From alok.juneja at ranbaxy.com Thu Oct 3 10:42:13 2002 From: alok.juneja at ranbaxy.com (ALOK JUNEJA) Date: Thu, 3 Oct 2002 20:12:13 +0530 Subject: [BiO BB] Micro Array System Message-ID: <3AC70875A08ED511AED20002557C54BB01D83B2D@gur_msg_01.Ranbaxy.com> Hello friends Would any one of you throw some light on which Micro Array System would be most efficient amongst the following? Amersham Perkin Elmer Axon It would be more beneficial if someone with practical hands guide me with his/her experience. Regards Alok Juneja From gudladona_radha at hotmail.com Tue Oct 1 02:06:04 2002 From: gudladona_radha at hotmail.com (Radha G) Date: Tue, 1 Oct 2002 11:36:04 +0530 Subject: [BiO BB] (no subject) Message-ID: Hi I am a IT profeccional and i am going take classes for programming concepts in c and c++ for bioinformatics students. Could you please give me info aboutspecific examples related in bioinformatics -------------- next part -------------- An HTML attachment was scrubbed... URL: From anton at ebi.ac.uk Tue Oct 1 17:39:07 2002 From: anton at ebi.ac.uk (Anton Enright) Date: Tue, 01 Oct 2002 17:39:07 -0400 Subject: [BiO BB] Announcing BioLayout JAVA v1.0b Message-ID: Dear Friends, We would like to announce the release of BioLayout JAVA v1.0b. This is a tool we've been developing for visualising protein-protein interaction networks and protein sequence similarity graphs. Although, the method should be able to lay out just about any type of graph. BioLayout JAVA uses a modified Fruchterman Rheingold graph layout algorithm which performs very nice layouts of complex graphs. The previous version was written in C and had many portability problems, the new version in JAVA, should run on just about any platform and has many new features. For best performance, we recommend running the application on a fast machine with plenty of memory (e.g. Mac G4 1.0Ghz, 250MB RAM). This is because large graphs may require a lot of processing, and memory. If you are interested in downloading BioLayout JAVA, or finding out about the algorithm, then please go to the project homepage at: http://www.ebi.ac.uk/research/cgg/services/layout Please feel free to let us know your comments and to report problems at: biolayout at ebi.ac.uk Many Thanks, The BioLayout Development Team. Anton Enright, Leon Goldovsky and Ildefonso Cases (Ouzounis Group). European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge. CB10 1SD, UK. From tina at digikore.com Wed Oct 2 08:01:54 2002 From: tina at digikore.com (Tina) Date: Wed, 2 Oct 2002 17:31:54 +0530 Subject: [BiO BB] an information query Message-ID: <006001c26a0b$85870c80$fe01a8c0@vsnl.net.in> Hi, My husband has just completed his MBBS and is extremely interested in a career in Bio / medical infomatics. He is currently taking his GREs and would like to apply to Universities in the US for a Master's program in the same. We would like to know wether there are any companies here in India that he could approach to get some project experience while he also studies the necessary software programs and computer languages etc. I was wondering if you could give us any guidance on what courses to take up, and which companies to approach, since i found other queries that people have sent you on the www. I am sorry to have bothered you if this is inapproppriate. Thanking you and hoping that you will respond Regards Tina Nangrani -------------- next part -------------- An HTML attachment was scrubbed... URL: From seabi at indiatimes.com Fri Oct 4 04:58:59 2002 From: seabi at indiatimes.com (seabi) Date: Fri, 04 Oct 2002 14:28:59 +0530 Subject: [BiO BB] an information query Message-ID: <200210040904.OAA30045@WS0005.indiatimes.com> hi go and mail to bio_delhi at indiatimes.com for more information seabi bio_bulletin_board at bioinformatics.org wrote: Hi, My husband has just completed his MBBS and is extremely interested in a career in Bio / medical infomatics. He is currently taking his GREs and would like to apply to Universities in the US for a Master's program in the same. We would like to know wether there are any companies here in India that he could approach to get some project experience while he also studies the necessary software programs and computer languages etc. I was wondering if you could give us any guidance on what courses to take up, and which companies to approach, since i found other queries that people have sent you on the www. I am sorry to have bothered you if this is inapproppriate. Thanking you and hoping that you will respond Regards Tina Nangrani Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From seabi at indiatimes.com Fri Oct 4 05:03:53 2002 From: seabi at indiatimes.com (seabi) Date: Fri, 04 Oct 2002 14:33:53 +0530 Subject: [BiO BB] Micro Array System Message-ID: <200210040909.OAA31489@WS0005.indiatimes.com> hi visit: www.uml.edu and raise quary to be answered to mr. john fray. he is the right personality for this seabi bio_bulletin_board at bioinformatics.org wrote: Hello friends Would any one of you throw some light on which Micro Array System would be most efficient amongst the following? Amersham Perkin Elmer Axon It would be more beneficial if someone with practical hands guide me with his/her experience. Regards Alok Juneja _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From alok.juneja at ranbaxy.com Fri Oct 4 10:52:37 2002 From: alok.juneja at ranbaxy.com (ALOK JUNEJA) Date: Fri, 4 Oct 2002 20:22:37 +0530 Subject: [BiO BB] Micro Array System Message-ID: <3AC70875A08ED511AED20002557C54BB01D83B34@gur_msg_01.Ranbaxy.com> Thanks Seabi regards alok juneja -----Original Message----- From: seabi [mailto:seabi at indiatimes.com] Sent: Friday, October 04, 2002 2:34 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Micro Array System hi visit: www.uml.edu and raise quary to be answered to mr. john fray. he is the right personality for this seabi bio_bulletin_board at bioinformatics.org wrote: Hello friends Would any one of you throw some light on which Micro Array System would be most efficient amongst the following? Amersham Perkin Elmer Axon It would be more beneficial if someone with practical hands guide me with his/her experience. Regards Alok Juneja _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _____ Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From drjohn08318 at yahoo.com Fri Oct 4 13:12:02 2002 From: drjohn08318 at yahoo.com (John Hoey) Date: Fri, 4 Oct 2002 10:12:02 -0700 (PDT) Subject: [BiO BB] Micro Array System In-Reply-To: <3AC70875A08ED511AED20002557C54BB01D83B34@gur_msg_01.Ranbaxy.com> Message-ID: <20021004171202.11824.qmail@web14410.mail.yahoo.com> I am well-versed in all of these systems and I can without hesitation that Amersham is buy far the best instrument for Microarray analysis. If anyone is interested in knowing why I say this, please contact me. Sincerely, JGH ALOK JUNEJA wrote:Thanks Seabi regardsalok juneja-----Original Message----- From: seabi [mailto:seabi at indiatimes.com] Sent: Friday, October 04, 2002 2:34 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Micro Array System hi visit: www.uml.edu and raise quary to be answered to mr. john fray. he is the right personality for this seabi bio_bulletin_board at bioinformatics.org wrote: Hello friends Would any one of you throw some light on which Micro Array System would be most efficient amongst the following? Amersham Perkin Elmer Axon It would be more beneficial if someone with practical hands guide me with his/her experience. Regards Alok Juneja _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --------------------------------- Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! -------------- next part -------------- An HTML attachment was scrubbed... URL: From senthil at cdfd.org.in Fri Oct 4 05:36:15 2002 From: senthil at cdfd.org.in (Senthil Kumar M.) Date: Fri, 4 Oct 2002 02:36:15 -0700 Subject: [BiO BB] (no subject) In-Reply-To: Message-ID: Dear Radha G, Your question is not clear about what you want. If you want to know about the ongoing projects you can see them very well on www.bioinformatics.org. There are numerous .org sites that cater to the need of bioinformatics. For eg you might be interested in www.bioperl.org or www.biojava.org. It depends on what you want to do. If you are interested in a good course in BLAST etc you might have a look at the NCBI site http://www.ncbi.nlm.nih.gov . Hope this helps. Also, in your future mails you might include a relevant subject line so that people can respond to your mails more readily. -- Senthil X*********************************************X # Senthil Kumar M. # # Senior Research Fellow, # # Center for DNA fingerprinting & Diagnostics,# # ECIL Road, Hyderabad 500 076, India. # # email: senthil at cdfd.org.in # # senthil at operamail.com # X*********************************************X On Tue, 1 Oct 2002, Radha G wrote: > Hi > > I am a IT profeccional and i am going take classes for programming > concepts in c and c++ for bioinformatics students. Could you please give > me info aboutspecific examples related in bioinformatics > From cysu at nlg.csie.ntu.edu.tw Mon Oct 7 10:17:44 2002 From: cysu at nlg.csie.ntu.edu.tw (Chia-Yu Su) Date: Mon, 7 Oct 2002 22:17:44 +0800 Subject: [BiO BB] How to apply for a UMLS license number? Message-ID: <009701c26e0c$4e360060$431f708c@nlgpc2> Hi, I am wondering if someone could help me with the question about getting the account for UMLS. I would like to download the MetaMap Technology Transfer package(MMTx) from the website of National Library of Medicine(NLM). http://umlsks.nlm.nih.gov/ However, it requires a UMLS license number to get a login ID for this webpage. Do I have to print the UMLS license agreement on http://www.nlm.nih.gov/research/umls/license.html and mail it to NLM after filling the form? Then NLM would give me an account? Thanks in advance. Chia-Yu ------ Chia-Yu Su Lab of Natural Language Processing Dept. of Computer Science and Information Engineering National Taiwan University email: cysu at nlg.csie.ntu.edu.tw phone: 886 2-2362-5336 fax : 886 2-2362-8167 Lab 301, Dept. of Computer Science and Information Engineering, No.1, Sec.4, Roosevelt Rd., Taipei, R.O.C. Taiwan -------------- next part -------------- An HTML attachment was scrubbed... URL: From balajior at rediffmail.com Wed Oct 9 11:12:15 2002 From: balajior at rediffmail.com (Balaji R) Date: 9 Oct 2002 15:12:15 -0000 Subject: [BiO BB] phylogenetic tree Message-ID: <20021009151215.17207.qmail@webmail2.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From Joel.Dudley at asu.edu Thu Oct 10 17:12:04 2002 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Thu, 10 Oct 2002 14:12:04 -0700 Subject: [BiO BB] phylogenetic tree Message-ID: <7D2FB294FA311F4299D03CC8D390437002D3AC73@mainex5.asu.edu> Balaji, MEGA is a very powerful Phylogenetic Analysis and Tree Building application. You can find it at http://www.megasoftware.net . Joel Dudley Faculty Research Associate Arizona State University Center for Evolutionary and Functional Genomics http://lsweb.la.asu.edu/skumar/ -----Original Message----- From: Balaji R [mailto:balajior at rediffmail.com] Sent: Wednesday, October 09, 2002 8:12 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] phylogenetic tree hi, has any one tried out with the phylogenetic SW available and found out which among them is the better one . if so can you let me know about it, this is basically to develop phylogenetic trees.., thanks, balaji Enjoy the little things in life,for one day you may look back and realize they were the big things. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Knowledge is Power, and Power is Respect, With the Knowledge we learn TODAY may we Earn the Respect (and Money) for TOMORROW!!! Peace & Love be with you... _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From sravan_111 at rediffmail.com Fri Oct 11 10:16:47 2002 From: sravan_111 at rediffmail.com (sravan sravan) Date: 11 Oct 2002 14:16:47 -0000 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #330 - 8 msgs Message-ID: <20021011141647.664.qmail@webmail8.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From tmi0m0 at spi.power.uni-essen.de Fri Oct 11 07:17:22 2002 From: tmi0m0 at spi.power.uni-essen.de (=?iso-8859-1?Q?Johannes_H=FCsing?=) Date: Fri, 11 Oct 2002 13:17:22 +0200 Subject: [BiO BB] phylogenetic tree In-Reply-To: <7D2FB294FA311F4299D03CC8D390437002D3AC73@mainex5.asu.edu>; from Joel Dudley on Thu, Oct 10, 2002 at 02:12:04PM -0700 References: <7D2FB294FA311F4299D03CC8D390437002D3AC73@mainex5.asu.edu> Message-ID: <20021011131722.34946@spi.power.uni-essen.de> On Thu 2002-10-10 (14:12), Joel Dudley wrote: > Balaji, > MEGA is a very powerful Phylogenetic Analysis and Tree Building > application. You can find it at http://www.megasoftware.net . > It seems to me that the license of this package is not free. This is a feature Balaji did not specifically ask for, but at least something which should be mentioned in the context of this list. See also http://bioinformatics.org/mailman/listinfo/bio_bulletin_board Thanks and regards Johannes From karen at scientecpersonnel.com Fri Oct 11 23:23:29 2002 From: karen at scientecpersonnel.com (Karen Tok) Date: Sat, 12 Oct 2002 11:23:29 +0800 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #330 - 8 msgs In-Reply-To: <20021011141647.664.qmail@webmail8.rediffmail.com> Message-ID: Hi guys, We are a Head hunting company for the Life Science/Healthcare/IT industry in Asia, located in Singapore. If you, or know of anyone who is looking for a job in the Life sciences area and are willing to be relocated to Asia, please contact us. You may visit our website www.scientecpersonnel.com for the list of available jobs. Regards, Karen Tok Business Development Manager (Asia) Biomedical sciences, Healthcare, IT ScienTec Personnel No 5, Shenton Way, #37-02 UIC Building, Singapore 068808 Tel : 62253272 Fax : 62257282 HP : 91072139 karen at scientecpersonnel.com www.scientecpersonnel.com When one door closes, another opens. Seize the opportunity while the path remains lit. --->-----Original Message----- --->From: bio_bulletin_board-admin at bioinformatics.org --->[mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of sravan --->sravan --->Sent: Friday, October 11, 2002 10:17 PM --->To: bio_bulletin_board at bioinformatics.org --->Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #330 - 8 msgs ---> ---> ---> --->Hi all, --->I am a postgraduate in biochemistry and and a post MSc diploma --->holder in Bioinformatics. I am presentlty working in CENTER FOR --->DNA FINGERPRINTING AND DIAGNOSTICS under DR. SHEKHAR MANDE in the --->area of computational and structural biology.I wish to join in PHD --->in GERMANY , --->SWEEDON or in other contries in the area oF COMPUTATIONAL --->/STRUCTURAL BIOLOGY --->I request all the group members of the organization to give your --->kind suggestions and please send me the list of universities I can --->apply for. --->I have yet to clear TOEFL AND GRE. --->Thanks to all. --->yours sincerely --->sravan. ---> --->_______________________________________________ --->BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org --->https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From seabi at indiatimes.com Sat Oct 12 05:33:51 2002 From: seabi at indiatimes.com (seabi) Date: Sat, 12 Oct 2002 15:03:51 +0530 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #330 - 8 msgs Message-ID: <200210120920.OAA10880@WS0005.indiatimes.com> please visit www.gnacademy.org hope it will help u. seabi bio_bulletin_board at bioinformatics.org wrote: Hi all, I am a postgraduate in biochemistry and and a post MSc diploma holder in Bioinformatics. I am presentlty working in CENTER FOR DNA FINGERPRINTING AND DIAGNOSTICS under DR. SHEKHAR MANDE in the area of computational and structural biology.I wish to join in PHD in GERMANY , SWEEDON or in other contries in the area oF COMPUTATIONAL /STRUCTURAL BIOLOGY I request all the group members of the organization to give your kind suggestions and please send me the list of universities I can apply for. I have yet to clear TOEFL AND GRE. Thanks to all. yours sincerely sravan. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in Change the way you talk. Indiatimes presents "Valufon", Your PC to Phone service with clear voice at rates far less than the normal ISD rates. Go to http://www.valufon.indiatimes.com. Choose your plan. BUY NOW. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hzi at uol.com.br Sun Oct 13 16:10:50 2002 From: hzi at uol.com.br (Henry) Date: 13 Oct 2002 18:10:50 -0200 Subject: [BiO BB] MSPCrunch and Bioperl Message-ID: <1034539852.17870.35.camel@samadhi> Hello - Has anyone used the MSPCrunch from bioperl? Can this substitute the original one at the swedish site (the only difference being that this one is implemented in Perl)? The original site for MSPCrunch is always down, and I can't get me a working binary copy. I have to much data to process via web interfaces. Thank you Best regards, Henry -- (((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( Micro$oft-Free Human 100% Debian GNU/Linux Not buzz-word compliant www.debian-rs.org www.debian-br.cipsga.org.br wwww.debian.org )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))) Microsoft turns standards into incompatibilities - you don't need them. From sravan_111 at rediffmail.com Mon Oct 14 01:45:42 2002 From: sravan_111 at rediffmail.com (sravan sravan) Date: 14 Oct 2002 05:45:42 -0000 Subject: [BiO BB] (no subject) Message-ID: <20021014054542.2590.qmail@webmail9.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From seabi at indiatimes.com Mon Oct 14 07:19:59 2002 From: seabi at indiatimes.com (seabi) Date: Mon, 14 Oct 2002 16:49:59 +0530 Subject: [BiO BB] (no subject) Message-ID: <200210141105.QAA04130@WS0005.indiatimes.com> you can visi the following site . hope this may help u ::::: www.mec.cuny.edu/academic_afairs/science_tech_school/biology/biocourses.htm seabi bio_bulletin_board at bioinformatics.org wrote: Hello Madam, I am working in the area of computational biology.I am involved in generation of a fine non-redundant fold library. Rightnow I can't explain my work due to some officieal restrictions As this we are using to develop a software that is commercial. As I am a from a biology background Iam feeling littlebit tough. But Iam sure that I could do well. I wish to join a PHD in computational biology further. Sorry for not revealing the things, Yours sincerely P.sravana kumar. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From Joel.Dudley at asu.edu Mon Oct 14 11:15:22 2002 From: Joel.Dudley at asu.edu (Joel Dudley) Date: Mon, 14 Oct 2002 08:15:22 -0700 Subject: [BiO BB] phylogenetic tree Message-ID: <7D2FB294FA311F4299D03CC8D390437002D3AC77@mainex5.asu.edu> Correct, although MEGA does not cost anything it is not "free" as we define the word in the context of this list. I can say, however, that an open-source strategy for MEGA and other applications are currently being considered by the producing lab. Joel Dudley Faculty Research Associate Arizona State University Center for Evolutionary and Functional Genomics http://lsweb.la.asu.edu/skumar/ -----Original Message----- From: Johannes H?sing [mailto:tmi0m0 at spi.power.uni-essen.de] Sent: Friday, October 11, 2002 4:17 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] phylogenetic tree On Thu 2002-10-10 (14:12), Joel Dudley wrote: > Balaji, > MEGA is a very powerful Phylogenetic Analysis and Tree Building > application. You can find it at http://www.megasoftware.net . > It seems to me that the license of this package is not free. This is a feature Balaji did not specifically ask for, but at least something which should be mentioned in the context of this list. See also http://bioinformatics.org/mailman/listinfo/bio_bulletin_board Thanks and regards Johannes _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From akarayol at anadolu.edu.tr Tue Oct 15 04:36:25 2002 From: akarayol at anadolu.edu.tr (AHMET KARAYOL) Date: Tue, 15 Oct 2002 12:36:25 +0400 Subject: [BiO BB] (no subject) Message-ID: Does anyone help me about bioinformatics links on the internet. Tahanks... From akarayol at anadolu.edu.tr Tue Oct 15 04:33:41 2002 From: akarayol at anadolu.edu.tr (AHMET KARAYOL) Date: Tue, 15 Oct 2002 12:33:41 +0400 Subject: [BiO BB] (no subject) Message-ID: Hi I am Ahmet Karayol from Turkey.I am working in the area of computational biology.I'm undergraduate student at biology department at Anatolian University in Turkey.I'm graduating this year and if so I want to continue to this subject.Could anyone help me work in company or other about biology and bioinformatics and If somebody send the charters studying abroad I wll be pleased of that.after graduating I want to go abroad.I know Engish well.I look forardto seeing your messages. Best regards From akarayol at anadolu.edu.tr Tue Oct 15 04:33:41 2002 From: akarayol at anadolu.edu.tr (AHMET KARAYOL) Date: Tue, 15 Oct 2002 12:33:41 +0400 Subject: [BiO BB] (no subject) Message-ID: Hi I am Ahmet Karayol from Turkey.I am working in the area of computational biology.I'm undergraduate student at biology department at Anatolian University in Turkey.I'm graduating this year and if so I want to continue to this subject.Could anyone help me work in company or other about biology and bioinformatics and If somebody send the charters studying abroad I wll be pleased of that.after graduating I want to go abroad.I know Engish well.I look forardto seeing your messages. Best regards From akarayol at anadolu.edu.tr Tue Oct 15 04:33:41 2002 From: akarayol at anadolu.edu.tr (AHMET KARAYOL) Date: Tue, 15 Oct 2002 12:33:41 +0400 Subject: [BiO BB] (no subject) Message-ID: Hi I am Ahmet Karayol from Turkey.I am working in the area of computational biology.I'm undergraduate student at biology department at Anatolian University in Turkey.I'm graduating this year and if so I want to continue to this subject.Could anyone help me work in company or other about biology and bioinformatics and If somebody send the charters studying abroad I wll be pleased of that.after graduating I want to go abroad.I know Engish well.I look forardto seeing your messages. Best regards From letondal at pasteur.fr Tue Oct 15 07:39:58 2002 From: letondal at pasteur.fr (Catherine Letondal) Date: Tue, 15 Oct 2002 13:39:58 +0200 Subject: [BiO BB] bioinformatics links on the internet In-Reply-To: Your message of "Tue, 15 Oct 2002 12:36:25 +0400." Message-ID: <200210151139.g9FBdxuY511974@electre.pasteur.fr> "AHMET KARAYOL" wrote: > Does anyone help me about bioinformatics links on the internet. > Tahanks... You have a look here: http://www.pasteur.fr/recherche/BNB/bnb-en.html -- Catherine Letondal -- Pasteur Institute Computing Center From sravan_111 at rediffmail.com Tue Oct 15 09:25:31 2002 From: sravan_111 at rediffmail.com (sravan sravan) Date: 15 Oct 2002 13:25:31 -0000 Subject: [BiO BB] (no subject) Message-ID: <20021015132531.21689.qmail@webmail4.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: curriculum_vite.doc Type: application/msword Size: 29184 bytes Desc: not available URL: From marge_geek at yahoo.com Tue Oct 15 19:18:18 2002 From: marge_geek at yahoo.com (marge marge) Date: Tue, 15 Oct 2002 16:18:18 -0700 (PDT) Subject: [BiO BB] The so called National Bioinformatics Institute (NBI) Message-ID: <20021015231818.39782.qmail@web13706.mail.yahoo.com> Hello everyone, The first time I came across the name of 'National Bioinformatics Institute' (NBI) ( http://www.bioinfoinstitute.com/default.htm ) was on an ad by a vocational school for a certification program in bioinformatics. I checked NBI's web site and it sounded great and exactly what I wanted. I have all the needed programing skills and I have most of the required computational biology and sequence analysis algorithms that are needed in bioinformatics. Since I didn't have any professional experience in the field, I figured some certification would be very useful. I didn't know any people working in the industry to consult so I decided to register in one of these programs. There are many schools offering such programs leading to NBI's "certified bioinformatics specialist" (CBS) and it seems that it has become popular . For example, http://128.242.53.21/ http://www.xintrausa.com/bioinf_pg.htm These schools are good for people wanting to get certified in IT fields. The level and standard of what they teach is not very high but at least the certification exams are written and administered by companies like Microsoft, Sun, Oracle, Cisco, etc. However, for bioinformatics, this NBI outfit sounds very suspect to say the least and I am afraid tens of people are wasting lots of money on programs and certifications. The first thing I noticed about NBI's material was the FAQ. It was copied from bioinformatics.org with no credit or at least a link. So I decided to examine the content of the web site further and it turns out that nearly every thing on the site is copied from other sources with no trace of credit or acknowledgment. The sections titled "Bioinformatics Resources", "Genomics", "Education", "Employment", "Software", "Pharmaceutical Companies" are copied from the "Biotechnology Information Directory" Section of "The World Wide Web Virtual Library" : http://www.cato.com/biotech/index.html The section titled "Job Market News - Bioinfo Events" is copies (not links) of articles from other sources (including the copyright notice and logos of the original publisher.) If copying links and FAQS without credit is not bad enough, it gets worse! The documentation of their own certification program, http://www.bioinfoinstitute.com/bio_certi.htm is copied from bioninformatics.ca (with few words changed) : http://www.bioinformatics.ca/programhandbook.pdf NBI also just started a chemoinformatics certification program but, you guessed it, the material on this program seems to be swiped from elsewhere. The section titled "chemoinformatics resources" is exactly the same as this page at Indiana University: http://www.indiana.edu/~cheminfo/informatics/cinformhome.html The material on "what is chemoinformatics" and "chemoinformatics certification" also appears on NC State' s computer training unit: http://www.ncsu.edu/ctu/codes/chem.htm but I am not sure who is copying from whom in this case. The person(s) behind NBI might be qualified or even experienced in bioinformatics and the exam might be very good but judging from the material on the web site, I wouldn't hold my breath. I have decided not to take the exam although I paid for the program (not for the NBI exam luckily!). I don't think any of the people registering in these course and paying $400 to NBI for the exam know any of the info I just posted. If you get a chance to publicize how NBI seems not to care about ethics and plagiarism, please do. Marge. __________________________________________________ Do you Yahoo!? Faith Hill - Exclusive Performances, Videos & More http://faith.yahoo.com From cchao at rcsb.rutgers.edu Tue Oct 15 20:44:50 2002 From: cchao at rcsb.rutgers.edu (Jimmy Chao) Date: Tue, 15 Oct 2002 20:44:50 -0400 Subject: [BiO BB] The so called National Bioinformatics Institute (NBI) References: <20021015231818.39782.qmail@web13706.mail.yahoo.com> Message-ID: <00e901c274ad$410e0fc0$65b20680@VMwin2k> Marge, You did an excellent job in digging out these info about NBI. Actually I went to their seminar once to figure out what they are offering. From the material they offer, I would say the certificate worth nothing. Because the material and exam are too simple. It just offer an introductory about bioinfromatics for people who have no much background. They even take student without any biology or computer background. The course is about 2-3 months, it covers basic molecule & genetics biology, and perl, GCG, bioinformatics databases etc. A person can only pick up very little with very short period of time. I am working in Protein Data Bank as developer for complex search engine. I have both biology and computer science degree, and working on my Ph.D. in biomedical informatics as well. I have been looking for a job in bioinformatics industry for about 2 years. Although some recruiters called me up, but never get a chance to interview. The reason is simple, the bioinformatics industry needs people who is an expert in biology and know something about computer. The main issues stay in biology problem and only the biologist know what to do. If they need someone to develop software, they don't need junior programmer to know biology. The need very experience programmer/developer and the biologist can tell them what to do. Besides, bioinformatics is a term for any combination of biology and computer. The most interesting part is to find gene related to a disease, and design a drug to cure that disease. However, this model haven't prove to work the way people expect. Maybe it's still too early to exam the result. Maybe there are some drugs being developed this way (come on, it's business secret). I would say using bioinformatics technique may reduce a bit trial and error effort, but majority work still rely on a lot of wet lab experiment and pre-clinical trial. NBI exaggerate the job market in bioinformatics and their certificate is just their own program. Who care about this piece of paper? It's not worth wasting time & money for that certificate. Their ceriticate won't be as valuable as MCSE, JAVA, ORACLE or CISCO. You may know Protein Data Bank is the world-wide depository of protein & nucleic acid structures. You may have a beter idea about PDB at this link http://www.bio-itworld.com/archive/100902/banking.html This is a purely bioinformatics field, and many researchers rely on 3D structure to develope drugs and other application. And New Jersey is a based for many pharmaceutical companies, such as Johnson & Johnson, Merch, Aventis, Schering-Plough, etc. However, staffs in PDB don't find many job oppertunity in industry. For me, I feel frustrate in job hunting for two years. I'll either focus on drug design or bioinformatics data mining/search engine. The drug design may lead me to find a job in pharmaceutical company, while bioinformatics data mining/search engine may keep my job in PDB to build plateform that for public access for free. =========================================================== Chi-Ming Jimmy Chao http://ndb.dyndns.org Protein Data Bank http://www.pdb.org Research Collaboratory for Structural Bioinformatics Department of Chemistry and Chemical Biology Rutgers, The State University of New Jersey Phone: (732) 397-8840 Fax: (732) 445-4320 =========================================================== ----- Original Message ----- From: "marge marge" To: Sent: Tuesday, October 15, 2002 7:18 PM Subject: [BiO BB] The so called National Bioinformatics Institute (NBI) > Hello everyone, > > The first time I came across the name of 'National > Bioinformatics Institute' (NBI) ( > http://www.bioinfoinstitute.com/default.htm ) was on > an ad by a vocational school for a certification > program in bioinformatics. I checked NBI's web site > and it sounded great and exactly what I wanted. I have > all the needed programing skills and I have most of > the required computational biology and sequence > analysis algorithms that are needed in bioinformatics. > Since I didn't have any professional experience in the > field, I figured some certification would be very > useful. I didn't know any people working in the > industry to consult so I decided to register in one of > these programs. There are many schools offering such > programs leading to NBI's "certified bioinformatics > specialist" (CBS) and it seems that it has become > popular . For example, > > http://128.242.53.21/ > http://www.xintrausa.com/bioinf_pg.htm > > These schools are good for people wanting to get > certified in IT fields. The level and standard of what > they teach is not very high but at least the > certification exams are written and administered by > companies like Microsoft, Sun, Oracle, Cisco, etc. > However, for bioinformatics, this NBI outfit sounds > very suspect to say the least and I am afraid tens of > people are wasting lots of money on programs and > certifications. > > The first thing I noticed about NBI's material was the > FAQ. It was copied from bioinformatics.org with no > credit or at least a link. So I decided to examine the > content of the web site further and it turns out that > nearly every thing on the site is copied from other > sources with no trace of credit or acknowledgment. > > The sections titled "Bioinformatics Resources", > "Genomics", "Education", "Employment", "Software", > "Pharmaceutical Companies" are copied from the > "Biotechnology Information Directory" Section of "The > World Wide Web Virtual Library" : > > http://www.cato.com/biotech/index.html > > The section titled "Job Market News - Bioinfo Events" > is copies (not links) of articles from other sources > (including the copyright notice and logos of the > original publisher.) > > If copying links and FAQS without credit is not bad > enough, it gets worse! The documentation of their own > certification program, > > http://www.bioinfoinstitute.com/bio_certi.htm > > is copied from bioninformatics.ca (with few words > changed) : > > http://www.bioinformatics.ca/programhandbook.pdf > > NBI also just started a chemoinformatics certification > program but, you guessed it, the material on this > program seems to be swiped from elsewhere. The section > titled "chemoinformatics resources" is exactly the > same as this page at Indiana University: > > http://www.indiana.edu/~cheminfo/informatics/cinformhome.html > > > The material on "what is chemoinformatics" and > "chemoinformatics certification" also appears on NC > State' s computer training unit: > > http://www.ncsu.edu/ctu/codes/chem.htm > > but I am not sure who is copying from whom in this > case. > > The person(s) behind NBI might be qualified or even > experienced in bioinformatics and the exam might be > very good but judging from the material on the web > site, I wouldn't hold my breath. I have decided not to > take the exam although I paid for the program (not for > the NBI exam luckily!). I don't think any of the > people registering in these course and paying $400 to > NBI for the exam know any of the info I just posted. > If you get a chance to publicize how NBI seems not to > care about ethics and plagiarism, please do. > > Marge. > > __________________________________________________ > Do you Yahoo!? > Faith Hill - Exclusive Performances, Videos & More > http://faith.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From zoope80 at rediffmail.com Wed Oct 16 13:32:07 2002 From: zoope80 at rediffmail.com (Ashis mathew philip) Date: 16 Oct 2002 17:32:07 -0000 Subject: [BiO BB] Please Help Me !!!! Message-ID: <20021016173207.14838.qmail@webmail18.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From gene.quantification at wzw.tum.de Wed Oct 16 11:39:54 2002 From: gene.quantification at wzw.tum.de (Gene Quantification Homepage) Date: Wed, 16 Oct 2002 17:39:54 +0200 Subject: [BiO BB] Gene Quantification Newsletter - 10/2002 Message-ID: <5.0.2.1.0.20021016173932.03e5fc58@pollux.wzw.tum.de> Gene Quantification Newsletter - 10/2002 October 2002 Introduction: Main focus of the GENE QUANTIFICATION web page http://www.wzw.tum.de/gene-quantification/ is, to describe and summarize all technical aspects involved in quantitative gene expression analysis using real-time (kinetic) PCR & RT-PCR: e.g. detection chemistry, assay specificity, sensitivity, reproducibility, robustness, intra- & inter-assay variations, kinetic PCR efficiency calculation, quantification strategies, optimisation strategy, data calculation and statistics, etc. etc. The GENE QUANTIFICATION web page illustrates the usefulness of reliable quantification strategies, e.g. absolute-, relative-quantification assays, and the difference between them in kinetic PCR & kinetic RT-PCR. Main focus of the PHYSIOLOGY web page is, to describe all kind of kinetic RT-PCR applications in molecular Physiology, molecular Endocrinology, and molecular Immunology (mainly mammary gland immunology) are summarized on my new homepage http://www.wzw.tum.de/gene-quantification/physiology.shtml ############################################# NEW features: Determination of real-time PCR efficiency - NEW EQUATIONS http://www.wzw.tum.de/gene-quantification/efficiency.html Endocrinology & Mammary Gland Immunology - NEW PUBLICATIONS http://www.wzw.tum.de/gene-quantification/physiology.shtml Steroid receptors: AR, ERa, ERb, PR Adrenergic receptors: alpha-1-subtypes & alpha-2-subtypes & beta-subtypes (publications in press) Somatotropic axis: GHR, IGF-1, IGF2, both IGF receptors & IGF-BP1 to BP3 Serotonin receptors (coming soon) NEW MOVIES http://www.wzw.tum.de/gene-quantification/movie.html e.g. PCR, RPA, Electrophoresis, Northern- & Southern-Blot NEW PUBLICATIONS about kinetic PCR http://www.wzw.tum.de/gene-quantification/real-time.html and http://www.wzw.tum.de/gene-quantification/chemistry.html and http://www.wzw.tum.de/gene-quantification/hkg.html and http://www.wzw.tum.de/gene-quantification/literature.html sections: RT-PCR and real-time RT-PCR (in general) LightCycler specific technical notes absolute quantification using kinetic PCR relative quantification using kinetic PCR classical block RT-PCR & competitive RT-PCR normalisation & housekeeping gene problems in real-time PCR verification of DNA array results quantification software: REST, REST-XL, Q-Gene, geNorm kinetic RT-PCR poster board Poster boards (a little bit slow !!!): http://www.wzw.tum.de/gene-quantification/poster-a.html methodological poster board A: Array verification physiological poster board B: IGFs - Early Response Genes physiological poster board C: Steroid receptors physiological poster board D: Zinc metabolism physiological poster board E: Immunological relevant factors New links & databases: http://www.wzw.tum.de/gene-quantification/link.html e.g. - Dictionary of Nucleic Acid Structures (DNAS) - Glossary iSenseIT - Molecular Biology Glossary - A Hypermedia Glossary of Genetic Terms pick from an alphabetical list of Terms with 656 entries http://www.realtimeprimerdatabase.ht.st http://www.realtimeprimers.org/ http://www.pcrlinks.com http://www.cyclertest.com/ The COMPLETE Alkami Quick GuideTM for PCR is a (158 pages) http://www.wzw.tum.de/gene-quantification/quick-guide-pcr.pdf LightCycler University (LCU) http://www.wzw.tum.de/gene-quantification/real-time.html#lcu Please send the NEWSLETTER and the home page links to further scientists and friends who are interested in real-time PCR, new quantification strategies, relative or absolute gene quantification using kinetic PCR. best regards Michael Pfaffl ############################################# For further QUESTIONS concerning real-time PCR and if you want to SUBSCRIBE to our monthly appearing GENE QUANTIFICATION NEWSLETTER please contact gene.quantification at wzw.tum.de You will receive all NEW FEATURES and future REST & REST-XL updates. GENE QUANTIFICATION web page and the GENE QUANTIFICATION NEWSLETTER are non-commercial, educational sites with the only purpose of facilitating access to biology-related information over the internet. The web page is optimised for Netscape Navigator version 4.7 & Internet Explorer version 5.0 (and higher versions) with an optimal screen resolution of 1024 x 768 pixels. GENE QUANTIFICATION web page visits and DOWNLOAD statistics are listed here: http://www.wzw.tum.de/gene-quantification/contact.html#server If you want UN-SUBSCRIBE from all future NEWSLETTERS please contact gene.quantification at wzw.tum.de and type REMOVE into the subject line. You will be removed instantly from our mailing list. ******************************************************************** Gene Quantification @ wzw.tum.de e-mail: gene.quantification at wzw.tum.de homepage: http://www.wzw.tum.de/gene-quantification/index.shtml homepage: http://www.wzw.tum.de/gene-quantification/physiology.shtml responsible Senior Scientist: Dr. Michael W. Pfaffl Institute of Physiology Life Science Center Weihenstephan, Technical University of Munich Weihenstephaner Berg 3 D-85350 Freising-Weihenstephan GERMANY ******************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From alohse at asmusa.org Wed Oct 16 17:04:12 2002 From: alohse at asmusa.org (alohse at asmusa.org) Date: Wed, 16 Oct 2002 17:04:12 -0400 Subject: [BiO BB] AMERICAN ACADEMY OF MICROBIOLOGY REPORT RECOMMENDS RESEARCH AGENDA FOR ECOGENOMICS Message-ID: <9FC11E38265F974DB80EFC018870C94F0114712F@asmex1.asmusa.org> AMERICAN ACADEMY OF MICROBIOLOGY REPORT RECOMMENDS RESEARCH AGENDA FOR ECOGENOMICS Washington D.C.--Microbes have dominated life on Earth for most of its 4.5 billion year history. They outnumber all other living things, inhabit every imaginable environment and control the biological, geological, and chemical cycles that shape the planet and make life possible. Knowledge of the microbial world promises medical and agricultural breakthroughs, improved understanding of evolution, methods for protecting the environment and ways of predicting global change. This scientific revolution is not only underway, but ready for its next steps, a new report from the American Academy of Microbiology says. "Microbial Ecology and Genomics: A Crossroads of Opportunity," recommends an agenda to advance scientific understanding of the incredible diversity, complex organization and crucial interactions of microbial organisms and their environments. Ecogenomics, the intersection of ecology and genome science, focuses on analyzing microbial systems at many levels of biocomplexity-single cells, communities, and entire ecosystems. The goal is to examine the real environmental contexts where genomes evolve and shed light on the communities that control the biogeochemical cycles sustaining the biosphere. Technology has made "watching" the microbial world in action possible like never before. Better and faster genome sequencing, DNA microarrays, and the bioinformatics methods that store and manipulate massive amounts of data have produced an explosion of information. Culture-independent molecular techniques have revealed unexplored worlds in geothermal vents, cold oceans, soils, animal digestive tracts, and even the human mouth. It is now recognized that the microbial world is so vast that the majority of microbes have never been cultured and characterized. Advanced technologies can provide the tools for research that goes beyond identifying uncultured microbes and decoding genomes, the report says, to answer central questions about the origin and ongoing development of life. The report presents the conclusions of thirty (30) prominent scientists with expertise in microbiology, informatics, biostatistics, genomics, ecology and systematics. Issues outlined include the possibility of redefining microbial families, genera, and species based on genomic information; the implications of horizontal gene transfer; the factors driving microbial speciation; and the biochemical contributions of microbial communities. The document makes recommendations for a 10-year plan of developing new methods, outreach and training and specific research programs that will integrate genomics with microbial systematics, evolution and ecology. The American Academy of Microbiology (AAM) is an honorific leadership group within the American Society for Microbiology (ASM) whose mission is to recognize excellence and foster knowledge in the microbiological sciences. Its programs include convening critical issues colloquia and developing consensus-building position papers that provide expert scientific opinion on current and emerging issues in microbiology. AAM reports can be downloaded for free: http://www.asmusa.org/acasrc/academy.htm For more information and to get a hard copy of "Microbial Ecology and Genomics: A Crossroads of Opportunity," contact Andrea Lohse at the American Academy of Microbiology (202)942-9292 or alohse at asmusa.org. Andrea Lohse Manager, American Academy of Microbiology American Society for Microbiology 1752 N Street, NW Washington DC 20036 202.942.9292 202.942.9353 alohse at asmusa.org From seabi at indiatimes.com Thu Oct 17 02:49:05 2002 From: seabi at indiatimes.com (seabi) Date: Thu, 17 Oct 2002 12:19:05 +0530 Subject: [BiO BB] Phd. in computational bio Message-ID: <200210170634.MAA20751@WS0005.indiatimes.com> hi hope the following link will help u www.krasnow.gmu.edu/bioinformatics/bioinf_resrch.htm seabi bio_bulletin_board at bioinformatics.org wrote: Hi all, I am a postgraduate in biochemistry and working as project assistant in CDFD,hyderabad.I wish to do PhD in bioinformatics and computational biology. Kindly send your kind suggestions and let me know the information aboaut positions available. Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy Music, Video, CD-ROM, Audio-Books and Music Accessories from http://www.planetm.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From priyaa_b at hotmail.com Thu Oct 17 00:49:04 2002 From: priyaa_b at hotmail.com (padma priya) Date: Thu, 17 Oct 2002 04:49:04 +0000 Subject: [BiO BB] query Message-ID: hello, i'm a postgraduate in biochem and currntly studying bioinformatics. i would like to know what is expression profile and what the databases used. thank u. priya _________________________________________________________________ Get faster connections?-- switch to?MSN Internet Access! http://resourcecenter.msn.com/access/plans/default.asp From yadhukumar at hotmail.com Thu Oct 17 06:23:05 2002 From: yadhukumar at hotmail.com (yadhu kumar) Date: Thu, 17 Oct 2002 15:53:05 +0530 Subject: [BiO BB] phylogenetic tree Message-ID: Hello Balaji, ARB is a software program developed at Technical University of Munich, Germany, to construct the phlogenetic trees using most common methods like parsimony, maximum likelyhood, distance matrix methods, etc., What makes it unique is its built in database of the aligned sequences for eg., there are about 20 thousands aligned 16s rRNA sequences. You can do lot with ARB starting from probe match, primer design, export,import sequences, sequence editing, tree building, and so on. One more important feature is its inbuilt secondary structure editor where one can visualize the rRNA structures and take them into consideration to improve the alignment, on which a quality of phylogenetic tree depends on. Its a open source free software and you can download from www.arb-home.de. Unfortunately it works only on Linux and solaris machines. Mac versions are also available. Hope it helps. If you have any questions regarding the same, feel free to mail me. with regards yadhu Bioinformatics Unit Department of Microbiology Technical University of Munich Munich , Germany +49 89 28922370 (O) +49 89 21021897 (R) +49 172 8204198 (M) _________________________________________________________________ Surf the Web without missing calls!?Get MSN Broadband. http://resourcecenter.msn.com/access/plans/freeactivation.asp From pajailwala at yahoo.com Thu Oct 17 09:54:01 2002 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Thu, 17 Oct 2002 06:54:01 -0700 (PDT) Subject: [BiO BB] query In-Reply-To: Message-ID: <20021017135401.94312.qmail@web12308.mail.yahoo.com> The term expression is used in bioinformatics to represent 'transcription'. An expression profile tells you what genes(ESTs) were expressed or transcribed in a cell at a certain point in time, under certain conditions. Microarrays capture expression profiles. Databases : none so far, though stanford university has some publicly available microarray datasets. --- padma priya wrote: > hello, > i'm a postgraduate in biochem and currntly studying > bioinformatics. i would like to know what is expression profile > and what the > databases used. > thank u. > priya > > _________________________________________________________________ > Get faster connections?-- switch to?MSN Internet Access! > http://resourcecenter.msn.com/access/plans/default.asp > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ===== ------------------------------------------------------------------------------------------ Never take the first step before considering the last. ------------------------------------------------------------------------------------------ Parthav Jailwala Ph : Home : (414) 283 0403 Mobile : (414) 305 9633 __________________________________________________ Do you Yahoo!? Faith Hill - Exclusive Performances, Videos & More http://faith.yahoo.com From priyaa_b at yahoo.com Fri Oct 18 09:34:00 2002 From: priyaa_b at yahoo.com (padma priya) Date: Fri, 18 Oct 2002 06:34:00 -0700 (PDT) Subject: [BiO BB] query In-Reply-To: <20021017135401.94312.qmail@web12308.mail.yahoo.com> Message-ID: <20021018133400.12187.qmail@web13509.mail.yahoo.com> hi parthav, thanx so much for the info u 've gvn me. priya --- Parthav Jailwala wrote: > The term expression is used in bioinformatics to > represent > 'transcription'. An expression profile tells you > what genes(ESTs) > were expressed or transcribed in a cell at a certain > point in > time, under certain conditions. Microarrays capture > expression > profiles. Databases : none so far, though stanford > university has > some publicly available microarray datasets. > > > --- padma priya wrote: > > hello, > > i'm a postgraduate in biochem and > currntly studying > > bioinformatics. i would like to know what is > expression profile > > and what the > > databases used. > > thank u. > > priya > > > > > _________________________________________________________________ > > Get faster connections?-- switch to?MSN Internet > Access! > > > http://resourcecenter.msn.com/access/plans/default.asp > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > ===== > ------------------------------------------------------------------------------------------ > Never take the first step before considering the > last. > ------------------------------------------------------------------------------------------ > Parthav Jailwala > Ph : Home : (414) 283 0403 > Mobile : (414) 305 9633 > > __________________________________________________ > Do you Yahoo!? > Faith Hill - Exclusive Performances, Videos & More > http://faith.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________________________ Do you Yahoo!? Faith Hill - Exclusive Performances, Videos & More http://faith.yahoo.com From agelder at mentornet.net Mon Oct 21 13:43:56 2002 From: agelder at mentornet.net (Ann Gelder) Date: Mon, 21 Oct 2002 10:43:56 -0700 Subject: [BiO BB] E-mentors needed for women students Message-ID: <20021021175138.083C263A86@www.bioinformatics.org> Dear Friends, You already know that women are underrepresented in engineering, mathematics, and science careers. For example, in today's U.S. workforce, women are just over 9% of the engineers and approximately 30% of the scientists. Here's something you can do today to help increase those numbers: Become an online mentor for MentorNet, the Presidential Award winning E- Mentoring Network for Women in Engineering and Science! Mentoring is a proven strategy for increasing the retention rates of women in engineering, mathematics, and science. With two weeks left in our recruiting drive, we have a particular need for mentors in biotechnology and biological science fields. Last year, students in these fields represented a full 16% of all participating students, and we are seeing an even stronger demand this year. Below, you can find out more about the MentorNet program and how to sign up. And please pass this message along to your friends and colleagues, so they don't miss out on this great volunteer opportunity! What is MentorNet? *MentorNet is an electronic mentoring network. Our award-winning One-on- One Mentoring Program pairs women engineering and science students with professionals all over the world. We match community college, undergraduate, and graduate women with engineers and scientists working in corporations, national laboratories, and government. How does it work? *During the school year, mentors and students communicate by email about career goals, balancing work and life, course work, and many other topics of their choice. There's no need for previous mentoring experience: mentors and students receive topics and training online to ensure a successful e-mentoring relationship. This is a great way for employees to receive free training in mentoring and staff development skills. What other benefits does the program offer? *MentorNet also offers you the opportunity to take part in an online e- community which focuses on issues of interest to our mentors and students. It's a perfect opportunity to expand your own network and to share your experiences with engineers and scientists worldwide. What if I don't have much time? * As an e-mentor, you can make a big difference in a student's life with a relatively small time commitment. Mentors who participated in last year's One-on-One Mentoring Program reported spending an average of just 20 minutes per week. Because you communicate entirely by email, you can write whenever and wherever it's convenient for you. Who can serve as mentors? *We encourage applications from both women and men, with an educational or professional background in engineering, science, or related technologies, who are currently employed in private industry or government sectors. How do I sign up? * Go to www.MentorNet.net and follow this 2-step process: 1) Join the Community: Click on "Community" and register/sign in as a new/returning Community member. 2) Apply for the One-on-One Program: Follow the One-on-One Mentoring Program links to the Mentor section and fill out the application. The deadline is October 31, 2002. MentorNet has been growing rapidly since its inception in 1997. Since then we have paired over 6,500 students with mentors. We hope you will be one of them! MentorNet's sponsors include 3M, Alcoa Foundation, AT&T, Elizabeth and Stephen J. Bechtel Jr. Foundation, Cisco Systems, Engineering Information Foundation, EMC, Google, IBM, Intel, The International Society for Optical Engineering, Lawrence Livermore National Laboratory, Lawrence Berkeley National Laboratory, Los Alamos National Laboratory, Maui Economic Development Board, Motorola, NASA Ames Research Center, National Science Foundation, Sandia National Laboratory, SAP Labs, Schlumberger, University Aviation Administration, U.S. Department of Education's FIPSE, and U.S. Department of Transportation. From concini at brenta.dit.unitn.it Tue Oct 22 05:58:13 2002 From: concini at brenta.dit.unitn.it (Michela de Concini) Date: Tue, 22 Oct 2002 11:58:13 +0200 Subject: [BiO BB] CMSB03 - deadline approaching Message-ID: Computational Methods in Systems Biology University of Trento 24-26 February, 2003 Rovereto, Italy www.science.unitn.it/~priami/cmsb.html Molecular biology has until now mainly focussed on individual molecules, on their properties as isolated entities or as complexes in very simple model systems. However, biological molecules in living systems participate in very complex networks, including regulatory networks for gene expression, intracellular metabolic networks and both intra- and intercellular communication networks. Such networks are involved in the maintenance (homeostasis) as well as the differentiation of cellular systems of which we have a very incomplete understanding. Nevertheless, the progress of molecular biology has made possible the detailed description of the components that constitute living systems, notably genes and proteins. Large scale genome sequencing means that we can (at least in principle) delimneate all macromolecular components of a given cellular system, and microarray experiments as well as large scale proteomics will soon give us large amounts of experimental data on gene regulation, molecular interactions and cellular networks. The challenge of the 21st century will be to understand how these individual components integrate to complex systems and the function and evolution of these systems, thus scaling up from molecular biology to systems biology. By combining experimental data with advanced formal theories from computer science, "the formal language for biological systems" to specify dynamic models of interacting molecular entities would be essential for 1. understanding normal behaviour of cellular processes, and how changes may affect the processes and cause disease. It may be possible to correlate genetic properties and symptoms in new and more efficient ways, based on an actual understanding of how various processes interact. 2. Providing predictability and flexibility to academic, pharmaceutical, biotechnology and medical researchers studying gene or protein functions. In particular, it may save time by reducing the number of experiments needed, if inadequate hypotheses could be excluded by computer simulation. Topics of interest include, but are not limited to: Modelling languages for Systems Biology Concurrency theory in Systems Biology Constraint programming in Systems Biology Logical methods in Systems Biology Formal methods to analyse biomolecular systems Quantitative analysis of biomolecular systems Simulation techniques for Systems Biology Case studies IMPORTANT DATES Nov 9, 2002 Submission deadline for papers and demos Nov 30, 2002 Notification of acceptance Dec 16, 2002 Camera-ready version due PROCEEDINGS The proceedings will be published in the Springer LNCS series and will be available at the workshop. SUBMISSION Authors are invited to submit .ps or .pdf original research papers as well as survey or tutorial papers of no more than 12 pages in LNCS format (see http://www.springer.de/comp/lncs/authors.html for instructions) at the address concini at dit.unitn.it For further information please contact us at the addresses [concini,priami]@dit.unitn.it. The papers will pass a peer review process and the accepted ones will appear in the proceedings. INVITED SPEAKERS Ehud Shapiro, Weizmann Institute of Science, Israel To be announced PROGRAMME COMMITTEE Charles Auffray, CNRS, Villejuif (F) Cosima Baldari, Universit? di Siena (I) Alexander Bockmayr, Universit? Henri Poincar?, Nancy (F) Luca Cardelli, Microsoft Research Cambridge (UK) Vincent Danos, Universit? Paris VII (F) Pierpaolo Degano, Universit? di Pisa (I) Fran?ois Fages, INRIA Rocquencourt (F) Drabl?s Finn, , Norwegian University of Science and Technology, Trondheim (N) Monika Heiner, Brandenburg University of Technology at Cottbus - (D) Ina Koch, University of Applied Sciences Berlin, (D). John E. Ladbury, University College London (UK) Patrick Lincoln, SRI (USA) Satoru Miyano, University of Tokyo (JP) Gordon Plotkin, University of Edinburgh (UK) Simon Plyte, Pharmacia Corporation (I) Corrado Priami (CHAIR), Universit? di Trento (I) Aviv Regev, Weizmann Institute of Science (IL) Magali Roux-Rouqui?, BSMI Pasteur Institute (F) Vincent Schachter, Hybrigenics Paris (F) Masaru Tomita, Keio University (JP) Adelinde Uhrmacher, University of Rostock (D) Alfonso Valencia, CNB-CSIC Centro Nacional de Biotecnologia, Cantoblanco Madrid, (E) Olaf Wolkenhauer, UMIST, Manchester (UK) ORGANIZING COMMITTEE Linda Brodo, Michela de Concini, Corrado Priami, Debora Schuch da Rosa Machado -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From parl17 at hotmail.com Tue Oct 29 13:11:10 2002 From: parl17 at hotmail.com (P L) Date: Tue, 29 Oct 2002 19:11:10 +0100 Subject: [BiO BB] Laboratory Information Management System (LIMS) Message-ID: An HTML attachment was scrubbed... URL: From parl17 at hotmail.com Tue Oct 29 13:32:26 2002 From: parl17 at hotmail.com (P L) Date: Tue, 29 Oct 2002 19:32:26 +0100 Subject: [BiO BB] Laboratory Information Management System (LIMS) Message-ID: Hi, It appears my last post did not work! I am Par Larsson, working with bioinformatics at the Swedish Defence Research Agency in Umea, Sweden. I have looked for open source alternatives to the commercial LIMS available on the market and have found a couple of projects. All, however, appear dead. If I am wrong, please correct me! With the help from a Swedish venture capitalist I have contacted, and CodeFactory, a local software company devoted to open source projects, I would like to initiate the development of an open LIMS/AIMS. I'm posting this to inquire about the general interest for such a project. If you do have any comments or would like to contribute should the project become alive, don't hesitate to contact me. Best regards, P?r Par Larsson parl17 at hotmail.com (I will reply from my permanent email account) _________________________________________________________________ Get a speedy connection with MSN Broadband.? Join now! http://resourcecenter.msn.com/access/plans/freeactivation.asp From bio_resources at yahoo.se Tue Oct 29 15:36:16 2002 From: bio_resources at yahoo.se (=?iso-8859-1?q?Jonathan=20Esguerra?=) Date: Tue, 29 Oct 2002 21:36:16 +0100 (CET) Subject: [BiO BB] RE: LIMS Message-ID: <20021029203616.71286.qmail@web12901.mail.yahoo.com> Hej! If you mean tools such as those offered by Spotfire, as far as I know, too, there is no open source LIMS available except for this one which deals exclusively with microarray exptl data. I chanced upon it in a conference in Sk?vde, Sweden a month ago wherein these guys from Lund Univ presented their work. It is called BASE for BioArray Software Environment. Homepage is at: http://base.thep.lu.se/ Probably one can pattern another LIMS open-source project to theirs. Best regards, ./jonathan ===== Jonathan LS Esguerra Structural Chemistry Department of Medical Biochemistry Gothenburg University, Sweden _____________________________________________________ Gratis e-mail resten av livet p? www.yahoo.se/mail Busenkelt! From juha.muilu at helsinki.fi Wed Oct 30 06:09:52 2002 From: juha.muilu at helsinki.fi (Juha Muilu) Date: Wed, 30 Oct 2002 13:09:52 +0200 Subject: [BiO BB] Laboratory Information Management System (LIMS) References: Message-ID: <007201c28004$e1a756a0$6340d680@tehi> Hi P?r, Thanks for the mail. I am very interested in this. Currently we are looking for alternatives for our commercial LIMS which is used to store genotype data. Can you please send more information? Best Regards, Juha -- Juha Muilu, Ph.D. Head of Database Operations, Database Coordinator Finnish Genome Center/National Public Health Insitute/HIIT Biomedicum P.O. Box 63, 00014 Helsinki FINLAND Email: juha.muilu at helsinki.fi Phone: +358(0)9 191 25479 ----- Original Message ----- From: "P L" To: Sent: Tuesday, October 29, 2002 8:32 PM Subject: [BiO BB] Laboratory Information Management System (LIMS) > Hi, > > It appears my last post did not work! > > I am Par Larsson, working with bioinformatics at the Swedish Defence > Research Agency in Umea, Sweden. > > I have looked for open source alternatives to the commercial LIMS available > on the market and have found a couple of projects. All, however, appear > dead. If I am wrong, please correct me! > > With the help from a Swedish venture capitalist I have contacted, and > CodeFactory, a local software company devoted to open source projects, I > would like to initiate the development of an open LIMS/AIMS. > > I'm posting this to inquire about the general interest for such a project. > If you do have any comments or would like to contribute should the project > become alive, don't hesitate to contact me. > > > Best regards, > > P?r > > Par Larsson > parl17 at hotmail.com > (I will reply from my permanent email account) > > > _________________________________________________________________ > Get a speedy connection with MSN Broadband. Join now! > http://resourcecenter.msn.com/access/plans/freeactivation.asp > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From franciswyeung at yahoo.com Wed Oct 30 10:37:31 2002 From: franciswyeung at yahoo.com (Francis Yeung) Date: Wed, 30 Oct 2002 07:37:31 -0800 (PST) Subject: [BiO BB] Laboratory Information Management System (LIMS) In-Reply-To: Message-ID: <20021030153731.43953.qmail@web14308.mail.yahoo.com> I am very interested in this. Is this a brand new development or a modified version of existing open source software. --- P L wrote: > Hi, > > It appears my last post did not work! > > I am Par Larsson, working with bioinformatics at the > Swedish Defence > Research Agency in Umea, Sweden. > > I have looked for open source alternatives to the > commercial LIMS available > on the market and have found a couple of projects. > All, however, appear > dead. If I am wrong, please correct me! > > With the help from a Swedish venture capitalist I > have contacted, and > CodeFactory, a local software company devoted to > open source projects, I > would like to initiate the development of an open > LIMS/AIMS. > > I'm posting this to inquire about the general > interest for such a project. > If you do have any comments or would like to > contribute should the project > become alive, don't hesitate to contact me. > > > Best regards, > > P?r > > Par Larsson > parl17 at hotmail.com > (I will reply from my permanent email account) > > > _________________________________________________________________ > Get a speedy connection with MSN Broadband.?Join > now! > http://resourcecenter.msn.com/access/plans/freeactivation.asp > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________________________ Do you Yahoo!? HotJobs - Search new jobs daily now http://hotjobs.yahoo.com/ From fmaia at gmx.net Wed Oct 30 15:35:26 2002 From: fmaia at gmx.net (Filipe Maia) Date: Wed, 30 Oct 2002 20:35:26 +0000 Subject: [BiO BB] Laboratory Information Management System (LIMS) In-Reply-To: References: Message-ID: <20021030203526.052209d2.fmaia@gmx.net> > With the help from a Swedish venture capitalist I have contacted, and > CodeFactory, a local software company devoted to open source projects, I > would like to initiate the development of an open LIMS/AIMS. > > I'm posting this to inquire about the general interest for such a project. > If you do have any comments or would like to contribute should the project > become alive, don't hesitate to contact me. I'm also very interested in knowing more about this. -- *----------------------------------------------------------------* | .''`. | Filipe Maia | | : :' : | email: fmaia at gmx.net | | `. `'` | | | `- | Debian GNU/Linux: | *----------------------------------------------------------------* From pkerrwall at psu.edu Thu Oct 31 11:23:13 2002 From: pkerrwall at psu.edu (Kerr Wall) Date: Thu, 31 Oct 2002 11:23:13 -0500 Subject: [BiO BB] Laboratory Information Management System (LIMS) In-Reply-To: Message-ID: <0D6CE980-ECED-11D6-8191-003065B572CC@psu.edu> Hi Par, I've spent the last six months writing a LIMS system for the Floral Genome Project at Penn State University. The project is an EST project so my tables are broken down into organism, tissue, library, plate, and clone. The web interface is written in Java (servlets & jsp) but I am really interested in porting this to Perl/Bioperl/CGI. I have added several additional features to the system including a plate-based blast against the arabidopsis and rice genomes which generates summary blasts results that are linked in from the LIMS system. Because we have many universities working on this project, I have written the system as a web interface which allows the user (at each university) to login and then upload finished plates from the sequencing labs, view blast results, add/edit/update information in the database, etc Because we have several libraries already finished, I have moved on to further downstream analysis and haven't had a chance to go back and change and update a lot of the features of the LIMS system that I have built. I would be very interested in helping you guys out. Please contact me for further details. Kerr Wall On Tuesday, October 29, 2002, at 01:32 PM, P L wrote: > Hi, > > It appears my last post did not work! > > I am Par Larsson, working with bioinformatics at the Swedish Defence > Research Agency in Umea, Sweden. > > I have looked for open source alternatives to the commercial LIMS > available on the market and have found a couple of projects. All, > however, appear dead. If I am wrong, please correct me! > > With the help from a Swedish venture capitalist I have contacted, and > CodeFactory, a local software company devoted to open source projects, > I would like to initiate the development of an open LIMS/AIMS. > > I'm posting this to inquire about the general interest for such a > project. If you do have any comments or would like to contribute > should the project become alive, don't hesitate to contact me. > > > Best regards, > > P?r > > Par Larsson > parl17 at hotmail.com > (I will reply from my permanent email account) > > > _________________________________________________________________ > Get a speedy connection with MSN Broadband.? Join now! > http://resourcecenter.msn.com/access/plans/freeactivation.asp > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From bioinfo at biosystemsconsulting.com Thu Oct 31 12:23:35 2002 From: bioinfo at biosystemsconsulting.com (bioinfo) Date: Thu, 31 Oct 2002 12:23:35 -0500 Subject: [BiO BB] Laboratory Information Management System (LIMS) In-Reply-To: <20021030153731.43953.qmail@web14308.mail.yahoo.com> Message-ID: <003201c28102$3f58d820$65fea8c0@raptor> Hello, Check out www.alkahest.org there is a automated processing pipeline tool that is being created by my group. Eventually we plan to integrate LIMS data into the package. We are in the beginning phases of the project and have focused initially on areas that we need. The software is funded by a grant but is going to be completely open source. The premise behind the project is to, initially, create a genomic analysis pipeline and database with web based interfaces that has a unified install tool. This means that any small lab could install it and have access to the pipeline and database in an integrated format. We are going to add the LIMS component soon. We would love to have others join us on this project. mark -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Francis Yeung Sent: Wednesday, October 30, 2002 10:38 AM To: bio_bulletin_board at bioinformatics.org Cc: aurora_yeung at msn.com Subject: Re: [BiO BB] Laboratory Information Management System (LIMS) I am very interested in this. Is this a brand new development or a modified version of existing open source software. --- P L wrote: > Hi, > > It appears my last post did not work! > > I am Par Larsson, working with bioinformatics at the > Swedish Defence > Research Agency in Umea, Sweden. > > I have looked for open source alternatives to the > commercial LIMS available > on the market and have found a couple of projects. > All, however, appear > dead. If I am wrong, please correct me! > > With the help from a Swedish venture capitalist I > have contacted, and > CodeFactory, a local software company devoted to > open source projects, I > would like to initiate the development of an open > LIMS/AIMS. > > I'm posting this to inquire about the general > interest for such a project. > If you do have any comments or would like to > contribute should the project > become alive, don't hesitate to contact me. > > > Best regards, > > P?r > > Par Larsson > parl17 at hotmail.com > (I will reply from my permanent email account) > > > _________________________________________________________________ > Get a speedy connection with MSN Broadband.?Join > now! > http://resourcecenter.msn.com/access/plans/freeactivation.asp > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________________________ Do you Yahoo!? HotJobs - Search new jobs daily now http://hotjobs.yahoo.com/ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board