March 1997 - chemweb - imperial.ac.uk

CML and XML
by Peter＠ursus.demon.co.uk 24 Mar '97

24 Mar '97

Chemical Markup Language (CML) has been written to be an application of the new Web language, XML. XML, which is a simple dialect of SGML, has recently been announced at two conferences and received considerable interest. Indeed it is being presented as a split between the two largest browser manufacturers (Netscape and Microsoft). A typical article on the potential of XML is described in: http://www.webweek.com/97Mar24/software/split.html where CML gets an honourable (and essentially accurate) mention! There is a lot of hype about XML (which is being launched at the WWW6 conference next month and where we hope to have a CML/JUMBO demo at the developers' forum). Obviously if XML *does* become a Web standard, it makes it that much easier for people to support CML (and other similar applications). Browsers, parsers, search engines (non-chemical), authoring tools, database front-ends, etc. will all be built for generic applications. The molecular community will 'get this without effort'. However, even if XML does not get adopted by Microsoft and Netscape, this will have no impact on CML, since it is based on industry-strength SGML implementation. Chemistry is sufficiently complex that it requires the power of SGML or the equivalent representation in Object-oriented language. Indeed CML can be used to create an IDL (Interface Definition Language) from which any API (e.g. C++, Java) can be automatically compiled. Put another way, CML is sufficiently powerful that it can be algorithmically transformed into whatever language is or will be used in the next few years. The current Java implementation of CML (JUMBO and related tools) uses a generic approach to structured documents which maps directly onto XML/SGML but could be trivially transformed into any other structured document technology. I am starting to get enquiries and volunteers for writing input routines for JUMBO. If anyone has a 'file format' that they have responsibility for that they would like to input into JUMBO, please let me know. I am naturally particularly keen to see chemical/* MIME types supported, but any files in common use can be considered (especially if they are well documented and stable!) P. -- Peter Murray-Rust, domestic net connection Virtual School of Molecular Sciences http://www.vsms.nottingham.ac.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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Crystal structure viewing & manipulation
by Paul May 24 Mar '97

24 Mar '97

Hi, Can anyone recommend a Windows/PC program that can display crystal structures (with a given number of unit cells along each axis direction), rotate them in 3D, and allow the user to manipulate the structure, e.g. remove surface atoms, move atoms about, create/break bonds, etc. We want to examine how the surface of a diamond crytal might reconstruct to graphite as the terminating groups leave, and there must be a better way to do this than than handheld straw models? The Weblab viewer from MSI can do some of this, but it doesn't have all the functionality I'd like. Anyone know of a similar program written specifically for crystals? 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 "If you broke a mirror with a horseshoe, would you get 7 years of ambiguity?" ----------------------------------------------------------------------------- ----- 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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Job Vacancy> Webmaster
by Paul Deards 22 Mar '97

22 Mar '97

Apologies if ChemWeb's remit doesn't extend to job ads, but this one seems particularly relevant. ============= The Society of Chemical Industry's newly created IT Department has the following vacancy for full-time staff based at its London offices. Webmaster SCI has 6 successful web sites (listed at http://sci.mond.org/pubs.html) which are visited by over 6000 people each week. We have a vacancy for a webmaster who will be responsible for maintaining and generating content for the sites, including writing daily science and business news, and participating in the development of new sites. The successful candidate will have a science or business background. S/he will have some writing experience, and an enthusiasm for writing for the new media. Knowledge of HTML, although useful, is not required. Annual salary: Stg15,000 . To apply, send your CV and a covering letter to : Paul Deards, IT Manager, SCI, 14/15 Belgrave Square, London SW1X 8PS. Email applications (ASCII only please) should be sent to: pauld(a)chemind.demon.co.uk. Review of applications will begin immediately and will continue until the posts are filled. Please note that we will only pay interview travelling expenses to applicants based in the UK or Ireland. ================= -------------------------- Paul Deards IT Manager Society of Chemical Industry 0171-2353681 x233 pauld(a)chemind.demon.co.uk http://sci.mond.org/ -------------------------- Advertising with SCI 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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CSML
by Dr Douglas J. Chappell 17 Mar '97

17 Mar '97

Hi, Can someone please tell me the location of the documentation for CSML - I've searched far & wide but so far have only found example scripts. Thanks, Doug |---------------------------------------| | Dr Doug Chappell | | Department of Biochemistry | | The University of Sydney, 2006 | | NSW AUSTRALIA | | Phone: 61-2-9351-2511 | | Facsimile: 61-2-9351-4726 | | Email: D.Chappell(a)biochem.usyd.edu.au| |---------------------------------------| ----- 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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Top 5% Chemistry Site - Award
by Rolf Claessen 12 Mar '97

12 Mar '97

Top 5% Chemistry Site ===================== This award is given monthly to the best 5% of submissions to either "Rolf Claessen's Chemistry Index" http://www.geocities.com/Tokyo/5243/index.htm or "Homepage for Chemists" http://www-public.rz.uni-duesseldorf.de/~knecht/chempage.htm Rolf Claessen http://www.geocities.com/Tokyo/5243/index.htm (frames) http://www.geocities.com/Tokyo/5243/home_en.htm (no frames) s101264(a)stud-amil.uni-wuerzburg.de Rolf Claessen http://www.geocities.com/Tokyo/5243 s101264(a)stud-mail.uni-wuerzburg.de Tel. +49 931 701814 ----- 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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word processing packages on unix system
by dychen＠cheyenne.bgsu.edu 12 Mar '97

12 Mar '97

hello everyone, sorry if this subject isn't so chemweb-related, i figure you are the most resourceful group, here it goes. our department would like to know your opinions on word processing softwares on unix system (we understand that mac and pc can do good jobs too). either free/share (latex) or licensed packages (framemaker). please forward your responses to me directly. many thanks!! chen ----- 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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Using an intelligent agent
by Jelle Smit 12 Mar '97

12 Mar '97

A few days ago i downloaded the intelligent agent Autonomy at http://www.agentware.com/download.htm; only use the US sites the UK site expires immediately! (the US software expires 60 days after you first install it). I find this agent very usefull. Simply type your query in the form of a sentence like: synthesis of fullerenes using metal catalysts and the search dog of Autonomy search for you on WWW, reads the documents and presents the most relevant ones. It is possible to train your search dog for an optimal result. Jelle Smit Library University of Technology Delft, The Netherlands ----- 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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Short Introduction to WWW - Publishing Chemistry (VRML, Chmie, J
by Rolf Claessen 12 Mar '97

12 Mar '97

At http://www.geocities.com7Tokyo/5243/pub_en.htm I wrote a short introduction to publishing chemistry using vrml, java, chime, .... with short code examples. Yours sincerely, Rolf Claessen University of Wuerzburg, Germany http://www.geocities.com/Tokyo/5243 ************** Rolf Claessen 0931 - 701814 ************** http://www.geocities.com/Tokyo/5243/index.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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Re: Electronic conferences
by Janet Ash 08 Mar '97

08 Mar '97

Thank you to Henry Rzepa for the helpful comments on electronic conferences from an organisers point of view. I should still be interested to hear more views from people who have taken part in electronic conferences, either through making a presentation or just "attending". Janet Ash Chairman Chemical Structure Association ------------------------------------------- Janet Ash Herengracht 14E 1015 BK Amsterdam The Netherlands Tel/Fax: +31 20 6269610 e-mail: ash(a)euronet.nl or 100547.562(a)compuserve.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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Re: paperless submission of Student Cousework
by Bernard Blessington 07 Mar '97

07 Mar '97

On Thu, 6 Mar 1997 19:25:01 GMT "Jeffrey L. Nauss" <Jeffrey.Nauss(a)UC.Edu> wrote: > On Mar 6, 6:40pm, RICHARD SINGER wrote: > > Dr Nauss wrote regarding marking emailed UG work.... > I think this is an important point and coincides with with what I had > previously stated - "Students may have to learn the software. They probably > would need to become fairly adept at using it for attachments and such." > Teaching the proper use of the computers and software would probably have to > be a significant part of the course - at least for now. I agree,: word processing, spreadsheets, graphs, chemical structure-drawing,email(with MIME attachments), www and file managing(local and networked)are now basic techniques for chemistry. We teach them from day 1 and find some students need considerable help, others can nearly teach us!. > > the thought of 150 word processed first year experiment > > reports with bitmap graphics appearing on my hard drive is > > frightening! Fear not !! I teach 250-300 students(1st & Second Year UK University) in a single, totally electronic, class(Organic Chemistry and Molecules of Life), comprising mainly Pharmaceutical & Forensic Chemists/Pharmacists. The way I get round the above problem is to divide the class into sets(about 10 students per set). They work on specified exercises, mounted on a central server, and then circulate, using email with MIME attachments, within the set their individual answers. Each member saves his answer and those received from other set members on a floppy, then checks the answers of the other members of the set. The set then discuss their answers and circulate corrections amongst themselves. A specified time is given for both stages . After this time the set "leader" sends me a simple email list( cc to all his set members) of all who have contributed to the set discussion( and more importantly anyone who has not). I can also request copies of any set's work & discussion(email+ attachments). For the next exercise the set "leader" moves alphabetically down the set and the procedure is repeated. At the end of the series of exercises I ask each member of the set to assign and email me integer marks(-2 to +2) to others in the set which they feel reflects their contribution to the set's activities. The chemistry material in the exercises also forms the basis of a traditional short answer exam at the end of the course. This approach is still in its early stages(1 year experience + 1 year trial run) and is still evolving. Overall student feedback is that it is good, interesting,novel stimulating( and very modern!!). Workshy students do not like it at all. Clearly a sympathetic and careful pace is essential if students with initially poor IT skills are to be encouraged rather than discouraged . I apologise for possible duplication but I am cross posting this reply to Chem-education list in response to the similar enquiries arisng there( see: d.c.nonhebel(a)strath.ac.uk ..... I have been asked to chair an ECEN group - an education group of the EU -investigating the teaching of Communication and Management Skills in Chemistry programmes within the EU.......) Bernard ---------------------- Dr.Bernard Blessington . Bradford University . Dept. of Pharmaceutical Chemistry. Bradford BD7 1DP, England. Tel +44 (0) 1274 384704 FAX +44 (0) 1274 305340 e mail - b.blessington(a)bradford.ac.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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