From gcg-users@www.bioinformatics.uthscsa.edu Thu Nov 29 15:54:43 2001 From: gcg-users@www.bioinformatics.uthscsa.edu (Borries Demeler) Date: Thu, 29 Nov 2001 09:54:43 -0600 (CST) Subject: [GCG-Users] GCG server move Message-ID: <200111291554.fATFshK26358@bioc09.v19.uthscsa.edu> To all users of the GCG server: On Tuesday, Dec. 4th at 10 am, we will temporarily disconnect the GCG server to move it to its new location in the bioinformatics core facility in room 420 D. During the move the server and the Accelrys software packages will be unavailable. After Tuesday, the machine will also get a new hostname and IP address (old: gcg.v26.uthscsa.edu, new: gcg.v19.uthscsa.edu), the current alias name (gcg.uthscsa.edu) will however stay the same, but will probably require one day until the University name server is updated in order to resolve properly. Please plan accordingly to avoid conflicts during the down time, which should not last more than a couple of hours. As soon as we know the new IP address, we will inform you again. If you have any questions regarding this move, feel free to contact me at: demeler@biochem.uthscsa.edu, Room 420 D, x7-6592 Thank you, -Borries --- Borries Demeler, Ph.D. The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From demeler@bioc09.v19.uthscsa.edu Thu Nov 29 09:54:43 2001 From: demeler at bioc09.v19.uthscsa.edu (Borries Demeler) Date: Tue Apr 27 19:36:56 2004 Subject: [GCG-Users] GCG server move Message-ID: <200111291554.fATFshK26358@bioc09.v19.uthscsa.edu> To all users of the GCG server: On Tuesday, Dec. 4th at 10 am, we will temporarily disconnect the GCG server to move it to its new location in the bioinformatics core facility in room 420 D. During the move the server and the Accelrys software packages will be unavailable. After Tuesday, the machine will also get a new hostname and IP address (old: gcg.v26.uthscsa.edu, new: gcg.v19.uthscsa.edu), the current alias name (gcg.uthscsa.edu) will however stay the same, but will probably require one day until the University name server is updated in order to resolve properly. Please plan accordingly to avoid conflicts during the down time, which should not last more than a couple of hours. As soon as we know the new IP address, we will inform you again. If you have any questions regarding this move, feel free to contact me at: demeler@biochem.uthscsa.edu, Room 420 D, x7-6592 Thank you, -Borries --- Borries Demeler, Ph.D. The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From gcg-users@www.bioinformatics.uthscsa.edu Wed Apr 3 02:25:49 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Borries Demeler) Date: Tue, 2 Apr 2002 20:25:49 -0600 (CST) Subject: [GCG-Users] GCG/SeqWeb moved & updated Message-ID: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> Dear GCG user: Thanks to help from Steve Hardies, we have now completed the installation of the updated GCG and SeqWeb software suites to the bioinformatics Linux server. This week on Friday, 4/5 at 5:00 pm, we will turn off access to the old GCG server and move the GCG.UTHSCSA.EDU domain name to the new GCG server. In order to make the transition as smooth as possible, we ask that each current GCG user please check the following steps: 1. If you do not have an account on the bioinformatics server yet, please visit http://www.biochem.uthscsa.edu/apply/bioinf.html to apply for an account. When applying for an account, please keep in mind to: a) limit your desired login name to 8 characters max. b) select a secure password from the listing at http://biochem.uthscsa.edu/cgi-bin/passwords if you do not choose a secure password, one will be assigned. c) you will no longer need different passwords and logins for the bioinformatics shell account and the GCG/SeqWeb logins - bot will authenticate from the same password file. d) Please include a valid telephone number and e-mail address where we can reach you in case of questions. e) If you already have an account on the bioinformatics server, but would like a new password or would like to update your account information, simply fill out the application again with the updated information. Once you have an account on the bioinformatics server, you will be able to access both the web based SeqWeb software and the command line based gcg software. The command line version will only be available through secure shell (ssh). For documentation on ssh please visit the bioinformatics web server (http://www.bioinformatics.uthscsa.edu) 2. Please finish all your GCG-related projects on the current server until the end of this week and arrange with Jeremy Mann (x7-2672) to transfer any data you might have on the old server to the new server. If you can't finish a project by Friday of this week, please let us know, and we will make special arrangements for you. Note: Even after the old GCG server goes off-line, it will still be possible to transfer your data to the new system. 3. Starting Monday of next week (4/8), you will be able to connect to the new gcg installation by pointing your browser to: https://gcg.uthscsa.edu (Please note the "s" in https, gcg is now served over a secure webserver) The login procedure is much the same as before, except the secure server will issue a certificate each time you log in, and your login and password will be different. Please not that the old address http://gcg.uthscsa.edu and http://gcg.v19.uthscsa.edu will no longer be accessible after Friday 5:00 pm. Access will only be possible through the secure webserver https://gcg.uthscsa.edu or https://www.gcg.uthscsa.edu Databases: We have installed all databases with the exception of GenBank. We are working on obtaining additional diskspace to install nightly updates on the most popular databases, until then we ask that you use the respective online services such as netblast etc. Because the new installation runs on a 4-processor 700 MHZ Xeon, you should see a significant improvement in performance over the old DEC Alpha installation. Please address all questions regarding GCG to gcg-users@biochem.uthscsa.edu. Borries Demeler, Ph.D., Dept. of Biochemistry demeler@biochem.uthscsa.edu, (210) 567-6592 Susan L. Naylor, Ph.D., Dept. of Cellular and Structural Biology naylor@uthscsa.edu, (210) 567-3842 John Littlefield, Ph.D., Academic Information Services littlefield@uthscsa.edu, (210) 567-2283 From gcg-users@www.bioinformatics.uthscsa.edu Wed Apr 3 13:55:15 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Anthony B. Firulli, Ph.D) Date: Wed, 03 Apr 2002 07:55:15 -0600 Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> References: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> Message-ID: Borries, I have no idea if I have an account on the new server or not. I have been using telenet and terminal emulation to access GCG on a UNIX machine. What will happen to all my files on that machine? will they be transfered will the old machine be maintained? if there a functional version of seqlab for MAC. I am not a computer guy and I use GCG often please let me know what is going on. ABF >Dear GCG user: > >Thanks to help from Steve Hardies, we have now completed the installation >of the updated GCG and SeqWeb software suites to the bioinformatics Linux >server. This week on Friday, 4/5 at 5:00 pm, we will turn off access to >the old GCG server and move the GCG.UTHSCSA.EDU domain name to the new >GCG server. > >In order to make the transition as smooth as possible, we ask that each >current GCG user please check the following steps: > >1. If you do not have an account on the bioinformatics server yet, >please visit http://www.biochem.uthscsa.edu/apply/bioinf.html to >apply for an account. When applying for an account, please keep in >mind to: > > a) limit your desired login name to 8 characters max. > > b) select a secure password from the listing at > http://biochem.uthscsa.edu/cgi-bin/passwords > if you do not choose a secure password, one will be assigned. > > c) you will no longer need different passwords and logins for the > bioinformatics shell account and the GCG/SeqWeb logins - bot will > authenticate from the same password file. > > d) Please include a valid telephone number and e-mail address where > we can reach you in case of questions. > > e) If you already have an account on the bioinformatics server, > but would like a new password or would like to update your > account information, simply fill out the application again with > the updated information. > >Once you have an account on the bioinformatics server, you will be >able to access both the web based SeqWeb software and the command line >based gcg software. The command line version will only be available >through secure shell (ssh). For documentation on ssh please visit the >bioinformatics web server (http://www.bioinformatics.uthscsa.edu) > >2. Please finish all your GCG-related projects on the current server >until the end of this week and arrange with Jeremy Mann (x7-2672) >to transfer any data you might have on the old server to the new server. >If you can't finish a project by Friday of this week, please let us know, >and we will make special arrangements for you. Note: Even after the old >GCG server goes off-line, it will still be possible to transfer your data >to the new system. > >3. Starting Monday of next week (4/8), you will be able to connect to >the new gcg installation by pointing your browser to: > > https://gcg.uthscsa.edu > >(Please note the "s" in https, gcg is now served over a secure webserver) > >The login procedure is much the same as before, except the secure >server will issue a certificate each time you log in, and your login >and password will be different. > >Please not that the old address http://gcg.uthscsa.edu and >http://gcg.v19.uthscsa.edu will no longer be accessible after Friday >5:00 pm. Access will only be possible through the secure webserver >https://gcg.uthscsa.edu or https://www.gcg.uthscsa.edu > >Databases: We have installed all databases with the exception of GenBank. >We are working on obtaining additional diskspace to install nightly updates >on the most popular databases, until then we ask that you use the respective >online services such as netblast etc. > >Because the new installation runs on a 4-processor 700 MHZ Xeon, you should >see a significant improvement in performance over the old DEC Alpha >installation. > >Please address all questions regarding GCG to gcg-users@biochem.uthscsa.edu. > >Borries Demeler, Ph.D., Dept. of Biochemistry >demeler@biochem.uthscsa.edu, (210) 567-6592 > >Susan L. Naylor, Ph.D., Dept. of Cellular and Structural Biology >naylor@uthscsa.edu, (210) 567-3842 > >John Littlefield, Ph.D., Academic Information Services >littlefield@uthscsa.edu, (210) 567-2283 > >_______________________________________________ >GCG-Users mailing list >GCG-Users@www.bioinformatics.uthscsa.edu >http://biochem.uthscsa.edu/mailman/listinfo/gcg-users ___________________________________________________________________ Anthony B. Firulli, Ph.D MC 7756 Department of Physiology The University of Texas Health Science Center at San Antonio 7703 Floyd Curl Drive San Antonio TX, 78229-3900 office (210) 567-4401 lab 567-4352 FAX 567-4410 mobile 213-8429 Department home page http://physiology.uthscsa.edu/physiology.html ___________________________________________________________________ From gcg-users@www.bioinformatics.uthscsa.edu Wed Apr 3 14:18:55 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Borries Demeler) Date: Wed, 3 Apr 2002 08:18:55 -0600 (CST) Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: from "Anthony B. Firulli, Ph.D" at Apr 03, 2002 07:55:15 AM Message-ID: <200204031418.g33EItE00355@bioc09.v19.uthscsa.edu> > Borries, > > I have no idea if I have an account on the new server or not. I have > been using telenet and terminal emulation to access GCG on a UNIX > machine. What will happen to all my files on that machine? will they > be transfered will the old machine be maintained? if there a > functional version of seqlab for MAC. I am not a computer guy and I > use GCG often please let me know what is going on. > > ABF For all users with the same question: If you have never applied for an account on bioinformatics, you don't have one and you will have to set up an account so you can continue to use GCG. The old gcg computer will be disconnected on Friday, so please finish off any projects you have running on the old system before then. If you want to transfer files over to the new system, please contact Jeremy Mann at x7-2672, and he will assist you with that, even after Friday. IMPORTANT! Please follow the procedure outlined in the message I sent yesterday in applying for a new account, especially when selecting user names and passwords. Usernames have to be 8 characters or shorter, passwords have to be secure. If you don't submit a secure password, you increase our workload unnecessarily, and it will take longer to set up your account. We will have to call you back with a password that we have assigned. Passwords will be rejected if they match any of the criteria below: * contain a name or word found in a dictionary * contain only numbers * contain only letters * are less than 8 characters long A secure password contains a mix of upper and lower case letters, mixed with numbers or characters (!@#$%^&A*_+-~), is not found in a dictionary, and is at least 8 characters long. To make it easy, select one from our random password generator: http://www.biochem.uthscsa.edu/cgi-bin/passwords Here are the account application rules: a) limit your desired login name to 8 characters max. b) select a secure password from the listing at http://biochem.uthscsa.edu/cgi-bin/passwords if you do not choose a secure password, one will be assigned. c) you will no longer need different passwords and logins for the bioinformatics shell account and the GCG/SeqWeb logins - bot will authenticate from the same password file. d) Please include a valid telephone number and e-mail address where we can reach you in case of questions. e) If you already have an account on the bioinformatics server, but would like a new password or would like to update your account information, simply fill out the application again with the updated information. About your other questions: * The old gcg machine will not be maintained any longer, although the user account files will be backed up and can be accessed in the future. However, if you plan to have the files transferred over to the new system, we would ask you to do to call Jeremy within the next couple of weeks for assistance with that. * No, there is no Mac version. SeqLab is a Unix program and only runs on Unix machines. Currently, only Compaq's True64 and Linux are supported. Regards, -Borries --- Borries Demeler, Ph.D. Assistant Professor The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From gcg-users@www.bioinformatics.uthscsa.edu Wed Apr 3 14:48:26 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Naylor, Sue) Date: Wed, 03 Apr 2002 08:48:26 -0600 Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: References: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> Message-ID: <3CAAC1DA.8672.3EF23@localhost> Tony, I think you were using WebSeq (the Web interface). The web version should still be functional. Sue Date sent: 0000,0000,8000Wed, 03 Apr 2002 07:55:15 -0600 From: 0000,0000,8000"Anthony B. Firulli, Ph.D" < Subject: 0000,0000,8000Re: [GCG-Users] GCG/SeqWeb moved & updated To: 0000,0000,8000gcg-users@bioc09.v19.uthscsa.edu Send reply to: 0000,0000,8000gcg-users@bioc09.v19.uthscsa.edu 0000,8000,0000[ Double-click this line for list subscription options ] Borries, I have no idea if I have an account on the new server or not. I have been using telenet and terminal emulation to access GCG on a UNIX machine. What will happen to all my files on that machine? will they be transfered will the old machine be maintained? if there a functional version of seqlab for MAC. I am not a computer guy and I use GCG often please let me know what is going on. ABF 0000,0000,0000>Dear GCG user: > >Thanks to help from Steve Hardies, we have now completed the installation >of the updated GCG and SeqWeb software suites to the bioinformatics Linux >server. This week on Friday, 4/5 at 5:00 pm, we will turn off access to >the old GCG server and move the GCG.UTHSCSA.EDU domain name to the new >GCG server. > >In order to make the transition as smooth as possible, we ask that each >current GCG user please check the following steps: > >1. If you do not have an account on the bioinformatics server yet, >please visit http://www.biochem.uthscsa.edu/apply/bioinf.html to >apply for an account. When applying for an account, please keep in >mind to: > > a) limit your desired login name to 8 characters max. > > b) select a secure password from the listing at > http://biochem.uthscsa.edu/cgi-bin/passwords > if you do not choose a secure password, one will be assigned. > > c) you will no longer need different passwords and logins for the > bioinformatics shell account and the GCG/SeqWeb logins - bot will > authenticate from the same password file. > > d) Please include a valid telephone number and e-mail address where > we can reach you in case of questions. > > e) If you already have an account on the bioinformatics server, > but would like a new password or would like to update your > account information, simply fill out the application again with > the updated information. > >Once you have an account on the bioinformatics server, you will be >able to access both the web based SeqWeb software and the command line >based gcg software. The command line version will only be available >through secure shell (ssh). For documentation on ssh please visit the >bioinformatics web server (http://www.bioinformatics.uthscsa.edu) > >2. Please finish all your GCG-related projects on the current server >until the end of this week and arrange with Jeremy Mann (x7-2672) >to transfer any data you might have on the old server to the new server. >If you can't finish a project by Friday of this week, please let us know, >and we will make special arrangements for you. Note: Even after the old >GCG server goes off-line, it will still be possible to transfer your data >to the new system. > >3. Starting Monday of next week (4/8), you will be able to connect to >the new gcg installation by pointing your browser to: > > https://gcg.uthscsa.edu > >(Please note the "s" in https, gcg is now served over a secure webserver) > >The login procedure is much the same as before, except the secure >server will issue a certificate each time you log in, and your login >and password will be different. > >Please not that the old address http://gcg.uthscsa.edu and >http://gcg.v19.uthscsa.edu will no longer be accessible after Friday >5:00 pm. Access will only be possible through the secure webserver >https://gcg.uthscsa.edu or https://www.gcg.uthscsa.edu > >Databases: We have installed all databases with the exception of GenBank. >We are working on obtaining additional diskspace to install nightly updates >on the most popular databases, until then we ask that you use the respective >online services such as netblast etc. > >Because the new installation runs on a 4-processor 700 MHZ Xeon, you should >see a significant improvement in performance over the old DEC Alpha >installation. > >Please address all questions regarding GCG to gcg-users@biochem.uthscsa.edu. > >Borries Demeler, Ph.D., Dept. of Biochemistry >demeler@biochem.uthscsa.edu, (210) 567-6592 > >Susan L. Naylor, Ph.D., Dept. of Cellular and Structural Biology >naylor@uthscsa.edu, (210) 567-3842 > >John Littlefield, Ph.D., Academic Information Services >littlefield@uthscsa.edu, (210) 567-2283 > >_______________________________________________ >GCG-Users mailing list >GCG-Users@www.bioinformatics.uthscsa.edu >http://biochem.uthscsa.edu/mailman/listinfo/gcg-users ___________________________________________________________________ Anthony B. Firulli, Ph.D MC 7756 Department of Physiology The University of Texas Health Science Center at San Antonio 7703 Floyd Curl Drive San Antonio TX, 78229-3900 office (210) 567-4401 lab 567-4352 FAX 567-4410 mobile 213-8429 Department home page http://physiology.uthscsa.edu/physiology.html ___________________________________________________________________ _______________________________________________ GCG-Users mailing list GCG-Users@www.bioinformatics.uthscsa.edu http://biochem.uthscsa.edu/mailman/listinfo/gcg-users Susan L. Naylor, Ph.D. Department of Cellular & Structural Biology University of Texas Health Science Center 7703 Floyd Curl Dr. San Antonio, TX 78229-3900 Telephone: (210) 567-3842 FAX: (210) 567-6781 E-mail: Naylor@UTHSCSA.edu From gcg-users@www.bioinformatics.uthscsa.edu Wed Apr 3 14:50:39 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Borries Demeler) Date: Wed, 3 Apr 2002 08:50:39 -0600 (CST) Subject: [GCG-Users] GCG transition help document Message-ID: <200204031450.g33Eodd00914@bioc09.v19.uthscsa.edu> Steve Hardies has prepared some help documentation that should help you with the transition from the old setup to the new. You can access this document now from the bioinformatics site at: http://www.bioinformatics.uthscsa.edu just click the "Documentation" button for several help documents. Eventually, we will move all documentation into the new "Bioinformatics Core Facility Documentation System" which Jeremy has set up and can be accessed from the same site. It will help us to better organize the various documentation. Regards, -Borries --- Borries Demeler, Ph.D. Assistant Professor The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From gcg-users@www.bioinformatics.uthscsa.edu Wed Apr 3 21:43:08 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Anthony B. Firulli, Ph.D) Date: Wed, 03 Apr 2002 15:43:08 -0600 Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: <3CAAC1DA.8672.3EF23@localhost> References: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> <3CAAC1DA.8672.3EF23@localhost> Message-ID: >Tony, > >I think you were using WebSeq (the Web interface). The web version >should still be functional. >Sue > Hi Sue I was using Nasca telenet 2.6 the old fashion way ABF ___________________________________________________________________ Anthony B. Firulli, Ph.D MC 7756 Department of Physiology The University of Texas Health Science Center at San Antonio 7703 Floyd Curl Drive San Antonio TX, 78229-3900 office (210) 567-4401 lab 567-4352 FAX 567-4410 mobile 213-8429 Department home page http://physiology.uthscsa.edu/physiology.html ___________________________________________________________________ From gcg-users@www.bioinformatics.uthscsa.edu Wed Apr 3 23:14:32 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Jeremy Mann) Date: Wed, 3 Apr 2002 17:14:32 -0600 (CST) Subject: [GCG-Users] way to speed up your jobs Message-ID: <32911.24.162.180.254.1017875672.squirrel@biochem.uthscsa.edu> I have noticed with some types of jobs/searchs, SeqWeb has an option for Number of Processors. You can use up to 4 (FOUR) processors to dramatically accerlerate your jobs. Just thought I'd pass this along. -- Jeremy Mann jeremy@biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility Phone: (210) 567-2672 From demeler@bioc09.v19.uthscsa.edu Tue Apr 2 20:25:49 2002 From: demeler at bioc09.v19.uthscsa.edu (Borries Demeler) Date: Tue Apr 27 19:36:56 2004 Subject: [GCG-Users] GCG/SeqWeb moved & updated Message-ID: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> Dear GCG user: Thanks to help from Steve Hardies, we have now completed the installation of the updated GCG and SeqWeb software suites to the bioinformatics Linux server. This week on Friday, 4/5 at 5:00 pm, we will turn off access to the old GCG server and move the GCG.UTHSCSA.EDU domain name to the new GCG server. In order to make the transition as smooth as possible, we ask that each current GCG user please check the following steps: 1. If you do not have an account on the bioinformatics server yet, please visit http://www.biochem.uthscsa.edu/apply/bioinf.html to apply for an account. When applying for an account, please keep in mind to: a) limit your desired login name to 8 characters max. b) select a secure password from the listing at http://biochem.uthscsa.edu/cgi-bin/passwords if you do not choose a secure password, one will be assigned. c) you will no longer need different passwords and logins for the bioinformatics shell account and the GCG/SeqWeb logins - bot will authenticate from the same password file. d) Please include a valid telephone number and e-mail address where we can reach you in case of questions. e) If you already have an account on the bioinformatics server, but would like a new password or would like to update your account information, simply fill out the application again with the updated information. Once you have an account on the bioinformatics server, you will be able to access both the web based SeqWeb software and the command line based gcg software. The command line version will only be available through secure shell (ssh). For documentation on ssh please visit the bioinformatics web server (http://www.bioinformatics.uthscsa.edu) 2. Please finish all your GCG-related projects on the current server until the end of this week and arrange with Jeremy Mann (x7-2672) to transfer any data you might have on the old server to the new server. If you can't finish a project by Friday of this week, please let us know, and we will make special arrangements for you. Note: Even after the old GCG server goes off-line, it will still be possible to transfer your data to the new system. 3. Starting Monday of next week (4/8), you will be able to connect to the new gcg installation by pointing your browser to: https://gcg.uthscsa.edu (Please note the "s" in https, gcg is now served over a secure webserver) The login procedure is much the same as before, except the secure server will issue a certificate each time you log in, and your login and password will be different. Please not that the old address http://gcg.uthscsa.edu and http://gcg.v19.uthscsa.edu will no longer be accessible after Friday 5:00 pm. Access will only be possible through the secure webserver https://gcg.uthscsa.edu or https://www.gcg.uthscsa.edu Databases: We have installed all databases with the exception of GenBank. We are working on obtaining additional diskspace to install nightly updates on the most popular databases, until then we ask that you use the respective online services such as netblast etc. Because the new installation runs on a 4-processor 700 MHZ Xeon, you should see a significant improvement in performance over the old DEC Alpha installation. Please address all questions regarding GCG to gcg-users@biochem.uthscsa.edu. Borries Demeler, Ph.D., Dept. of Biochemistry demeler@biochem.uthscsa.edu, (210) 567-6592 Susan L. Naylor, Ph.D., Dept. of Cellular and Structural Biology naylor@uthscsa.edu, (210) 567-3842 John Littlefield, Ph.D., Academic Information Services littlefield@uthscsa.edu, (210) 567-2283 From firullia@uthscsa.edu Wed Apr 3 07:55:15 2002 From: firullia at uthscsa.edu (Anthony B. Firulli, Ph.D) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> References: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> Message-ID: Borries, I have no idea if I have an account on the new server or not. I have been using telenet and terminal emulation to access GCG on a UNIX machine. What will happen to all my files on that machine? will they be transfered will the old machine be maintained? if there a functional version of seqlab for MAC. I am not a computer guy and I use GCG often please let me know what is going on. ABF >Dear GCG user: > >Thanks to help from Steve Hardies, we have now completed the installation >of the updated GCG and SeqWeb software suites to the bioinformatics Linux >server. This week on Friday, 4/5 at 5:00 pm, we will turn off access to >the old GCG server and move the GCG.UTHSCSA.EDU domain name to the new >GCG server. > >In order to make the transition as smooth as possible, we ask that each >current GCG user please check the following steps: > >1. If you do not have an account on the bioinformatics server yet, >please visit http://www.biochem.uthscsa.edu/apply/bioinf.html to >apply for an account. When applying for an account, please keep in >mind to: > > a) limit your desired login name to 8 characters max. > > b) select a secure password from the listing at > http://biochem.uthscsa.edu/cgi-bin/passwords > if you do not choose a secure password, one will be assigned. > > c) you will no longer need different passwords and logins for the > bioinformatics shell account and the GCG/SeqWeb logins - bot will > authenticate from the same password file. > > d) Please include a valid telephone number and e-mail address where > we can reach you in case of questions. > > e) If you already have an account on the bioinformatics server, > but would like a new password or would like to update your > account information, simply fill out the application again with > the updated information. > >Once you have an account on the bioinformatics server, you will be >able to access both the web based SeqWeb software and the command line >based gcg software. The command line version will only be available >through secure shell (ssh). For documentation on ssh please visit the >bioinformatics web server (http://www.bioinformatics.uthscsa.edu) > >2. Please finish all your GCG-related projects on the current server >until the end of this week and arrange with Jeremy Mann (x7-2672) >to transfer any data you might have on the old server to the new server. >If you can't finish a project by Friday of this week, please let us know, >and we will make special arrangements for you. Note: Even after the old >GCG server goes off-line, it will still be possible to transfer your data >to the new system. > >3. Starting Monday of next week (4/8), you will be able to connect to >the new gcg installation by pointing your browser to: > > https://gcg.uthscsa.edu > >(Please note the "s" in https, gcg is now served over a secure webserver) > >The login procedure is much the same as before, except the secure >server will issue a certificate each time you log in, and your login >and password will be different. > >Please not that the old address http://gcg.uthscsa.edu and >http://gcg.v19.uthscsa.edu will no longer be accessible after Friday >5:00 pm. Access will only be possible through the secure webserver >https://gcg.uthscsa.edu or https://www.gcg.uthscsa.edu > >Databases: We have installed all databases with the exception of GenBank. >We are working on obtaining additional diskspace to install nightly updates >on the most popular databases, until then we ask that you use the respective >online services such as netblast etc. > >Because the new installation runs on a 4-processor 700 MHZ Xeon, you should >see a significant improvement in performance over the old DEC Alpha >installation. > >Please address all questions regarding GCG to gcg-users@biochem.uthscsa.edu. > >Borries Demeler, Ph.D., Dept. of Biochemistry >demeler@biochem.uthscsa.edu, (210) 567-6592 > >Susan L. Naylor, Ph.D., Dept. of Cellular and Structural Biology >naylor@uthscsa.edu, (210) 567-3842 > >John Littlefield, Ph.D., Academic Information Services >littlefield@uthscsa.edu, (210) 567-2283 > >_______________________________________________ >GCG-Users mailing list >GCG-Users@www.bioinformatics.uthscsa.edu >http://biochem.uthscsa.edu/mailman/listinfo/gcg-users ___________________________________________________________________ Anthony B. Firulli, Ph.D MC 7756 Department of Physiology The University of Texas Health Science Center at San Antonio 7703 Floyd Curl Drive San Antonio TX, 78229-3900 office (210) 567-4401 lab 567-4352 FAX 567-4410 mobile 213-8429 Department home page http://physiology.uthscsa.edu/physiology.html ___________________________________________________________________ From demeler@bioc09.v19.uthscsa.edu Wed Apr 3 08:18:55 2002 From: demeler at bioc09.v19.uthscsa.edu (Borries Demeler) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: from "Anthony B. Firulli, Ph.D" at Apr 03, 2002 07:55:15 AM Message-ID: <200204031418.g33EItE00355@bioc09.v19.uthscsa.edu> > Borries, > > I have no idea if I have an account on the new server or not. I have > been using telenet and terminal emulation to access GCG on a UNIX > machine. What will happen to all my files on that machine? will they > be transfered will the old machine be maintained? if there a > functional version of seqlab for MAC. I am not a computer guy and I > use GCG often please let me know what is going on. > > ABF For all users with the same question: If you have never applied for an account on bioinformatics, you don't have one and you will have to set up an account so you can continue to use GCG. The old gcg computer will be disconnected on Friday, so please finish off any projects you have running on the old system before then. If you want to transfer files over to the new system, please contact Jeremy Mann at x7-2672, and he will assist you with that, even after Friday. IMPORTANT! Please follow the procedure outlined in the message I sent yesterday in applying for a new account, especially when selecting user names and passwords. Usernames have to be 8 characters or shorter, passwords have to be secure. If you don't submit a secure password, you increase our workload unnecessarily, and it will take longer to set up your account. We will have to call you back with a password that we have assigned. Passwords will be rejected if they match any of the criteria below: * contain a name or word found in a dictionary * contain only numbers * contain only letters * are less than 8 characters long A secure password contains a mix of upper and lower case letters, mixed with numbers or characters (!@#$%^&A*_+-~), is not found in a dictionary, and is at least 8 characters long. To make it easy, select one from our random password generator: http://www.biochem.uthscsa.edu/cgi-bin/passwords Here are the account application rules: a) limit your desired login name to 8 characters max. b) select a secure password from the listing at http://biochem.uthscsa.edu/cgi-bin/passwords if you do not choose a secure password, one will be assigned. c) you will no longer need different passwords and logins for the bioinformatics shell account and the GCG/SeqWeb logins - bot will authenticate from the same password file. d) Please include a valid telephone number and e-mail address where we can reach you in case of questions. e) If you already have an account on the bioinformatics server, but would like a new password or would like to update your account information, simply fill out the application again with the updated information. About your other questions: * The old gcg machine will not be maintained any longer, although the user account files will be backed up and can be accessed in the future. However, if you plan to have the files transferred over to the new system, we would ask you to do to call Jeremy within the next couple of weeks for assistance with that. * No, there is no Mac version. SeqLab is a Unix program and only runs on Unix machines. Currently, only Compaq's True64 and Linux are supported. Regards, -Borries --- Borries Demeler, Ph.D. Assistant Professor The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From naylor@uthscsa.edu Wed Apr 3 08:48:26 2002 From: naylor at uthscsa.edu (Naylor, Sue) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: References: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> Message-ID: <3CAAC1DA.8672.3EF23@localhost> A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 6094 bytes Desc: not available Url : http://biochem.uthscsa.edu/pipermail/gcg-users/attachments/20020403/e3f42fff/attachment.bin From demeler@bioc09.v19.uthscsa.edu Wed Apr 3 08:50:39 2002 From: demeler at bioc09.v19.uthscsa.edu (Borries Demeler) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] GCG transition help document Message-ID: <200204031450.g33Eodd00914@bioc09.v19.uthscsa.edu> Steve Hardies has prepared some help documentation that should help you with the transition from the old setup to the new. You can access this document now from the bioinformatics site at: http://www.bioinformatics.uthscsa.edu just click the "Documentation" button for several help documents. Eventually, we will move all documentation into the new "Bioinformatics Core Facility Documentation System" which Jeremy has set up and can be accessed from the same site. It will help us to better organize the various documentation. Regards, -Borries --- Borries Demeler, Ph.D. Assistant Professor The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From firullia@uthscsa.edu Wed Apr 3 15:43:08 2002 From: firullia at uthscsa.edu (Anthony B. Firulli, Ph.D) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] GCG/SeqWeb moved & updated In-Reply-To: <3CAAC1DA.8672.3EF23@localhost> References: <200204030225.g332Pna28818@bioc09.v19.uthscsa.edu> <3CAAC1DA.8672.3EF23@localhost> Message-ID: >Tony, > >I think you were using WebSeq (the Web interface). The web version >should still be functional. >Sue > Hi Sue I was using Nasca telenet 2.6 the old fashion way ABF ___________________________________________________________________ Anthony B. Firulli, Ph.D MC 7756 Department of Physiology The University of Texas Health Science Center at San Antonio 7703 Floyd Curl Drive San Antonio TX, 78229-3900 office (210) 567-4401 lab 567-4352 FAX 567-4410 mobile 213-8429 Department home page http://physiology.uthscsa.edu/physiology.html ___________________________________________________________________ From jeremy@bioc09.v19.uthscsa.edu Wed Apr 3 17:14:32 2002 From: jeremy at bioc09.v19.uthscsa.edu (Jeremy Mann) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] way to speed up your jobs Message-ID: <32911.24.162.180.254.1017875672.squirrel@biochem.uthscsa.edu> I have noticed with some types of jobs/searchs, SeqWeb has an option for Number of Processors. You can use up to 4 (FOUR) processors to dramatically accerlerate your jobs. Just thought I'd pass this along. -- Jeremy Mann jeremy@biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility Phone: (210) 567-2672 From gcg-users@www.bioinformatics.uthscsa.edu Wed Aug 21 14:50:39 2002 From: gcg-users@www.bioinformatics.uthscsa.edu (Jeremy Mann) Date: Wed, 21 Aug 2002 08:50:39 -0500 (CDT) Subject: [GCG-Users] Updated SeqWeb Message-ID: <32861.129.111.69.228.1029937839.squirrel@biochem.uthscsa.edu> The current version of SeqWeb has been updated to 2.1. This is a major fix and enhancement release from Accelrys. - Browser Support: Seqweb 2.1 now works on the following browsers: Netscape versions 4.77, 4.78, 4.79, 6.2 and 6.2.3 for Windows 98/Me/NT/2000, Unix and Macintosh Internet Explorer 5.5 and 6.0 for Windows 98/Me/NT/2000 Internet Explorer 5.0 and 5.1x for Macintosh - Java Applets: Seqweb 2.1 now supports running Java applets in Internet Explorer for MacOS 8, 9 and 10. - Enhancements: Seqweb 2.1 has been optimized to reduce the loading time of several components and pages, included all analysis pages, all manager pages and the sequence selector and manager applets. Added support for the PSI-BLAST and TransMem applications that are available in Version 10.3 of the Wisconsin Package. - Changes/Fixes: Allows you to rename the results file from within the Results Manager. This option is available through the Edit function, where you may specify the new name of the results file as well as a new description. A search utility has been added to the project management functions that are available through the Sequence Manager applet. This utility makes it easier for you to search for specific user names in the given user list. Two new buttons have been added to the Sequence Selector that appear in all analysis forms that accept multiple-sequences as input. These two buttons are Select All and Deselect All. WebLab ViewerLite, from Accelry's, is now distributed with SeqWeb. This viewer provides high-quality molecular visualization on the Windows and Macintosh platforms. Instructions for user installation of this desktop tool are available in Appendix D, "Add-on software for Molecular Visualization" of the SeqWeb 2.1 online help. As with any new release, there will probably some problems at first. Please report these to me immediately. My contact information is below. Enjoy the new release. -- Jeremy Mann jeremy@biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility Phone: (210) 567-2672 From jeremy@bioc09.v19.uthscsa.edu Wed Aug 21 09:50:39 2002 From: jeremy at bioc09.v19.uthscsa.edu (Jeremy Mann) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] Updated SeqWeb Message-ID: <32861.129.111.69.228.1029937839.squirrel@biochem.uthscsa.edu> The current version of SeqWeb has been updated to 2.1. This is a major fix and enhancement release from Accelrys. - Browser Support: Seqweb 2.1 now works on the following browsers: Netscape versions 4.77, 4.78, 4.79, 6.2 and 6.2.3 for Windows 98/Me/NT/2000, Unix and Macintosh Internet Explorer 5.5 and 6.0 for Windows 98/Me/NT/2000 Internet Explorer 5.0 and 5.1x for Macintosh - Java Applets: Seqweb 2.1 now supports running Java applets in Internet Explorer for MacOS 8, 9 and 10. - Enhancements: Seqweb 2.1 has been optimized to reduce the loading time of several components and pages, included all analysis pages, all manager pages and the sequence selector and manager applets. Added support for the PSI-BLAST and TransMem applications that are available in Version 10.3 of the Wisconsin Package. - Changes/Fixes: Allows you to rename the results file from within the Results Manager. This option is available through the Edit function, where you may specify the new name of the results file as well as a new description. A search utility has been added to the project management functions that are available through the Sequence Manager applet. This utility makes it easier for you to search for specific user names in the given user list. Two new buttons have been added to the Sequence Selector that appear in all analysis forms that accept multiple-sequences as input. These two buttons are Select All and Deselect All. WebLab ViewerLite, from Accelry's, is now distributed with SeqWeb. This viewer provides high-quality molecular visualization on the Windows and Macintosh platforms. Instructions for user installation of this desktop tool are available in Appendix D, "Add-on software for Molecular Visualization" of the SeqWeb 2.1 online help. As with any new release, there will probably some problems at first. Please report these to me immediately. My contact information is below. Enjoy the new release. -- Jeremy Mann jeremy@biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility Phone: (210) 567-2672 From demeler@bioc09.v19.uthscsa.edu Tue Oct 1 23:46:01 2002 From: demeler@bioc09.v19.uthscsa.edu (Borries Demeler) Date: Tue, 1 Oct 2002 17:46:01 -0500 (CDT) Subject: [GCG-Users] Scheduled Maintenance Message-ID: <200210012246.g91Mk1X0002537@bioc09.v19.uthscsa.edu> To all bioinformatics server users: Tomorrow 10/2/02 from 8:00 pm to 10:00 pm the bioinformatics server will be unavailable due to scheduled maintenance. We will replace a faulty SCSI cable to allow access to another 500 gigabytes of RAID 5 storage. During this time the GCG Wisconsin package will be unavailable and the modems will not be functional. Please plan accordingly. Thanks, -Borries P.S. apologies if you receive duplicate mailings - some recipients are subscribed to both the bioinformatics server list and the gcg users list. --- Borries Demeler, Ph.D. Assistant Professor The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From demeler@bioc09.v19.uthscsa.edu Tue Oct 1 18:46:01 2002 From: demeler at bioc09.v19.uthscsa.edu (Borries Demeler) Date: Tue Apr 27 19:36:57 2004 Subject: [GCG-Users] Scheduled Maintenance Message-ID: <200210012246.g91Mk1X0002537@bioc09.v19.uthscsa.edu> To all bioinformatics server users: Tomorrow 10/2/02 from 8:00 pm to 10:00 pm the bioinformatics server will be unavailable due to scheduled maintenance. We will replace a faulty SCSI cable to allow access to another 500 gigabytes of RAID 5 storage. During this time the GCG Wisconsin package will be unavailable and the modems will not be functional. Please plan accordingly. Thanks, -Borries P.S. apologies if you receive duplicate mailings - some recipients are subscribed to both the bioinformatics server list and the gcg users list. --- Borries Demeler, Ph.D. Assistant Professor The University of Texas Health Science Center at San Antonio Dept. of Biochemistry, 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900 Voice: 210-567-6592, Fax: 210-567-4575, Email: demeler@biochem.uthscsa.edu From jeremy@biochem.uthscsa.edu Tue Jun 21 09:27:25 2005 From: jeremy at biochem.uthscsa.edu (Jeremy Mann) Date: Wed Jun 22 08:21:07 2005 Subject: [GCG-Users] GCG in a 64bit environment Message-ID: <55702.129.111.174.49.1119360445.squirrel@biochem.uthscsa.edu> This message is for all GCG users on bcf.uthscsa.edu. Since we have switched to a 64bit environment, if you try and run GCG you will be presented with a list of library errors. This can be fixed by adding an environment variable to your .bashrc or .cshrc files (depending on which shell you are using). For Bash: export LD_ASSUME_KERNEL=2.4.19 For Csh: setenv LD_ASSUME_KERNEL 2.4.19 -- Jeremy Mann jeremy@biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672