December 1996 - 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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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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New version of ISIS/Draw available for download -- supports polymers, too.
by David W. Hughes 30 Dec '96

30 Dec '96

(This message is being simultaneously posted to several lists; please forgive any duplicate messages. And please forward to any list you feel may be interested.) Just in time for the New Year... We've placed ISIS/Draw 2.1 for Windows up on our WWW site, for free download for academic use and/or personal use at home. This version * supports Windows 95 and Windows NT as a 32-bit application, and supports "tool tips", long file names, and the use of the right mouse button. (a 16-bit version is also available for Windows 3.1.x) * can create 2D polymer representations, in the manner in which polymer chemists are familiar * makes it possible to annotate structures by attaching data to specific portions of a structure. The Macintosh version of ISIS/Draw 2.1 will be available soon. You can obtain a copy of ISIS/Draw 2.1 for Windows (or an updated ISIS/Draw 2.0.2 for Macintosh) at http://www.mdli.com or at our UK mirror site http://www.mdli.co.uk Don't forget to get a copy of the updated help file, too. Enjoy! -- ------------------------------------------------------------------ David Hughes Group Manager, Material Science Marketing 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 ------------------------------------------------------------------ Message sent to: 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 ----- 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 peter murray rust 24 Dec '96

24 Dec '96

On Mon, 23 Dec 1996, John Maher wrote: [...] > We are involved in a JISC/JTAP project for the delivery of multiple choice > questions in chemistry (and mathematics). See : > http://emrs.chm.bris.ac.uk/john/jisc.html > and is part of the UK's JISC/JTAP projects : http://www.jtap.ac.uk/ > and http://www.jtap.ac.uk/projects/index.html therein. > > The questions are being held as a question bank in > an Oracle database. 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. The next option is to do-your-own-thing and hope that the rest of the world follows. Occasionally it does as with HTML - which in purists' eyes is seriously flawed, but it works 90% of the time. Unfortunately chemistry tends to be in the 10% :-(. However the success of the WWW is based on the experiements that didn't work as well as the ones that did - globally it is a very cost-effective way of developing acceptable solutions. The third option is to wait for (or encourage) a 'standards' body to help. For example, there is now a move to introduce standards for distance education, which would certainly be extremely useful - e.g. student records, registration, learning contracts, etc. I doubt you are at this stage yet. Finally, therefore, there is the possibility of building 'virtual critical mass' for your community. An area where we are starting to do this is in the creation of (hyper)glossaries - see http://www.venus.co.uk/ where we have helped people create their own hyperglossaries under a common technology (in that case SGML/CML). It seems likely that you will need a common technology if you are to act as a source of interchange of material and re-use. To do this you will need at least: - a common technology for the actual material. (I doubt that you will find HTML robust enough, and my own suggestion would be SGML). It must allow searching, clear identification of the information components and a clear separation of syntax and semantics. You are also (IMO) likely to need glossaries and/or data dictionaries. - a common namespace for addressing. You need to be able to locate questions precisely and (I assume) correlate the answers with the questions, so I expect that unique IDs for each question-answer become essential. You will also have to decide whether there is any hierarchy in your information, e.g. 'Read the following passge which relates to the next 5 questions'. If glossary experience is anything to go by, this will be quite a tricky problem. I suspect that it will help a lot if you can get a small number of mutually interested groups to get together on this. The real-life component of virtual projects can be important :-) P. > Peter Murray-Rust (PeterMR, ) Director, Virtual School of Molecular Sciences Pharmaceutical Sciences, Nottingham University, NG7 2RD, UK; Tel 44-115-9515100 Fax 5110 http://www.nottingham.ac.uk/vsms/; OMF: http://www.ch.ic.ac.uk/omf/ ----- 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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Article on virtual reality on the Web
by Ian Winship, Univ Northumbria Info Services 23 Dec '96

23 Dec '96

This may be of interest: KRIEGER, JH Doing chemistry in a virtual world Chemical & engineering news 9 December 1996, 35-41 - using VRML (Virtual Reality Modelling Language). also at http://pubs.acs.org/hotartcl/cenear/961209/virtual.html ========================================================================== Ian Winship Information Services Dept. | e-mail: ian.winship(a)unn.ac.uk University of Northumbria at Newcastle | phone: 0191 227 4132 City Campus Library | fax: 0191 227 4563 Newcastle upon Tyne | NE1 8ST | UK | =========================================================================== ----- 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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Online, but unnoticed?
by Paul Deards 23 Dec '96

23 Dec '96

I've just written the following article for the Chemistry & Industry web site (http://ci.mond.org) However, as the subject is particularly appropriate for this mailing list, I'm copying it here for discussion. ------------ On-line, but unnoticed? Electronic chemistry journals and conferences have yet to make a significant impact, and aren't seen as "serious" publications. That's the conclusion of Chemical Abstracts (CA) after a year of reviewing articles on the world wide web. However, a new wave of journals from major publishers in 1997 could give the new medium the weight and authority it currently lacks. A healthy list of CA citations can be invaluable for a scientist's career prospects. CA started indexing electronic documents in April 1995. By the beginning of December this year, CA had indexed 210 papers from 14 on-line journals and 45 papers from 2 on-line conferences (see table). This is a vanishingly small figure when compared with the half a million articles CA abstracts in a year from more traditional sources. Editor David Weisgerber attributes the small figures to a lack of regard for electronic journals. "There is a lack of awareness of on-line journals, but also a general perception about the lack of recognized credentials for these publications, a concern for gaining little visibility and readership among one's peers, and the view that publication in such journals may not 'count' towards career goals," he comments Yet on-line journals would appear to have the edge over their printed counterparts. They have lower production costs, the ability to offer multimedia, and can be easily accessible world-wide without the need for a local library archive. The low figures are down to the youth of the medium, comments Patrick van der Valk, of consultants BetaCyte. In a medium where very little is more than five years old, most on-line chemistry journals have been around for less than a few years. "It will be a couple of years before they are taken seriously," he predicts. In fact, a look behind the headline figures shows a healthier picture for web publications than CA paints. CA say that a good fraction, about three-quarters, of the papers it looks at on the web fit its selection criteria - that is, they report new scientific findings and are publicly available. Also, CA's policy on papers distributed in several media distorts the figures downwards. When an article is available in different forms, CA indexes only one, preferring paper to CD-ROM, and the latter to web publications. Many web journals and conferences are therefore missing from the figures. For example, two on-line conferences generated 110 citations between them last year, but are missing from the figures because the citation is to the CD-ROM published at the end of the conferences. Electronic versions of printed journals are also missing - citations are to the paper versions. CA says that this policy reflects the stability of the media, but also because "our users will probably find it easier to go from our print document citations to the corresponding CD-ROM or on-line formats than trace the reverse path". CA also note that monitoring the web involves disproportionate amounts of time and staff. Henry Rzepa, of Imperial College, London, comments that this could mean that CA is missing out on some of the things that are going on. "There is no established mechanism for the author of internet related materials to easily bring them to the attention of CA," he says, adding that this could be related to the fact that almost all web materials have not been subjected to quality control via peer review machanisms. "Clearly a top priority for the chemical community is to establish such mechanisms, and a formal channel to bring them to the attention of agencies such as CA", he adds. One cloud on the horizon for electronic journals is the issue of permanence. One of CA's criteria for indexing an article is some degree of 'relative permanence'. When paper journals go out of business, there is likely to be a physical archive in some universities or in national collections. National collections, however, don't collect copies of web documents, nor do subscribing libraries keep a physical archive. The death of a web-only journal is likely to be accompanied by the disappearance of its archive into the electronic ether. Weisgerber reports that CA was concerned that some electronic documents would be so short lived that citations would have little value in a few years' time. However, CA decided to take a lenient view, assuming that web documents will be available indefinitely in order to avoid being too restrictive on the new medium. Problems such as permanence and stability are still awaiting solutions, yet it looks like the next 12 months could be a defining period for electronic chemistry journals. Until now, on-line publications have tended to be new journals taking advantage of the low start-up costs of the internet. Now, several publishers have announced plans to put on-line versions of print journals on the web. The Royal Society of Chemistry, for example, is producing on-line versions of all of its 12 primary journals beginning in the New Year. With the weight of publishing companies and the reputations of recognised titles behind them, 1997 could be the year that on-line journals are taken seriously by the chemical community. (For Table: Abstracting the virtual: Web-only chemistry related journals and conferences abstracted by CA <see article on web site, http://ci.mond.org/connect.html>) ------------------ -------------------------- Paul Deards Internet Publisher Chemistry and Industry 0171-2353681 x233 pauld(a)chemind.demon.co.uk http://ci.mond.org/ -------------------------- Advertising with C&I electronic publications is a cost-effective way of reaching a target audience of scientists. For more details, contact us at advertising(a)chemind.demon.co.uk -------------------------- ----- 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 John Maher 23 Dec '96

23 Dec '96

Rzepa, Henry wrote: > > >does anybody know of contributions, reflections or recommendations > > >from chemists or from a chemical point of view in the context of the > > >metadata discussion which is connected with the keywords of "Dublin > > >Core" or Warwick Framework". (For those who are interested see URL: > > >http://purl.org/metadata/dublin_core) I know of the CML project which > > >in my opinion goes in this direction. Are there others ? and this was followed by Peter Muaary Rust : > It is my intention to get a frozen version of CML out over this (in our > country) holiday period. CML has the same syntactic provision for META as > HTML, but it is up to the molecular community how that is used. I have > also (recently) introduced an <ADMIN>...</ADMIN> element which was driven > by the needs of hyperglossaries in CML but is relevant to any chemical > document. This is a flexible container and so can contain people, > e-mails, addresses, etc. It could, for example, contain a list of the > molecules in a paper (e.g. as SMILES strings or CAS regnos). I'd welcome > suggestions :-) We are involved in a JISC/JTAP project for the delivery of multiple choice questions in chemistry (and mathematics). See : http://emrs.chm.bris.ac.uk/john/jisc.html and is part of the UK's JISC/JTAP projects : http://www.jtap.ac.uk/ and http://www.jtap.ac.uk/projects/index.html therein. The questions are being held as a question bank in an Oracle database. 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. John Maher ----- 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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Metadata discussion and chemistry
by Thomas Hapke 20 Dec '96

20 Dec '96

Hello, does anybody know of contributions, reflections or recommendations from chemists or from a chemical point of view in the context of the metadata discussion which is connected with the keywords of "Dublin Core" or Warwick Framework". (For those who are interested see URL: http://purl.org/metadata/dublin_core) I know of the CML project which in my opinion goes in this direction. Are there others ? Thank you 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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UK Research Selectivity Excercises
by Rzepa, Henry 19 Dec '96

19 Dec '96

I though it might interest people in either the UK or further afield that Web technology is now the preferred method for disseminating important matters such as national university research profiles. The results for the UK chemistry were posted on http://back.niss.ac.uk/education/hefc/rae96/1_96/t18.html within minutes of the "press embargo" being lifted. 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/ (Eudora Pro 3.0) ----- 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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