From owner-biocore-l@ks.uiuc.edu Wed Feb 26 16:38:17 2003 Received: (from majordom@localhost) by ks.uiuc.edu (8.11.2/8.11.2) id h1QMcFM00927 for biocore-l-outgoing; Wed, 26 Feb 2003 16:38:15 -0600 (CST) X-Authentication-Warning: havana.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from ostia.ks.uiuc.edu (ostia.ks.uiuc.edu [130.126.120.70]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id h1QMcEl00923 for ; Wed, 26 Feb 2003 16:38:14 -0600 (CST) Received: (from kvandivo@localhost) by ostia.ks.uiuc.edu (8.11.6+Sun/8.9.1) id h1QMcEv23279 for biocore-l@ks.uiuc.edu; Wed, 26 Feb 2003 16:38:14 -0600 (CST) Date: Wed, 26 Feb 2003 16:38:14 -0600 From: Kirby Vandivort To: biocore-l@ks.uiuc.edu Subject: recent server changes Message-ID: <20030226223813.GA23174@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk Recent changes that have occurred on our local server: February 26, 2003 * Control Panel:Beta Feature: Tabs can be turned on or off now via a checkbox on the summary page. If a new message comes in on a hidden tab, it will cause itself to appear (rb). * Fixed some typos in email that is sent to new project members (mb). * Fixed a bug that was causing project deletions to not work properly (mb). * VMD Saved States:Fixed a bug that was causing users to not be properly warned if they tried to save a state with a local file (mb). * Revised the number of entries that show up in the Control Panel chat history web pages from 20 to 50 (mb). February 12, 2003 * Cleaned up the text in some of the email messages that are being sent to users when they join projects, change email addresses (mb, kv). * Control Panel: Added menu items that point to the list of public projects and the FAQ (mb). * Public Projects: Made it so that the administrator can change viewable areas in both the public and private side (mb). * Hidden Projects: Fixed various issues with the Control Panel display so that it is accurate (mb). -- Kirby Vandivort Theoretical and Computational Biophysics Email: kvandivo@ks.uiuc.edu 3051 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA From owner-biocore-l@ks.uiuc.edu Mon Mar 24 17:46:22 2003 Received: from havana.ks.uiuc.edu (localhost [127.0.0.1]) by ks.uiuc.edu (8.12.8/8.11.2) with ESMTP id h2ONkMEF025780 for ; Mon, 24 Mar 2003 17:46:22 -0600 (CST) Received: (from majordom@localhost) by havana.ks.uiuc.edu (8.12.8/8.12.8/Submit) id h2ONkMPU025779 for biocore-l-outgoing; Mon, 24 Mar 2003 17:46:22 -0600 (CST) X-Authentication-Warning: havana.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from ostia.ks.uiuc.edu (ostia.ks.uiuc.edu [130.126.120.70]) by ks.uiuc.edu (8.12.8/8.11.2) with ESMTP id h2ONkLEF025775 for ; Mon, 24 Mar 2003 17:46:21 -0600 (CST) Received: (from kvandivo@localhost) by ostia.ks.uiuc.edu (8.11.6+Sun/8.9.1) id h2ONkLS12175 for biocore-l@ks.uiuc.edu; Mon, 24 Mar 2003 17:46:21 -0600 (CST) Date: Mon, 24 Mar 2003 17:46:21 -0600 From: Kirby Vandivort To: biocore-l@ks.uiuc.edu Subject: New Server Release Message-ID: <20030324234620.GB12160@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk There was a new server release today. These changes are already in the server running at http://biocore.ks.uiuc.edu and they are available for users to download for their own servers. * VMD Saved States:If the user attempts to save a state this is using a local file they are now prompted to upload the file to the BioFS. Future views of the state will then use the file from the BioFS (mb). * Control Panel:Tabs that are denoting "activity" (by changing colors) now also have an asterisk appear in front of their name. This was required because of the way that the new version of Java on the Macintosh handles tabs (rb). * Control Panel:The state of tabs (whether turned on or off) is now saved across Control Panel startups (rb). * WebDAV:Files saved via WebDAV now send notification to the Control Panel (sk). * Fixed an SQL bug that was causing problems with creation of public projects (mb). * Control Panel:Fixed a bug that was causing the initial window to not get redrawn (rb). * Preferences:Fixed a long-standing bug that would cause Netscape 4.x to crash if the window was resized while on a "color chooser" page (dd). * Changed references from BioCoRE User Agreement to BioCoRE User License (kv). -- Kirby Vandivort Theoretical and Computational Biophysics Email: kvandivo@ks.uiuc.edu 3051 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA From owner-biocore-l@ks.uiuc.edu Mon Mar 24 17:51:29 2003 Received: from havana.ks.uiuc.edu (localhost [127.0.0.1]) by ks.uiuc.edu (8.12.8/8.11.2) with ESMTP id h2ONpTEF025839 for ; Mon, 24 Mar 2003 17:51:29 -0600 (CST) Received: (from majordom@localhost) by havana.ks.uiuc.edu (8.12.8/8.12.8/Submit) id h2ONpTDv025838 for biocore-l-outgoing; Mon, 24 Mar 2003 17:51:29 -0600 (CST) X-Authentication-Warning: havana.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from uiuc.edu (dhcp31.ks.uiuc.edu [130.126.120.231]) by ks.uiuc.edu (8.12.8/8.11.2) with ESMTP id h2ONpREF025831; Mon, 24 Mar 2003 17:51:27 -0600 (CST) Date: Mon, 24 Mar 2003 17:51:22 -0600 Reply-To: biocore@ncsa.uiuc.edu Subject: BioCoRE@NCSA Collaborative Research Environment Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v551) From: Robert Brunner To: biocore-l@ks.uiuc.edu Content-Transfer-Encoding: 7bit Message-Id: <8415DEA0-5E53-11D7-ACAD-0030654E438A@uiuc.edu> X-Mailer: Apple Mail (2.551) Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk March 24, 2003: Urbana, Illinois - The Theoretical and Computational Biophysics (TCB) Group at the University of Illinois is proud to announce the initial public release of BioCoRE@NCSA, a collaborative research environment at the National Center for Supercomputer Applications. The TCB Group develops BioCoRE with support from the NIH's National Center for Research Resources. The BioCoRE@NCSA effort is also funded by the NSF. BioCoRE is a collaborative work environment for biomedical research, research management and training. A resource-centered platform, BioCoRE offers scientists, working together or alone, a seamless interface to a broad range of local and remote technologies such as discipline-specific and general tools, data, and visualization solutions. In creating unprecedented proximity to colleagues' expertise and knowledge, BioCoRE empowers scientists everywhere, establishing equal access to research and training opportunities. To harness and streamline collaborative capabilities across temporal and physical boundaries in research and training, BioCoRE builds on the transparent use of and communication between technological resources (hardware and software) and databases. BioCoRE features powerful yet easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features. For additional information, please visit the BioCoRE@NCSA website at http://biocore.ncsa.uiuc.edu/ The TCB Group encourages BioCoRE@NCSA users to be closely involved in the development process through reporting bugs, contributing fixes, regular feedback mechanisms, periodic surveys and via other means. Questions or comments may be directed to biocore@ncsa.uiuc.edu. We are eager to hear from you, and thank you for using our software! From owner-biocore-l@ks.uiuc.edu Fri Apr 11 11:28:55 2003 Received: from havana.ks.uiuc.edu (localhost [127.0.0.1]) by ks.uiuc.edu (8.12.9/8.11.2) with ESMTP id h3BGStT5015769 for ; Fri, 11 Apr 2003 11:28:55 -0500 (CDT) Received: (from majordom@localhost) by havana.ks.uiuc.edu (8.12.9/8.12.9/Submit) id h3BGStl8015768 for biocore-l-outgoing; Fri, 11 Apr 2003 11:28:55 -0500 (CDT) X-Authentication-Warning: havana.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from ostia.ks.uiuc.edu (ostia.ks.uiuc.edu [130.126.120.70]) by ks.uiuc.edu (8.12.9/8.11.2) with ESMTP id h3BGSsT5015764 for ; Fri, 11 Apr 2003 11:28:54 -0500 (CDT) Received: (from kvandivo@localhost) by ostia.ks.uiuc.edu (8.11.6+Sun/8.9.1) id h3BGSrp10222 for biocore-l@ks.uiuc.edu; Fri, 11 Apr 2003 11:28:53 -0500 (CDT) Date: Fri, 11 Apr 2003 11:28:53 -0500 From: Kirby Vandivort To: biocore-l@ks.uiuc.edu Subject: New Version of BioCoRE Server at UIUC Message-ID: <20030411162852.GA10187@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4.1i Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk We've just installed an updated version of the server we run here in the TCB Group. Updates include: # Control Panel: Tabs no longer change to have an asterisk to denote activity. Rather, the summary table cell background for a particular project changes if there is activity. This works cleaner on various platforms (rb). # VMD Saved States: Fixed a problem with "local files getting uploaded" that was occuring on Windows (mb). # WebDAV: Fixed some bugs that was causing the Linux mount.dav to not be able to write correctly, and fixed a timezone bug (sk). # Control Panel: There is now an Edit menu that has Copy and Paste options. Mac OS X Java wasn't able to Cut and Paste without this. It does work for other platforms as well (rb). # In addition, we are now using a new version of the Database Manager and this will hopefully make BioCoRE more responsive. -- Kirby Vandivort Theoretical and Computational Biophysics Email: kvandivo@ks.uiuc.edu 3051 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA From owner-biocore-l@rama.ks.uiuc.edu Wed Nov 12 11:43:55 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hACHhtu6015275 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 12 Nov 2003 11:43:55 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id hACHhtdT015274 for biocore-l-outgoing; Wed, 12 Nov 2003 11:43:55 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from jerusalem.ks.uiuc.edu (jerusalem.ks.uiuc.edu [130.126.120.53]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hACHhsu5015270 for ; Wed, 12 Nov 2003 11:43:54 -0600 (CST) Received: (from kvandivo@localhost) by jerusalem.ks.uiuc.edu (8.11.6/8.9.3) id hACHhsP15827 for biocore-l@ks.uiuc.edu; Wed, 12 Nov 2003 11:43:54 -0600 Date: Wed, 12 Nov 2003 11:43:54 -0600 From: Kirby Vandivort To: biocore-l@ks.uiuc.edu Subject: Revisions to webpage Message-ID: <20031112174352.GC8408@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk We've just released some small revisions to the webpage. The main change is a reorganization of some links that provides more visibility to Documentation. Hopefully this will help users find information that they are looking for more quickly and efficiently. We've also added a spotlight for WebDAV access to BioFS. -- Kirby Vandivort Theoretical and Senior Research Programmer Computational Biophysics Email: kvandivo@ks.uiuc.edu 3051 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA From owner-biocore-l@rama.ks.uiuc.edu Fri Nov 14 10:37:16 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hAEGbGu6019697 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Fri, 14 Nov 2003 10:37:16 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id hAEGbGgf019696 for biocore-l-outgoing; Fri, 14 Nov 2003 10:37:16 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from jerusalem.ks.uiuc.edu (jerusalem.ks.uiuc.edu [130.126.120.53]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hAEGbGu5019692 for ; Fri, 14 Nov 2003 10:37:16 -0600 (CST) Received: (from kvandivo@localhost) by jerusalem.ks.uiuc.edu (8.11.6/8.9.3) id hAEGbGn05069 for biocore-l@ks.uiuc.edu; Fri, 14 Nov 2003 10:37:16 -0600 Date: Fri, 14 Nov 2003 10:37:15 -0600 From: Kirby Vandivort To: biocore-l@ks.uiuc.edu Subject: biocore-l: Recent changes to the TCB BioCoRE Server Message-ID: <20031114163714.GB3264@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk ======================================================================= For archives and subscription information about this Mailing List, visit the BioCoRE homepage at http://www.ks.uiuc.edu/Research/biocore/ It's been a while since I've sent one of these out, but I wanted to acquaint everyone with some of the recent changes to the main BioCoRE server here in the TCB group. Some of these changes haven't made their way into the server download yet, as we use our main server for testing new changes before they are unleashed upon the world. * There is a new version of the VMD/BioCoRE tool that streamlines usage quite a bit. We have redesigned the interface so that it is quite easy to publish views to BioCoRE and if you haven't tried it out before we encourage you to do so. * WebDAV is becoming more and more polished within BioCoRE. WebDAV is a technology that lets you "mount" the BioFS (BioCoRE's shared filesystem) onto your local computer so that it looks just like a normal folder on your hard drive. This is a really slick feature that we highly invite you to use. More information on both of these features is available under the "Documentation" heading on the BioCoRE homepage at http://www.ks.uiuc.edu/Research/biocore/ Additional changes are described in the change log, located at http://www.ks.uiuc.edu/Research/biocore/announce/changeLog.shtml -- Kirby Vandivort Theoretical and Senior Research Programmer Computational Biophysics Email: kvandivo@ks.uiuc.edu 3051 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA From owner-biocore-l@rama.ks.uiuc.edu Mon Nov 17 09:10:37 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hAHFAau6004767 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Mon, 17 Nov 2003 09:10:36 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id hAHFAanH004766 for biocore-l-outgoing; Mon, 17 Nov 2003 09:10:36 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from jerusalem.ks.uiuc.edu (jerusalem.ks.uiuc.edu [130.126.120.53]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hAHFAau5004762 for ; Mon, 17 Nov 2003 09:10:36 -0600 (CST) Received: (from kvandivo@localhost) by jerusalem.ks.uiuc.edu (8.11.6/8.9.3) id hAHFAaX26753 for biocore-l@ks.uiuc.edu; Mon, 17 Nov 2003 09:10:36 -0600 Date: Mon, 17 Nov 2003 09:10:36 -0600 From: Kirby Vandivort To: biocore-l@ks.uiuc.edu Subject: biocore-l: Updates to main BioCoRE server Message-ID: <20031117151034.GA24969@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk I've just released a new version of the BioCoRE server here in the TCB group. On Mac OS X, the VMD launcher should now work with VMD 1.8.2 as well as recent earlier versions. Fixed a bug in the Control Panel that was causing people to disappear from the User List right after they logged in. To test out these and other changes, point your browser to: http://www.ks.uiuc.edu/Research/biocore/ -- Kirby Vandivort Theoretical and Senior Research Programmer Computational Biophysics Email: kvandivo@ks.uiuc.edu 3051 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA From owner-biocore-l@rama.ks.uiuc.edu Wed Dec 10 16:02:54 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hBAM2rtX008665 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 10 Dec 2003 16:02:53 -0600 (CST) Received: (from majordom@localhost) by rama.ks.uiuc.edu (8.12.10/8.12.9/Submit) id hBAM2rFH008664 for biocore-l-outgoing; Wed, 10 Dec 2003 16:02:53 -0600 (CST) X-Authentication-Warning: rama.ks.uiuc.edu: majordom set sender to owner-biocore-l@ks.uiuc.edu using -f Received: from jerusalem.ks.uiuc.edu (jerusalem.ks.uiuc.edu [130.126.120.53]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hBAM2rtW008660 for ; Wed, 10 Dec 2003 16:02:53 -0600 (CST) Received: (from kvandivo@localhost) by jerusalem.ks.uiuc.edu (8.11.6/8.9.3) id hBAM2rT02159 for biocore-l@ks.uiuc.edu; Wed, 10 Dec 2003 16:02:53 -0600 Date: Wed, 10 Dec 2003 16:02:53 -0600 From: Kirby Vandivort To: biocore-l@ks.uiuc.edu Subject: biocore-l: New version of server released in the TCBG group Message-ID: <20031210220252.GC29932@ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Sender: owner-biocore-l@ks.uiuc.edu Precedence: bulk We've just uploaded a new version of the code to the TCBG server. Changes include: # Notebook: Added option to always have BioCoRE send email when a new message is posted. This is set via the Utilities page by selecting 'Email Options' under the Current Project. # WebDAV: Fixed a bug where users could move project directories. # Notebook: Tweaked search to make it work again for private projects as well as for speed. # VMD Launch: New beta version. Minor changes in the layout as a response to user comments and a couple of bug fixes. Please give it a try and let us know what you think. http://www.ks.uiuc.edu/Research/biocore/ -- Kirby Vandivort Theoretical and Senior Research Programmer Computational Biophysics Email: kvandivo@ks.uiuc.edu 3051 Beckman Institute http://www.ks.uiuc.edu/~kvandivo/ University of Illinois Phone: (217) 244-5711 405 N. Mathews Ave Fax : (217) 244-6078 Urbana, IL 61801, USA