From dag at sonsorol.org Thu Mar 23 15:17:19 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 23 Mar 2006 15:17:19 -0500 Subject: [OBF-developers] Important news for all developers with open-bio.org CVS access Message-ID: Hello, ** All developer accounts are being moved to a new server this weekend; details enclosed ** This mailing list was freshly created a few minutes ago by parsing out the email addresses listed in the user account data on pub.open- bio.org, the OBF machine that hosts the following open source CVS repositories: * /home/repository/biopython * /home/repository/biojava * /home/repository/bioperl * /home/repository/biodas * /home/repository/moby * /home/repository/biocorba * /home/repository/biosql * /home/repository/bioruby * /home/repository/emboss If you receive this email, it means we think you are a developer. If you are a developer, we have really important news for you, please keep reading! The folks running the OBF servers have always had a plan in place to transition onto more modern server hardware, especially hardware purpose built with "lights out" remote management in mind. The remote management techniques allow any of our admin volunteers to have complete control of the server as if they were standing next to the machine. Since our machines are locked in a cage in a Boston data- center and our admin staff is located all over the globe, this is important. Our new hardware is great - we have complete remote control of the console, BIOS settings and even electrical power from anywhere in the world. Sorry for raving about hardware, I'm a geek. What can I say? If you want to see pictures of the new server cage and OBF hardware you can see them at this URL: http://bioteam.net/gallery/bioteamBDC Going back in time, our way-cool legacy hardware can be seen in this gallery: http://gallery.open-bio.org/gallery2/v/obf-servers/ The new hardware has been up and running for quite some time now in "testing" mode. However, recent circumstances have forced us to actually commit to a formal transition. This transition has already begun, it will complete this weekend. Moving all of the developers and the real CVS repositories is the final step. The reason for the move is that the company that currently hosts portal.open-bio.org and pub.open-bio.org (Wyeth Research, Cambridge MA USA) is making changes to their internet connection that will remove the ability for them to host internet-facing servers in their Cambridge, MA facilities. This change is going to happen on the evening of Monday March 27th and once it occurs our old servers currently sitting in Wyeth will be disconnected from the internet. On behalf of the OBF I'd just like to thank Wyeth one more time for their amazing support over the years. Our servers consume non-trivial amounts of internet bandwidth and have been freely hosted on their corporate internet circuit for many years now. Paying for such hosting would have cost us many thousands of dollars per year. With internet hosting you only really notice the ISP when the service goes down and many of our servers at Wyeth exceeded 500+ days of continuous uptime with no disruption or loss of network connectivity. Our new server hardware is located within a colocation cage belonging to BioTeam Inc (my employer). BioTeam has donated the cost of the new server hardware and will be donating the ongoing costs of power, cooling, hosting and bandwidth. It's nice to work for a company that understands, values and supports the OBF's various projects and efforts. The hosting facility is solid. Infrastructure folks will enjoy these links: http://www.bostondatacenters.com/specs.html http://www.bostondatacenters.com/network.html http://www.bostondatacenters.com/facility.html The following transitions have already occurred: (1) All of our mailing lists (57!) have been consolidated onto http:// lists.open-bio.org -- all subscribers, preferences, settings and mailing list archives transfered over just fine (2) All of our websites have been consolidated on the new server newportal.open-bio.org (3) Behind the scenes OBF has a helpdesk/ticketing system to help with support issues. Emailing "support at open-bio.org" is the proper way to get into the system. It's been working great and it is far easier to respond quickly to issues and make sure that nothing falls through the cracks. (4) Our server replacement for cvs.open-bio.org (the anonymous CVS server) is still on order so we've built a temporary server as a VMWare virtual host. The new server also offers anonymous RSYNC access which is a new addition for us. Surf on over to http:// cvs.open-bio.org for the details. With email, websites and anonymous-CVS transitioned, the final step is to get the developer environment migrated. We have a new machine just for everyone on this list. It is called "dev.open-bio.org" and it will be the new home for developers using CVS as well as the people who want to switch over to using Subversion. dev.open-bio.org is where the repositories will be moved to. This is the machine you'll have SSH access to and this is the machine you'll be CVS/SVN committing to. Remember this hostname! dev.open-bio.org (we'll also alias dev.biomoby.org, dev.biojava.org etc. etc.) Technically, its a pretty easy process to mirror over the repositories, user accounts and all of your user home directories and files. I've already actually done this. The nasty part is user passwords. Those can't be migrated. The old server stores hashed passwords in a way that is not compatible with the methods used on the new server. This means that while we can move your user account and all your files over to the new machine, your password is going to have to be changed. You'll need to communicate with support at open-bio.org for a password reset before you can regain access to the system. While a painful process for our admin staff, this is also a good way for us to weed out dormant or inactive accounts. I'm guessing a significant portion of the accounts we move over will never be reactivated. This is good housekeeping for us to be doing anyway. How this process is going to work: (1) Sometime on Saturday the 25th we will disable all access to the existing CVS machine (2) User accounts, home directories, files and all CVS repositories will be mirrored and migrated to dev.open-bio.org (3) We will begin altering and resetting user passwords for access to dev.open-bio.org It would help if you could refrain from doing any CVS commits on Saturday the 25th. While not required this will help make sure the mirror and migration process works perfectly. ===================================================== HOW TO GET YOUR PASSWORD FOR DEV.OPEN-BIO.ORG ===================================================== Easy. Email "support at open-bio.org" and MAKE SURE you provide all of the following information: ------------------------------------------------------------------------ ------ Full Name: Organization/Institution/Employer: Working email address (for notices such as this): Existing unix username: Project/CVS affiliation: ------------------------------------------------------------------------ ------ We'll start taking dev.open-bio.org password reset/access requests right now but we'll ask that you do not login to dev.open-bio.org until Sunday the 26th or until you receive notice that the migration has been completed. This will ensure that you don't alter, delete or change any files that will then get lost when we do our final mirror and sync operations. ===================================================== HELP US FIND AND SQUASH PROBLEMS ===================================================== This is a really complicated migration of a ton of different servers, services and users. I'm sure stuff will get flaky during the transition and I'm sure that I'm forgetting about some things. If you notice anything not working or experience any sort of problem PLEASE email support at open-bio.org or just contact me directly. I'll be pretty much tethered to my computer during the upcoming days. How to reach me: Chris Dagdigian dag at sonsorol.org 617-877-5498 Ichat/AOL Instant messenger: 'bioteamdag' From dag at sonsorol.org Sat Mar 25 18:39:20 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 25 Mar 2006 18:39:20 -0500 Subject: [OBF-developers] transition to the new open-bio developer server is complete Message-ID: Hi everyone, dev.open-bio.org is now the official server you should be using for CVS/SVN commits and checkins. The final mirror and sync actions went just fine. I've changed the DNS entry for "pub.open-bio.org" to point to this new machine but just to be safe (and in case you have existing code checkouts with the old machine name hard coded into the CVS root somewhere) please make sure that the DNS switch has propagated out to you before you try to connect to (or CVS commit) against "pub.open- bio.org". The IP address of dev.open-bio.org is 207.154.17.71 If you run the command "host pub.open-bio.org" or "nslookup pub.open- bio.org" and you get back an IP address of 207.154.17.71 then you know the DNS has propagated to your local server and it is OK to use pub.open-bio.org interchangeably with dev.open-bio.org. If you get back 65.246.187.177 then you know you still have the old DNS cached somewhere within your organization -- it should age out and re-update within 24 hours. Please give the new system a whirl. I did migrate over the python / usr/local/bin/syncmail script that many people use to autogenerate CVS commit email messages. As you start committing code again let me know if the commit messages are going out smoothly. Let me know if you need software, libraries or other things installed. Ruby, perl and python are all present on the system along with the usual compilers and dev tools. I still need to install a modern Java SDK. Many people have already requested and received their new password information. Hopefully you found the process smooth - its a good intro to how our ticketing/support system works if you've never dealt with it before. For those of you finding yourselves locked out of the new server, here is the info to regain access: ===================================================== HOW TO GET YOUR PASSWORD FOR DEV.OPEN-BIO.ORG ===================================================== Easy. Email "support at open-bio.org" and MAKE SURE you provide all of the following information: ------------------------------------------------------------------------ Full Name: Organization/Institution/Employer: Working email address (for notices such as this): Existing unix username: Project/CVS affiliation: ------------------------------------------------------------------------ From darin.london at duke.edu Tue Mar 28 09:42:45 2006 From: darin.london at duke.edu (Darin London) Date: Tue, 28 Mar 2006 09:42:45 -0500 Subject: [OBF-developers] Announcing BOSC 2006 Message-ID: <44294B65.4050207@duke.edu> MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 14th International Conference on Intelligent Systems for Molecular Biology. Please consult The Official BOSC 2006 Website at http://www.open-bio.org/wiki/BOSC_2006 for details and information. In addition, a BOSC weblog has been setup to make it easier to desiminate all BOSC related announcements: http://wiki.open-bio.org/boscblog/ And if you have an ICAL compatible Calendar, there is an EventDB calendar set up with all BOSC related deadlines. http://eventful.com/groups/G0-001-000014747-0 More information about ISMB can be found at the Official ISMB 2006 Website: http://ismb2006.cbi.cnptia.embrapa.br/ Thank You, and we look forward to seeing you all, The BOSC Organizing Committee. From dag at sonsorol.org Thu Mar 23 20:17:19 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu, 23 Mar 2006 15:17:19 -0500 Subject: [OBF-developers] Important news for all developers with open-bio.org CVS access Message-ID: Hello, ** All developer accounts are being moved to a new server this weekend; details enclosed ** This mailing list was freshly created a few minutes ago by parsing out the email addresses listed in the user account data on pub.open- bio.org, the OBF machine that hosts the following open source CVS repositories: * /home/repository/biopython * /home/repository/biojava * /home/repository/bioperl * /home/repository/biodas * /home/repository/moby * /home/repository/biocorba * /home/repository/biosql * /home/repository/bioruby * /home/repository/emboss If you receive this email, it means we think you are a developer. If you are a developer, we have really important news for you, please keep reading! The folks running the OBF servers have always had a plan in place to transition onto more modern server hardware, especially hardware purpose built with "lights out" remote management in mind. The remote management techniques allow any of our admin volunteers to have complete control of the server as if they were standing next to the machine. Since our machines are locked in a cage in a Boston data- center and our admin staff is located all over the globe, this is important. Our new hardware is great - we have complete remote control of the console, BIOS settings and even electrical power from anywhere in the world. Sorry for raving about hardware, I'm a geek. What can I say? If you want to see pictures of the new server cage and OBF hardware you can see them at this URL: http://bioteam.net/gallery/bioteamBDC Going back in time, our way-cool legacy hardware can be seen in this gallery: http://gallery.open-bio.org/gallery2/v/obf-servers/ The new hardware has been up and running for quite some time now in "testing" mode. However, recent circumstances have forced us to actually commit to a formal transition. This transition has already begun, it will complete this weekend. Moving all of the developers and the real CVS repositories is the final step. The reason for the move is that the company that currently hosts portal.open-bio.org and pub.open-bio.org (Wyeth Research, Cambridge MA USA) is making changes to their internet connection that will remove the ability for them to host internet-facing servers in their Cambridge, MA facilities. This change is going to happen on the evening of Monday March 27th and once it occurs our old servers currently sitting in Wyeth will be disconnected from the internet. On behalf of the OBF I'd just like to thank Wyeth one more time for their amazing support over the years. Our servers consume non-trivial amounts of internet bandwidth and have been freely hosted on their corporate internet circuit for many years now. Paying for such hosting would have cost us many thousands of dollars per year. With internet hosting you only really notice the ISP when the service goes down and many of our servers at Wyeth exceeded 500+ days of continuous uptime with no disruption or loss of network connectivity. Our new server hardware is located within a colocation cage belonging to BioTeam Inc (my employer). BioTeam has donated the cost of the new server hardware and will be donating the ongoing costs of power, cooling, hosting and bandwidth. It's nice to work for a company that understands, values and supports the OBF's various projects and efforts. The hosting facility is solid. Infrastructure folks will enjoy these links: http://www.bostondatacenters.com/specs.html http://www.bostondatacenters.com/network.html http://www.bostondatacenters.com/facility.html The following transitions have already occurred: (1) All of our mailing lists (57!) have been consolidated onto http:// lists.open-bio.org -- all subscribers, preferences, settings and mailing list archives transfered over just fine (2) All of our websites have been consolidated on the new server newportal.open-bio.org (3) Behind the scenes OBF has a helpdesk/ticketing system to help with support issues. Emailing "support at open-bio.org" is the proper way to get into the system. It's been working great and it is far easier to respond quickly to issues and make sure that nothing falls through the cracks. (4) Our server replacement for cvs.open-bio.org (the anonymous CVS server) is still on order so we've built a temporary server as a VMWare virtual host. The new server also offers anonymous RSYNC access which is a new addition for us. Surf on over to http:// cvs.open-bio.org for the details. With email, websites and anonymous-CVS transitioned, the final step is to get the developer environment migrated. We have a new machine just for everyone on this list. It is called "dev.open-bio.org" and it will be the new home for developers using CVS as well as the people who want to switch over to using Subversion. dev.open-bio.org is where the repositories will be moved to. This is the machine you'll have SSH access to and this is the machine you'll be CVS/SVN committing to. Remember this hostname! dev.open-bio.org (we'll also alias dev.biomoby.org, dev.biojava.org etc. etc.) Technically, its a pretty easy process to mirror over the repositories, user accounts and all of your user home directories and files. I've already actually done this. The nasty part is user passwords. Those can't be migrated. The old server stores hashed passwords in a way that is not compatible with the methods used on the new server. This means that while we can move your user account and all your files over to the new machine, your password is going to have to be changed. You'll need to communicate with support at open-bio.org for a password reset before you can regain access to the system. While a painful process for our admin staff, this is also a good way for us to weed out dormant or inactive accounts. I'm guessing a significant portion of the accounts we move over will never be reactivated. This is good housekeeping for us to be doing anyway. How this process is going to work: (1) Sometime on Saturday the 25th we will disable all access to the existing CVS machine (2) User accounts, home directories, files and all CVS repositories will be mirrored and migrated to dev.open-bio.org (3) We will begin altering and resetting user passwords for access to dev.open-bio.org It would help if you could refrain from doing any CVS commits on Saturday the 25th. While not required this will help make sure the mirror and migration process works perfectly. ===================================================== HOW TO GET YOUR PASSWORD FOR DEV.OPEN-BIO.ORG ===================================================== Easy. Email "support at open-bio.org" and MAKE SURE you provide all of the following information: ------------------------------------------------------------------------ ------ Full Name: Organization/Institution/Employer: Working email address (for notices such as this): Existing unix username: Project/CVS affiliation: ------------------------------------------------------------------------ ------ We'll start taking dev.open-bio.org password reset/access requests right now but we'll ask that you do not login to dev.open-bio.org until Sunday the 26th or until you receive notice that the migration has been completed. This will ensure that you don't alter, delete or change any files that will then get lost when we do our final mirror and sync operations. ===================================================== HELP US FIND AND SQUASH PROBLEMS ===================================================== This is a really complicated migration of a ton of different servers, services and users. I'm sure stuff will get flaky during the transition and I'm sure that I'm forgetting about some things. If you notice anything not working or experience any sort of problem PLEASE email support at open-bio.org or just contact me directly. I'll be pretty much tethered to my computer during the upcoming days. How to reach me: Chris Dagdigian dag at sonsorol.org 617-877-5498 Ichat/AOL Instant messenger: 'bioteamdag' From dag at sonsorol.org Sat Mar 25 23:39:20 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 25 Mar 2006 18:39:20 -0500 Subject: [OBF-developers] transition to the new open-bio developer server is complete Message-ID: Hi everyone, dev.open-bio.org is now the official server you should be using for CVS/SVN commits and checkins. The final mirror and sync actions went just fine. I've changed the DNS entry for "pub.open-bio.org" to point to this new machine but just to be safe (and in case you have existing code checkouts with the old machine name hard coded into the CVS root somewhere) please make sure that the DNS switch has propagated out to you before you try to connect to (or CVS commit) against "pub.open- bio.org". The IP address of dev.open-bio.org is 207.154.17.71 If you run the command "host pub.open-bio.org" or "nslookup pub.open- bio.org" and you get back an IP address of 207.154.17.71 then you know the DNS has propagated to your local server and it is OK to use pub.open-bio.org interchangeably with dev.open-bio.org. If you get back 65.246.187.177 then you know you still have the old DNS cached somewhere within your organization -- it should age out and re-update within 24 hours. Please give the new system a whirl. I did migrate over the python / usr/local/bin/syncmail script that many people use to autogenerate CVS commit email messages. As you start committing code again let me know if the commit messages are going out smoothly. Let me know if you need software, libraries or other things installed. Ruby, perl and python are all present on the system along with the usual compilers and dev tools. I still need to install a modern Java SDK. Many people have already requested and received their new password information. Hopefully you found the process smooth - its a good intro to how our ticketing/support system works if you've never dealt with it before. For those of you finding yourselves locked out of the new server, here is the info to regain access: ===================================================== HOW TO GET YOUR PASSWORD FOR DEV.OPEN-BIO.ORG ===================================================== Easy. Email "support at open-bio.org" and MAKE SURE you provide all of the following information: ------------------------------------------------------------------------ Full Name: Organization/Institution/Employer: Working email address (for notices such as this): Existing unix username: Project/CVS affiliation: ------------------------------------------------------------------------ From darin.london at duke.edu Tue Mar 28 14:42:45 2006 From: darin.london at duke.edu (Darin London) Date: Tue, 28 Mar 2006 09:42:45 -0500 Subject: [OBF-developers] Announcing BOSC 2006 Message-ID: <44294B65.4050207@duke.edu> MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 14th International Conference on Intelligent Systems for Molecular Biology. Please consult The Official BOSC 2006 Website at http://www.open-bio.org/wiki/BOSC_2006 for details and information. In addition, a BOSC weblog has been setup to make it easier to desiminate all BOSC related announcements: http://wiki.open-bio.org/boscblog/ And if you have an ICAL compatible Calendar, there is an EventDB calendar set up with all BOSC related deadlines. http://eventful.com/groups/G0-001-000014747-0 More information about ISMB can be found at the Official ISMB 2006 Website: http://ismb2006.cbi.cnptia.embrapa.br/ Thank You, and we look forward to seeing you all, The BOSC Organizing Committee.