- chemweb - imperial.ac.uk

Web Chemistry Course and Conferencing Tools
by Rzepa, Henry 19 Jun '97

19 Jun '97

As more people are thinking about developing structured courses of teaching and training Web-based materials in chemistry, so the need arises to think how such courses might operate in a multi-author, multi-course, many student and symmetric ( ie students need to submit files as well as read documents) environment. None of this is specific to chemistry, but it turns out there are many interesting tools emerging for this type of application. We have heard very good reports about WebCT http://homebrew1.cs.ubc.ca/webct/ although there are other (perhaps more expensive) products such as FirstClass etc. Does anyone have any experiences of using such tools? One of my concerns is that we will all end up using different tools, and the global reach of the web will start "Balkanising" into lots of little local Intranets, all pretty much incompatible. 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/ chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: Web Chemistry Course and Conferencing Tools
by Paul Heelis 19 Jun '97

19 Jun '97

At 08:49 19/06/97 +0100, Rzepa, Henry wrote: >As more people are thinking about developing structured courses of >teaching and training Web-based materials in chemistry, so the need arises >to think how >such courses might operate in a multi-author, multi-course, many >student and symmetric ( ie students need to submit files as well as >read documents) environment. > >None of this is specific to chemistry, but it turns out there >are many interesting tools emerging for this type of application. >We have heard very good reports about WebCT >http://homebrew1.cs.ubc.ca/webct/ >although there are other (perhaps more expensive) products >such as FirstClass etc. > >Does anyone have any experiences of using such tools? > > We are evaluating Topclass from WBT systems in Ireland. Having just had a quick glance at the WebCT site it appears to offer a similar approach, but we have found it to be very bug ridden and unstable (hopefully WBT do not subscribe to this list!). However I would be grateful for information on any other systems that others have tried. Dr Paul Heelis Reader in Chemistry School of Science and Technology North East Wales Institute Mold Rd Wrexham Ll11 2AW UK Tel +44 1978 293372 fax +44 1978 290008 e-mail heelisp(a)newi.ac.uk editor(a)netsci.u-net.com Internet Journal of Science- Biological Chemistry http://www.netsci-journal.com First internet Conference on Photochemistry and Photobiology http://www.netsci-journal.com/97v3/ Infochem - chemist's database http://www.infochem.co.uk chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: Web Chemistry Course and Conferencing Tools
by Myles Danson 19 Jun '97

19 Jun '97

At 08:49 19/06/97 +0100, you wrote: >As more people are thinking about developing structured courses of >teaching and training Web-based materials in chemistry, so the need arises >to think how >such courses might operate in a multi-author, multi-course, many >student and symmetric ( ie students need to submit files as well as >read documents) environment. > >None of this is specific to chemistry, but it turns out there >are many interesting tools emerging for this type of application. >We have heard very good reports about WebCT >http://homebrew1.cs.ubc.ca/webct/ >although there are other (perhaps more expensive) products >such as FirstClass etc. > >Does anyone have any experiences of using such tools? > Though I do not have such experience yet, I do know of two other similar commercial systems. These are: WBT/TopClass http://www.wbtsystems.com Web Course in a Box http://www.madduck.com I believe that these pages hold details of participating institutions. A related issue is that of Computer Assisted Assessment engines using the WWW, perhaps combined within such course management systems. The Birmingham Medical School MedWeb is a good example in my opinion as is the Clyde Virtual Assessment Engine. Both have low client requirements: http://medweb.bham.ac.uk/teaching.html http://cvu.strath.ac.uk/campus.html specific details are at: http://cvu.strath.ac.uk/ae Another interesting development on the CAA / web side is TML (tutorial mark up language) at Bristol: http://www.ilrt.bris.ac.uk/mru/netquest/tml/ Please post this to the list of you think it is of use. Myles Danson Teaching Support / IT Coordinator Chemistry Department Loughborough University Loughborough Leicestershire UK chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Announce: Chemistry Models in Virtual Reality
by Matt Becker 19 Jun '97

19 Jun '97

I would like to draw your attention to a breakthrough in chemistry modeling. There are exceptional 3D chemistry models that are currently produced through Virtual Reality Modeling Language (VRML). The site features a VRML search engine that contains many beautiful representations of molecular and membrane structure at: http://vrml.sgi.com Go To: Once the site has loaded, there will be an blank entry field at the top of the homepage that has a Dive In button next to it. Enter the word chemistry in the field and click on the Dive In button. This will load an index of the "VRML worlds" which depict chemistry models. It is necessary to download a VRML browser to view these models. It is a simple and free download from the same page. *Here are a few quotes from an article entitled "VRML, Chemistry and the Web- A New Reality" by Alan J. Robinson of the Molecular Modeling Group, Department of Physical and Theoretical Chemistry, University of Oxford, Oxford, UK. "This article is an attempt firstly to introduce the concept of VRML which brings 3-D virtual reality to the Internet, secondly to describe how straightforward it is to use it and thirdly how we are now applying it to our research in chemistry to analyse and report results." "But why should chemists (and other scientists) be interested in VRML? Already as chemists we are used to dealing with VR programs such as QUANTA (Ref. 12), Sybyl (Ref. 13) and RasMol (Ref. 9) that display chemical structures and most will agree that these programs are beneficial in understanding a molecule compared to a flat representation on paper." "When analysing complex data it is often only possible to rationalise it by visualising it in 3-D, however this is notoriously difficult to transfer to the flat page of a journal. VRML gives us a medium through which we can easily create 3-D representations of the data that others may down-load and explore. Furthermore, it is intended that future versions of VRML will be capable of both animation and motion physics (i.e. objects moving according to physical laws), so the development of properties through time may be traced, obviously an important concern for chemists." The full article can be located at: http://alcyone.pcl.ox.ac.uk/people/alan/VRML/Paper/vrml.html Please address any questions or comments to Matt Becker <matt(a)cybernautics.com>. Matt Becker Cybernautics, Inc. 415.289.1580 x128 matt(a)cybernautics.com chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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netscape bug fix progress
by Michael Barker 18 Jun '97

18 Jun '97

Hi All, Nobody seems to have mentioned the security problems recently spotted in Netscape 4 and also found in earlier versions... so here is the news as of the 16/06. *------------------------------------------------------------* | Michael H. Barker GRSC The University of Liverpool | | Department of Chemistry | | E-mail: mhbarker(a)liv.ac.uk Oxford Street | | Liverpool | | Tel: +44 151 794 2274 L69 7ZD | | Fax: +44 151 794 3588 United Kingdom | | | | http://www.liv.ac.uk/Chemistry/Links/links.html | | "WWW Links for Chemists" @ The University of Liverpool, UK | *------------------------------------------------------------* http://home.netscape.com/flash3/misc/security_update.html SECURITY UPDATE June 16, 1997 ------------------------------------------------------------------------- The reported privacy bug affecting Netscape Navigator has been identified and fixed. It is now being thoroughly tested by Netscape, and a fix will be released by Wednesday, June 18. The bug, reported by an Internet consultant, affects Netscape Navigator 2.0 and 3.0, and Netscape Communicator 4.0 on all platforms (Windows, Macintosh, and Unix). Netscape will test the fix extensively before releasing it in an updated version of Communicator 4.0 during the week of June 16. A fix for Navigator 3.0 will follow shortly after the Communicator fix. Netscape knows of no reports of successful exploitation of this privacy bug, and no customer incidents have been reported. The privacy bug can allow malicious Web site operators to retrieve known files from the hard disks of visiting users by mimicking the submission of a form. Under ordinary circumstances, users browsing on known, trusted sites are not at risk. However, if a user visits an unknown, untrusted site, the operator of that site can potentially retrieve files from a user's hard disk through an obscure series of steps. For this attack to work, the hacker must know the exact name and path of the file. To completely remove any risk of this bug, Navigator users should download the updated version of Communicator (or Navigator), which includes the fix. In the interim, users of Navigator 3.0 and Communicator 4.0 can take the following steps to enable warning dialog boxes to detect and cancel form submissions: * In Navigator 3.0: Go to the Options menu and select Security Preferences. Select the "Submitting a Form Insecurely" preference to enable that warning dialog box. * In Navigator 4.0: Select the lock in the toolbar to open the Security Advisor. Select Navigator, then select the "Sending Unencrypted Information to a Site" preference to enable that warning dialog box. Although the Internet consultant was unwilling to release the technical details of the bug, he has subsequently released them to Netscape. The information that he provided matches what Netscape determined independently. Netscape will post a fix by June 18. Customers and partners will find download details and updates on the Netscape home page when the fix is available. ------------------------------------------------------------------------- [Navigation bar] Corporate Sales: 415/937-2555; Personal Sales: 415/937-3777; Government Sales: 415/937-3678 If you have any questions, please visit Customer Service, or contact your nearest sales office. Copyright ) 1997 Netscape Communications Corporation chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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ChemStarter - Online Discussion Forum
by Rolf Claessen 16 Jun '97

16 Jun '97

ChemStarter - Online Discussion Forum I added an online discussion forum to the ChemStarter at http://destille.chemie.de/HyperNews/get/forums/chemstarter.html It is possible to use html. So you can include images, vrml, chime, ... into your messages to illustrate the discussion about chemistry problems. Yours Rolf Claessen claessen(a)chemie.de chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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RSC CIG/CSA Autumn Meeting - Chemical structures and networking
by john blackmore 13 Jun '97

13 Jun '97

(apologies for multiple list postings) This is the first announcement of a Joint Royal Society of Chemistry Chemical Information Group (RSC CIG) and the Chemical Structure Association (CSA) meeting The all-day meeting entitled: Chemical structures and networking - an overview of recent developments and trends is to be held on Thursday, October 16th 1997, Burlington House, Piccadilly, London. Rapid development continues in the application of increasingly sophisticated computer technology, both hardware and software, to the location, retrieval, registration, manipulation and exploitation of chemical structure and related data. These developments are helping users cope with the new demands arising from the continuing growth in the volumes and complexity of data, especially from such techniques as combinatorial chemistry and high-throughput screening. All of this is taking place alongside the continuing growth in the use of Internet/Intranet technology. Most of the new developments allow the use of a browser interface, and many of them are accessible via the Internet. This meeting will review recent developments and trends in the availability of tools for manipulating chemical structure and related data. Key presentations will provide overviews which will be supplemented by presentations and demonstrations from major systems suppliers. After the presentations, there will be a (free) wine and cheese reception, which will provide a further opportunity to network and to view the various demonstrations. This one-day meeting presents a highly cost-effective way of keeping up to date with this fast-moving field. The cost is 20 to members of the RSC CIG or CSA and 25 to non-members. The number of attendees will be be limited to 50, so early booking is advisable. Further details and registration forms are available from: Doug Veal Doverton Ltd 46 The Knoll Hayes Bromley Kent BR2 7DHP Phone/fax 0181-325-7608 e-mail: doverton(a)compuserve.com announcement posted by john blackmore, RSC CIG johnb(a)infonol.demon.co.uk chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Babel and XCART
by Trevor Gilson 11 Jun '97

11 Jun '97

I don't recall the Babel molecular structure file format conversion utility referred to recently - might be a good time to remind folk that it may be obtained from: http://mercury.aichem.arizona.edu/babel.html - and while we are on the subject, I wrote to Arizona recently about an ambiguity over Cambridge cssr files. This format is used by Desk Top Molecular Modeler for PC, but it chooses to allow the atom 'label' (usually an integer) (columns 7-10) to be seperated by a space from its atom (symbol), so long as it is in its correct column. BABEL, by contrast, seems to interpret the label as the x-coordinate when it occurs. I suspect that BABEL is going on columns encountered rather than on the old-fashioned (and horrible) rigid FORTRAN-type format? It is not particularly difficult to edit the DTMM file into BABEL compliance, just a nuisance to do it every time! I recommend the DOS technical editor Tech-Edit 2.61 which processes or removes columns with dexterity. I also have a DOS based molecular coordinate/structure constructor/viewer utility, xcart with xtick - see http://www.soton.ac.uk/~trg/acad/xcart.html (Requires chime to view). I don't recommend this as user-friendly, but it can be useful for smallish difficult molecules particularly in inorganic chemistry and it outputs pdb files, one of the main chemical mime specified formats. It can also be used to add connectivity information to any raw list of atom coordinates (up to 255 atoms). I have used a development of the package (not yet online) for the production of raytraced vibrational animations, as used to generate the animated gifs on my home page. Trevor Gilson chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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xyz2rgb molecular animations
by Paul May 11 Jun '97

11 Jun '97

Hi, I was recently sent this, which might be of interest here: > > > xyz2rgb makes pretty pictures and movies of molecules. It expects input > in the form of an XYZ file, one of the file formats frequently used by > computational chemists. As output, it produces one or more line-interlaced RGB > files. These can be converted to other formats using the ImageMagick image > processing toolkit. Conversion between a wide variety of molecule file formats > can be accomplished using a program called Babel. > > Information on xyz2rgb (including source code) is available at > http://world.std.com/~wware/xyz2rgb.html > xyz2rgb is GPL-ware. > - ------------------------------------------------------------- > Will Ware email: wware[at]world[dot]std[dot]com Regards, ------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 9287667, fax: +44 (0)117 9251295 <mailto:paul.may@bris.ac.uk> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "Why don't you just leave me alone with my thought" Homer Simpson ------------------------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Register now for Chemistry Webmasters 3
by ALLENB＠rsc.org 10 Jun '97

10 Jun '97

If you have not yet done so, NOW IS THE TIME TO REGISTER for CHEMISTRY WEBMASTERS 3 - Future Technologies for Chemistry on the Internet on Thursday 10 July 1997, at the University of Oxford Chemistry Sub-Faculty Organised by The Royal Society of Chemistry and the University of Oxford on behalf of the CLIC consortium, this FREE meeting will be a mixture of presentations, posters and workshops. Speakers include Dr Henry Rzepa on 'Publishing CD-ROMs of Internet Sites and Electronic Conferences', Dr Mark Winter on 'Stylish chemistry web pages and how to plug them', Dr Peter Murray-Rust on 'Chemical Data on the Internet - CML and XML' and Omer Casher on 'Programming web sites - Hyperwave and Netscape 4'. Workshops will include Dr Karl Harrison's Virtual Chemistry Lab, to be used in teaching for the first time this autumn, and Dr Mark Winter will chair what is sure to be a lively discussion on future directions and funding issues. Full details of the programme are at http://chemistry.rsc.org/rsc/chemwebm.htm To register email Becky Allen at allenb(a)rsc.org chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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