- chemweb - imperial.ac.uk

HOLA!!!!
by Adaris López 07 Oct '05

07 Oct '05

My name is Adaris . I am graduated of radiochemistry and master in analytical chemistry. I want to know the international event that will realize in the next years. I am from Cuba. I wait for your answer. Thanks in advance

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Report
by Wendy Warr 22 Sep '05

22 Sep '05

Chemical Information and Computation 2005, Number 1 Report on the 229th ACS National Meeting and Exposition Our report on the Spring 2005 National Meeting of the American Chemical Society, held in San Diego, went to press in August. Apart from the usual news section, covering about 70 companies, this 160-page report, with colour graphics, carries transcripts of all the presentations given in the award symposium honouring Peter Willett as winner of the COMP Award for Computers in Chemical and Pharmaceutical Research, plus transcripts of papers on the future of scientific publishing, safe exchange of chemical information, ADME, molecular mechanics and simulation, and drug discovery. The last of the 34 transcripts records the open meeting of the ACS committees on ACS Publications and CAS. The line up of speakers includes Steve Bachrach, Pieter Bolman, Bob Clark, Tim Clark, Jason Cole, Simon Coles (Southampton), John Delaney, René Deplanque, Jonathan Essex, Johnny Gasteiger, Steve Heller, Chris Lipinski, Larry Marnett, Brian Masek, Peter Murray-Rust, Anthony Nicholls, Marc Nicklaus, Tudor Oprea, Stephen Pickett, Henry Rzepa, Mark Seierstad, Bill Town, Andrea Twiss-Brooks, Eric Vangrevelinghe, Hugo Villar, Wendy Warr, Peter Willett, Ann Wolpert, and others. The full contents list is available at http://warr.com/morepubs.html. 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

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Workshop on Innovations in Scholarly Communications
by Wendy Warr 22 Sep '05

22 Sep '05

The notice below will be of interest to some subscribers to this list. 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 -----Original Message----- From: UKEIG: the UK eInformation Group [mailto:LIS-UKEIG@JISCMAIL.AC.UK] On Behalf Of Chris Awre Sent: 22 September 2005 11:10 To: LIS-UKEIG(a)JISCMAIL.AC.UK Subject: [LIS-UKEIG] OAI4 Workshop on Innovations in Scholarly Communications **With apologies for cross-posting** CERN Workshop on Innovations in Scholarly Communication - OAI4 20-22 October 2005 The 4th CERN Workshop on Open Access is still open for bookings. 155 firm bookings have already been made, and only a small number of vacant places now remain. The Programme can be found at http://oai4.web.cern.ch/OAI4/, where details on how to register are also available. The series of CERN Workshops has established itself as one of the premier meetings on Open Access in Europe. The 2005 Programme reflects a wide spectrum of interest in the Open Access movement, with papers and workshops to interest librarians, funders, academics and technical specialists. If you are interested in attending the Workshop, please book without delay to avoid disappointment. Please circulate this e-mail to colleagues in your organisation who may be interested in attending at CERN. Regards, Chris Awre *********************************** Chris Awre Integration Architect e-Services Integration Group Brynmor Jones Library University of Hull Cottingham Road Hull HU6 7LY t: 01482 46 5441 e: c.awre(a)hull.ac.uk ***********************************

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CINF-IO Informatics Scholarship for Scientific Excellence
by Wendy Warr 21 Sep '05

21 Sep '05

Posted on behalf of Guenter Grethe CINF-IO Informatics Scholarship for Scientific Excellence The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by IO Informatics is designed to reward graduate students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Five scholarships valued at $1,000 each will be given out at both the Spring and Fall ACS National Meetings in a given year for a total of $10,000/year. Additionally, the winners will receive an annual license, free-of-charge, of IO Informatic's software Sentinent for their academic institution. The grants have been awarded for the first time at the 230th National Meeting of ACS in Washington, DC. Applicants must be enrolled at a certified college or university. They have to present a poster at the respective National Meeting. Abstracts for the poster have to be submitted according to ACS rules on or before the deadline for electronic submission using OASYS (http://oasys.acs.org/oasys.htm) Point to the division (CINF) and select Poster session. Applications are accepted for the 2006 Spring ACS Meeting in Atlanta (March 26 - 30, 2006). The deadline for submission of an abstract is November 23, 2005. Additionally, a 2,000-word long abstract describing the work to be presented has to be sent in electronic form before February 1st, 2006, to the chair of the selection committee at ggrethe(a)comcast.net. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on content, presentation and relevance of the poster and will be announced at the meeting. The content shall reflect upon the student's work and describe research in the field of chemoinformatics and related sciences. Winning posters will be marked "Winner of the CINF-IO Informatics Scholarship for Scientific Excellence" at the poster session. Guenter Grethe Dr. Guenter Grethe 352 Channing Way Alameda, CA 94502-7409 Tel/Fax: 510-865-5152 Mobile: 510-333-7526 e-mail: ggrethe(a)comcast.net 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

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XHTML 1.0 -- onward, ho!
by Bob Hanson 16 Sep '05

16 Sep '05

Thanks very much for the XHTML tips of late. I would like to hear from others who are working on moving in this direction. Have you figured out some effective tricks for making the transition to XHTML Strict? How would one ever replace iframes? (I'm guessing their's an iframe-like object, but I don't know.) I've been pointed to two different parsers: http://validator.w3.org/ and http://schneegans.de/sv/ The first is far more friendly, by the way. See: http://validator.w3.org/check?uri=www.stolaf.edu/people/hansonr/jmol/docs vs. http://schneegans.de/sv/?url=http://www.stolaf.edu/people/hansonr/jmol/docs I should point out, though, that neither of these really checks the validation for this page. In this case the page is produced by browser-based JavaScript, so true validation requires validating the FINAL "rendered" HTML, not just the <script> tags. (This is mentioned in the XHTML specs.) In order to do this, I had to add additional flags in the code to deliver "source" rather than "actual" HTML. This was important - when I did that the first time (my first XHTML page ever) I was greeted by the message: "Failed validation, 3161 errors" I still don't know if there is a simple way to do this; you can't just "look at the source" anymore, even with Netscape, to see how your code is writing. If anyone knows a good solution to this -- validating browser-generated XHTML code, do let me know! Right now I write this "pseudo code" that looks something like this: s=s.replace(/\&lt/g,"&lt") .replace(/\<\/)/g,"</") .replace(/\</g,"<br /><") prior to writing, and then clip the screen, run a little batch DOS job that wraps it into an XHTML strict framework, and then upload it to w3c for validation. Is there a simpler way to do this? -Bob Hanson -- Robert M. Hanson, hansonr(a)stolaf.edu, 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:hansonr@stolaf.edu http://www.stolaf.edu/people/hansonr

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chemical web services
by Ferenc Csizmadia 01 Sep '05

01 Sep '05

Hi all, Can anyone direct me to SOAP-based web services that can input chemical structures in a common format (SMILES, CML, Molfile, etc.) and output calculated/predicted properties? Regards, Ferenc PS: Sorry for multiple postings --- Ferenc Csizmadia fcsiz(a)chemaxon.com

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http://live.watchmactv.com/: Podcasts => Videocasts
by Rzepa, Henry 14 Aug '05

14 Aug '05

http://live.watchmactv.com/ represents an interesting "fusion" cooking of Internet technologies. At the site, one can subscribe via RSS to videofeeds from the site, encoded in the new h.264 codec. A 2 minute download using broadband can produce 2-3 minutes of video at a very good image size (640 by 480). All this it is presumed will be "squirtable" into an iPod more or less automatically. It seems to have some interesting pedagogic potential. Combined with eg the CMLRSS way of entraining molecules in a feed, and the potential of including RDF information (RDF is a way of associating formal information about the purpose of a link) it seems the scope for re-inventing chemical publishing continues unabated. I suppose the ultimate incarnation is that one's iPod could contain in effect a personalised issue of a chemical journal, but enhanced with eg molecule coordinates and other chemical information, in association with other articles, audio, video, etc etc. And just to complete the full range of geekery, http://www.fingergear.com/ would allow all of this to be accessed only if the appropriate biometric identification is supplied! -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Green Chemistry Assistant Web Site
by Bob Hanson 06 Aug '05

06 Aug '05

Friends and Colleagues, I have the pleasure of announcing a new web site focused on Green Chemistry -- The St. Olaf College/EPA Green Chemistry Assistant http://fusion.stolaf.edu/gca The Green Chemistry Assistant is more than just a web site -- it is a fully functional web application. The overall objective of the site is to help you analyze chemical processes that you are interested in in terms of Green Chemistry. But you will find, if you explore a little, that the Green Chemistry Assistant is useful far beyond the typical confines of that field. With this web site you can: * do simple green chemistry calculations such as atom economy, theoretical yield, relative excess, experimental atom economy, process mass efficiency, and E-factor. * better organize the "prelaboratory" work associated with carrying out chemical reactions in the student or research laboratory, * graphically analyze a chemical process in terms of a variety of "greenness" measures, * consider the health and environmental hazards associated with a chemical process, * generate "Green Process Analysis Reports" that summarize a process in terms of inputs, outputs, and safety, and * save your work by sending the data and report to yourself or others via email. The Green Chemistry Assistant is primarily geared toward students: * General chemistry students can use this site to learn about basic green chemistry calculations such as atom economy, limiting reactant, theoretical yield, and percent yield. * Organic chemistry students can use this site to prepare "prelab" reports that summarize the number of moles and mass of reactants and products and take into account hazards. * Advanced chemistry students will find this site helpful for obtaining CAS registry numbers as well as physical and safety information relating to over 68,000 compounds from the U.S. Environmental Protection Agency Green Chemistry Database. While designed primarily for students, we hope that this web application will be an important contribution to both the Green Chemistry and the synthesis/pharmaceutical communities. Of course, we'll be interested in hearing from anyone for whom the site does not behave properly. We believe it is well tested on Windows machines using a variety of browsers; due to the complexity of browser/operating system combinations on Macintoshes, we are less confident that it will work entirely properly on those systems, but we encourage you to try it out and tell us what needs fixing. Enjoy! Bob Hanson -- Robert M. Hanson, hansonr(a)stolaf.edu, 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:hansonr@stolaf.edu http://www.stolaf.edu/people/hansonr

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JCIM issue on escience
by Wendy Warr 19 Jun '05

19 Jun '05

Later this year I will be editing a special issue of the Journal of Chemical Information and Modeling (formerly J. Chem. Inf. Comput. Sci.) with a focus on collaboratories, virtual laboratories, grid computing and other e-science issues. Since April, I have been contacting teams in this field with a view to getting them to submit a manuscript, with a deadline of September 1, 2005. I am hoping for a publication date early in 2006; papers would appear on the Web from the end of 2005. The Web manuscript submission page is at https://paragon.acs.org/paragon/index.jsp. It is important that authors state in their cover letter that the paper is for my focus issue on e-science. Manuscripts will be peer reviewed, of course, so I cannot promise publication: only contributions that meet the usual standards of JCIM will be accepted. I would appreciate any help you can give me in publicizing this. 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

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Fwd: Action Alert: Stop Efforts to Shutdown NIH's PubChem
by Rzepa, Henry 30 May '05

30 May '05

Excuse the cross posting, but the events described below are of seminal importance >from: >https://mx2.arl.org/Lists/SPARC-OAForum/Message/1939.html > > >Dear SPARC Member, > >I am writing to ask that you weigh in on an important issue now under discussion in Congress. > >The American Chemical Society (ACS) is calling on Congress to shut down the NIH's PubChem, a freely accessible database that connects chemical information with biomedical research and clinical information, organizing facts in numerous public databases into a unified whole. It is a critical component of NIH's Molecular Libraries Initiative, which in turn is a key element of the NIH strategic "roadmap" to speed new medical treatments and improve healthcare. > >ACS claims that PubChem competes with Chemical Abstracts Service (CAS). In reality, PubChem and the Chemical Abstracts Service databases are complementary, not duplicative. If ACS succeeds in eliminating PubMed, scientific progress will be throttled. > >ACS lobbying efforts are targeting: >* the Ohio delegation in Congress, >* Rep. Ralph Regula (OH), Chairman of the House Appropriations Subcommittee on Labor, Health and Human Services, Education, and Related Agencies, and >* Senator Arlen Specter (PA), Chairman of the Senate Appropriations Subcommittee on Labor, Health and Human Services, Education and Related Agencies. > >Please consider contacting Rep. Regula (tel. 202-225-3876, fax 202-225-3059> and Senator Specter (tel. 202-224-4254, fax 202-228-1229). If you live in Ohio, please also contact your U.S. Representative and Senators (Ohio delegation contact information is available at <http://www.senate.gov/> and <http://www.house.gov/>.) > >Thank you for your help! > >Rick Johnson >SPARC > >* * * KEY POINTS * * * > >PubChem Background > >* PubChem is a freely accessible database created by NIH in 2004 to provide information about small molecules. It is designed for use as a research tool and as a starting point that may lead to the development of new medications. The database connects chemical information with biomedical research and clinical information, organizing facts in numerous databases into a unified whole. > >* PubChem is a critical part of the Molecular Libraries initiative of the NIH Roadmap for Medical Research. It combines new data generated by NIH with data available from other public sources to create a powerful new research tool. It is part of the powerful family of integrated databases operated by the National Library of Medicine -- including GenBank, PubMed and a host of other resources that are utilized millions of times a day by scientists all over the world. The integration of these databases makes the whole much greater than the sum of its parts. > >Situation > >* ACS/CAS has expressed concern that PubChem is a threat to the financial survival of the Chemical Abstracts Service (CAS). PubChem provides free access to its database; CAS charges a fee for researchers to use its database. ACS has demanded that NIH shut down PubChem or substantially alter it so as not to compete with CAS. > >* NIH met with ACS officials to seek a solution that would resolve the society's concern. Since the initial meeting, there have been multiple communications between NIH and ACS leadership. ACS has effectively broken off discussions, leaving the issues unresolved. NIH is willing to continue discussions with ACS/CAS to benefit the scientific community and biomedical research. For example, NIH has said it is willing to link to the CAS database, essentially providing CAS with access to a new market. Medical researchers infrequently use CAS at this time. > >* Opposition to PubChem is from the ACS leadership. It is not clear if ACS members are aware of the issue and if they would agree with the ACS leadership's position. > >* NIH staff analysis shows that PubChem and CAS overlap relatively little in terms of content (see attached charts). PubChem and CAS differ widely in scope and resources: > >Budget -- CAS budget is reported to be $260 million; PubChem budget is $3 million. >Staffing -- CAS staff is reported to be 1,300; PubChem staff is 13. >Scope -- CAS has information on 25 million unique chemicals; PubChem has information on 850,000 unique chemicals (though this number is expected to grow). >Purpose -- CAS provides chemical, commercial and patent information to chemists; PubChem integrates medical information for medical researchers. >Overlap -- PubChem and CAS content are complementary resources aimed at different segments of the scientific community. > >Why PubChem is needed > >* It is a critical new tool that will speed the development of new treatments for America's most important health problems. >* It brings information about the biological activities of chemical substances to biomedical researchers on a broad scale. >* A fundamental NIH principle is that medical research information developed with public funds must be made freely and publicly available for the good of advancing medical research to cure disease. > -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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