From idoerg at cc.huji.ac.il Wed Jul 4 09:36:51 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Wed, 4 Jul 2001 16:36:51 +0300 (GMT+0300) Subject: [BiO BB] Threader, anyone? Message-ID: Hi all, Can anybody recommend me a good threading program? By "threading" I mean a program which accepts a protein sequence, and produces a fold prediction based on energy minimization by alignment to known folds. More specifically I'm looking for: 1) A standalone program, preferably on a Linux machine. 2) A program which can produce meaningful results for pairwise threading, that is, compare several given query sequences against a single fold. But a library-based threader (such as GenThreader) is also good. unfortunately the latter is temporarily unavailable for download, AFAIK. 3) Hopefully well documented, easy to use, etc. etc. Thanks, Iddo -- Iddo Friedberg | Tel: +972-2-6758647 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From jeff at bioinformatics.org Wed Jul 4 21:05:05 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 04 Jul 2001 21:05:05 -0400 Subject: [BiO BB] Threader, anyone? References: Message-ID: <3B43BD41.7787BCDC@bioinformatics.org> (bio_bulletin_board-admin at bioinformatics.org only goes to me) >From "Mathura, Venkatarajan S." : ------------------------------------ Iddo, Did you try to get PROSPECT ? If not, just for your info: It is from ORNL, USA. The reference for PROSPECT is : Ying Xu and Dong Xu. Protein threading using PROSPECT:Design and evaluation. Proteins: Structure, Function, and Genetics. 40:343-354. 2000. The website for the program is http://compbio.ornl.gov/structure/prospect/. PROSPECT has performed very well in CASP4. The program can be installed as a stand alone and works in LINUX OS. You can contact Dr. Dong Xu (xud at ornl.gov) or Dr. Ying Xu (xyn at ornl.gov) to get the software. You can also clarify your question as to whether PROSPECT can query several sequences to a single fold with them! All the best. Venkat Computational Biology Lab, SCSB, UTMB Galveston, Tx 77555 From indraneel at indialine.org Sat Jul 7 20:35:59 2001 From: indraneel at indialine.org (Indraneel Majumdar) Date: Sat, 7 Jul 2001 19:35:59 -0500 Subject: [BiO BB] need sugesstion In-Reply-To: <3B373224.6818C6B1@sgi1.chemie.uni-hamburg.de> References: <20010615112710.88580.qmail@web14004.mail.yahoo.com> <20010623193452.C12706@indialine.org> <20010625.5274900@siddhi.samsara.org> <3B373224.6818C6B1@sgi1.chemie.uni-hamburg.de> Message-ID: <20010707193559.A7653@indialine.org> Hi, On Mon, Jun 25, 2001 at 02:44:20PM +0200, Jan-Christoph Westermann wrote: > Usuario Universo Online wrote: > >> > >> I'm not too sure of this either. AFAIK the fees being charged are quite > >> high to justify joining, but then the software and equipment being used > >> there costs a lot too. That does not mean that you need all that to > >> learn. Open alternatives like `O' and `VMD' exist for us poorer people > >> running Debian GNU/Linux. > > > > Can you explain what 'O' and 'VMD' are, briefly? > > VMD: Visual Molecular Dynamics > > http://www.ks.uiuc.edu/Research/vmd/ and `O' is: "O is the end of FRODO" http://www.imsb.au.dk/~mok/o/ This is a cool program and worth the pain to install it. And same for molscript (just search on google.com ) \Indraneel -- http://www.indialine.org/indraneel/ From tribiosys at scientist.com Wed Jul 11 06:27:14 2001 From: tribiosys at scientist.com (TriBioSys) Date: Wed, 11 Jul 2001 15:57:14 +0530 Subject: [BiO BB] Bioinformatics jobs in Pune, India Message-ID: Bioinformaticians required in Pune, India An international bioinformatics company based in the US, is looking for a core team to be based in Pune, India. The company is focused on satisfying the drug discovery and development needs of the pharmaceutical industry through managing genomic, proteomic, and other research data. The company has an experienced founding team with strong backgrounds in the healthcare informatics, IT services, biotech, and pharmaceutical sectors. You must be at least a Masters in any life-science discipline. Others with a science background may be considered, depending upon their aptitude. Those with at least one of the following skillsets have an added advantage: 1. Computational Tools and Databases in Sequence Analysis, Gene Structure, Regulatory Regions, Transcription Factors, Protein Analysis, Phylogeny, Data Mining and Annotation. 2. Experience in RDBMS, programming in C++/Perl/Corba/Java, on Unix/Linux/NT platforms. 3. Experience in the use of molecular modelling packages. Contact: tribiosys at mail.com Send your resumes in text format, mentioning your reasons for choosing bioinformatics as a career. Include TBS1104 as a reference code in the subject line of your email. Also mention expected salary and the best time you can be contacted on the phone, for the initial interviews. From molconus at yahoo.com Thu Jul 12 03:01:21 2001 From: molconus at yahoo.com (Molecular Connections) Date: Thu, 12 Jul 2001 00:01:21 -0700 (PDT) Subject: [BiO BB] (no subject) Message-ID: <20010712070121.18240.qmail@web14103.mail.yahoo.com> Dear Sir, Request you to post this in your bulletin board. - thank you. Molcon, based in Bangalore, is the bioinformatics joint venture of a leading healthcare focused incubator in India and a reputed technology lab based in Singapore. Molcon is in the process of recruiting talent across various levels (including some senior executive level positions). Please mail to molconus at yahoo.com in case you would like to know further details about the company. __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From paolo at ist.unige.it Fri Jul 13 06:25:16 2001 From: paolo at ist.unige.it (Paolo Romano) Date: Fri, 13 Jul 2001 12:25:16 +0200 (DFT) Subject: [BiO BB] NETTAB Abstracts' Book freely available Message-ID: <200107131025.MAA20726@ist.unige.it> Dear colleagues, a limited number of Abstracts' Book of the NETTAB workshop on "CORBA and XML: towards a bioinformatics integrated network environment", held in Genoa on last May 17-18, is now available for free distribution. Information on the Workshop can be found at the following URL: http://www.cba.unige.it/Events/NETTAB/ http://www.bioinformatics.org/NETTAB/ If you are interested in receiving a copy of the Abstracts' Book, please email to Assunta Manniello at mam at ist.unige.it (or reply to this message) by specifying your full surface mail address. Best regards. Paolo Romano PS: This message is sent to many mailing lists. I'm sorry for possible duplications. -- Paolo Romano (paolo at ist.unige.it) Biotechnology Department, National Cancer Research Institute - Genova c/o Advanced Biotechnology Centre Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From antonioneme at hotmail.com Fri Jul 13 12:23:37 2001 From: antonioneme at hotmail.com (Antonio Neme) Date: Fri, 13 Jul 2001 12:23:37 Subject: [BiO BB] NETTAB Abstracts' Book freely available Message-ID: Hi! I am interested on it. My address is: Sericultura 139, Col. 20 de Noviembre Del. Venustiano Carranza Mexico, D.F. Mexico Thank you in advance. Antonio >Dear colleagues, > >a limited number of Abstracts' Book of the NETTAB workshop >on "CORBA and XML: towards a bioinformatics integrated network >environment", held in Genoa on last May 17-18, is now available >for free distribution. > >Information on the Workshop can be found at the following URL: >http://www.cba.unige.it/Events/NETTAB/ >http://www.bioinformatics.org/NETTAB/ > >If you are interested in receiving a copy of the Abstracts' >Book, please email to Assunta Manniello at mam at ist.unige.it >(or reply to this message) by specifying your full surface >mail address. > >Best regards. Paolo Romano >PS: This message is sent to many mailing lists. I'm sorry for > possible duplications. >-- >Paolo Romano (paolo at ist.unige.it) >Biotechnology Department, >National Cancer Research Institute - Genova >c/o Advanced Biotechnology Centre >Largo Rosanna Benzi, 10, I-16132, Genova, Italy >Tel: +39-010-5737-288 Fax: +39-010-5737-295 > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From jeff at bioinformatics.org Fri Jul 13 11:26:40 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 13 Jul 2001 11:26:40 -0400 Subject: [BiO BB] [Fwd: Posters] Message-ID: <3B4F1330.7676B677@bioinformatics.org> -------------- next part -------------- An embedded message was scrubbed... From: Yolanda Hollingsworth Subject: Posters Date: Fri, 13 Jul 2001 10:52:38 -0400 Size: 865 URL: From allyd2002 at yahoo.com Sat Jul 14 00:57:29 2001 From: allyd2002 at yahoo.com (Ally Duck) Date: Fri, 13 Jul 2001 21:57:29 -0700 Subject: [BiO BB] Unsubscribe In-Reply-To: <200107111600.MAA03743@www.bioinformatics.org> Message-ID: -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] Sent: July 11, 2001 9:00 AM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #58 - 1 msg 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. Bioinformatics jobs in Pune, India (TriBioSys) --__--__-- Message: 1 From: "TriBioSys" To: Subject: [BiO BB] Bioinformatics jobs in Pune, India Date: Wed, 11 Jul 2001 15:57:14 +0530 charset="iso-8859-1" Reply-To: bio_bulletin_board at bioinformatics.org Bioinformaticians required in Pune, India An international bioinformatics company based in the US, is looking for a core team to be based in Pune, India. The company is focused on satisfying the drug discovery and development needs of the pharmaceutical industry through managing genomic, proteomic, and other research data. The company has an experienced founding team with strong backgrounds in the healthcare informatics, IT services, biotech, and pharmaceutical sectors. You must be at least a Masters in any life-science discipline. Others with a science background may be considered, depending upon their aptitude. Those with at least one of the following skillsets have an added advantage: 1. Computational Tools and Databases in Sequence Analysis, Gene Structure, Regulatory Regions, Transcription Factors, Protein Analysis, Phylogeny, Data Mining and Annotation. 2. Experience in RDBMS, programming in C++/Perl/Corba/Java, on Unix/Linux/NT platforms. 3. Experience in the use of molecular modelling packages. Contact: tribiosys at mail.com Send your resumes in text format, mentioning your reasons for choosing bioinformatics as a career. Include TBS1104 as a reference code in the subject line of your email. Also mention expected salary and the best time you can be contacted on the phone, for the initial interviews. --__--__-- _______________________________________________ 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!? Get your free @yahoo.com address at http://mail.yahoo.com From yadhukumar at hotmail.com Sat Jul 14 12:30:52 2001 From: yadhukumar at hotmail.com (yadhu kumar) Date: Sat, 14 Jul 2001 22:00:52 +0530 Subject: [BiO BB] NETTAB Abstracts' Book freely available Message-ID: An HTML attachment was scrubbed... URL: From jeff at bioinformatics.org Sat Jul 14 13:37:11 2001 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Sat, 14 Jul 2001 13:37:11 -0400 Subject: [BiO BB] replies Message-ID: <3B508347.843384F8@bioinformatics.org> Please note that when you reply to a message posted here, your reply gets addressed to this list, not to the original sender. 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 vidya_dhote at hotmail.com Sun Jul 15 23:15:13 2001 From: vidya_dhote at hotmail.com (Vidya Dhote) Date: Mon, 16 Jul 2001 08:45:13 +0530 Subject: [BiO BB] NETTAB Abstracts' Book freely available Message-ID: Dear sir, I would be glad if you can send me the Abstracts' Book of the NETTAB workshop to the following address. Vidya Dhote, Jubilant Biosys (P) Ltd., 8th Floor, The Estate, #121, Dickenson Road, Bangalore 560 042 INDIA Warm regards, Vidya. >From: Paolo Romano >Reply-To: bio_bulletin_board at bioinformatics.org >To: biopython-announce at biopython.org, >bio_bulletin_board at bioinformatics.org, bioxml-announce at bioxml.org, >biojava-l at biojava.org, biocorba-announce-l at biocorba.org, >bioperl-announce-l at bioperl.org >CC: paolo at ist.unige.it, mam at ist.unige.it >Subject: [BiO BB] NETTAB Abstracts' Book freely available >Date: Fri, 13 Jul 2001 12:25:16 +0200 (DFT) > >Dear colleagues, > >a limited number of Abstracts' Book of the NETTAB workshop >on "CORBA and XML: towards a bioinformatics integrated network >environment", held in Genoa on last May 17-18, is now available >for free distribution. > >Information on the Workshop can be found at the following URL: >http://www.cba.unige.it/Events/NETTAB/ >http://www.bioinformatics.org/NETTAB/ > >If you are interested in receiving a copy of the Abstracts' >Book, please email to Assunta Manniello at mam at ist.unige.it >(or reply to this message) by specifying your full surface >mail address. > >Best regards. Paolo Romano >PS: This message is sent to many mailing lists. I'm sorry for > possible duplications. >-- >Paolo Romano (paolo at ist.unige.it) >Biotechnology Department, >National Cancer Research Institute - Genova >c/o Advanced Biotechnology Centre >Largo Rosanna Benzi, 10, I-16132, Genova, Italy >Tel: +39-010-5737-288 Fax: +39-010-5737-295 > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From bioinformaticsckk at yahoo.co.in Wed Jul 18 02:14:35 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Wed, 18 Jul 2001 07:14:35 +0100 (BST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #63 - 1 msg In-Reply-To: <200107161600.MAA10048@www.bioinformatics.org> Message-ID: <20010718061435.76009.qmail@web8005.mail.in.yahoo.com> 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 From rmp at sanger.ac.uk Wed Jul 18 05:55:39 2001 From: rmp at sanger.ac.uk (Roger Pettett) Date: Wed, 18 Jul 2001 10:55:39 +0100 (BST) Subject: [BiO BB] Ensembl v 1.1.0 Released Message-ID: 17th July 2001 The latest version of Ensembl is available at http://www.ensembl.org/ Ensembl 1.1.0 carries the April freeze dataset, and covers 90% of known genes. The website now incorporates the Distributed Annotation System (DAS); 3.5 million human ESTs from dbEST; Exportview - allowing the export of data from any feature or region; Anchorview - jump into a contigview between two features; has improved displays and is highly configurable. For further details please see http://www.ensembl.org/whatsnew/ Ensembl is a joint project between EMBL - EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust. R. -- +---------------------------------------------------------------+ Roger Michael Pettett Email: rmp at sanger.ac.uk Webmaster, Web: http://www.sanger.ac.uk The Sanger Centre Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA +---------------------------------------------------------------+ From goswami at archeanit.com Wed Jul 18 13:05:07 2001 From: goswami at archeanit.com (Satyakam Goswami) Date: Wed, 18 Jul 2001 22:35:07 +0530 (IST) Subject: [BiO BB] Sun's Computational Biology SIG Message-ID: <1102.192.168.0.2.995475907.squirrel@mail.archeanit.net> Sun's Computational Biology SIG Sun's vision in Computational Biology is based on three factors: The Sun Platform, Open Standards, and Community Support. Computational Biology is a progressive segment comprised of Bioinformatics, Macromolecular Structure, BioSimulation/BioNetworks, Bioengineering and the interface with Medical Informatics. As part of our efforts to support both open standards and the computational community, as well as to keep the Sun Computational Biology Community up-to-date on Sun products, we have formed a Special Interest Group in Computational Biology. This group is open to all of Sun's Education and Research customers. The Steering Committee will be comprised of the principals of the relevant Sun Centers of Excellence, as well as key Sun program managers. To join the CB-SIG, please send email to compbio-sig-info at sun.com with your contact information, Sun equipment, CB applications and any ideas and comments. The email list (compbio-sig at sun.com) and website (www.sun.com/edu/hpc/compbio-sig) are also for discussions, coordination of activities, articles, literature, copies of presentations, etc. Discussion topics for the CB-SIG will come from topics of interest to the membership, as well as Sun's Informatics Advisory Council (IAC), and the open-standards Interoperable Informatics Infrastructure Consortium (I3C), and other initiatives. Meetings will, initially, be held in conjunction with the HPC Constortium meetings (www.sun.com/edu/hpc). The first such meeting will be held at the HPC Consortium meeting in Heidelberg on June 19, 2001. -- Archean Infotech Victory Vihar,Himayatnagar Hyderabad 500029,www.archeanit.com Ph:3228666,6570704,3228674 Mobile:9849016667 ----------------------------------------- This email was sent using SquirrelMail. "Webmail for nuts!" http://squirrelmail.org/ From senthil at bioinformatics.org Sun Jul 22 04:20:29 2001 From: senthil at bioinformatics.org (Mr M senthil kumar) Date: Sun, 22 Jul 2001 01:20:29 -0700 (PDT) Subject: [BiO BB] NETTAB Abstracts' Book freely available In-Reply-To: <200107131025.MAA20726@ist.unige.it> Message-ID: Hi, Could you please send me the abstract book to the following address. Regards, Senthil -- X*********************************************X # Senthil Kumar M. # # Junior Research Fellow, # # Center for DNA fingerprinting & Diagnostics,# # ECIL Road, Hyderabad 500 076, India. # # email: senthil at www.cdfd.org.in # # senthil at operamail.com # X*********************************************X On Fri, 13 Jul 2001, Paolo Romano wrote: > Dear colleagues, > > a limited number of Abstracts' Book of the NETTAB workshop > on "CORBA and XML: towards a bioinformatics integrated network > environment", held in Genoa on last May 17-18, is now available > for free distribution. > > Information on the Workshop can be found at the following URL: > http://www.cba.unige.it/Events/NETTAB/ > http://www.bioinformatics.org/NETTAB/ > > If you are interested in receiving a copy of the Abstracts' > Book, please email to Assunta Manniello at mam at ist.unige.it > (or reply to this message) by specifying your full surface > mail address. > > Best regards. Paolo Romano > PS: This message is sent to many mailing lists. I'm sorry for > possible duplications. > -- > Paolo Romano (paolo at ist.unige.it) > Biotechnology Department, > National Cancer Research Institute - Genova > c/o Advanced Biotechnology Centre > Largo Rosanna Benzi, 10, I-16132, Genova, Italy > Tel: +39-010-5737-288 Fax: +39-010-5737-295 > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From mam at ist.unige.it Tue Jul 24 07:08:55 2001 From: mam at ist.unige.it (Assunta Manniello) Date: Tue, 24 Jul 2001 13:08:55 +0200 Subject: [BiO BB] NETTAB Abstracts' Book freely available In-Reply-To: References: <200107131025.MAA20726@ist.unige.it> Message-ID: <5.0.2.1.1.20010724130619.00a8fb20@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 At 01.20 22/07/01 -0700, you wrote: >Hi, >Could you please send me the abstract book to the following address. >Regards, >Senthil > >-- >X*********************************************X ># Senthil Kumar M. # ># Junior Research Fellow, # ># Center for DNA fingerprinting & Diagnostics,# ># ECIL Road, Hyderabad 500 076, India. # ># email: senthil at www.cdfd.org.in # ># senthil at operamail.com # >X*********************************************X > >On Fri, 13 Jul 2001, Paolo Romano wrote: > > > Dear colleagues, > > > > a limited number of Abstracts' Book of the NETTAB workshop > > on "CORBA and XML: towards a bioinformatics integrated network > > environment", held in Genoa on last May 17-18, is now available > > for free distribution. > > > > Information on the Workshop can be found at the following URL: > > http://www.cba.unige.it/Events/NETTAB/ > > http://www.bioinformatics.org/NETTAB/ > > > > If you are interested in receiving a copy of the Abstracts' > > Book, please email to Assunta Manniello at mam at ist.unige.it > > (or reply to this message) by specifying your full surface > > mail address. > > > > Best regards. Paolo Romano > > PS: This message is sent to many mailing lists. I'm sorry for > > possible duplications. > > -- > > Paolo Romano (paolo at ist.unige.it) > > Biotechnology Department, > > National Cancer Research Institute - Genova > > c/o Advanced Biotechnology Centre > > Largo Rosanna Benzi, 10, I-16132, Genova, Italy > > Tel: +39-010-5737-288 Fax: +39-010-5737-295 > > > > _______________________________________________ > > 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