July 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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Molecule of the Month
by Paul May 31 Jul '98

31 Jul '98

Hi, August's Molecule of the Month is Finasteride (tradename Propecia), which is a drug used to treat male pattern baldness recently approved by the FDA in America. It has been submitted by Matthew J. Dowd from the Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA, USA. Versions: HTML: <http://www.phc.vcu.edu/feature/finasteride/finasteride.html> CHIME: <http://www.phc.vcu.edu/feature/finasteride/finasteride2.html> MOTM Home: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> Regards, ------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927, fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "Now listen brain, you know I don't like you, and you don't like me, but let's just get through this test and I can get back to killing you with beer", Homer Simpson. ------------------------------------------------------------------------- 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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PISA
by Dr. Wendy A. Warr 28 Jul '98

28 Jul '98

Can anyone tell me anything about the Pharmaceutical Information Systems Association, PISA? What is their address? What do they do? Apologies for duplicate postings. 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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"Chemical samples preservation" to be discussed at ECSOC-2
by Shu-Kun Lin 24 Jul '98

24 Jul '98

Hi, colleagues, The disposal of old chemical samples is costly and generates environmental problem, while old samples can be used for many other screening purposes. However, there are many technical problems regarding samples management. As one of the two Section Conveners of Section E of The 2nd International Electronic Conference on Synthetic Organic Chemistry (ECSOC-2, at http://mdpi.org/ecsoc-2.htm) I would like to invite chemists contribute short papers expressing ideas on the samples preservation project. The format might be that of the short comments published in many journals. MDPI published MOLECULES (http://mdpi.org/molecules/) is the first journal encouraging chemists to deposit and exchange samples. In order to promote this activity, I thought about purchasing ca. 0.5 g ( or any amount 5mg-500g) of samples of the rare compounds described in any MOLECULES papers. The nonprofit organization MDPI has put great efforts on collecting all old samples from retired professors and in many cases pay cash to purchase all of them. MDPI further rewards sample contributor afterwards if any part of the samples are sold in the worldwide samples exchange project (For more information, please visit http://mdpi.org/ website). It has been my dream that no old samples are trashed but all are preserved by MDPI. I would like to open active discussions at Section E, where the topic includes "Information and Compound Archives Management and Internet Application: Molecular diversity studies, literature, databases, chemical sample libraries, and 2D and 3D structural presentation". If you have any comment, please let me know. I will appreciate it if you support us. Shu-Kun Lin President of MDPI Editor, MOLECULES (vol.3 1998) --------------------------------------------------------- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland http://www.mdpi.org/ MOLECULES http://www.mdpi.org/molecules/ ECSOC-2 http://www.mdpi.org/ecsoc-2.htm 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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Cyclodextrin
by Andrew Gee 23 Jul '98

23 Jul '98

I have been looking for a pdb of alpha, beta and gamma cyclodextrins. I have looked in many places but so far I haven't had any luck. Could someone please tell me where to find these. Thanks in advance. Andrew Gee 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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ECSOC-2 calling for papers
by Shu-Kun Lin 22 Jul '98

22 Jul '98

Dear Colleagues, The deadline for submission of papers to the Second International Electronic Conference in Organic Synthesis (ECSOC-2) is August 1st, 1998. This Conference will take place from September 1-30 on the Internet, providing the opportunity for immediate feedback and informal discussions. The organisers would like to encourage you to use this medium to have your research results made available to the global chemistry community. Please visit the Conference Website for further information. ECSOC-2 Website: http://www.mdpi.org/ecsoc-2.htm Dr. Esteban Pombo-Villar ECSOC-2 Chairman Novartis Pharma CH-4002 Basel, Switzerland phone +41 61 324 9865, fax +41 61 324 9794 e-mail ESTEBAN.POMBO(a)pharma.novartis.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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ChemInfo/MetaChem: efficient resource discovery for the chemical community
by Alan Arnold 22 Jul '98

22 Jul '98

Colleagues, Henry's "Needle in a Chemical Haystack" Webmasters4 paper http://www.ch.ic.ac.uk/talks/wm4/ and recent discussions here about search engine performance have prompted me to introduce myself and a project that I hope may be of interest to many of you. Among other things, I am principal investigator for an Australian Research Council (ARC) project "ChemInfo/MetaChem" whose primary aim is to create an internationally accessible electronic gateway to chemistry information resources of all kinds. As a consequence of widespread concerns in the Australian academic chemical community about the high costs of a number of the major sources of chemistry related information, both print and electronic, and the effect on ability of users of chemistry information to have convenient and reliable access to these resources, representatives of the Royal Australian Chemical Institute (RACI), Professors and Heads of Departments of Chemistry (PHoDs), CSIRO and CAUL (Council of Australian University Librarians) met some time ago to discuss ways of improving the chemical information research infrastructure in Australia. The outcome of this meeting was the development of a range of strategies designed to improve access to both print and electronic information sources. One of the strategies identified was the development of a chemistry gateway on the web which would provide access to a diverse range of evaluated information sources and services. The ChemInfo/MetaChem gateway will provide access to Internet information such as electronic chemistry publications and databases, research projects, data sources, software, online teaching modules, directories, conferences etc. In addition, the gateway will provide links, through library catalogues and document delivery services, to print information. Similar gateway initiatives have emerged from similarly concerned chemical communities in the US and UK and elsewhere. Some excellent ones that come to mind are ChemPort http://www.chemport.org/, ChemCenter http://www.Chemcenter.org/, ChemSoc http://www.chemsoc.org, ChemDex http://www.shef.ac.uk/chemistry/chemdex/ and it's 'commercial' development ChemDex+ http://chemweb.com/databases/chemdex/chemdex.exe, and the ChemWeb http://www.chemweb.com/ projects. We do not wish to reinvent these excellent wheels. However, we believe that a distinguishing feature of the ChemInfo/MetaChem gateway will be that each resource will be evaluated, described, classified and indexed by subject specialists - thus providing the element of trust that is crucial to efficient resource discovery in these times. The final result will be a database of metadata records providing information about, and links to, the resources and also their level of validity and authority as a basis for research and teaching activity. Discussions are underway to ensure that the metadata database will be mirrored in at least the US and UK. At the moment, the project is a collaborative effort involving 9 Australian university libraries and we expect that this number will increase as the utility of the gateway is recognised. Subject specialist librarians currently donate their time as an "in-kind" contribution to the $ provided by the ARC. Over the few 6 months, our librarians plan to produce metadata for up to 10000 records, using the MetaWeb suite of tools http://purl.nla.gov.au/metaweb/home developed by the Distributed Systems Technology Center (DSTC) - another of the project partners. As our primary aim is efficient resource discovery, Dublin Core http://128.253.70.110/DC5/UserGuide5.html has been chosen as our primary metadata schema, but as many resources out there are educational, these can also be well described by the EdNA (Education Network of Australia) metadata schema http://www.edna.edu.au/edna/owa/info.getpage?sp=auto&pagecode=5210. We are also very interested in the development of metadata that can be used to describe resources peculiar to the chemical community. Henry's prototype DC-Chem schema http://www.ch.ic.ac.uk/talks/wm4/9.html looks like it would be a good place to start. At the moment I have to confess that we do not have a fully developed web site for the gateway, but some background info can be found at http://www.ch.adfa.oz.au/metachem/ A more comprehensive and useable site is on the virtual drawing board. I would very much appreciate your comments, particularly in the areas of evaluation criteria, chemically-specific metadata elements, whose metadata will you trust, identifying our initial 10000 resources, etc. Please also do not hesitate to let me know if you can see anything we can do down-under to create productive international alliances and provide better access to information for the global chemical community. ___________________________________________________________________ Alan Arnold, School of Chemistry and Director of Flexible Education, University College (UNSW) Australian Defence Force Academy, CANBERRA ACT 2600 Australia voice:+61 2 6268 8080 fax:+61 2 6268 8002 web: http://www.ch.adfa.oz.au/apa/ 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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New Version of ChemistryWeb Internet Resources
by TSKoh 21 Jul '98

21 Jul '98

I've upgraded the interface to ChemistryWeb Internet Resources and revise the content recently. The new URL address is: http://www.ssc.ntu.edu.sg:8000/chemweb/htmlj/ I'm in the midst of beta testing. The javascript version is fully operational. I'm halfway through creating the mainly text version. I really appreciate any comments and suggestions especially the viewing of the pages by different browsers. Thank you. Thiam-Seng --------- Thiam-Seng KOH (Dr.) Division of Chemistry National Institute of Education Nanyang Technological University 469 Bukit Timah Road Singapore 259756 Tel: (65) 4605175 Fax: (65) 4698952 Email: kohts(a)nievax.nie.ac.sg 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" using Netscape: Commercial only?
by Rzepa, Henry 20 Jul '98

20 Jul '98

A few days ago, I posted the results of a "What's related" search using Netscape 4.5 of the following conference http://www.ch.ic.ac.uk/ectoc/echet98/ with the following results ORGANIC CHEMISTRY RESOURCES WORLDWIDE 2.Exorga, Inc. - Consultants in Organic Chemistry and Molecular Modeling 3.Basic reactions in organic chemistry. 4.Photochemical Reactions of Organic Compounds 5.IUPAC Nomenclature 6.Chemexper Chemical Directory 7.Unofficial Combinatorial Chemistry Website 8.Farchan Laboratories 9.Orgo-Tek 10.ChemKey Search 11.(null) 12.Search on this Topic... Having thought a bit more about it, I now realise several noteworthy points about this list a) All the sites are either .com, or are "selling" something b) Since ECHET98 is the fourth in a series, one might reasonably expect at least one of the first three to be present in this list! None are. c) The IUPAC entry is NOT to the official IUPAC pages (which are a .org) but to a mirror .com site. The site run by Gerry Moss for example (a university site) does not appear. c) A colleague has pointed out that Netscape make their money by charging (large organisations?) a lot of money to enable them to appear in lists such as this. Another organisation (SmartNames) charges $40 to translate an (otherwise obscure?) Internet name to a "smart name". I am forced to the conclusion that the result of a "What's related" seach is going to be driven almost entirely by commerce, ie presumably in part by who has paid Netscape to appear in such a list. This in turn has most interesting implications. Note for example the lack of any university sites (except No 10, and that's to a commercial operation located at a University). Do universities have the "purchasing power" to ever appear on such a list? This Netscape "portal" appears that it is not going to give you the most scientifically relevant information, but will attempt to direct you towards commerce at all times. Hardly a neutral or impartial system. One, I would have thought, to be avoided if you are searching for scientific rather than commercial answers. Or to put it another way, it appears true that you very rarely get something for nothing! So who IS going to look after the interests of the chemical community? 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. 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 "Smart browsing" using Netscape
by Adam Hodgkin 16 Jul '98

16 Jul '98

Colleague It really is time there was a clear path forward for Chemical content on the web. How can this happen? I do not know, but I suspect that it is going to get a lot clearer in the next year or two. It has to or the www will fail in a kind of alphabet soup (see note in InfoWorld http://www.infoworld.com/cgi-bin/displayStory.pl?980715.wipatrick.htm) One encouraging sign is that the Search Engines are growing up and are trying to differentiate themselves by becoming Portals and also by trying to offer exceptional specialised search services. One of these Portals needs to do a deal with CAS or Reed Elsevier and start offering specialised chemistry content searching function. Which will it be? AltaVista, Excite, InfoSeek, Yahoo, etc? What technology will they use? XML, simple text searching with metatags or some database derived technology? Some portion of the chemical community ought to show them how to do it. Or could this service be provided by a specialist Chemistry Portal. In which case ChemWeb (the other one) looks like the best bet. Any views? Adam --- --- Adam Hodgkin | e-mail: adam(a)cherwell.com Chairman | Phone: +44 (0)1865 784810 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.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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