December 1998 - chemweb - imperial.ac.uk

Molecule Editor in Java
by Denis M. Bayada 18 Feb '99

18 Feb '99

Dear all, I have just finished writing a molecule editor in JAVA. If anyone is interested, it is available at : http://www.chem.leeds.ac.uk/ICAMS/people/denis/moledit.html You may freely download the Java source code and modify it. Any comments are indeed welcome. Thank you Denis --------------------------------------------------------------------- Denis M. Bayada e-mail: denis(a)mi.leeds.ac.uk ICAMS voice: (44) (0)113 233 65 95 School of Chemistry fax: (44) (0)113 233 65 63 University of Leeds http://www.chem.leeds.ac.uk/ICAMS/people/denis Leeds LS2 9JT ENGLAND ... but as I proceeded in my labour, it became every day more horrible and irksome to me. Sometimes I could not prevail on myself to enter my laboratory for several days, and at other times I toiled day and night in order to complete my work. It was, indeed, a filthy process in which I was engaged. Frankenstein (Mary Shelley) --------------------------------------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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1998 MDPI Prize Announcement
by Shu-Kun Lin 23 Dec '98

23 Dec '98

1998 MDPI Prize Announcement The first recipient of 1998 MDPI Prize is Dr. Jean-Pierre Vigneron from Paris, France. He is rewarded with this prize for his contribution in molecular diversity preservation by depositing a large number of chemical samples, many of them are natural products. The recipient will receive 3000 Swiss Francs and will be invited to visit Basel in 1999. The selection of recipient is carried out by discussions among the MDPI Foundation members. MDPI Prize will be announced every year to recognize the great efforts of chemists who significantly contributed to MDPI activities. Dr. Shu-Kun Lin President of MDPI Basel, 23 December 1998 --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland http://www.mdpi.org/ E-mail lin(a)mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- 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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Smart browsing technology
by newingto＠kodak.com 14 Dec '98

14 Dec '98

From: Ian Newington Does anyone know of any smart browsing technology out ther applied to chemistry journals? What I'm thinking about is something which will pick up not just my main interests, for which I can set up a standard search profile to run regularly, but for those other items that one picks up when browsing titles and abstracts. I would then get a result set that was much broader than I get from regular profiles and would still enable those all-important connections to be made which generate novel ideas but without having to trawl through an ever-increasing sea of chemistry journals. In the general field of news items Wisewire (www.wisewire.com) does this and Autonomy (www.agentware.com) have some neat software which is trainable to your interests. Has anyone applied this to chemistry yet? Ian Newington Kodak European R&D Tel: +44-(0)181-424-4451 FAX: +44-(0)181-424-5788 email: ian_newington(a)kodak.com 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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The disagreement with Springer on Molecules is settled
by Shu-Kun Lin 11 Dec '98

11 Dec '98

Hi, The disagreement with Springer on the journal Molecules (http://www.mdpi.org/molecules/) is settled. Dr. Shu-Kun Lin (MDPI) and Dr. Rainer Stumpe (Springer) met in Basel today, 11 December 1998, and agreed (both signed on a "Memorandum of Understanding") that the two journal "Molecules" and "Molecules Online" have different scope and can co-exist. Neither party will, in future, interfere in any way with the other's rights to publish their respective journal. Afterwards, Dr. Lin has no further claims against Springer-Verlag. MDPI's Molecules immediately resumed publication this afternoon. Thanks! Happy new year of 1999 to all of you! Shu-Kun --------------------------------------------------------- Dr. Shu-Kun Lin Editor-in-Chief, Molecules (ISSN 1420-3049) Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland http://www.mdpi.org/ E-mail lin(a)mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- 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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Report on W3C Meeting, 8 December, London
by Rzepa, Henry 10 Dec '98

10 Dec '98

W3C, in case you did not know, is the World Wide Web Consortium, the body which manages Web standards. It has a UK office (one of 7 world wide) and this year, this office (at RAL) organised an open meeting to disseminate future developments. Lest you are wondering what the relevance to chemistry is, let me emphasize that as "small players", its essential we re-use generic technologies and methods in developing our own subject. What follows is a brief personal report of this meeting. 1) Jon Bosak on XML. XML is a data centric model (compared to HTML which might be described as a text-centric model). Jon emphasised that XML comes into its own with complex datasets, where data can be used in different ways, data with long life cycles, and data intended to drive scripts, Java, etc. All of which suits chemistry particularly well. He re-iterated the separation between data content, its structure and its presentation and how XML has been designed from the outset to achieve this separation. With this combination, Jon showed how online formatting of information will shortly be regarded as a superset of the print format. This will set the cat amongst the pigeons, since much of the chemistry community still regards "print" as the ultimate definer of "chemical knowledge". Jon concluded by describing how an association might be achieved between XML "elements" and application components, ie expressed as JavaBeans. He strongly recommended OASIS (Organisation for advancement of structured information standards; http://www.oasis-open.org/cover/ ). 2) Subsequent speakers developed the theme of the "document" as an application, and Reuters in particular showed how XML could play a vital role in their kind of business. Several presenters showed how a newspaper front page could be created from structured documents and applied styles. My thoughts turned to how an electronic journal article might be presented to the user in the context of how they might want to use it, as an alternative to the "house style". 3) Stu Weibel of OCLC (Mr metadata) empahasised the three "S" components, semantics, structure and syntax. Semantics is achieved via definitions such as the Dublin Core, structure via formalisms such as the RDF (Resource description framework) and Syntax using XML. RDF could eg be used to support XML conversions from one element set to another as a process for supporting inter-operability. Everything is pretty abstract at this level, and RDF is not in the "intuitive" category. 4) Other presenters showed how style sheets are evolving from 1st gen (CSS1) to second (CSS2) and how XSL (Extensible style sheets) used with XML could also be used to transform XML from one application to another. It was also noted that work on expressing HTML as an XML element set was well under way, ie HTML (5?) would in future be an implementation of XML. Mention was made of Internet Explorer 5.0, Netscape "GECKO" and Opera 3.5, the first two at least supporting XML. 5) There was an interesting presentation about Scalable Vector Graphics, and its intended role in replacing GIF images! SMIL is a multimdedia format with timelines etc for use in presentations; its more declarative than eg Macromedia director (ie relies less on use of scripts), although Microsoft have decided to go a different way with HTML-TIME. 6) Finally the BBC gave a presentation on the integration of digital broadcasting with the Web. The interesting concept of a URI (Uniform resource identifier) describing a time-dependent broadcast resource (ie a program) is something it seems we will have to get used to. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ If my digital email signature is invalid, download a new root at http://www.belsign.be/en/services/receive/install-ca.html 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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Call for bids: software for Molbank journal and/or lab notebook
by Shu-Kun Lin 10 Dec '98

10 Dec '98

Dear colleagues: Individual scientists or companies are invited to bid for supplying supporting software for MDPI electronic journals, particularly Molbank (ISSN 1422-8599, Vol. 1, 1999). Structure and spectrum display software developers are invited. The accepted supplier must have a demonstrated, working software based on Internet website browser. It will enable authors, manuscript referees and readers to upload (if permitted), download and view structural and spectroscopic as well as any other graphic numerical data and manipulate it on the internet comfortably. Visit http://www.ch.ic.ac.uk/ectoc/echet98/ for a perhaps the best example! For sample papers of Molbank, please visit the http://www.mdpi.org/molbank/indextemp.htm website. Molbank is the first chemistry journal preserving experimental data of individual compounds. It is evolved from the MolBank section of the journal Molecules. Structure and spectrum display software for Molbank journal must be a very promising product for electronic lab notebook. Therefore, Molbank will be regarded as an exhibition place for promoting your products. We will therefore not pay for any charge and will not collect any advertisement fee. The accepted provider will have the exclusive right of using its software within a period of 1 year. However, in order to promote fare competition and encourage innovation on software development, Molbank keeps its right to freely choose another software provider and switch to another software. Molbank will also publish the related software reviews, also free of charge. Please submit your proposal by e-mail to Dr. Shu-Kun Lin, Managing Editor, Molbank before the end of 1998. --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland http://www.mdpi.org/ E-mail lin(a)mdpi.org Tel. +41 79 322 3379, Fax +41 61 302 8918 -------------------------------------------------------- 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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marvin 1.2 applets drawing and displaying structures
by Ferenc Csizmadia 04 Dec '98

04 Dec '98

The 1.2 version of the Marvin applets for drawing and displaying chemical structures and substructures can now be downloaded at http://www.chemaxon.com/marvin. New features: - (Unique) SMILES/SMARTS output - Improvements in the user interface - More documentation Some other features: - Molfile input and output - Molfile compression/decompression for fast data transfer - Automatic charges and H atoms - checking valence errors - query atoms and bonds - stereo chemistry - advanced user interface - zooming - templates - merging of fragments Ferenc ~~~~~~ Ferenc Csizmadia, Ph.D. ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 Email: fcsiz(a)chemaxon.com. 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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"enhanced" Electronic Journals
by Rzepa, Henry 03 Dec '98

03 Dec '98

Following Paul May's http://www.rsc.org/ej/qu/1998/F9808830/index.htm I further note that "chiming" articles is "bandwaggoning" (I might add following the ground breaking examples from the CLIC project in 1996 and 1997, ie http://chemcomm.clic.ac.uk/navi.pl?clicenhanced/ccc/communications/c02788#s… ) For "imitations", see for example the J. Phys. Org. Chem http://www.rsc.org/ej/qu/1998/F9808830/index.htm who call the technique "dynamic electronic enhancement". The RSC also has such enhanced articles in its own Phys org journal, ie Perkin 2. See for example http://www.rsc.org/suppdata/perkin2/1998/2695/index.html (although in this case the enhancement is part of the supplemental data, is NOT part of the intrinsic journal article itself, and depends entirely on what the authors submit to the journal. Most of the supplemental data is in fact available as Word documents) Pity that the current Chime has many features disabled for non Windows NT computers (ie Macs), and will not be available at all for Unix. For example, the use of Linux is rapidly growing, but such users cannot take advantage of these enhanced articles. Personally, to address these issues, I think Java is the way! See for example http://origin.ch.ic.ac.uk/molda/ for a certificate-authenticated modelling tool which could e.g. become a component of an e-journal, or http://origin.ch.ic.ac.uk/vchemlab/cos/signed_applet.html for authenticated interfaces to databases etc. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ If my digital email signature is invalid, download a new root at http://www.belsign.be/en/services/receive/install-ca.html 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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Re: Virtual Journals, Chime & Jcamp (fwd)
by Dr. Wendy A. Warr 02 Dec '98

02 Dec '98

Gary Wiggins wrote: > > ---------- Forwarded message ---------- > Date: Tue, 1 Dec 1998 19:09:59 +0000 (GMT) > From: Paul May <paulmay(a)tlchm.bris.ac.uk> > To: Chemistry Wem-Users list <chemweb(a)ic.ac.uk> > Subject: Virtual Journals, Chime & Jcamp > > Hi, > > I thought you might be interested to know that a paper I submitted to the > new RSC e-Journal PhysChemComm has been published only 20 days after > submission! This is certainly a record for me, and probably goes to > highlight another advantage that e-Journals have over paper-only Journals > - if the paper is written in a web-friendly format and all the > correspondance is done via email, then the refereeing > time, handling time and admin time can be significantly reduced, and > *extremely rapid* publication times can result. > I am glad for Dr. May's sake that his paper was published so quickly. I have nothing against e-publishing (indeed many of my own business interests are in that area) but I would sound a note of caution. In my experience (as an editor of an ACS journal) it is unusual even for a reviewer to reply within 3 weeks. I am not writing this message as a criticism of our reviewers. Ninety-nine percent of them go to a lot of trouble reading papers with great care and writing really incisive reviews, despite the fact that they have a heavy burden of teaching and research (and increasing amounts of admin duties). Moreover, some of our reviewers are in industry and score no points at all for reviewing papers. It is no mean task to review fairly the sort of papers we receive, many of them packed with math and full of abstruse concepts. We also have many authors whose mother tongue is not English, whose work needs extensive editing, and not a few authors who do not have easy access to the sort of facilities US authors enjoy. Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com 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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[Fwd: Fifth International Conference on Chemical Structures - Call for Papers]
by Dr. Wendy A. Warr 01 Dec '98

01 Dec '98

-- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com

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