge to create free, open-source applications for biological research, but as I scan the lists of available software it seems like it has all been done (Which I know is FAR from the truth). What kind of open-source software would be useful to the bioinformatics community? All ideas and opinions welcome. - Joel _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From indraneel at indialine.org Tue Aug 21 23:36:08 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 21 Aug 2001 22:36:08 -0500 Subject: [BiO BB] open source ideas In-Reply-To: <3B82FBA5.CA0FB9A3@bioinformatics.org> References: <3B82FBA5.CA0FB9A3@bioinformatics.org> Message-ID: <20010821223608.B19144@indialine.org> On Tue, Aug 21, 2001 at 08:24:05PM -0400, J.W. Bizzaro wrote: > Joel Dudley wrote: > > > > I have the greatest urge to create free, open-source applications for > > biological research, but as I scan the lists of available software it seems > > like it has all been done all been done?? Please don't scare me like that, I still get a paycheck every month for writing (would be) open source code for Bioinfo. > If you're referring to projects list at BiO, most are just getting started or > are under development. I wouldn't say they're "done" ;-) You may want to > consider joining one of the projects, whatever interests you. or if you find other people's ideas difficult to follow, read up some semi-scientific articles (scientific american probably would be a good start, also new scientist), look at a biological problem (whatever interests you) from a programmer's/IT person's point of view and do something about it (code, code, code). I'm pretty certain nobody will have addressed it before, but you can check that at google.com before you start. best wishes, Indraneel -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Tue Aug 21 23:45:25 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 21 Aug 2001 22:45:25 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010821224525.C19144@indialine.org> On Tue, Aug 21, 2001 at 11:27:02PM -0400, bioinfo wrote: > Hello, > How about starting with a windows application that allows easy compilation ^^^^^^^ Is Perl included in the default installation? > of EST Sequences for submission. It could have a "interrogator" function > which allows the user to fill out all of the necessary fields then it > annotates each EST sequence file either with the existing file name or some > other format (for example a lab code and a number, the number could change > while the lab code did not). T hen the program could move all the annotated > files into one large file and add the final headers. The saved file could > then be emailed to ESTDB. I doubt the program would take a huge amount of > time to write and debug, but I bet it would save the average researcher (and > the PERL programmer) time by allowing the average scientist to use a windows > application to compile his or her own data. or make this a PHP/Apache or Perl/Apache hack so people everywhere can (re)use your code. It's a nice idea which need not be limited only to EST sequences. -- http://www.indialine.org/indraneel/ From bioinfo at biosystemsconsulting.com Tue Aug 21 23:56:09 2001 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Tue, 21 Aug 2001 23:56:09 -0400 Subject: [BiO BB] open source ideas In-Reply-To: <20010821224525.C19144@indialine.org> Message-ID: Hello, I agree it could be expanded to a much larger submission / compilation tool. I considered creating the application using Perl / CGI scripts with a Web interface and I came to the conclusion that it would be more user friendly if anyone could install it on their local machine and run a graphical interface that allowed easy director selection and data entry for the header files. While writing it as a Visual application does limit it to the windows platform if it were written in Java with an installer that queried the system for OS type then it could install the necessary Java components and it could run essentially platform independent. Anyway, I would love to see this program as an independent application rather than as PERL scripts on a website. Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Tuesday, August 21, 2001 11:45 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas On Tue, Aug 21, 2001 at 11:27:02PM -0400, bioinfo wrote: > Hello, > How about starting with a windows application that allows easy compilation ^^^^^^^ Is Perl included in the default installation? > of EST Sequences for submission. It could have a "interrogator" function > which allows the user to fill out all of the necessary fields then it > annotates each EST sequence file either with the existing file name or some > other format (for example a lab code and a number, the number could change > while the lab code did not). T hen the program could move all the annotated > files into one large file and add the final headers. The saved file could > then be emailed to ESTDB. I doubt the program would take a huge amount of > time to write and debug, but I bet it would save the average researcher (and > the PERL programmer) time by allowing the average scientist to use a windows > application to compile his or her own data. or make this a PHP/Apache or Perl/Apache hack so people everywhere can (re)use your code. It's a nice idea which need not be limited only to EST sequences. -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From indraneel at indialine.org Wed Aug 22 00:14:23 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Tue, 21 Aug 2001 23:14:23 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: <20010821224525.C19144@indialine.org> Message-ID: <20010821231423.E19144@indialine.org> Hi, You're right, possibly it'll make sense to keep this sort of thing stand alone. It releases the user from the clutches of the web admin. Also if one is content with a text interface, then it will be platform independent, I guess perl has posix conformance. And with the possibility of implementing things as modules, this can really be scaleable. (Of course i don't know Java, so am supporting perl). Now to find someone to code it! \indraneel On Tue, Aug 21, 2001 at 11:56:09PM -0400, bioinfo wrote: > Hello, > I agree it could be expanded to a much larger submission / compilation > tool. I considered creating the application using Perl / CGI scripts with a > Web interface and I came to the conclusion that it would be more user > friendly if anyone could install it on their local machine and run a > graphical interface that allowed easy director selection and data entry for > the header files. While writing it as a Visual application does limit it to > the windows platform if it were written in Java with an installer that > queried the system for OS type then it could install the necessary Java > components and it could run essentially platform independent. Anyway, I > would love to see this program as an independent application rather than as > PERL scripts on a website. > > Mark Burke -- http://www.indialine.org/indraneel/ From bioinfo at biosystemsconsulting.com Wed Aug 22 09:30:48 2001 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Wed, 22 Aug 2001 09:30:48 -0400 Subject: [BiO BB] open source ideas In-Reply-To: <20010821231423.E19144@indialine.org> Message-ID: Hello, If you do I would love to see it and use it when it is complete. Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Wednesday, August 22, 2001 12:14 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Hi, You're right, possibly it'll make sense to keep this sort of thing stand alone. It releases the user from the clutches of the web admin. Also if one is content with a text interface, then it will be platform independent, I guess perl has posix conformance. And with the possibility of implementing things as modules, this can really be scaleable. (Of course i don't know Java, so am supporting perl). Now to find someone to code it! \indraneel On Tue, Aug 21, 2001 at 11:56:09PM -0400, bioinfo wrote: > Hello, > I agree it could be expanded to a much larger submission / compilation > tool. I considered creating the application using Perl / CGI scripts with a > Web interface and I came to the conclusion that it would be more user > friendly if anyone could install it on their local machine and run a > graphical interface that allowed easy director selection and data entry for > the header files. While writing it as a Visual application does limit it to > the windows platform if it were written in Java with an installer that > queried the system for OS type then it could install the necessary Java > components and it could run essentially platform independent. Anyway, I > would love to see this program as an independent application rather than as > PERL scripts on a website. > > Mark Burke -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Joel.Dudley at DevelopOnline.com Wed Aug 22 11:00:41 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 22 Aug 2001 08:00:41 -0700 Subject: [BiO BB] open source ideas Message-ID: Alright already! I'll code it. :-) I am mainly a Unix programmer but Window's programming is easy so I can whip something together. There are some cross platform GUI toolkits like Motif or GTK but I am unsure about their quirks between platforms. I will probably write it in Visual C++ unless I find a better cross-platform solution (which would be preferred since I use Linux on all my machines). Maybe I can come up with my own simple widget set using a cross-platform graphics library like SDL. I will post the program to this list when I have the first alpha version done. I know PHP just as well but PHP+Apache can be a bear for the non-sysadmin savvy (even though it is very cool). I guess this would be a good time for an informal poll. What OS do you use for your daily Desktop? - Joel -----Original Message----- From: bioinfo [mailto:bioinfo at biosystemsconsulting.com] Sent: Wednesday, August 22, 2001 6:31 AM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] open source ideas Hello, If you do I would love to see it and use it when it is complete. Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Wednesday, August 22, 2001 12:14 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Hi, You're right, possibly it'll make sense to keep this sort of thing stand alone. It releases the user from the clutches of the web admin. Also if one is content with a text interface, then it will be platform independent, I guess perl has posix conformance. And with the possibility of implementing things as modules, this can really be scaleable. (Of course i don't know Java, so am supporting perl). Now to find someone to code it! \indraneel On Tue, Aug 21, 2001 at 11:56:09PM -0400, bioinfo wrote: > Hello, > I agree it could be expanded to a much larger submission / compilation > tool. I considered creating the application using Perl / CGI scripts with a > Web interface and I came to the conclusion that it would be more user > friendly if anyone could install it on their local machine and run a > graphical interface that allowed easy director selection and data entry for > the header files. While writing it as a Visual application does limit it to > the windows platform if it were written in Java with an installer that > queried the system for OS type then it could install the necessary Java > components and it could run essentially platform independent. Anyway, I > would love to see this program as an independent application rather than as > PERL scripts on a website. > > Mark Burke -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From reillywu at yahoo.com Wed Aug 22 11:01:39 2001 From: reillywu at yahoo.com (Chunlei Wu) Date: Wed, 22 Aug 2001 08:01:39 -0700 (PDT) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #74 - 2 msgs In-Reply-To: <200108211600.MAA30212@www.bioinformatics.org> Message-ID: <20010822150139.22845.qmail@web4903.mail.yahoo.com> Thanks,Thomas. I found a page at "http://www.ensembl.org/stats/" said file "ensembl-1.1.0_masked_golden_path.gz" is "DNA database (masked for repetitive sequences)". So I think that's the data I needed. Thank you very much. Newgene --- bio_bulletin_board-admin at bioinformatics.org wrote: > > Send BiO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body > 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it > is more specific than > "Re: Contents of BiO_Bulletin_Board digest...") > > > Today's Topics: > > 1. Is there a database available including all > non-repetitive sequences of human genome (Chunlei > Wu) > 2. Re: Is there a database available including all > non-repetitive sequences of human genome (Thomas > Sicheritz-Ponten) > > --__--__-- > > Message: 1 > Date: Tue, 21 Aug 2001 04:07:16 -0700 (PDT) > From: Chunlei Wu > Subject: [BiO BB] Is there a database available > including all non-repetitive sequences of human > genome > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > As title. > I know the repetitive sequences in human genome can > be > masked by > RepMasker. Did someone mask the entire human genome > and make available > the human genome sequnences without repetitive > sequences? > > Thanks > > Newgene > > > __________________________________________________ > Do You Yahoo!? > Make international calls for as low as $.04/minute > with Yahoo! Messenger > http://phonecard.yahoo.com/ > > --__--__-- > > Message: 2 > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Is there a database available > including all non-repetitive sequences of human > genome > From: Thomas Sicheritz-Ponten > Date: 21 Aug 2001 13:25:43 +0200 > Reply-To: bio_bulletin_board at bioinformatics.org > > Chunlei Wu writes: > > > As title. > > I know the repetitive sequences in human genome > can be > > masked by > > RepMasker. Did someone mask the entire human > genome > > and make available > > the human genome sequnences without repetitive > > sequences? > > > > Check what ensembl provides: www.ensembl.org > Maybe you can find a description about how > ftp://ftp.ensembl.org/pub/current/data/fasta/dna/ensembl-1.1.0_masked_golden_path.gz > has been masked. > > good luck > -thomas > > -- > Sicheritz-Ponten Thomas, Ph.D CBS, Department of > Biotechnology > thomas at biopython.org The Technical > University of Denmark > CBS: +45 45 252489 Building 208, DK-2800 > Lyngby > Fax +45 45 931585 > http://www.cbs.dtu.dk/thomas > > De Chelonian Mobile ... The Turtle Moves ... > > > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > --__--__---- > > End of BiO_Bulletin_Board Digest __________________________________________________ Do You Yahoo!? Make international calls for as low as $.04/minute with Yahoo! Messenger http://phonecard.yahoo.com/ From stein at fieldmuseum.org Wed Aug 22 11:25:28 2001 From: stein at fieldmuseum.org (Jennifer Steinbachs) Date: Wed, 22 Aug 2001 10:25:28 -0500 (CDT) Subject: [BiO BB] open source ideas In-Reply-To: Message-ID: On Wed, 22 Aug 2001, Joel Dudley wrote: >What OS do you use for your daily Desktop? Depends... usually Solaris... sometimes linux (either intel or powerpc)... much less frequently (and only because of special applications) MacOS of some flavor. Keep in mind that most hard core *biologists* use either windows or mac. Of those who are brave enough to venture into the unix world, most will not have root access to install server applications. Those that do have root access typically don't have developed sys admin skills. Just my observations... -jennifer From philipp.pagel at cmp.yale.edu Wed Aug 22 12:06:24 2001 From: philipp.pagel at cmp.yale.edu (Philipp Pagel) Date: Wed, 22 Aug 2001 12:06:24 -0400 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010822120624.A2566@merlin> Hi! On Wed, Aug 22, 2001 at 08:00:41AM -0700, Joel Dudley wrote: > Alright already! I'll code it. :-) I am mainly a Unix programmer but > Window's programming is easy so I can whip something together. There are > some cross platform GUI toolkits like Motif or GTK but I am unsure about > their quirks between platforms. I will probably write it in Visual C++ > unless I find a better cross-platform solution (which would be preferred > since I use Linux on all my machines). Maybe I can come up with my own > simple widget set using a cross-platform graphics library like SDL. I will I've been looking arround for a nice cross plattform GUI toolkit. There are plenty out there so I wouldn't try to reinvent the wheel and hack together another one. For a nice overview have a look at: http://www.geocities.com/SiliconValley/Vista/7184/guitool.html#free_toolkit Especially wxWindows looks quite good to me (no affiliation): http://www.wxwindows.org/ It seems to have originated in a UNIX environment and has been ported to an impressive number of platforms. If I really start to write the thing I'm thinking about I'll probably use this... cu Philipp -- Dr. Philipp Pagel Department of Cellular and Molecular Physiology phone: (203) 785-6835 SHM, B117 fax: (203) 785-4951 Yale University 333 Cedar ST New Haven, CT 06520 USA From Joel.Dudley at DevelopOnline.com Wed Aug 22 12:20:54 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 22 Aug 2001 09:20:54 -0700 Subject: [BiO BB] open source ideas Message-ID: Thanks! Wxwindows looks great! -----Original Message----- From: Philipp Pagel [mailto:philipp.pagel at cmp.yale.edu] Sent: Wednesday, August 22, 2001 9:06 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Hi! On Wed, Aug 22, 2001 at 08:00:41AM -0700, Joel Dudley wrote: > Alright already! I'll code it. :-) I am mainly a Unix programmer but > Window's programming is easy so I can whip something together. There are > some cross platform GUI toolkits like Motif or GTK but I am unsure about > their quirks between platforms. I will probably write it in Visual C++ > unless I find a better cross-platform solution (which would be preferred > since I use Linux on all my machines). Maybe I can come up with my own > simple widget set using a cross-platform graphics library like SDL. I will I've been looking arround for a nice cross plattform GUI toolkit. There are plenty out there so I wouldn't try to reinvent the wheel and hack together another one. For a nice overview have a look at: http://www.geocities.com/SiliconValley/Vista/7184/guitool.html#free_toolkit Especially wxWindows looks quite good to me (no affiliation): http://www.wxwindows.org/ It seems to have originated in a UNIX environment and has been ported to an impressive number of platforms. If I really start to write the thing I'm thinking about I'll probably use this... cu Philipp -- Dr. Philipp Pagel Department of Cellular and Molecular Physiology phone: (203) 785-6835 SHM, B117 fax: (203) 785-4951 Yale University 333 Cedar ST New Haven, CT 06520 USA _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From johann at egenetics.com Wed Aug 22 12:30:16 2001 From: johann at egenetics.com (Johann Visagie) Date: Wed, 22 Aug 2001 18:30:16 +0200 Subject: [BiO BB] open source ideas In-Reply-To: <20010822120624.A2566@merlin>; from philipp.pagel@cmp.yale.edu on Wed, Aug 22, 2001 at 12:06:24PM -0400 References: <20010822120624.A2566@merlin> Message-ID: <20010822183016.B52215@fling.sanbi.ac.za> Philipp Pagel on 2001-08-22 (Wed) at 12:06:24 -0400: > > http://www.geocities.com/SiliconValley/Vista/7184/guitool.html#free_toolkit Nice summary. > Especially wxWindows looks quite good to me (no affiliation): > > http://www.wxwindows.org/ wxWindows is excellent. The Python wrapper, wxPython (http://wxpython.org) makes cross-platform GUI development _particularly_ simple. One can almost start considering the use of the word "trivial". The standard methodology for using Python to prototype cross-platform apps goes something like: - Prototype the entire app in Python until it works - Profile, and if too slow: - Rip out performance-critical modules - Rewrite them in C(++) - Plug them back in - Lather, rinse, repeat Using wxPython and wxWindows, the above recipe can be extended from "cross-platform development" to "cross-platform _GUI_ development". -- V From cprjay at hotmail.com Wed Aug 22 12:31:08 2001 From: cprjay at hotmail.com (Chamath Placid Jayasuriya) Date: Thu, 23 Aug 2001 02:31:08 +1000 Subject: [BiO BB] help Message-ID: Hello, just a quick question: when using the program DBClustal why use the display alignment BLAST instead of DBClustal sequence order? hope someone can help _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From Joel.Dudley at DevelopOnline.com Wed Aug 22 15:34:50 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 22 Aug 2001 12:34:50 -0700 Subject: [BiO BB] open source ideas Message-ID: Just to be sure, the target database is dbEST at NCBI right? No other proprietary databases as targets? - Joel -----Original Message----- From: bioinfo [mailto:bioinfo at biosystemsconsulting.com] Sent: Wednesday, August 22, 2001 6:31 AM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] open source ideas Hello, If you do I would love to see it and use it when it is complete. Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Wednesday, August 22, 2001 12:14 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Hi, You're right, possibly it'll make sense to keep this sort of thing stand alone. It releases the user from the clutches of the web admin. Also if one is content with a text interface, then it will be platform independent, I guess perl has posix conformance. And with the possibility of implementing things as modules, this can really be scaleable. (Of course i don't know Java, so am supporting perl). Now to find someone to code it! \indraneel On Tue, Aug 21, 2001 at 11:56:09PM -0400, bioinfo wrote: > Hello, > I agree it could be expanded to a much larger submission / compilation > tool. I considered creating the application using Perl / CGI scripts with a > Web interface and I came to the conclusion that it would be more user > friendly if anyone could install it on their local machine and run a > graphical interface that allowed easy director selection and data entry for > the header files. While writing it as a Visual application does limit it to > the windows platform if it were written in Java with an installer that > queried the system for OS type then it could install the necessary Java > components and it could run essentially platform independent. Anyway, I > would love to see this program as an independent application rather than as > PERL scripts on a website. > > Mark Burke -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From bioinfo at biosystemsconsulting.com Wed Aug 22 16:12:33 2001 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Wed, 22 Aug 2001 16:12:33 -0400 Subject: [BiO BB] open source ideas In-Reply-To: Message-ID: Joel, That is the first submission area I was going to look at. There is no existing tool that makes assembling these sequences easy for the average bench scientist. Mark Burke PS if you want to take this discussion off the news group feel free to email me directly at mark_burke at ncsu.edu -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Joel Dudley Sent: Wednesday, August 22, 2001 3:35 PM To: 'bio_bulletin_board at bioinformatics.org' Subject: RE: [BiO BB] open source ideas Just to be sure, the target database is dbEST at NCBI right? No other proprietary databases as targets? - Joel -----Original Message----- From: bioinfo [mailto:bioinfo at biosystemsconsulting.com] Sent: Wednesday, August 22, 2001 6:31 AM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] open source ideas Hello, If you do I would love to see it and use it when it is complete. Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Wednesday, August 22, 2001 12:14 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Hi, You're right, possibly it'll make sense to keep this sort of thing stand alone. It releases the user from the clutches of the web admin. Also if one is content with a text interface, then it will be platform independent, I guess perl has posix conformance. And with the possibility of implementing things as modules, this can really be scaleable. (Of course i don't know Java, so am supporting perl). Now to find someone to code it! \indraneel On Tue, Aug 21, 2001 at 11:56:09PM -0400, bioinfo wrote: > Hello, > I agree it could be expanded to a much larger submission / compilation > tool. I considered creating the application using Perl / CGI scripts with a > Web interface and I came to the conclusion that it would be more user > friendly if anyone could install it on their local machine and run a > graphical interface that allowed easy director selection and data entry for > the header files. While writing it as a Visual application does limit it to > the windows platform if it were written in Java with an installer that > queried the system for OS type then it could install the necessary Java > components and it could run essentially platform independent. Anyway, I > would love to see this program as an independent application rather than as > PERL scripts on a website. > > Mark Burke -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From muppetman559 at hotmail.com Wed Aug 22 19:38:06 2001 From: muppetman559 at hotmail.com (James Thompson) Date: Wed, 22 Aug 2001 18:38:06 -0500 Subject: [BiO BB] open source ideas Message-ID: One idea that I have not heard from this discussion group is the use of a site such as sourceforge.net or bioinformatics.org to host the development of your work. Sites such as these offer free hosting space and an easy means for interested parties to find your applications. Also, if your project ever becomes large enough to require additional people, both of these places provide easy means to integrate work from multiple programmers. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From Joel.Dudley at DevelopOnline.com Wed Aug 22 19:56:40 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 22 Aug 2001 16:56:40 -0700 Subject: [BiO BB] open source ideas Message-ID: Well suggested. Once the project is in alpha I will hot it on Bioinformatics.org and begin looking for additional team members when needed. -----Original Message----- From: James Thompson [mailto:muppetman559 at hotmail.com] Sent: Wednesday, August 22, 2001 4:38 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas One idea that I have not heard from this discussion group is the use of a site such as sourceforge.net or bioinformatics.org to host the development of your work. Sites such as these offer free hosting space and an easy means for interested parties to find your applications. Also, if your project ever becomes large enough to require additional people, both of these places provide easy means to integrate work from multiple programmers. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From indraneel at indialine.org Wed Aug 22 23:29:58 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Wed, 22 Aug 2001 22:29:58 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010822222958.A23571@indialine.org> Great, thanks Joel, for a moment I thought Mark wanted me to code it. I'm also very happy today. My boss approved building a 8 node beowulf. On Wed, Aug 22, 2001 at 08:00:41AM -0700, Joel Dudley wrote: > Alright already! I'll code it. :-) I am mainly a Unix programmer but > Window's programming is easy so I can whip something together. There are ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (have to put this on the todo list then) > an informal poll. What OS do you use for your daily Desktop? guess what, my daily desktop has 'debian' scrawled all over it in huge letters! \Indraneel -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Wed Aug 22 23:39:56 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Wed, 22 Aug 2001 22:39:56 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010822223956.B23571@indialine.org> On Wed, Aug 22, 2001 at 10:25:28AM -0500, Jennifer Steinbachs wrote: > > Keep in mind that most hard core *biologists* use either windows or mac. where cp is copy, mv is rename, and rm is delete (nowadays it only takes a few clicks to trash the system though). Probably a self extracting archive with a (blue screen) installer is important to the survival of the code then. Or dump the .pl files in a directory and start the README with "Please ask your system administrator to install these files in c:\usr\local\bin" \indraneel -- http://www.indialine.org/indraneel/ From bioinformaticsckk at yahoo.co.in Thu Aug 23 00:41:12 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Thu, 23 Aug 2001 05:41:12 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #73 - 1 msg In-Reply-To: <200108181600.MAA11701@www.bioinformatics.org> Message-ID: <20010823044112.15616.qmail@web8001.mail.in.yahoo.com> Hello everyone, I want to know the different promoter-finding programs that are freely available. Where can i find a comprehensive information on the different promoters that are identified till now in the biological system (both prokaryotic and Eukaryotic). Thank you in advance. Regards, Kiran Kumar ____________________________________________________________ Do You Yahoo!? Send a newsletter, share photos & files, conduct polls, organize chat events. Visit http://in/ groups.yahoo.com From jwester at sgi1.chemie.uni-hamburg.de Thu Aug 23 04:09:52 2001 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Thu, 23 Aug 2001 10:09:52 +0200 Subject: [BiO BB] open source ideas References: Message-ID: <3B84BA50.950DD118@sgi1.chemie.uni-hamburg.de> Joel Dudley wrote: > What OS do you use for your daily Desktop? Linux (KDE), Irix (CDE) and Windows. jcw -- Jan-Christoph Westermann - jwester at sgi1.chemie.uni-hamburg.de Der Sinn einer jeden Sig ist doch klar: Sie dient als Mahnmal dafuer das nicht jede Tradition einen Sinn habn muss. Patrick `Pacifier` Multhaup in detebe From bioinfo at biosystemsconsulting.com Thu Aug 23 08:07:23 2001 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Thu, 23 Aug 2001 08:07:23 -0400 Subject: [BiO BB] open source ideas In-Reply-To: <20010822222958.A23571@indialine.org> Message-ID: Thanks as well Joel. I wasn't trying to push anyone to code it. It has been in the back of my mind for awhile and I haven't had the time (and it has been a long time since I have done any "real" coding). I look foreword to seeing the application develop and grow to something more than we have discussed already. Indraneel, what primary applications are you planning to use with the Beowulf? I am in the process of setting up a HPC environment and have looked at Linux clusters. I would be interested in hearing your thoughts about implementation and the applications you plan to use on it (if you can talk about it, that is...) Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Wednesday, August 22, 2001 11:30 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Great, thanks Joel, for a moment I thought Mark wanted me to code it. I'm also very happy today. My boss approved building a 8 node beowulf. On Wed, Aug 22, 2001 at 08:00:41AM -0700, Joel Dudley wrote: > Alright already! I'll code it. :-) I am mainly a Unix programmer but > Window's programming is easy so I can whip something together. There are ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (have to put this on the todo list then) > an informal poll. What OS do you use for your daily Desktop? guess what, my daily desktop has 'debian' scrawled all over it in huge letters! \Indraneel -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From stein at fieldmuseum.org Thu Aug 23 10:33:12 2001 From: stein at fieldmuseum.org (Jennifer Steinbachs) Date: Thu, 23 Aug 2001 09:33:12 -0500 (CDT) Subject: [BiO BB] HPC implementation In-Reply-To: Message-ID: On Thu, 23 Aug 2001, bioinfo wrote: > Indraneel, what primary applications are you planning to use with the >Beowulf? I am in the process of setting up a HPC environment and have >looked at Linux clusters. I would be interested in hearing your thoughts >about implementation and the applications you plan to use on it (if you can >talk about it, that is...) I set a cluster up last year and my husband set up a bigger one at his place of employment this past spring (and will likely set up a third next year). We've been toying with the idea of putting a FAQ up on my website for the biologically inclined who want (or think they want) a cluster. The targetted audience is an academic setting - based on both of our experiences. The focus of the FAQ would be on all the planning questions that one should be asking... e.g., once i buy the system, who will look after it? who will pay for upgrades? where will the beast go? etc. I haven't put this into full gear yet... would this be as useful as I think it would? -jennifer ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist http://compbiology.org ----------------------------------- From Joel.Dudley at DevelopOnline.com Thu Aug 23 11:40:59 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Thu, 23 Aug 2001 08:40:59 -0700 Subject: [BiO BB] open source ideas Message-ID: Ok, I am pretty sure I know how I am going to do this program. I need to tinker with the widget stuff so I can write it once and make it cross platform. From my poll it seems like many of you use Debian on your desktop (like me!) or some other flavor of Linux. It also seems that many of you are forced to use windows for research. Once I do some testing with WxWindows this weekend I should have an alpha version by the end of next week. At that time I will submit the program to the list for review and will then move it to bioinformatics.org for hosting. I am really excited about the support I am getting from this list for new program ideas. Let's keep it up! - Joel P.S. With all of the cluster talk today maybe the next project can be a modular clustering architecture with a slick GUI and management tools wrapped around linux. -----Original Message----- From: bioinfo [mailto:bioinfo at biosystemsconsulting.com] Sent: Thursday, August 23, 2001 5:07 AM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] open source ideas Thanks as well Joel. I wasn't trying to push anyone to code it. It has been in the back of my mind for awhile and I haven't had the time (and it has been a long time since I have done any "real" coding). I look foreword to seeing the application develop and grow to something more than we have discussed already. Indraneel, what primary applications are you planning to use with the Beowulf? I am in the process of setting up a HPC environment and have looked at Linux clusters. I would be interested in hearing your thoughts about implementation and the applications you plan to use on it (if you can talk about it, that is...) Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Wednesday, August 22, 2001 11:30 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Great, thanks Joel, for a moment I thought Mark wanted me to code it. I'm also very happy today. My boss approved building a 8 node beowulf. On Wed, Aug 22, 2001 at 08:00:41AM -0700, Joel Dudley wrote: > Alright already! I'll code it. :-) I am mainly a Unix programmer but > Window's programming is easy so I can whip something together. There are ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (have to put this on the todo list then) > an informal poll. What OS do you use for your daily Desktop? guess what, my daily desktop has 'debian' scrawled all over it in huge letters! \Indraneel -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From indraneel at indialine.org Thu Aug 23 11:49:22 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Thu, 23 Aug 2001 10:49:22 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: <20010822222958.A23571@indialine.org> Message-ID: <20010823104922.A25837@indialine.org> Hi Mark, On Thu, Aug 23, 2001 at 08:07:23AM -0400, bioinfo wrote: > Thanks as well Joel. I wasn't trying to push anyone to code it. It has > been in the back of my mind for awhile and I haven't had the time (and it Yes, it happens to all of us all the time. > > Indraneel, what primary applications are you planning to use with the > Beowulf? I am in the process of setting up a HPC environment and have > looked at Linux clusters. I would be interested in hearing your thoughts > about implementation and the applications you plan to use on it (if you can > talk about it, that is...) Thankfully, I can talk about what apps we are planning to run (the code is open too but will be released only after papers are published, I wish it could be made open now so people could point out the bugs). Actually the primary aim is to use it as a cluster of workstations (COW) since our multi processor (costly) servers running solaris are having a hard time keeping up with the jobs. This probably shall be running code that we develop inhouse, mainly protein structure analysis code. And since we shall be making a beowulf anyway, it does not make sense not to use MPICH and PVM, so hopefully we shall write our code to make best use of the cluster as a parallel machine. And while we are at it, we shall also be testing out the parallel implementations of different bioinformatics software, when we require them. The general plan is to use 8 diskless nodes using the AMD Athlon 1.4 GHz, Asus A7M266 motherboard, 512 MB DDR RAM, Netgear GA620 gigabit ethernet provided we can get them. A 200 GB dual athlon (AMD 1.2 GHz, Tyan thunder K7 S2462UNG, 2GB DDR RAM) file server per 8 nodes, and a gateway (same as node with Ultra ATA disks). Currently I am trying to search for maintainance and system software (like bwatch, schedulers etc) to see what is available and which are easy to use, while fulfilling our requirements. I'll gladly accept any suggestions you have to offer. TIA, Indraneel -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Thu Aug 23 11:54:04 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Thu, 23 Aug 2001 10:54:04 -0500 Subject: [BiO BB] HPC implementation In-Reply-To: References: Message-ID: <20010823105404.B25837@indialine.org> On Thu, Aug 23, 2001 at 09:33:12AM -0500, Jennifer Steinbachs wrote: > > I haven't put this into full gear yet... would this be as useful as I > think it would? More than useful, it's required. Once you set up the site also ask the www.beowulf.org people to put a link from their site. None of the sites talk much of exactly how the cluster is being managed and used from a sysad/netad point of view (it's become like the Linux books which only talk of configuration). If you can put that in, it'll be great. TIA, Indraneel -- http://www.indialine.org/indraneel/ From indraneel at indialine.org Thu Aug 23 12:07:52 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Thu, 23 Aug 2001 11:07:52 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010823110752.C25837@indialine.org> On Thu, Aug 23, 2001 at 08:40:59AM -0700, Joel Dudley wrote: > Ok, I am pretty sure I know how I am going to do this program. I need to Great, and best wishes. Remember to use the perl posix compliancy, else we'll have to sit down and change the /\ one way or the other /\/\/\ > > P.S. With all of the cluster talk today maybe the next project can be a > modular clustering architecture with a slick GUI and management tools > wrapped around linux. I hope that exists allready, if not I know on whom the axe will fall \Indraneel -- http://www.indialine.org/indraneel/ From Joel.Dudley at DevelopOnline.com Thu Aug 23 16:25:38 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Thu, 23 Aug 2001 13:25:38 -0700 Subject: [BiO BB] open source ideas Message-ID: Not going to use perl. -----Original Message----- From: Indraneel Majumdar [mailto:indraneel at indialine.org] Sent: Thursday, August 23, 2001 9:08 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas On Thu, Aug 23, 2001 at 08:40:59AM -0700, Joel Dudley wrote: > Ok, I am pretty sure I know how I am going to do this program. I need to Great, and best wishes. Remember to use the perl posix compliancy, else we'll have to sit down and change the /\ one way or the other /\/\/\ > > P.S. With all of the cluster talk today maybe the next project can be a > modular clustering architecture with a slick GUI and management tools > wrapped around linux. I hope that exists allready, if not I know on whom the axe will fall \Indraneel -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From michikami at yahoo.com Thu Aug 23 12:40:47 2001 From: michikami at yahoo.com (Michi Kami) Date: Thu, 23 Aug 2001 09:40:47 -0700 (PDT) Subject: [BiO BB] open source ideas (Beowulf) In-Reply-To: Message-ID: <20010823164047.87044.qmail@web20007.mail.yahoo.com> In case anyone isn't aware of it and would be interested - John Koza from Stanford has a 1000-Pentium Beowulf cluster set up. (As my 3-year old says, "that's a big puppy!") He has a write-up, and links to it, at http://www.xent.com/FoRK-archive/july99/0591.html His area is genetic algorithms (mine also, while bridging into bioinformatics), and the system runs Linux. -Mark bioinfo wrote: Thanks as well Joel. I wasn't trying to push anyone to code it. It has been in the back of my mind for awhile and I haven't had the time (and it has been a long time since I have done any "real" coding). I look foreword to seeing the application develop and grow to something more than we have discussed already. Indraneel, what primary applications are you planning to use with the Beowulf? I am in the process of setting up a HPC environment and have looked at Linux clusters. I would be interested in hearing your thoughts about implementation and the applications you plan to use on it (if you can talk about it, that is...) Mark Burke -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of Indraneel Majumdar Sent: Wednesday, August 22, 2001 11:30 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas Great, thanks Joel, for a moment I thought Mark wanted me to code it. I'm also very happy today. My boss approved building a 8 node beowulf. On Wed, Aug 22, 2001 at 08:00:41AM -0700, Joel Dudley wrote: > Alright already! I'll code it. :-) I am mainly a Unix programmer but > Window's programming is easy so I can whip something together. There are ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (have to put this on the todo list then) > an informal poll. What OS do you use for your daily Desktop? guess what, my daily desktop has 'debian' scrawled all over it in huge letters! \Indraneel -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Do You Yahoo!? Make international calls for as low as $0.04/minute with Yahoo! Messenger. -------------- next part -------------- An HTML attachment was scrubbed... URL: From indraneel at indialine.org Thu Aug 23 17:23:53 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Thu, 23 Aug 2001 16:23:53 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010823162353.B26800@indialine.org> On Thu, Aug 23, 2001 at 01:25:38PM -0700, Joel Dudley wrote: > Not going to use perl. will it run on my desktop? -- http://www.indialine.org/indraneel/ From jeff at bioinformatics.org Thu Aug 23 17:38:51 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 23 Aug 2001 17:38:51 -0400 Subject: [BiO BB] bioclusters Message-ID: <3B8577EB.331C55F4@bioinformatics.org> Michi Kami wrote: > > In case anyone isn't aware of it and would be interested - John > Koza from Stanford has a 1000-Pentium Beowulf cluster set up. > (As my 3-year old says, "that's a big puppy!") He has a write-up, > and links to it, at http://www.xent.com/FoRK-archive/july99/0591.html > His area is genetic algorithms (mine also, while bridging > into bioinformatics), and the system runs Linux. I've been considering starting a mailing list, and later posting some HOWTO's, for building computer clusters (e.g., Beowulf) for bioinformatics. There are at least two issues that make "bioclusters" unique, requiring discussions outside of those for traditional clusters: (1) some bioinformatics programs have special hardware requirements (e.g., "embarrassingly parallel" vs. parallel or serial), and (2) bioinformaticians/ists may want to find and help each other with locating or porting bioinformatics software to these clusters (e.g., where can one get a parallel version of BLAST?). I know some people who'd like to learn more (or anything) about building bioclusters, but we need some people with experience willing to give advise. It would be silly to have 200 people on a list with no one able to answer a single question. If you are able to help, please contact me at jeff at bioinformatics.org. Also, if anyone knows of an existing discussion forum with educational resources like what I'm proposing, please let us know. Maybe we don't want to reinvent the wheel. Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From dag at fedayi.sonsorol.org Thu Aug 23 17:40:43 2001 From: dag at fedayi.sonsorol.org (chris dagdigian) Date: Thu, 23 Aug 2001 16:40:43 -0500 (EST) Subject: [BiO BB] Re: bioclusters In-Reply-To: <3B8577EB.331C55F4@bioinformatics.org> Message-ID: Acually I just set up necluster.org over the past few months intending to use it as a platform for new england area discussion of clustering :) This idea came from some VA Linux guys that I was working with who thought that the critical mass of clusters in New England was large enough to support a regional interest group. I'm interested in helping out with HOWTO documents and actually I'm trying to get a presentation accepted at the ORA Bioinformatics conference in February where I can talk about production quality life science clusters. In particular I want to talk/write about the VAMPIRE cluster that I just built for Vertex Pharmaceuticals (PR-speak info available at http://www.vpharm.com/Pressreleases2001/pr081301.html :) Count me in as a member of any biocluster list that comes up and please let me know what you think of the "NECLUSTER" idea. I really do think that there could be a pretty good local area clustering user group that may or may not be life science specific depending on its members. Keep me in the loop! -Chris > Michi Kami wrote: > > > > In case anyone isn't aware of it and would be interested - John > > Koza from Stanford has a 1000-Pentium Beowulf cluster set up. > > (As my 3-year old says, "that's a big puppy!") He has a write-up, > > and links to it, at http://www.xent.com/FoRK-archive/july99/0591.html > > His area is genetic algorithms (mine also, while bridging > > into bioinformatics), and the system runs Linux. > > I've been considering starting a mailing list, and later posting some HOWTO's, > for building computer clusters (e.g., Beowulf) for bioinformatics. There are > at least two issues that make "bioclusters" unique, requiring discussions > outside of those for traditional clusters: (1) some bioinformatics programs > have special hardware requirements (e.g., "embarrassingly parallel" vs. > parallel or serial), and (2) bioinformaticians/ists may want to find and help > each other with locating or porting bioinformatics software to these clusters > (e.g., where can one get a parallel version of BLAST?). > > I know some people who'd like to learn more (or anything) about building > bioclusters, but we need some people with experience willing to give advise. > It would be silly to have 200 people on a list with no one able to answer a > single question. If you are able to help, please contact me at > jeff at bioinformatics.org. > > Also, if anyone knows of an existing discussion forum with educational > resources like what I'm proposing, please let us know. Maybe we don't want to > reinvent the wheel. > > Cheers. > Jeff > -- > J.W. Bizzaro jeff at bioinformatics.org > Director, Bioinformatics.org http://bioinformatics.org/~jeff > "As we enjoy great advantages from the inventions of others, we > should be glad of an opportunity to serve others by any invention > of ours; and this we should do freely and generously." > -- Benjamin Franklin > -- > From Joel.Dudley at DevelopOnline.com Thu Aug 23 17:48:35 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Thu, 23 Aug 2001 14:48:35 -0700 Subject: [BiO BB] open source ideas Message-ID: I will probably use C++ with a cross-platform widget set. I will be adamant about full windows and Linux compatibility from the same code base. If it does not run well on your desktop that is unacceptable to me, so I hope it will :-). - Joel -----Original Message----- From: Indraneel Majumdar [mailto:indraneel at indialine.org] Sent: Thursday, August 23, 2001 2:24 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] open source ideas On Thu, Aug 23, 2001 at 01:25:38PM -0700, Joel Dudley wrote: > Not going to use perl. will it run on my desktop? -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jfreeman at variagenics.com Thu Aug 23 17:56:56 2001 From: jfreeman at variagenics.com (jfreeman) Date: Thu, 23 Aug 2001 17:56:56 -0400 Subject: [BiO BB] Re: bioclusters References: Message-ID: <3B857C28.7CCD272C@variagenics.com> Hi Folks, I could have used such a group when I built our in house cluster at Variagenics last year, and there has been a great deal of evolution in the tools and techniques since then. I concur with Chris and would be happy to lend a hand to this group. Thanks for suggesting this Jeff, Jim Freeman chris dagdigian wrote: > > Acually I just set up necluster.org over the past few months intending to > use it as a platform for new england area discussion of clustering :) This > idea came from some VA Linux guys that I was working with who thought that > the critical mass of clusters in New England was large enough to support a > regional interest group. > > I'm interested in helping out with HOWTO documents and actually I'm trying > to get a presentation accepted at the ORA Bioinformatics conference in > February where I can talk about production quality life science > clusters. In particular I want to talk/write about the VAMPIRE cluster > that I just built for Vertex Pharmaceuticals (PR-speak info available at > http://www.vpharm.com/Pressreleases2001/pr081301.html :) > > Count me in as a member of any biocluster list that comes up and please > let me know what you think of the "NECLUSTER" idea. I really do think that > there could be a pretty good local area clustering user group that may or > may not be life science specific depending on its members. > > Keep me in the loop! > > -Chris > > > Michi Kami wrote: > > > > > > In case anyone isn't aware of it and would be interested - John > > > Koza from Stanford has a 1000-Pentium Beowulf cluster set up. > > > (As my 3-year old says, "that's a big puppy!") He has a write-up, > > > and links to it, at http://www.xent.com/FoRK-archive/july99/0591.html > > > His area is genetic algorithms (mine also, while bridging > > > into bioinformatics), and the system runs Linux. > > > > I've been considering starting a mailing list, and later posting some HOWTO's, > > for building computer clusters (e.g., Beowulf) for bioinformatics. There are > > at least two issues that make "bioclusters" unique, requiring discussions > > outside of those for traditional clusters: (1) some bioinformatics programs > > have special hardware requirements (e.g., "embarrassingly parallel" vs. > > parallel or serial), and (2) bioinformaticians/ists may want to find and help > > each other with locating or porting bioinformatics software to these clusters > > (e.g., where can one get a parallel version of BLAST?). > > > > I know some people who'd like to learn more (or anything) about building > > bioclusters, but we need some people with experience willing to give advise. > > It would be silly to have 200 people on a list with no one able to answer a > > single question. If you are able to help, please contact me at > > jeff at bioinformatics.org. > > > > Also, if anyone knows of an existing discussion forum with educational > > resources like what I'm proposing, please let us know. Maybe we don't want to > > reinvent the wheel. > > > > Cheers. > > Jeff > > -- > > J.W. Bizzaro jeff at bioinformatics.org > > Director, Bioinformatics.org http://bioinformatics.org/~jeff > > "As we enjoy great advantages from the inventions of others, we > > should be glad of an opportunity to serve others by any invention > > of ours; and this we should do freely and generously." > > -- Benjamin Franklin > > -- > > From jeff at bioinformatics.org Thu Aug 23 19:28:12 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 23 Aug 2001 19:28:12 -0400 Subject: [BiO BB] bioclusters mailing list Message-ID: <3B85918C.266A0FCA@bioinformatics.org> Okay, as I mentioned I would in my last message, I made a mailing list for discussions about computer clusters for bioinformatics. You can susbscribe via the Web: http://bioinformatics.org/mailman/listinfo/bioclusters E-mail: bioclusters at bioinformatics.org I'll also work on a website for FAQs, etc. See you there! Cheers. Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From jeff at bioinformatics.org Thu Aug 23 19:37:55 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 23 Aug 2001 19:37:55 -0400 Subject: [BiO BB] bioclusters mailing list References: <3B85918C.266A0FCA@bioinformatics.org> Message-ID: <3B8593D3.65730A88@bioinformatics.org> "J.W. Bizzaro" wrote: > > E-mail: > > bioclusters at bioinformatics.org Ooops. This is not the address for subscribing via e-mail. That can be done via bioclusters-request at bioinformatics.org You can send a message with 'help' in the subject line to...get help :-) Jeff -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin -- From indraneel at indialine.org Thu Aug 23 21:19:32 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Thu, 23 Aug 2001 20:19:32 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010823201932.A27495@indialine.org> On Thu, Aug 23, 2001 at 02:48:35PM -0700, Joel Dudley wrote: > I will probably use C++ with a cross-platform widget set. I will be adamant > about full windows and Linux compatibility from the same code base. If it > does not run well on your desktop that is unacceptable to me, so I hope it > will :-). Thanks, that's great. \Indraneel -- http://www.indialine.org/indraneel/ From naka at nethere.com Sat Aug 25 15:26:38 2001 From: naka at nethere.com (M----->) Date: Sat, 25 Aug 2001 12:26:38 -0700 Subject: [BiO BB] Re: Cluster alternative for large NT group References: <200108241600.MAA17198@www.bioinformatics.org> Message-ID: <3B87FBEE.5F38E354@nethere.com> Many firms have large inhouse secretarial and clerical NT boxes. Lucent a while ago implemented a process-freezing software for NT which allows a program and its data to be moved across an available network and find unoccupied machines. (The other approach is cooperating machines continuing to use intermediate results but spawning new processes) Has anybody tried Lucent's ? Thanks Reggie San Diego From Joel.Dudley at DevelopOnline.com Sat Aug 25 21:01:52 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Sat, 25 Aug 2001 18:01:52 -0700 Subject: [BiO BB] open source ideas Message-ID: For anyone interested, I am probably going to use QT after significant research. it has great support for Linux, Win32, and OS X. Plus it is C++ which is what I prefer for this situation. The open-source license is pretty palatable as well. It should prevent anyone from trying to make a slimy buck off of this program. - Joel Dudley -----Original Message----- From: Indraneel Majumdar To: bio_bulletin_board at bioinformatics.org Sent: 8/23/01 6:19 PM Subject: Re: [BiO BB] open source ideas On Thu, Aug 23, 2001 at 02:48:35PM -0700, Joel Dudley wrote: > I will probably use C++ with a cross-platform widget set. I will be adamant > about full windows and Linux compatibility from the same code base. If it > does not run well on your desktop that is unacceptable to me, so I hope it > will :-). Thanks, that's great. \Indraneel -- http://www.indialine.org/indraneel/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From indraneel at indialine.org Sun Aug 26 00:29:35 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Sat, 25 Aug 2001 23:29:35 -0500 Subject: [BiO BB] open source ideas In-Reply-To: References: Message-ID: <20010825232935.A12607@indialine.org> Hi, On Sat, Aug 25, 2001 at 06:01:52PM -0700, Joel Dudley wrote: > For anyone interested, I am probably going to use QT after significant > research. it has great support for Linux, Win32, and OS X. Plus it is C++ What about tcl/tk. I've seen Ousterhout's book on many a windows user's desk. > which is what I prefer for this situation. The open-source license is pretty > palatable as well. It should prevent anyone from trying to make a slimy buck > off of this program. guess it's GPL (since there is kde for debian now) \Indraneel -- http://www.indialine.org/indraneel/ From Joel.Dudley at DevelopOnline.com Mon Aug 27 13:15:39 2001 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Mon, 27 Aug 2001 10:15:39 -0700 Subject: [BiO BB] looking for an opportunity Message-ID: Hello all, I am looking for a part-time programming opportunity in the bioinformatics field (I will look at any full time positions). I would prefer to work as a contractor but I will consider anything. I am currently employed as a Unix Systems Architect/Linux programmer. I am also working on my Masters degree in Computational Biosciences and have a BS in Microbiology. No problems with my current employer, I just wish to focus more on Bioinformatics programming and system design. Thank you. - Joel Dudley From clarisca at cwpanama.net Tue Aug 28 10:08:05 2001 From: clarisca at cwpanama.net (Claris Castillo T.) Date: Tue, 28 Aug 2001 09:08:05 -0500 Subject: [BiO BB] Software for parallel computing. Message-ID: <001f01c12fca$dbcf9c00$3700a8c0@cwpanama.net> There is somebody working on software for parallel computing? You know Blast for clusters (example)? Maybe a research group is working on this, do you have any idea which one? Thanks in advance, Claris ---------------------------------------------------------------------- Ing. Claris Castillo T. Email clarisca at cwpanama.net Tel?fono (507) 213-8367 M?vil (507) 617-5992 Claris Castillo (R0004) Claris Castillo T. 8619 NW 68TH Street Aptdo 426 Miami, Fl 33166 Zona 9-A. USA Panam?, Panam? -------------- next part -------------- An HTML attachment was scrubbed... URL: From idoerg at cc.huji.ac.il Tue Aug 28 10:51:44 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Tue, 28 Aug 2001 17:51:44 +0300 (GMT+0300) Subject: [BiO BB] Hydrophobic Core recognition Message-ID: Hi all, Does anybody know of a program which, given a PDB (or DSSP or somesuch) file can recognize the hydrophobic core? Thanks, Iddo -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From stein at fieldmuseum.org Tue Aug 28 11:13:04 2001 From: stein at fieldmuseum.org (Jennifer Steinbachs) Date: Tue, 28 Aug 2001 10:13:04 -0500 (CDT) Subject: [BiO BB] Software for parallel computing. In-Reply-To: <001f01c12fca$dbcf9c00$3700a8c0@cwpanama.net> Message-ID: On Tue, 28 Aug 2001, Claris Castillo T. wrote: >There is somebody working on software for parallel computing? You know Blast for clusters (example)? Maybe a research group is working on this, do you have any idea which one? >Thanks in advance, >Claris The high performance computing group at UofChicago has a parallel version of blast, compiled using their parallel compilers. See http://www.hpcl.cs.uchicago.edu/cgi-bin/seqanalysisroot.pl -jennifer ----------------------------------- J. Steinbachs, Ph.D. Computational Biologist http://compbiology.org ----------------------------------- From idoerg at cc.huji.ac.il Tue Aug 28 11:39:58 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Tue, 28 Aug 2001 18:39:58 +0300 (GMT+0300) Subject: [BiO BB] Software for parallel computing. In-Reply-To: <001f01c12fca$dbcf9c00$3700a8c0@cwpanama.net> Message-ID: On Tue, 28 Aug 2001, Claris Castillo T. wrote: : There is somebody working on software for parallel computing? You know : Blast for clusters (example)? Maybe a research group is working on : this, do you have any idea which one? Thanks in advance, Check out the Bioaccelerator: http://sgbcd.weizmann.ac.il/ Iddo -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From jatp at lundbeck.com Tue Aug 28 12:15:59 2001 From: jatp at lundbeck.com (Jan Torleif Pedersen) Date: Tue, 28 Aug 2001 18:15:59 +0200 Subject: [BiO BB] Hydrophobic Core recognition References: Message-ID: <3B8BC3BF.1FF76BBA@lundbeck.com> Dear Iddo, Not a trivial question ! Use the Protein tools from Stepen Bryant at the NCBI. There is a core recognition built into their threading program. It may be in the ncbi-toolkit that you can download from ftp://ftp.ncbi.nlm.nih.gov - If not I recommend you send an email to Steve directly at NCBI - Hi core definition program is probably the best one around. Alternatively use DSSP from embl and select all residues which have low solvent accesibility. That gives you a pretty good core - but be aware ! If you have large cavities (which you have in most proteins) you will get a strange definition of the core. Regards -- Jan Iddo Friedberg wrote: > > Hi all, > > Does anybody know of a program which, given a PDB (or DSSP or somesuch) > file can recognize the hydrophobic core? > > Thanks, > > Iddo > > -- > > Iddo Friedberg | Tel: +972-2-6757374 > Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 > The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il > POB 12272, Jerusalem 91120 | > Israel | > http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Dr. Jan Torleif Pedersen Dep. Computational Chemistry H. Lundbeck A/S Ottiliavej 9 DK-2000 Valby - Copenhagen DENMARK phone : +45 36 44 24 25 ext 2887 FAX : +45 36 30 13 85 email : jatp at lundbeck.com From drkutty at goldstone.net Wed Aug 29 01:07:20 2001 From: drkutty at goldstone.net (Dr. Kutty) Date: Wed, 29 Aug 2001 10:37:20 +0530 Subject: [BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #79 - 5 msgs Message-ID: <23002CE09C53D511A51D00025558AFDD0C9F42@EXCHANGESERVER> Hi Claris, Centre for Development of Advance Computing(CDAC), Pune, India are working on parallel Algorithms. CDAC is a National Institution under the Ministry Of Information Technology, Govt of India, who have developed India's first Commercial Super Computer. You may contact its Director, Dr.Arora in the following address. Dr.R.K.Arora Executive Director CDAC, Pune Pune University Campus Ganesh Khind Pune 411007 Phone: +91-20-5650507 E-mail: rkarora at cdac.ernet.in I am also forwarding a copy of this to Dr.Arora for his information. With Best Regards, Dr.Kutty Chairman Goldstone Technologies Ltd S.D.Road Secunderabad 500003 A.P. , India Tel: +91-40-780 7640 Fax: +91-40-780 1910 Email: drkutty at goldstone.net Message: 2 >From: "Claris Castillo T." To: Subject: [BiO BB] Software for parallel computing. Date: Tue, 28 Aug 2001 09:08:05 -0500 boundary="----=_NextPart_000_001C_01C12FA0.F2A72E40" Reply-To: bio_bulletin_board at bioinformatics.org This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C12FA0.F2A72E40 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable There is somebody working on software for parallel computing? You know = Blast for clusters (example)? Maybe a research group is working on this, = do you have any idea which one? Thanks in advance, Claris ---------------------------------------------------------------------- I From joel.mossong at crp-sante.lu Wed Aug 29 04:37:36 2001 From: joel.mossong at crp-sante.lu (Joel Mossong) Date: Wed, 29 Aug 2001 10:37:36 +0200 Subject: [BiO BB] Job: bioinformatics postdoc in Luxembourg Message-ID: <1.5.4.32.20010829083736.011f4290@pop3.restena.lu> The Centre de Recherche Public-Sant? in Luxembourg is a dynamic and rapidly growing research institute of international acclaim in the medical and life sciences. Within the program of the "Fonds National de la Recherche of Luxembourg" the CRP-Sant? offers a post-doctoral position in Bioinformatics. The applicant will be a key member of a large interdisciplinary project, which focuses on setting up a functional genomics core facility. He/she will work on problems in biostatistics (analysis of gene expression patterns and genomic micro-array data) and biological systems (modelling and simulation of cellular networks and regulatory processes). His/her role is to provide core programming, algorithm development and statistical analysis. Applicants are required to have a PhD in bioinformatics / biostatistics / statistics backed with a certain level of experience in biology. The ideal applicant will have comprehensive knowledge of the UNIX environment and programming languages as well as the interpersonal skills necessary to succeed within a multi-disciplinary team. The post is funded for 30 months, but is renewable subject to review. To receive more information or to apply (by sending your CV), please contact: Dr Evelyne Friederich LABORATOIRE DE BIOLOGIE MOL?CULAIRE, D'ANALYSE G?NIQUE ET DE MOD?LISATION Centre de Recherche Public-Sant? 18, rue Dicks L-1417 Luxembourg T?l. : 00 352 45 32 13 33 Fax. : 00 352 45 32 19 E-mail: Evelyne.Friederich at crp-sante.lu ========================================================================= Dr Jo?l Mossong, CRESIS, CRP-Sant?, 18 rue Dicks, L-1417 Luxembourg. Tel: +352 45 32 13 40 Fax: +352 45 32 19 Email: joel.mossong at crp-sante.lu ========================================================================= From bioinformaticsckk at yahoo.co.in Wed Aug 29 04:54:31 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Wed, 29 Aug 2001 09:54:31 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #79 - 5 msgs In-Reply-To: <200108281600.MAA22414@www.bioinformatics.org> Message-ID: <20010829085431.38077.qmail@web8004.mail.in.yahoo.com> Hi I have two specific problems related to biology. i am looking for the following information in the net. Could anyone help me out? Is there any database on small molecule inhibitors which also has information on it's target protein and organism. Is there any database on different mutations in different mcorbial genomes that lead to resistance to the drugs/inhibitors? I hope i am clear in putting the questions. Thank you in advance. Kiran Kumar ____________________________________________________________ Do You Yahoo!? Send a newsletter, share photos & files, conduct polls, organize chat events. Visit http://in/ groups.yahoo.com From bioinformaticsckk at yahoo.co.in Wed Aug 29 04:55:59 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Wed, 29 Aug 2001 09:55:59 +0100 (BST) Subject: [BiO BB] information on database In-Reply-To: <200108281600.MAA22414@www.bioinformatics.org> Message-ID: <20010829085559.13748.qmail@web8005.mail.in.yahoo.com> Hi I have two specific problems related to biology. i am looking for the following information in the net. Could anyone help me out? Is there any database on small molecule inhibitors which also has information on it's target protein and organism. Is there any database on different mutations in different mcorbial genomes that lead to resistance to the drugs/inhibitors? I hope i am clear in putting the questions. Thank you in advance. Kiran Kumar ____________________________________________________________ Do You Yahoo!? For regular News updates go to http://in.news.yahoo.com From uysal at doctor.com Wed Aug 29 05:31:55 2001 From: uysal at doctor.com (huseyin uysal) Date: Wed, 29 Aug 2001 17:31:55 +0800 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #79 - 5 msgs Message-ID: <20010829093156.14082.qmail@mail.com> Hi, I need a web based service for prediction of 3D structure ( or tertiary structure) of a a protein from its primary sequence. Does anyone knows this type of web based service? Thanks. huseyin -- _______________________________________________ FREE Personalized E-mail at Mail.com http://www.mail.com/?sr=signup Talk More, Pay Less with Net2Phone Direct(R), up to 1500 minutes free! http://www.net2phone.com/cgi-bin/link.cgi?143 From JATP at Lundbeck.com Wed Aug 29 05:38:15 2001 From: JATP at Lundbeck.com (Jan Torleif Pedersen) Date: Wed, 29 Aug 2001 11:38:15 +0200 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #79 - 5 msgs Message-ID: For protein structure prediction there are a number of servers around that attempt to do this based on homology. I am not sure there are any ab-initio servers around that can do this: Check out Manuel Petisch SWISS-MODEL at expasy: http://www.expasy.ch Otherwise the Protein structure prediction center has links to sites that do structure and fold-recognition. http://predictioncenter.llnl.gov -- Jan Dr. Jan T. Pedersen H. Lundbeck A/S Ottiliavej 9, 2500 Valby email: jatp at lundbeck.com phone: +45 36 30 13 11 FAX : +45 36 30 13 85 -----Original Message----- From: huseyin uysal [mailto:uysal at doctor.com] Sent: 29. August 2001 11:32 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #79 - 5 msgs Hi, I need a web based service for prediction of 3D structure ( or tertiary structure) of a a protein from its primary sequence. Does anyone knows this type of web based service? Thanks. huseyin -- _______________________________________________ FREE Personalized E-mail at Mail.com http://www.mail.com/?sr=signup Talk More, Pay Less with Net2Phone Direct(R), up to 1500 minutes free! http://www.net2phone.com/cgi-bin/link.cgi?143 _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From JATP at Lundbeck.com Wed Aug 29 05:40:10 2001 From: JATP at Lundbeck.com (Jan Torleif Pedersen) Date: Wed, 29 Aug 2001 11:40:10 +0200 Subject: [BiO BB] information on database Message-ID: Dear Kiran, Checkout Mike Gilsons binding database site: http://www.bindingdb.org -- Jan Dr. Jan T. Pedersen H. Lundbeck A/S Ottiliavej 9, 2500 Valby, Denmark email: jatp at lundbeck.com phone: +45 36 30 13 11 FAX : +45 36 30 13 85 -----Original Message----- From: kiran challapalli [mailto:bioinformaticsckk at yahoo.co.in] Sent: 29. August 2001 10:56 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] information on database Hi I have two specific problems related to biology. i am looking for the following information in the net. Could anyone help me out? Is there any database on small molecule inhibitors which also has information on it's target protein and organism. Is there any database on different mutations in different mcorbial genomes that lead to resistance to the drugs/inhibitors? I hope i am clear in putting the questions. Thank you in advance. Kiran Kumar ____________________________________________________________ Do You Yahoo!? For regular News updates go to http://in.news.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From idoerg at cc.huji.ac.il Wed Aug 29 05:41:53 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Wed, 29 Aug 2001 12:41:53 +0300 (GMT+0300) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #79 - 5 msgs In-Reply-To: <20010829093156.14082.qmail@mail.com> Message-ID: Hi Huseyin, On Wed, 29 Aug 2001, huseyin uysal wrote: : Hi, : I need a web based service for prediction of 3D structure ( or tertiary structure) of a a protein from its primary sequence. Does anyone knows this type of web based service? : Thanks. Go to: http://www.expasy.ch/tools/#tertiary Several tools are listed there. One which isn't listed, but which I really like and recommend is: http://insulin.brunel.ac.uk/psiform.html On the first toggle menu, hit the 3rd choice ("Fold Recognition GENTHREADER"). : : huseyin : -- : : _______________________________________________ : FREE Personalized E-mail at Mail.com : http://www.mail.com/?sr=signup : : Talk More, Pay Less with Net2Phone Direct(R), up to 1500 minutes free! : http://www.net2phone.com/cgi-bin/link.cgi?143 : : : _______________________________________________ : BiO_Bulletin_Board maillist- BiO_Bulletin_Board at bioinformatics.org : http://bioinformatics.org/mailman/listinfo/bio_bulletin_board : : -- Iddo Friedberg | Tel: +972-2-6757374 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From bioinformaticsckk at yahoo.co.in Thu Aug 30 00:35:38 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Thu, 30 Aug 2001 05:35:38 +0100 (BST) Subject: [BiO BB] reply to huseyin Message-ID: <20010830043538.17027.qmail@web8001.mail.in.yahoo.com> Huseyin, There is a server called PHD predict protein where you can submit your protein sequence to get the co-ordinates of the 3D structure of the protein. Yes, you still may have to select the kind of server you want to use for threading. There are 4 servers for threading available. you may select sausage as i felt it gives better results. Check this URL http://www.embl-heidelberg.de/predictprotein/predictprotein.html Best of Luck, Kira Kumar ____________________________________________________________ Do You Yahoo!? Send a newsletter, share photos & files, conduct polls, organize chat events. Visit http://in/ groups.yahoo.com From atprelease at yahoo.com Fri Aug 31 18:46:47 2001 From: atprelease at yahoo.com (Ross Corriden) Date: Fri, 31 Aug 2001 15:46:47 -0700 (PDT) Subject: [BiO BB] Basic Bioinformatics question Message-ID: <20010831224647.97005.qmail@web14101.mail.yahoo.com> Dear BiO_Bulletin_Board subscribers, I recently graduated from college with a degree in Biochemistry and I am searching for resources on the internet that provide a basic overview of bioinformatics. If anyone knows about a site that contains this kind of information, I would greatly appreciate it if they would send the address of the page to my e-mail: atprelease at yahoo.com Thank you very much for your help. --Ross __________________________________________________ Do You Yahoo!? Get email alerts & NEW webcam video instant messaging with Yahoo! Messenger http://im.yahoo.com From jeff at bioinformatics.org Fri Aug 31 20:05:59 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 31 Aug 2001 20:05:59 -0400 Subject: [BiO BB] Basic Bioinformatics question References: <20010831224647.97005.qmail@web14101.mail.yahoo.com> Message-ID: <3B902667.1F665A34@bioinformatics.org> Hi Ross. The first thing I suggest whenever asked this question is to look at the FAQ: http://bioinformatics.org/faq/ Damian has done a great deal of work on it, and it is now very comprehensive. Cheers. Jeff Ross Corriden wrote: > > I recently graduated from college with a degree in > Biochemistry and I am searching for resources on the > internet that provide a basic overview of > bioinformatics. If anyone knows about a site that > contains this kind of information, I would greatly > appreciate it if they would send the address of the > page to my e-mail: -- J.W. Bizzaro jeff at bioinformatics.org Director, Bioinformatics.org http://bioinformatics.org/~jeff "As we enjoy great advantages from the inventions of others, we should be glad of an opportunity to serve others by any invention of ours; and this we should do freely and generously." -- Benjamin Franklin --