From jkl@ccl.net Sun Nov 2 13:59:57 2003 -0500 Return-Path: Reply-To: From: "Mark Thompson" To: chemistry..at..ccl.net Cc: Subject: ArgusLab 4.0 beta #2 available Date: Sun, 2 Nov 2003 10:20:58 -0800 Message-ID: <000101c3a16e$10544ae0$271ae70c@planaria> ArgusLab 4.0 beta release #2 is now available. You can obtain it from http://www.arguslab.com Beta #1 ceased to function on Oct 31. Simply install Beta #2 over your Beta #1 installation and you should be good for another 3 months. (We're having the beta releases time-out to simplify support issues so that we don't end up answering bug issues in older beta releases). We've fixed a few bugs, but are still working on some of the feature modification suggestions from users. Also, I've been putting the finishing touches on our drug-docking feature to get it into the next beta release. Thanks to everyone for the great suggestions, bug reports, and your willingness to use beta software. Mark Thompson *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark..at..arguslab.com http://www.arguslab.com *************************** From chemistry-request@ccl.net Sat Nov 1 13:15:25 2003 Received: from denver065.server4free.de (lilbits.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA1IErLj016119 for ; Sat, 1 Nov 2003 13:14:53 -0500 Received: by denver065.server4free.de (Postfix, from userid 500) id 0AF763A8213; Sat, 1 Nov 2003 19:14:52 +0100 (CET) Date: Sat, 1 Nov 2003 19:14:52 +0100 From: Eugen Leitl To: chemistry..at..ccl.net Subject: Re: CCL:Linux Cluster Message-ID: <20031101181452.GC27418..at..leitl.org> References: <3FA0CEC5.8010502..at..silex.dk> <1510089009.20031031094924..at..bancorp.ru> <3FA2258B.1010809..at..silex.dk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable On Fri, Oct 31, 2003 at 10:04:11AM +0100, Kenneth Geisshirt wrote: > My point is that building a cluster by hand does not scale well. If you= =20 This is true, but the real issue is power supply and air conditioning. The limit for this used to lie around 64 nodes, but is now probably lower d= ue to current increase in power dissipation density (1/4 KW in 1 U for dual Xe= ons): http://www.beowulf.org/pipermail/beowulf/2003-March/006107.html It is still feasible to dissipate the heat by venting a hall of loosely shelved desktop PCs into open air -- assuming one doesn't have to settle for existing, crammed building floorplan -- which is probably the case for the = majority of new installations in established institutions. > plan a large cluster (32+ nodes) you will need some kind of automated=20 All cluster-centric Linux distributions use some kind of install automation= . It's not rocket science, Beowulf list archives are full of references http://www.beowulf.org/pipermail/beowulf/ > tool. If you build a 4-node cluster and add a new node (different=20 > hardware e.g., an old office pc) you can do it by hand. Typically, it pays to NOT recycle old _and_ heterogenous hardware. Due to t= he current innovation rate any ~k$ office-grade PC node (currently averaging a= t=20 64-bit x86 (Opteron/AMD 64) and GBit Ethernet) will outperform a large asse= mbly of old recycled systems, even not considering scaling issues (even well-behave= d code tends to profit from comparatively expensive low latency message-passing fa= bric such as Myrinet or Infiniband -- latter's large-scale deployment being pioneered by= the Virginia 1100x G5 2GHz cluster). For small-budget installations 8-16 nodes would still tend to form a sweet = spot, due to recently-fallen prices for 8-16 port SOHO GBit switches with full backplane bandwidth. Whether these will actually do it for you still depends on benchmarking you= r code, or at least a representative mockup thereof. -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE From chemistry-request@ccl.net Sun Nov 2 11:30:25 2003 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA2GTrhP003504 for ; Sun, 2 Nov 2003 11:29:53 -0500 Received: (from mn1@localhost) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) id hA2GTpt39572300; Sun, 2 Nov 2003 11:29:51 -0500 (EST) Date: Sun, 2 Nov 2003 11:29:51 -0500 From: "M. Nicklaus" To: Donald Keidel cc: chemistry{at}ccl.net, "M. Nicklaus" Subject: CCL:Program to search SD/MDL formatted files from chemical companies In-Reply-To: <000101c39cf7$81cc2240$529c178a@dopetec> Message-ID: References: <000101c39cf7$81cc2240$529c178a@dopetec> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Don, The chemoinformatics toolkit CACTVS has very powerful substructure search capabilities. It is free for academic use. See http://www2.ccc.uni-erlangen.de/software/cactvs/. We have, e.g., based our online Enhanced NCI Database Browser (http://cactus.nci.nih.gov/ncidb2/) on it. We are using CACTVS to search in SD files numbering in the millions of compounds (although you get a huge additional speedup if you first convert them into the internal CACTVS format). We are working to put a more complete CACTVS documentation together - if you are interested, feel free to contact me. For all other questions, please contact the author of CACTVS, Wolf-Dietrich Ihlenfeldt (wdi{at}xemistry.com). Cheers, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1{at}helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design Group Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ On Mon, 27 Oct 2003, Donald Keidel wrote: > Hello, > > I am looking for a program to search SD/MDL formatted files (chemical > company libraries of compounds). I have found ISIS/Base and 3DFS, but I > was wondering if anyone knows of others that might be cheaper than > ISIS/Base (hopefully free), but commercial examples would be of great > help also. Thank you in advance to anyone who reads and responds to > this request. Have a great day. > > Don > > ------------------------------------------------------------------------ > --------------------------------------- > Donald J. Keidel > University of California, Riverside > Department of Biochemistry and Molecular Biology > Riverside, CA 92521 > phone: (909) 787-5493 > fax: (909) 787-4434 > dopetec{at}dslextreme.com > webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm