- chemweb - imperial.ac.uk

Java and CML (Was "Re: ANNOUNCE: CML (Chemical Markup Language) V1.0 -Reply")
by RANDALL BRINKHUIS 08 Jan '97

08 Jan '97

Re the use of Java in developing Internet applications. I do not have any direct experience in developing with Java, but the following article might provide some relevant information since it discusses a Java application that involves more than applets. The article appeared in the Washington Business section of the Washington Post last week: "Untangling the Web, Automatically: Tiny Fairfax Firm's Software May Make Hunting for Information Vastly Easier," Washington Business, Jan. 3, 1997, p. B10-B11. (The article should also be on the Post's Web site at http://www.washingtonpost.com; sorry, but I don't have a specific URL.) This article describes TransactNet's new Java automatic query application. The software, called Web Interface Toolkit, will enable Web users to automatically track data on specific Web sites. Free test copies are available on the company's Web site [no URL given in the article, but I have been informed it is http://www.transactnet.com/products.html] Before the software can be used, however, it must be customized to a particular organization's needs. The company will charge $2,500 for each application an organization creates using the toolkit. Disclaimer: Personal views only; this is not intended to be an endorsement of TransactNet. Randall Brinkhuis, M.S.L.S. Environmental Protection Specialist U.S. EPA Office of Pollution Prevention and Toxics ----- 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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Re: Java and Firewalls
by Nick Lynch 08 Jan '97

08 Jan '97

>>From the announcement of the new release of Chemical Markup Language, and >other discussions on the list it seems that Java is becoming an integral >part of the chemical web. However, it appears that moving down this road >could exclude many people from our sites. > The use of the web is changing slightly as more companies make use of intranets and hence have more control over the type of applications and content of pages that their users are viewing. We have found during the development of ChemSymphony, http://www.cherwell.com/cherwell/chemsymphony that much of the interest has come from companies wishing to use the product internally and therefore using the cross-platform benefits of Java. The speed of compilers at the present time means that internal use will provide better results than relying on bandwidth issues. The security problems of Java have been discussed at length on a number of forums but there are many built in security issues that make Java a secure web development language. However, I do not believe this will be problem in the future. Now that there are a number of applications in Java from the main software vendors, the issue of security will disappear. Best wishes Nick --- --- Dr Nick Lynch | e-mail: nick(a)cherwell.com Commissioning Editor | Phone: +44 (0)1865 784812 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | http://www.cherwell.com/cherwell --- --- ----- 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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Re: Metadata discussion and chemistry
by Thomas Hapke 07 Jan '97

07 Jan '97

On Tue, 24 Dec 1996 Peter Murray-Rust wrote: > On Mon, 23 Dec 1996, John Maher wrote: > [...] >> The question of the classification of this material, to > > enable the proper automatic selection of questions has arisen. We would be > > very interested in contacting other chemists interested in the > > 'Dublin Core' and such meta classification of chemistry information. > > Classification is a notoriously difficult subject and one in which almost > everyone has a view :-). I am not an expert in library sciences, and > clearly one approach is to use existing library technology for such > classification. So, for example, subjects like 'thermodynamics' will have > precise hierarchical numbering and this may be a useful approach. On the > other hand it involves a lot of work, and you'll find that half the world > (or more) disagrees with the classification scheme you have chosen. > > The major problem is that with new problems - like cyber chemistry and > distance education - none of the existing methods are likely to be > appropriate. You risk squeezing the problem into the wrong shape of > flask. > [...] Peter Murray-Rust outlined the problems with every classification IMHO also from a librarian point of view ! 8-) But I am thinking about another aspect of classification and metadata: I understand the Dublin Core Set (DC) as the "least common denominator" between the full-text-indexing of WWW search engines and for example the librarian marc records. DC should enable the author or creator of a document-like object (DLO) to add metadata to every DLO, because he wants that his DLO, for example the full-text-document about the specific behavior of a mercury compound in the environment, will be retrieved by others 8-), and to allow search engines to index the specific DC-Elements separately to allow a better retrieval. For example, the word "mercury" in a quick-and dirty-search in Altavista would retrieve thousands of documents, some from a company named Mercury Ltd. or from the pop star Freddie Mercury and also some of the metal mercury. Sure, you can combine search words, for example mercury with for example environment. But what is do, if you want to know something about the behavior of a specific mercury compound in the environment. (It is clear, in the moment you would search CA for such a question. 8-) But in the future, when every author of his specific mercury compound has his paper in the web or something similar ?) And now to the theme "classification". Sorry for this long run ! The DC element Subject allows the author to describe the topic of his work in keywords and also in any classification code. In the library area there are some international used classification as DDC, UDC or LoC-Classification. But no "normal" scientific author is willing to use such a classification, because he don't know it ! 8-) You can add the type of the classification codes as qualifiers to the DC element. But that is not the problem, but which classification code should use the chemist. Other subjects have their own, specific, widely known classification scheme, the mathematicians will use the AMS classification, the computer scientists the ACM classification, the physicists the PACS (Physics & Astronomy Classification System). All these are used for the indexing also the specific online databases (Mathematical Revies, Physicvs Abstracts ...). One possibility for the chemist would be the CA Section Codes, but are these specific enough ? Are there other possibilities ? It would be very easy to use this. But makes this sense ? Any commentary is welcome ? Or is this discussion only important from a librarian point of view about the chaos of the internet ? 8-) For our example, the future user of a WWW search engine would search in the "DC-Element-"Subject"-Index for example with the qualifier "CAS-RN" the specific mercury compound and combine it with the qualifier "CAS-Section Code" with one of the CAS section codes 58 or 59. Assumed that the author has added this to the DC-Elements of his DLO and the search engines will use this meta information to build their indexes and to allow a retrieval in these sub-indexes, the future would perhaps get the desired information ! Or not !? 8-) Sorry again for this long message. Yours, Thomas Hapke Thomas Hapke, Subject Librarian for Chemical Engineering University Library, Technical University Hamburg-Harburg D-21071 Hamburg, Germany e-mail: hapke(a)tu-harburg.d400.de, phone: 40 7718-3365, fax: 40 7718-2248 WWW: http://www.tu-harburg.de/b/hapke/t_hapke.html ----- 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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New Internet Journal
by Dr Paul Heelis 03 Jan '97

03 Jan '97

Call for papers A new completely on-line journal of science has been launched. The Internet Journal of Science - biological chemistry can be found at http://www.netsci-journal.com/ All aspects of Chemistry are included, but with particular emphasis on studies of biologically important molecules. In addition, the journal would like to promote the application of Computers in chemistry such as Molecular Modelling, Cheminformatics and Bioinformatics. There will be 2 sections to each issue. The Journal This will contain peer reviewed articles, Regular papers. Communications. Reviews, both invited and contributed The Magazine This will contain more topical issues, News and views, comments on current trends Educational articles such as practical experiments, teaching articles, computer applications Software reviews and commercial announcements Student section - this will give both post and under-graduate students the opportunity to write papers The journal will host Electronic conferences on its Web Site. Sincerely, The editor, Dr. Paul F.Heelis, North East Wales Institute, UK p.s. My apologises if you receive this message more than once. Dr. Paul F Heelis Editor, Internet Journal of Science, Faculty of Science and Technology North East Wales Institute, PP19 Mold Rd Wrexham LL11 2AW UK Tel +44 1978 293004 Fax +44 1978 290008 e-mail editor(a)netsci.u-net.com ----- 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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CCL:New Journal - Call for papers
by Rzepa, Henry 03 Jan '97

03 Jan '97

I forward a message first posted to the CCL list (apologies for those on that list). I suspect this may be the first of several such announcements in 1997. In view of Paul Deards' article about CAS abstracting relatively few Internet-only items, I wonder whether the journal noted below will be included by CAS. ================== > >Call for papers > >A new completely on-line journal of science has >been launched. The Internet Journal of Science - >biological chemistry can be found at http://www.netsci-journal.com/ > >All aspects of Chemistry and Biochemistry are included. >In particular the journal will cover the applications of >Computers to Science such as MOLECULAR MODELLING, Cheminformatics >and Bioinformatics. > >There will be 2 sections to each issue. > >The Journal > >This will contain peer reviewed articles, >Regular papers. >Communications. >Reviews, both invited and contributed > >The Magazine > >This will contain more topical issues, >News and views, comments on current trends >Educational articles such as practical experiments, teaching articles, >computer applications >Software reviews and commercial announcements >Student section - this will give both post and under-graduate students >the opportunity to write papers >The journal will host Electronic conferences on its Web >Site. > >Sincerely, >The editor, Dr. Paul F.Heelis, North East Wales Institute, UK Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ ----- 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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WebElements - the periodic table on the WWW - new version
by Mark Winter 03 Jan '97

03 Jan '97

Dear colleague This is to announce a new version (2 beta 6) of WebElements, the periodic table on the WWW. and to request feedback. The URL is http://www.shef.ac.uk/~chem/web-elements/ WebElements has undergone a major overhaul to include a frames interface and stylesheets so I'd be particularly pleased to hear from those of you with MicroSoft InterNet Explorer versions that support style sheets. Users who do not use style sheets (currently all NetScape users) should not notice any problems, but do let me know if you do. Users who do not have a frames-capable browser can still use the old version until I manage to produce a non-frames version. All of the many chemical errors that observant users have reported are still there, and the next step is to correct these. I do thank everyone who has taken time to make comments and to point out errors. The main reasons for the new layout were user feedback (over 1500 messages). See - I do listen sometimes! The new layout has considerably smaller files and so should allow better download times from outside the UK. Also, I hope the new layout allows for easier navigation. There are still rough edges in the new layout and I'll fix these when I get back from holiday. PLEASE NOTE new phone number below Dr Mark J Winter (Deputy Head of Department) Department of Chemistry, The University, Sheffield S3 7HF, England tel: +44 (0)114 222 9304 fax: +44 (0)114 273 8673 e-m: mark.winter(a)sheffield.ac.uk http://www.shef.ac.uk/~chem/staff/mjw/mark-winter.html WebElements is the periodic table on the world-wide web: http://www.shef.ac.uk/~chem/web-elements/ The Sheffield Chemdex is a listing of chemistry sites on the world-wide web: http://www.shef.ac.uk/~chem/chemdex/ ----- 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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MOTM
by Paul May 02 Jan '97

02 Jan '97

Hi, Happy New Year to everyone on the list! January's Molecule of the Month is now available for your inspection. It's C60, which is appropriate both for the recent Nobel prize connection, and for the fact that it's been provided by Henry's Imperial College MOTM collection (who provided the very first MOTM a year ago). The author is Wyn Locke, and the URL is: http://www.ch.ic.ac.uk/motm/c60.html and it's on the MOTM page at: http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm ----------- Another plea: The MOTM idea seems to have been a great success - at least it's survived a year and the number of MOTMs available on-line is now building into quite a useful resource. But I still need more. I have one more ready for Feb, (plus a few that I've personally written that I'm keeping as spares) - but I don't have *any* MOTMs from sites other than Bristol ready for March onwards. So if you feel like contributing one, please let me know. It only takes a couple of hours to write one, and it can get your web site publicity (the Bristol MOTM page gets as many hits as the entire main Bristol Chemistry Home page...). Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 9287667, fax: +44 (0)117 9251295 email: paul.may(a)bris.ac.uk WWW: http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm ----------------------------------------------------------------------------- ----- 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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Chime 1.0
by Mark Winter 02 Jan '97

02 Jan '97

For information: >X-Sender: bryan@mttam (Unverified) >Mime-Version: 1.0 >Date: Wed, 1 Jan 1997 07:32:12 -0800 >To: bryan(a)mdli.com (Bryan Van Vliet) >From: bryan(a)mdli.com (Bryan Van Vliet) >Subject: Chime 1.0 >Cc: chime-feedback(a)mdli.com > >Happy New Year's Day, > >The Chemscape Team at MDL Information Systems, Inc. is proud to announce >that Chime 1.0 is now available from our US (http://www.mdli.com) and >UK (http://www.mdli.co.uk) web servers. Highlights of Chime 1.0 include: > >* It is free to all users (subject to the conditions of the license.) >* It has no expiration date. >* It supports MDL Rxnfiles. >* It supports printing. >* It has a direct "hot-link" to ISIS/Draw. >* It provides enhanced support for scripting and animations. > >Please see the release notes on our web sites for more details: > > http://www.mdli.com/chemscape/chime/release-1.0.html > http://www.mdli.co.uk/chemscape/chime/release-1.0.html > >After you have installed Chime 1.0 please try out out our Chemscape Server >search engine by accessing either: > > http://www.mdli.com/chemscape/clientserver/product.html > http://www.mdli.co.uk/chemscape/clientserver/product.html > >This completely functional Chemscape Server application provides full >structure search capabilities (substructure, similarity, and exact match) >over the NCI-3D database of over 126,000 compounds and has been available >since the end of September. It is also available on http://ChemWeb.Com >(which will have other databases accessible via Chemscape Server sometime >this quarter.) > >I would like to thank the Chemscape Team for their hard work on this >release: Tim Maffett (the principal architect of Chime), Mitch Miller, >Frankie Wu, Tom Blackadar, and Randy Bumgardner; John Laufer from our >ISIS/Draw group for his work on our 2D rendering library; Roger Sayle >for his work on the RasMol 3D rendering and scripting code; GlaxoWellcome >for entering into a collaboration with MDL for future RasMol development; >Eric Martz for his very compelling Chime tutorials (go to >http://www.umass.edu/microbio/chime/index.html if you haven't seen them); >and, finally, MDL for providing the resources to make Chime possible. > >If you have any questions or comments about Chime 1.0 please e-mail us >at chime-feedback(a)mdli.com. > >Bryan Van Vliet > > >--------------------------------------------------------------------------- >| Bryan Van Vliet bryan(a)mdli.com | >| Project Manager, Internet Technologies 510.895.1313 x1160 (Voice) | >| MDL Information Systems, Inc. 510.352.2870 (Fax) | >| 14600 Catalina Street, San Leandro, CA 94577 http://www.mdli.com | >--------------------------------------------------------------------------- > PLEASE NOTE new phone number below Dr Mark J Winter (Deputy Head of Department) Department of Chemistry, The University, Sheffield S3 7HF, England tel: +44 (0)114 222 9304 fax: +44 (0)114 273 8673 e-m: mark.winter(a)sheffield.ac.uk http://www.shef.ac.uk/~chem/staff/mjw/mark-winter.html WebElements is the periodic table on the world-wide web: http://www.shef.ac.uk/~chem/web-elements/ The Sheffield Chemdex is a listing of chemistry sites on the world-wide web: http://www.shef.ac.uk/~chem/chemdex/ ----- 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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browser profiles over the last 11 months
by Mark Winter 31 Dec '96

31 Dec '96

Happy New Year! For your interest I enclose percentage browser stats for the last 12 months. There's all sorts of reasons why these numbers aren't scientific but the apparent trends are interesting anyway. You may find these numbers helpful when deciding what features to implement on your pages. Browsers ver Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec MSIE all 3.9 3.6 5.8 6.4 5.2 5.7 7.3 7.5 9.8 10.2 12.1 14.2 Mosaic al 3.1 3.1 2.9 3.0 2.4 2.0 1.8 1.6 1.1 0.8 0.6 0.5 NetScape 0.9 1.6 0.8 0.9 0.5 0.6 0.4 0.3 0.2 0.1 0.2 0.1 0.1 NetScape 1 7.0 4.2 3.0 2.5 2.8 2.0 1.1 0.9 1.0 0.8 0.6 0.5 NetScape 1.1 30.3 25.8 21.7 18.3 14.9 12.6 9.0 7.8 4.8 4.9 3.6 2.4 NetScape 1.2 22.7 19.1 16.9 11.8 13.4 9.8 6.7 6.8 6.0 5.0 3.9 2.8 NetScape 2 26.8 37.2 44.0 51.3 50.4 53.3 53.4 52.7 44.8 40.4 38.0 35.5 NetScape 3 0 0 0.1 2.2 6.0 11.1 17.8 20.2 29.7 35.0 38.8 41.5 NetScape 4 0.1 All other browsers are very small. Note the falling % for Mosaic. NetScape Version 3 use is increasing rapidly and is now more used than version 2. Version 2 is dropping as version 3 picks up, while the proportion of version 1 users is also dropping slowly. NetScape 4! Not sure if it's a wind-up but there were a significant number of hits from multiple address using browsers identified as "Mozilla/4.0b1 (Win95; I)" and "Mozilla/4.0b1 (WinNT; I)" MS InterNet Explorer (all versions) is rising and is now around 14%. I note that MicroSoft itself rates itself at better than 20% - perhaps this reflects chemists having different software? Anyway, this is at the expense of NetScape and the minor browsers. More than 91% of all hits come from [NetScape v2 or better + MSIE]. About 98% of all hits are NetScape + MSIE so it appears barely worth bothering to use other than these for site testing. Platform Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Macintosh 23.2 23.5 24.9 25.5 19.6 22.3 26.7 19.8 18.3 20.6 21.4 19.3 PC 64.3 62.3 61.9 59.9 63.2 62.6 59.4 66.7 71.8 71.0 71.1 72.5 Unix 11.9 12.9 12.1 12.4 15.6 13.6 12.6 12.1 9.0 7.4 6.5 6.9 At first sight it looks as though UNIX users are disappearing, but it's more likely that they aren't, rather that PC/Mac users are increasing more rapidly. PS - Style sheets work well in MSIE on the Mac. Assume they will be more popular very soon. PPS - A lot of people must have had a sad Christmas, Dec 25th was not a quiet day on my site here - 32000 html files ! PLEASE NOTE new phone number below Dr Mark J Winter (Deputy Head of Department) Department of Chemistry, The University, Sheffield S3 7HF, England tel: +44 (0)114 222 9304 fax: +44 (0)114 273 8673 e-m: mark.winter(a)sheffield.ac.uk http://www.shef.ac.uk/~chem/staff/mjw/mark-winter.html WebElements is the periodic table on the world-wide web: http://www.shef.ac.uk/~chem/web-elements/ The Sheffield Chemdex is a listing of chemistry sites on the world-wide web: http://www.shef.ac.uk/~chem/chemdex/ ----- 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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Additional ISIS/Draw template pages, and contest announcement!
by David W. Hughes 30 Dec '96

30 Dec '96

Have you ever created a template page for ISIS/Draw that you're particularly proud of? Think anyone else might like to use it? Maybe there is a template page that you've always wished "someone" would create? Please read on... We deliver ISIS/Draw with over 240 structure templates and 30 "template pages" (collections of related templates you can graphically select). You can also create and use your own custom templates and template pages -- this makes ISIS/Draw easy to customize to your particular needs. We have now created a page on our WWW site where we will post new template pages as they become available. There are now three new template pages available at our WWW site (http://www.mdli.com) or at our UK mirror site (http://www.mdli.co.uk) Simply select the "Download" button up at the top, and then select the link to the Templates. ----> C O N T E S T ! ! <---- To celebrate the New Year, the introduction of the new Template Page page, and to mark the release of ISIS/Draw 2.1 for Windows, we've put together a "Template Page" contest. Prizes range from official ISIS/Draw polo shirts to $200 in cash. For details, come to our WWW site (or our UK mirror site), go to the template page download page, and look for a link to the contest details. Have fun! ------------------------------------------------------------------ David Hughes Group Marketing Manager MDL Information Systems, Inc. phone: (510) 895-1313, x.1432 14600 Catalina Street fax: (510) 352-2870 San Leandro, CA 94577 email: davidh(a)mdli.com ------------------------------------------------------------------ This message has been sent to the following lists: ACSMEDI(a)LISTS.WAYNE.EDU CHEMWEB(a)IC.AC.UK CHMINF-L(a)IUBVM.UCS.INDIANA.EDU MOL-DIVERSITY(a)LISTSERV.ARIZONA.EDU STS-L(a)UTKVM1.UTK.EDU ISISFORUM-L(a)MDLI.COM ISISDEV-L(a)MDLI.COM ----- 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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