With the help of a bursary from the Chemical Structure Association Trust I was able to attend the 2000 Chemistry and the Internet conference (ChemInt2000). As in previous years, the conference was held at Georgetown University in Washington DC. My reasons for attending the conference were primarily to present a poster detailing my recent work on ChiMeraL - 'A Universal Approach to Web-based Chemistry using XML and CML' and to attend the markup language tutorial being run by Henry Rzepa (my supervisor) and Peter Murray-Rust (collaborator on ChiMeraL). I did however have other reasons for going. I wanted to take the opportunity to meet people I knew only by e-mail or just as names on homepages. In particular, I wished to discover how much (if at all) XML languages are being used or developed and for what purposes (outside the immediate focus of CML). I should probably also admit to a strong desire to explore Washington, since I had never visited the States before!
The integration of these techniques with existing XML compliant languages, such as XHTML and SVG (Scaleable Vector Graphics) results in the production of electronic documents with significant advantages of data retrieval and flexibility over existing HTML/plugin solutions. An example of this is demonstrated by my project report (www.xml-cml.org). This combined XHTML, CML, SVG and a simple document language. Transforming this with XSL stylesheets optimises the document for various outputs; online browsing in IE5, HTML files on a CD or an Acrobat file for printing (via Apache's FOP). The same process was also used to create slides and my poster.
Many of these concepts were mentioned in the Markup Language Tutorial held on Sunday, September 24th. This started with an overview of markup and XHTML by Henry Rzepa. Unsurprisingly, a show of hands revealed that almost everyone in the room was experienced at editing HTML, allowing 'well formed' and 'valid' documents to be explained quickly with references to HTML, Tex and SGML. The contrast between presentational markup (used in HTML) and meaningful markup (XML languages) is extremely important, and herein lie the main limitations of commonly used HTML and plugin solutions. These can be summarised as the requirements for human comprehension and the loss of information due to the use of gif pictures and legacy files. Henry followed this with a brief overview of XHTML ('HTML as XML'), describing how to convert existing HTML pages to XHTML using George Gkoutos's JChemDig and JChemTidy.
Miloslav Nic followed with a more in-depth look at the syntax of XML and how it can be displayed using stylesheets. CSS (Cascading Stylesheets) can be used with XML languages in the same way as with HTML, to define formatting and display details (e.g. colour or position on the screen). The more powerful XSL (Extensible Stylesheet Language) can be used to search, select and transform XML documents to any other XML language (e.g. CML to SVG). There are many useful tutorials on his site (www.zvon.org).
On Monday, Egon Willghagen demonstrated server side conversion of XML to existing MIME types. This is the alternative approach to that used in ChiMeraL and has the advantage of not requiring an XML parser on the client. Two other XML languages were also presented, SpecML from Christopher Steinbeck and techniques for marking up basis sets (used for ab initio calculations) both in CML 1.0 and a dedicated language, from Alk Dransfeld and Balazs Hajgato.
I found ChemInt2000 to be a fascinating experience and would like to thank the CSA Trust for making it possible for me to attend.
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About 50 young chemists, chemistry lecturers, sponsors and organisers assembled on September 29 in the splendid surroundings of the Scientific Societies Lecture Theatre, just off Regent Street in London, for the first prizewinners meeting of the ExemplarChem competition. ExemplarChem is an Internet exhibition of exemplary chemistry student project work. Initiated by Henry Rzepa of Imperial College, the competition was established by a working group consisting of Dr Henry Rzepa, Dr Karl Harrison of Oxford University, Dr Paul May of Bristol University, and Dr Sean McWhinnie, Professor Rodney Townsend and Dr Sarah Vallence, all of the Royal Society of Chemistry.
As a result of generous sponsorship (from Pfizer, GlaxoWellcome, Unilever, SmithKline Beecham, Organon, ISI and the CSA), the Royal Society of Chemistry was able to organise an excellent programme of seven speakers, as well as providing lunch and a wine reception. Henry Rzepa opened the proceedings by giving the background to the setting up of ExemplarChem. The idea was seeded in 1997 when course work had to be submitted by students at Imperial College, and one student had mounted his project on his father's website. After three months this student had received 100,000 hits and was receiving letters from throughout the world, several of which addressed the student as Professor! This was clearly recognition on a global scale for work done by this student. One of the achievements of the first year of the ExemplarChem competition is to enable many more students to be internationally recognised for the work they have undertaken.
In the opening lecture Peter Murray-Rust, talking on 'New Directions and Opportunities', pointed out that none of the students knew about ExemplarChem when they started on their project work. He gave inspiration to the students by quoting James Kendall who, in 1953, stated that very few significant discoveries in chemistry were not attributed to young people. Now, in the age of the Internet, regional and national boundaries are broken down, and it is an amazing time to be alive. Publication enables precise communication of what you have done, and, using the Internet, anyone can show what they have achieved. Furthermore, you can now publish in ways that were never possible on paper, e.g. integrating documents and data; collaborating with people in a different country.
Ryan Sheppard from ISI had some interesting statistics about publishing and the perceived value of papers. ISI produces the most comprehensive, multidisciplinary bibliographic database of research information, based on citations. Examining the number of cited references for a period of 5 years from 1995 to 1999, the US came top of the list, with the UK in 4th place, but Europe overall received a higher percentage than the US. At the moment, ISI only index citations, but there are plans in the future to capture website hits also.
The last lecture before lunch was given by David Alker, from Pfizer, who made it clear what large companies like Pfizer are looking for when they receive job applications from students. He sees that getting a job is a partnership between job applicant and the employer, not just Big Brother watching over you, and said that getting an ExemplarChem award would certainly be a very positive factor in your favour. Employers are looking for a breadth of technical knowledge and understanding, and the ability to use that knowledge to solve problems, as well as motivation and a positive attitude. However, learning should not stop after the students have received their degrees but should continue throughout their careers, as they face new challenges and more independence.
The afternoon, chaired by Rodney Townsend of the Royal Society of Chemistry, started with a talk by Peter Tallack from Weidenfield and Nicholson, publishers of popular science books. In spite of the fact that chemistry is everywhere around us, chemistry has a bad public image, and is usually portrayed in a negative way. There is an urgent need to publicise and market chemistry in such a way as to spark the imagination of the public. The best scientific books come from working scientists, who have more authority than the average journalist, but for a book to become popular, it must have a story and avoid jargon. It is possible that a revival of chemistry publishing could come via the Web.
Andrew Doran, of SmithKline Beecham, showed how robotics are used in Drug Discovery Chemistry to help increase productivity in the pharmaceutical industry, while maintaining quality. The use of combinatorial chemistry and high throughput screening enables initial leads to be turned into drug candidates in the shortest possible time. Every step in the integrated process of drug production is automated, but you cannot remove the human intervention necessary between each step.
At the Eindhoven University of Technology, web technology is used for chemistry teaching and learning. Jetse Reijenga described the 'Notebook Project' in the chemistry department, whereby all students have a notebook computer, so that they can access digital knowledge anywhere, anytime. The students have to pay half the cost of the PC, but can get a loan. Their lecture schedules, tests, internet resources, databases for experimental work and so on are all put up on the web. The students submit reports and collaborate via e-mail, discussion groups, webcam, and video-conferencing. In addition, a multidisciplinary group of students at Eindhoven are collaborating with students in Singapore. Students are picking up the new technology faster than their teachers and in many cases it is the students that are helping the teachers to cope!
Mike Hann, from GlaxoWellcome, concluded the afternoon's lectures by another lecture from the pharmaceutical industry, describing drug production in a virtual world. Mike likened the difficulty of synthesising a new drug to the problem of finding a needle in a haystack. The computer can handle far more molecules than can be made, but molecules must be put into a high dimensional chemical space to see where the active molecules appear. One of the major problems is that activity can occur as an island in a sea of inactivity, and minor changes in the structure of a molecule can have very significant effect on the activity of the molecule.
The highlight of the day was naturally the presentation of the prizes to the winners. A total of 19 departments registered interest in the competition and this resulted in 39 entries from 10 departments. The 8 winners were:
Michael Wright receiving his ExemplarChem prize
There are plans to make the ExemplarChem Competition an annual event, and to involve more universities and more students. Further information may be found on the Exemplar-Chem website at www.chem-soc.org/exemplarchem/home.htm.
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Around 35 people attended the one-day joint meeting of the Chemical Structure Association and the Royal Society of Chemistry Chemical Information Group on the topic 'Balancing the Budget - Cost Effectiveness of Provision of Chemical Information' at Burlington House on October 4th, 2000. The talks were organised so that views of different interest groups such as suppliers, intermediaries and users could be heard. The first speaker was Dr John Buckingham (Chapman & Hall/CRC Press). He posed some interesting questions, which he only answered in part, in an effort to get everyone thinking about the problems encountered in chemical information. The general tenor of his remarks was that we now have so much 'information' available that this in itself can be a problem. This information overload means that intermediaries are necessary, and he listed several searching questions which customers ought to be asking of their suppliers. He was followed by Dr Julian Hayward (Synopsys), who reviewed his company's products. He stressed the importance of selectivity in providing information, that a good user interface is essential, and that the better systems are those produced by chemists for chemists - features which are applicable to any product in this area.
The next two speakers were representing intermediaries, i.e. organisations that do not necessarily sell databases or other information, but offer access to them. Dave Fletcher gave the view of Daresbury Chemical Information Service, which is largely used by the academic community of the UK. The centralised provision of the service offers a considerable cost saving to the users (approximately 2500, cost ~ Ł100/user/year), and allows for support, training, and information about the databases held. Next, Carolyn Anderson (Swets/Blackwell) described how centralised purchasing of both paper and electronic journals, and specialised search access to a wide range of journals, can significantly reduce the cost of traditional library facilities by saving administrative work.
After lunch, a portal view was provided by Jan Kuras of Chemweb. This organisation attempts to provide a one-site service for all information requirements of chemists. It currently has over 200,000 registered users, who can access over 170 journals and 35 databases on-line, thus possibly replacing or duplicating the role of a learned society. It also offers a virtual shopping mall for books, software and laboratory equipment. Helen Schofield from UMIST followed, offering the perspective of the academic user. In academia, costs always present a major problem in the provision of information. Most chemists really need to use SciFinder, but few universities can afford it (only six in the UK have it). Electronic journal access is another problem, where most organisations (the RSC is a notable exception) charge 15% above the cost of the printed copy, but then offer free access to their other titles, which may be largely irrelevant to most chemists.
The final user viewpoint was from Sue Jackson (Roche). Pharmaceutical companies are huge users of chemical information, but even there, costs and use must be justified, despite the spending being on a large scale ($70M/year worldwide, including telecoms hardware, for 3,600 scientific staff on six sites). The guiding principles are:
Is it needed?
Can it be done?
Is it in line with objectives?
Interestingly, support and maintenance is about 80% of the resource cost. In the end, it is the use of the information which is important.
The meeting closed with an overview from Fytton Rowland (Loughborough University), who showed that he had been hard at work during the meeting by producing one-line key-point summaries of the seven talks, with additional comments and thoughts of his own, the key point being that chemistry is different! There is a huge industrial market for information, with lots of value in secondary services, whereas the academic market cannot afford as much as it would like, and is confronted by demands from its students who expect everything on the web!
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You are cordially invited to attend the CSA Dinner at 7.00 for 7.30 pm on Monday 4th December 2000 at
75 Sloane Street,
London SW1X 9SG
The cost is Ł35 to include one pre-dinner drink and 3-course dinner with wine, coffee and mince pies.
Please send a cheque for Ł35, payable to the CSA, with your name and address to
TN17 2EP, UK
Tel/fax: +44 (0)1580 852270 e-mail: email@example.com
Numbers are strictly limited, so early booking is advised. Overseas members may pay on the night, but must book in advance.
R.S.V.P. by 27th November
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The 2000 AGM will be held at 4.00 pm on Monday 4th December at the Linnaen Society, Burlington House, Piccadilly, London.
Janet Ash and Peter Nichols are eligible for re-election. Barbara Nicholson and Eleanor Ricketts wish to stand down. Gez Cross has completed 6 years on the Committee and is not eligible for re-election.
All of the Ordinary Members are eligible for re-election. Nominations for membership of the Committee should be sent to the Secretary, Barbara Nicholson, by 20th November 2000.
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Dr Steve Heller and Dr Bill Milne are the co-recipients of this year's Herman Skolnik Award from the American Chemical Society's Chemical Information Division. The Division established the Skolnik Award in 1976 to recognise outstanding contributions to and achievements in the theory and practice of chemical information science. The Award is named in honour of the first recipient, Herman Skolnik. Steve Heller is a long-term member of the CSA, and an authority on information technology in the areas of scientific numeric and factual databases, chemical information and electronic publishing. From 1984 until his recent retirement, he held the position of research scientist in the US Agricultural Research Service's Beltsville, MD laboratory. He was also a guest researcher at NIST in Gaithersburg, MD, and the informatics project leader for the Plant Genome Research Program from 1990 to 1997. He currently serves on the editorial board of the Internet Journal of Chemistry, and is the co-organiser of the Chemistry and the Internet Conference. He has recently taken up the post of principal strategic planner at MDL.
The winner of the CSA Trust award for 2000 was announced on 23rd October by Dr Bill Town, Chair of the CSA Trust, at a ceremony in Annecy. The award was won by Dr Zaneta Nikolovska-Coleska who receives Ł1000 to assist with her travel to Georgetown University Medical School in Washington DC, US. There she will be taking up a postdoctoral fellowship with Professor Wang. Dr Nikolovska-Coleska will be working on molecular modelling methods aimed at the de novo design of enzyme inhibitors.
Dr Nikolovska-Coleska obtained her Ph.D. in 1999 from the University 'SS. Ciryl and Methodius' in Skopje, Macedonia. She is currently an Assistant Professor at the Institute of Pharmaceutical Chemistry and Drug Design in Skopje. She worked for three years at the National Institute of Chemistry in Ljubljana, Slovenia, where her supervisor was Dr Tomaz Solmajer. Her dissertation, 'Rational Approach in Design, Synthesis and Biological Evaluation of New Flavonoid Analogs as p56 lck Tyrosine Kinase Inhibitors' was awarded a Certificate of Merit by the judges of the 1999 Amersham Pharmacia Biotech & Science Prize for Young Scientists.
Nominees for the 2001 Patterson-Crane Award are being sought by the Dayton and Columbus, Ohio Sections of the American Chemical Society. The biennial award, consisting of a $2000 honorarium and a personalised commendation, is given in honour of Austin M. Patterson and E. J. Crane, previous editors of Chemical Abstracts.
An international honour, the Patterson-Crane Award acknow-ledges outstanding contributions to the field of chemical information, including the design, development, production or management of chemical information systems or services; electronic access and retrieval of chemical information; critically evaluated data compilations; information technology applications in chemistry; or other significant chemical documentation.
The 2001 Patterson-Crane Award will be presented on 8 May 2001 at an awards dinner to be held in Dayton, Ohio.
Nominations for the award must be in writing and should discuss the nominee's contributions to the field and provide an evaluation of accomplishments. Materials supporting the nomination should include a biography and bibliography of publications and presentations relevant to the award. Seconding letters are required.
Nominations will be judged by a seven-member selection committee consisting of Dayton and Columbus Section members as well as the Chair of the American Chemical Society Division of Chemical Information.
One copy of the nomination materials should be submitted for receipt by 31 January 2001 to:
The Patterson-Crane Award Committee,
Melinda Greer, Chair,
University of Dayton Chemistry Department,
300 College Park, Dayton, OH 45469-2357
For more detailed information, see the ACS Dayton Section web page (www.udayton.edu/~acs) or contact Melinda Greer at (937) 229-2666.
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The Chemical Structure Association and the Molecular Graphics and Modelling Society announce the Second Joint Sheffield Conference on Chemoinformatics. This event follows the highly successful conference, entitled 'Computational Approaches to the Design and Analysis of Combinatorial Libraries', held in Sheffield in April 1998. There has been an excellent response to the Call for Papers, and the organisers expect a very high standard of papers covering the following topics:
The conference will consist of oral presentations, poster presentations and a commercial exhibition.
The venue for the conference is Stephenson Hall, Sheffield University's oldest and most attractive hall of residence. The Conference Dinner will be held on the evening of Wednesday 10th April at the magnificent Cutlers' Hall, Sheffield. A full programme will be available shortly, and will be posted on the conference website at cisrg.shef.ac.uk/shef2001/
For further information, contact:
The Department of Information Studies,
University of Sheffield,
Sheffield S10 2TN, UK
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The prestigious Queen's Award for Enterprise was presented to Tripos Receptor Research, Ltd., the primary chemical production facility for Tripos, Inc., in a ceremony at the facility's campus in Bude, Cornwall, UK. Her Majesty the Queen recognised the company for successive incremental increases in the export of chemical compounds to countries outside the UK from 1997 to 1999.
Lady Mary Holborow JP, Lord Lieutenant for Cornwall, acted on behalf of Her Majesty the Queen and presented the award in a specially arranged ceremony at the Tripos Receptor Research Laboratories on October 12, 2000.
Tripos Receptor Research designs and manufactures libraries of highly-focused chemical compounds for leading pharmaceutical and biotechnology companies to use in their quest for new drugs. Tripos' LeadQuestTM chemical compounds are featured in some of the world's largest pharmaceutical companies to identify promising drug candidates.
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AMD and Derwent Information announced at the en the 10 millionth patent record to be added to the Derwent World Patents Index(r) (Derwent WPI). According to the U.S. Patent and Trademark Office, patent applications have increased by more than 50% since 1992.
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The 27 millionth CAS Registry Number (297728-24-6) was assigned on October 20, 2000 to an inosine-5'-monophosphate dehydrogenase inhibitor. Inosine-5'-monophosphate dehydrogenase (IMPDH) is an enzyme involved in the de novo synthesis of guanine nucleotides.
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This new release from MSI offers improved 3D information management through enhanced conformational model generation, the ability to handle databases of arbitrary size and the introduction of partial query handling. Catalyst uses conformational model generation to explore the possible active shape of drug molecules. The resulting pharmacophore description can then be used to mine leads from 3D databases and to predict activities for novel or proposed compounds. More information is available at www.msi.com.
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CAS and MicroPatent will offer patent document delivery directly through the ChemPort Connection. CAS search services include SciFinder and SciFinder Scholar, STN Express, STN Easy and STN on the Web. The ChemPort Connection is included with these services to provide links to full-text chemical literature and patents. MicroPatent documents will be accessible through links in ChemPort. MicroPatent's Global TOPS (Total On-demand Patent Solution) subscribers can now download full-text patents in addition to full-text documents through the ChemPort Connection, including articles from over 1,900 journals while using any of the CAS search services. Other customers will be able to access MicroPatent documents through a separate link for a small additional charge.
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CA Lexicon on STN is a powerful thesaurus tool for guiding searchers through the intricacies of scientific vocabulary. CA Lexicon employs intelligence that lets users apply the expertise of vocabulary experts. The principal features are a Concept/General Subject vocabulary; a Taxonomic vocabulary for biological genus and species terms; and Compound classes, including the chemical substances most frequently indexed by CAS, common synonyms, relationships, and more. CA Lexicon is due for release in December. The CAS website is at www.cas.org and more information on ChemPort is available at www.chemport.org.
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Users of the Derwent World Drug Alerts (Derwent WDA) database on Derwent Discovery can now to link directly from the patent abstract to images of the full patent document via the MicroPatent website. In addition, customers will be able to display the whole document at the click of a button, and from there, download, print or distribute the PDF formatted document. Derwent WDA covers patents from the World Intellectual Property Organisation (WIPO) and USPTO, as well as from the patent offices of the EPO, Britain, France, Germany and Japan; under the agreement links to all these documents will be available within days of publication. Useful websites are www.derwent-discovery.com and www.micropat.com.
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ChemOffice Ultra 2001 includes ChemDraw Ultra 6.0, Chem3D Ultra 6.0, ChemFinder Ultra 6.0, the E-Lab Notebook and ChemFinder for Word, CombiChem and ChemFinder for Excel. ChemDraw Ultra 6.0 offers multi-page documents, stereochemistry display and recognition, structure-spectrum correlations in ChemNMR, right-button context menus, and interactive structure-checking. ChemFinder 6.0 recognises and classifies structure references in Microsoft Word. The E-Lab Notebook stores collections of pages created by ChemDraw, Microsoft Excel and Microsoft Word, searchable by text, structure and substructure. The ChemACX database features over 200 supplier catalogues and hundreds of thousands of chemical products. ChemINDEX now includes the National Cancer Institute database of over 200,000 molecules, with anti-HIV and anti-cancer assay data, as well as the complete contents of the ChemFinder.Com database. As in previous versions of ChemOffice, the ChemDraw and Chem3DPlugins turn the chemist's desktop into a structure-intelligent network client. ChemDraw is also available as a Java applet. For more information, e-mail: firstname.lastname@example.org
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The newest version of Current Drugs' pharmaceutical intelligence database IDdb3 tracks drugs in development from the first patent publication through to eventual launch or discontinuation. IDdb3 is updated daily, making it one of the fastest information providers on pharmaceuticals in development. The database has details on over 16,000 investigational drugs, 30,000 therapeutic patents and 44,000 chemical structures, and it also provides users with additional intelligence, such as the market view of the commercial and scientific significance of emerging drugs, expert comment on and evaluation of scientific, commercial and forecast data. The website is at: www.current-drugs.com/news/.
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Kurt L. Loening died aged 76 on July 12, 2000, in Columbus, Ohio. For 39 years he had worked at CAS in Columbus, retiring in 1990 as Director of Nomenclature, Chemical Abstracts.
Kurt was born in Berlin, Germany, in 1924. He came to the US as a young man, and graduated from high school in New York City in 1942, receiving his B.Sc. degree in chemistry from Ohio State University in 1944. After a tour of duty with the US Army Chemical Warfare Service, he completed a PhD in physical chemistry at Ohio in 1951 and joined CAS.
There he worked with E. J. Crane, Austin M. Patterson, Leonard T. Capell and W. Russell Stemen. In 1964, Kurt succeeded Capell as Director of Nomenclature at CAS. His early contribution to the development and application of chemical nomenclature to the CA Volume and Collective Indexes was a thorough documentation of CAS naming and indexing policies, of which the present Appendix IV of the CA Index Guide is a direct descendant.
He was chairman of the ACS Committee on Nomenclature for 25 years. He participated in the work of all of the Nomenclature Commissions of IUPAC. He was chairman of the IUPAC Commission on Macromolecular Nomenclature from1968 to 1977, and guided the IUPAC Interdivisional Committee on Nomenclature and Symbols (IDCNS) from 1976-1987.
In 1987, he received the prestigious Patterson-Crane Award of the ACS Columbus and Dayton Local Sections for work in the documentation of chemistry in the development of chemical nomenclature and terminology. In 1990 he received the ACS Executive Director's Award for his years of distinguished service to the ACS. He was elected a Fellow of the American Association for the Advancement of Science (AAAS).
He gave a keynote address at the Chemical Nomenclature meeting in London, March 24-26, 1981, which the CSA, among others, was involved in organising with the Laboratory of the Government Chemist.
On retirement he was co-founder of a terminology consulting firm, Topterm. He was a co-founder and a co-editor of the journal TERMINOLOGY. Kurt was also Senior Research Associate in the Department of Chemistry of the Ohio State University, at which the Kurt Loening Endowment Fund in Chemical Nomenclature and Chemical Information has been established.
Thanks to W. Val Metanomski, CINF Archivist/Historian, from whose obituary of Kurt Loening this has been adapted.
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We are delighted to welcome six new UK members to the CSA.
Richard Compton is the business development director for life sciences at Molecular Simulations Ltd (MSI) in Cambridge.
Alison Eyles is the managing editor for Chemistry, at Current Drugs in London.
Diane Lightowler is working for Merck Sharp & Dohme at their Neuroscience Research Centre in Harlow, Essex.
Dr Anthony Williams is pharmaceutical information manager for De Novo Pharmaceuticals in Cambridge.
Dr Gillian Tozer-Hotchkiss works for the Derwent Reaction Service in London, and is assistant editor of Thielheimer's Synthetic Methods of Organic Chemistry, published by Karger.
John Wickenden has worked for Eli Lilly at Windlesham, Surrey, for over 30 years in the Library and Information department.
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David Ricketts is now vice president, business development, at Inpharmatica, a leading innovator in the application of structural bioinformatcs in pharmaceutical research. He was previously with Cambridge Discovery Chemistry as vice president business development. He brings substantial international experience in informatics and multi-disciplinary discovery collaborations, having worked in drug design at both Glaxo and British Biotechnology before becoming one of the original successful team at Oxford Molecular. He has spent three years working in the US west coast biotechnology industry, and has extensive experience of establishing and managing collaborations, with particular success in Japan.
Roger Thornely has sadly died. We send our condolences to his wife Theresa.
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