From owner-chemistry@ccl.net Mon Apr 12 15:05:01 2010 From: "D. Boyd dboyd()iupui.edu" To: CCL Subject: CCL: Gordon Research Conference on Computational Chemistry Message-Id: <-41646-100412140751-28509-pim2JxRVHdT+yVuwgui01g()server.ccl.net> X-Original-From: "D. Boyd" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 12 Apr 2010 13:12:55 -0400 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: "D. Boyd" [dboyd#%#iupui.edu] Prof. Dr. Walter Thiel (Max-Planck-Institut fur Kohlenforschung, Mulheim, Germany) is chairing the 2010 Gordon Research Conference on Computational Chemistry. The conference is being held August 29 - September 3, 2010 at Les Diablerets, Switzerland, the beautiful Swiss valley where the conference met in 2006. For information on the program and applying, please go to http://www.grc.org/programs.aspx?year=2010&program=compchem For background about this biennial conference series, please go to http://www.chem.iupui.edu/rcc/grccc.html Donald B. Boyd, Ph.D. Research Professor of Chemistry Editor Emeritus, Reviews in Computational Chemistry Department of Chemistry and Chemical Biology Indiana University-Purdue University at Indianapolis From owner-chemistry@ccl.net Mon Apr 12 20:44:00 2010 From: "Joseph Durant Joseph.Durant|symyx.com" To: CCL Subject: CCL: KNIME question Message-Id: <-41647-100412142157-21435-MER7+ERLzZINH5Lwsbh+gA..server.ccl.net> X-Original-From: Joseph Durant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 12 Apr 2010 09:54:18 -0700 MIME-Version: 1.0 Sent to CCL by: Joseph Durant [Joseph.Durant===symyx.com] Hi! An unofficial answer... KNIME passes information in a data table from node to node; the data types are specified for each data column. Their Chemistry Extensions provide readers/writes for Mol, Mol2, SDF and Smiles. Their CDK nodes include translators between CDK and Mol, Mol2, Smiles, and CML. Other node providers may define data types, although there is pressure to minimize this, and to provide translators to the core types used by KNIME. Schroedinger has a format for their nodes which supports capturing quantum chemical information. The KNIME group has placed great emphasis on interoperability of different vendors nodes. To this end they held an interoperability workshop last year at which representatives from KNIME, Symyx, Tripos, Schroedinger and Infocom met, together with representatives from various pharmaceutical companies, to construct workflows using multiple vendor nodes. And yes, we were able to construct real workflows using all the vendor nodes which ran. Joe P.S. In the interests of full disclosure, I am the project lead for the Symyx Chemistry Extensions for KNIME. Joseph M Leonard jleonard42*gmail.com wrote: > Question for the KNIME users: > > How is chemical data passed from node to node? Is there a (or several) > standard formats used? Is the data supposed to be self-describing? Can > it handle structural and quantum data, or merely structural data? > > I know that other dataflow systems had chemical datatypes long ago, > which was an effort to improve interoperability. Is this the case with > KNIME, or is it up to each author to define the format used? > > Thanks in advance! > > Joe Leonard > jleonard42()gmail.com > > -- > Disclaimer: I do not speak for my employer. If it's too early in the > morning, I am not sure I speak for myself... > -- Joe Durant Joseph.Durant~!~symyx.com Symyx Technologies, Inc. 2440 Camino Ramon, Suite 300, San Ramon, CA 94583 voice: (925) 543-7511 -------------- "A man doesn't begin to attain wisdom until he recognizes that he is no longer indispensable." Admiral Richard Byrd ======= Notice: This e-mail message, together with any attachments, contains information of Symyx Technologies, Inc. or any of its affiliates or subsidiaries that may be confidential, proprietary, copyrighted, privileged and/or protected work product, and is meant solely for the intended recipient. If you are not the intended recipient, and have received this message in error, please contact the sender immediately, permanently delete the original and any copies of this email and any attachments thereto.