- chemweb - imperial.ac.uk

More on (Chemical) RSS Metadata feeds
by Rzepa, Henry 12 Sep '03

12 Sep '03

I posted several months ago on RSS feeds. This is by way of an update since a number of interesting developments have occurred recently. Firstly, an excellent article detailing some of the standards (and not so standard) evolution in this area is available at http://www.xml.com/pub/a/2003/07/23/rssone.html I strongly recommend that for a balanced overview. What is more interesting is that the examples shown in this article actually relate to chemistry! Thus the Tetrahedron journal is now publishing an RSS feed (the URI for which I have not yet managed to find! Can anyone help?) as is the science journal Nature (http://nurture.nature.com/rss/rss.rdf ) I dont believe any of the learned society publishers have yet adopted this approach, but if anyone spots RSS feeds from them, please tell this list! Secondly, the metadata content of RSS (by default based on DC, or Dublin core) is now being extended specifically for journals using a namespace called PRISM (Publishing Requirements for Industry Standard Metadata ) which contains items such as <prism:publicationName>Tetrahedron</prism:publicationName> <prism:volume>59</prism:volume> <prism:number>28</prism:number> <prism:startingPage>5215</prism:startingPage> Interestingly the overtly chemical content is still carried (and recognised as chemical by humans only!) as <title>New 5-(2-ethenylsubstituted)-3(2H)-furanones with in vitro antiproliferative activity</title> We anticipate its only a matter of time before discrete chemical namespaces appear (such as contained in http://www.xml-cml.org/cml.rss ; see eg the Internet Journal of Chemistry RSS feed at http://www.ijc.com/abstracts/rss.xml, with a reprint of this article at http://www.ch.ic.ac.uk/rzepa/rss/, Part 2 is to be submitted shortly) We should remind ourselves however that in many ways the handling of metadata is still at the stage where the web was around 1993-1994 (although now arguably, the driving force is no longer from the academic environment but from the business sectors!) -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax)

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More on (Chemical) RSS Metadata feeds
by Gillian.Sinclair＠man.ac.uk 03 Sep '03

03 Sep '03

I shall be out of the office from Friday 22nd August - Wednesday 3rd September. I will deal with all email queries as soon as possible after this date. Thank you.

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Peter Willemsen/CONO/Jotun is out of the office.
by Peter Willemsen 01 Sep '03

01 Sep '03

I will be out of the office starting 01.09.2003 and will not return until 03.09.2003. I will respond to your message when I return.

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Marvin 3.2 and JChem 2.1 released
by Gillian.Sinclair＠man.ac.uk 01 Sep '03

01 Sep '03

I shall be out of the office from Friday 22nd August - Wednesday 3rd September. I will deal with all email queries as soon as possible after this date. Thank you.

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Marvin 3.2 and JChem 2.1 released
by Ferenc Csizmadia 01 Sep '03

01 Sep '03

Apologies for multiple postings. Marvin 3.2 and JChem 2.1 has been released. The packages contain Java applications and software development tools for chemistry, which are portable (run under Windows, Mac OS X, Unix, etc.) Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects. JChem modules: JChem Base (chemical database searching and database integration), JChem Cartridge for Oracle, Standardizer (structure canonization), Screen (virtual screening), Reactor (reaction modeling), Fragmenter (generating building blocks), JKlustor (clustering and diversity calculations). Some recent changes in Marvin: - Enhanced stereochemical representation (according to MDL's new specification. - Improved Charge, logP and pKa calculation. - MarvinSketch can open 3D viewer windows. Some recent changes in JChem: - New piece: JChem Cartridge for Oracle (accessing many JChem functions, such as structure searching or property predictions, from within Oracle's SQL) - Enhanced performance of substructure search, especially in case of reactions. - Substructure hit coloring and hit alignment - Improvements in Screen: fuzzy smoothing in pharmacophore fingerprints, median hypothesis, better pharmacophore perception (mapping), GenerateMD replaces GenerFP * ChemAxon will have a booth at the upcoming ACS meeting * New York, September 8-10, Booth 1112 http://www.chemistry.org/portal/a/c/s/1/acsdisplay.html?DOC=meetings\newyor… We will be showcasing our old and new products and will also have open computers to try live versions. Regards, Ferenc PS: The software can be tried/downloaded at http://www.chemaxon.com/products.html Online demos and examples Movies: http://www.chemaxon.com/demos.html Marvin Applications through Java Web Start: http://www.chemaxon.com/marvin/jnlp/index.html Marvin applet demos: http://www.chemaxon.com/marvin/demos.html Marvin examples for developers: http://www.chemaxon.com/marvin/doc/dev#examples JChem: http://www.jchem.com/examples.html FREE: - Marvin Applets are free for free web sites. - MarvinSketch and MarvinView applications accessed from ChemAxon's web site http://www.chemaxon.com/marvin/jnlp/index.html - Locally installed MarvinSketch, MarvinView, and MolConverter applications. -- Dr. Ferenc Csizmadia CEO ChemAxon http://www.chemaxon.com

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Re: [chemweb] Plugins and Patents
by Gillian.Sinclair＠man.ac.uk 29 Aug '03

29 Aug '03

I shall be out of the office from Friday 22nd August - Wednesday 3rd September. I will deal with all email queries as soon as possible after this date. Thank you.

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Plugins and Patents
by Anthony Lewis 29 Aug '03

29 Aug '03

Hello, I've been reading about the possibility that plugins may have been patented, which would have, I think, some implications for the interactive display chemical data. I'm wondering if anyone has any views or further insight they may care to share? All the best, Anthony Lewis C. Anthony Lewis Petroleum & Environmental Geochemistry Group, School of Earth, Ocean and Environmental Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, U.K. tel: +44 (0)1752 233000 ext. 2988 FAX: +44 (0)1752 233035 e-mail: calewis(a)plymouth.ac.uk

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RE: [chemweb] Plugins and Patents
by Anthony Lewis 29 Aug '03

29 Aug '03

Oops, I had forgotten about that post... I guess I should (re-)read my [chemweb] messages! It may be old hat but it does seem to have resurfaced and there is current discussion regarding this on xml-dev and by the W3C (see http://www.w3.org/2003/08/patent) I've not read the patent in question but I may have used "plugin" incorrectly. I think I should have used "embedded object" and to my, possibly naive, way of thinking this includes Java applets (whether open source or not). I have to admit to being confused by this and look forward to being enlightened. The IC chemistry homepage has always been interesting (I can see the molecule), although I find that almost all Java is very slow to load on my machine... I support open source, although purely as a user and not a programmer. Anthony Lewis -----Original Message----- From: Rzepa, Henry [mailto:h.rzepa@imperial.ac.uk] Sent: 29 August 2003 15:24 To: Chemistry Webmasters Discussion list Subject: Re: [chemweb] Plugins and Patents >Hello, > >I've been reading about the possibility that plugins may have been patented, which would have, I think, some implications for the interactive display chemical data. This was an ancient rumour which surfaced about 2 years ago. I posted to this list a month or so back, urging all to adopt an opensource solution to the above, recommending jmol (http://jmol.sourceforge.net ). As it happens, if you go to http://www.ch.ic.ac.uk/ the molecule which (might) appear on the right is displayed using JMol, and indeed its encoded as a CML file > >I'm wondering if anyone has any views or further insight they may care to share? Having mentioned opensource, I would bring this to people's attention "On September 1st the European Commission is going to vote a revised version of the European Patentability rules. The proposed revision contains a set of serious challenges to Open Source development since regulation regarding software patents will be broadly extended and might forbid independent development of innovative (Open Source and not) software-based solutions. The European Open Source community is very concerned about the upcoming new regulation and has organized a demo protest for August 27, asking Open Source supporting sites to change their home pages to let everyone know what is going on at the European Parliament. The Apache Software Foundation has decided to support this initiative, and this is why you are seeing this page. For further information please see http://swpat.ffii.org and http://petition.eurolinux.org . -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. _______________________________________________ chemweb mailing list chemweb(a)imperial.ac.uk http://mailman.ic.ac.uk/mailman/listinfo/chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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organic spectroscopy program - new version
by Adrian Blackman 25 Aug '03

25 Aug '03

If you teach introductory organic spectroscopy then you might be interested in WinTorg, a new version (3.3) of which has just been released. WinTorg simulates the process of identifying unknown organic compounds. It is suitable for use at early university or college level. Spectroscopy is emphasised. There are 100 compounds each having pmr, cmr, ir, ms spectra and uv data and other properties. (The shareware version has only 3 compounds). The unknowns can be identified by spectroscopy alone or in combination with chemical tests. Of the several improvements and new features, the main one is the inclusion of 5 spectroscopic calculators. More information and a free demonstration version of this Windows based program are available from: http://www.chem.utas.edu.au/staff/blackman/shareware/torganal.htm Thanks Adrian Blackman (author) ____________________________________________________________________ Dr Adrian Blackman Phone: (03) 6226 2183 Int'l 61 3 6226 2183 School of Chemistry Fax: (03) 6226 2858 Int'l 61 3 6226 2858 University of Tasmania Private Bag 75 Hobart Tasmania 7001 Australia Email: Adrian.Blackman(a)utas.edu.au WWW: http://www.chem.utas.edu.au/staff/blackman/ajb.htm ____________________________________________________________________

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Listadmin: New mail system
by Rzepa, Henry 22 Aug '03

22 Aug '03

Please note that a new mail system is now handling this list. This is both a test, and to serve as an example of the new headers and footers assciated with the postings. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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