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Micosoft and scholarly communication
by Wendy Warr 21 Oct '09

21 Oct '09

This news item may interest subscribers. Apologies for duplicate postings. Dear ICSTI Member Below is a message from Lee Dirks of Microsoft, who of course are ICSTI members, which highlights the release by Microsoft Research of a new collection of essays ‘The Fourth Paradigm: Data-Intensive Scientific Discovery’ edited by Tony Hey et al. This is a timely review by top drawer contributors of a subject area that builds on the vision of computer scientist Jim Gray and will resonate with the interests of many ICSTI members. Note that since the book is published under a creative commons licence articles are free to download. Make sure that you also click on the interview with Tony Hey in which he refers to Professor Carol Goble who was the winner of the first Jim Gray eScience Award, and who will be presenting at the ICSTI Summer Conference in Helsinki in June 2010. Best regards Tony Llewellyn Executive Director, ICSTI ********************************************************************************************************************************* Our group in MSR External Research published this work and it was announced/released yesterday. There is a special section on Scholarly Communication. [And it is published under a creative commons license for free download of any article so it is definitely an open success publication!] We will also have a print-on-demand book version and versions for the Kindle and Sony eBook Reader ... Tony Hey, Stewart Tansley, and Kristin Tolle, eds., The Fourth Paradigm: Data-Intensive Scientific Discovery, published by Microsoft Research, October 16, 2009. See especially the section "Scholarly Communication": http://research.microsoft.com/en-us/collaboration/fourthparadigm/ Lee Dirks, Introduction Clifford Lynch, Jim Gray's fourth paradigm and the construction of the scientific record Paul Ginsparg, Text in a data-centric world Herbert Van de Sompel and Carl Lagoze, All aboard: toward a machine-friendly scholarly communication system Anne Fitzgerald, Brian Fitzgerald, and Kylie Pappalardo, The future of data policy John Wilbanks, I have seen the paradigm shift, and it is us Timo Hannay, From web 2.0 to the global database. Also see this interview with Tony Hey: http://research.microsoft.com/en-us/news/features/fourthparadigm-101609.aspx Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England +44 (0)1477 533837 wendy(a)warr.com<mailto:wendy@warr.com> http://www.warr.com<http://www.warr.com/>

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ICSTI Workshop
by Wendy Warr 12 Oct '09

12 Oct '09

RESERVE THE DATE - 8 FEBRUARY 2010 Interactive Publications and the Record of Science A One-Day ICSTI Workshop Universite Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France. Monday 8 February 2010 - 9.00am to 5.30pm (Check-in and breakfast from 8.15am) Why attend The Web is by nature an interactive environment, yet online journals are mostly static, consistent with their traditional role as a never-changing scholarly record. However, this traditional role is increasingly challenged as browser technologies leap forward, dynamic visualization and presentation tools proliferate, and primary data are linked to research articles. In an important and timely event arranged by ICSTI (the International Council for Scientific and Technical Information), publishers, publishing service providers, librarians, editors and authors will meet in Paris for a full one-day workshop to survey the most exciting and challenging of the new developments and to begin to identify the necessary infrastructure for including interactive content within the record of science. Session topics are: (I) Interactive visualizations; (II) Adding value with enriched content and semantic links; (III) The archival problem and infrastructure for solutions; (IV) W(h)ither journals? Speakers include representatives from the Nature Publishing Group, National Library of Medicine, Royal Society of Chemistry, International Union of Crystallography, OECD, Concept Web Alliance, SciVee, British Library, CrossRef and Cell Press. REGISTRATION WILL OPEN OCTOBER 23, 2009 Programme and Registration Because seats are limited, advance registration is required. The registration fee, which includes continental breakfast, lunch and refreshment breaks, is 150 Euros for ICSTI members, 200 Euros for non-members and 80 Euros for students. Members of ALPSP, IATUL, ISSN, NFAIS and STM, which are all associate member of ICSTI are eligible for the member rate for this event, as are members of ICSU's scientific unions, CODATA, and IFLA, as well as CENDI with whom ICSTI has a new partnership relationship. Check the ICSTI Events URL http://www.icsti.org/events.php for updates, the final programme/speaker details and registration form. ______________________________________________________________________ For more information, contact the organizers Brian McMahon, Research and Development office, IUCr, bm(a)iucr.org<mailto:bm@iucr.org>, Tony Llewellyn, ICSTI Executive Director, aj.llewellyn(a)btinternet.com<mailto:aj.llewellyn@btinternet.com>, or the ICSTI Secretariat. ICSTI Secretariat: 33, rue de Naples - 75008 Paris, France Email : icsti(a)icsti.org<mailto:icsti@icsti.org> & icsti(a)voila.fr<mailto:icsti@voila.fr> Tel : +33 (0)1 45 25 65 92 Cell: +33 (0)6 14 65 16 57

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Reaxys Mini-symposium United Kingdom
by Wendy Warr 09 Oct '09

09 Oct '09

Sorry for the repetition. I forgot to send details of how to register: To register : http://mail.elsevier-alerts.com/go.asp?/mL1HJJA/bECU001 Reaxys Mini-symposium United Kingdom "WORKFLOW TOOLS IN CHEMICAL RESEARCH" Thursday 22nd October 2009, British Library Conference Centre 9.30 - 10.00 Registration 10.00 - 10.10 Welcome and Brief overview of Chemical Research Output in United Kingdom Farhana Hoque, Sr. Account Manager, Elsevier 10.10 - 10.30 Current Trends in Synthetic Chemistry: Overview of the Research Landscape Prof. Elizabeth Hounsell School of Biological and Chemical Sciences Birkbeck University of London 10.30 - 11.00 Use of Reaxys in synthetic chemistry research Dr. Jonathan Goodman, Reader in Chemistry, University of Cambridge, Department of Chemistry 11.00 - 11.15 Break 11.15 - 12.00 Innovations in Chemistry: An Elsevier Perspective Karel Nederveen, Publishing Director Chemistry, Elsevier 12.00 - 12.45 Maximising the Synthetic Chemistry Research Workflow: Reaxys David Evans, Director R&D Reaxys, Elsevier 12.45 - 13.15 30min Moderated Question & Answers and Closing Remarks Karel Nederveen 13.15 Lunch

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Reaxys mini-symposium
by Wendy Warr 09 Oct '09

09 Oct '09

I have been asked by Elsevier to post this invitation. Reaxys Mini-symposium United Kingdom "WORKFLOW TOOLS IN CHEMICAL RESEARCH" Thursday 22nd October 2009, British Library Conference Centre 9.30 - 10.00 Registration 10.00 - 10.10 Welcome and Brief overview of Chemical Research Output in United Kingdom Farhana Hoque, Sr. Account Manager, Elsevier 10.10 - 10.30 Current Trends in Synthetic Chemistry: Overview of the Research Landscape Prof. Elizabeth Hounsell School of Biological and Chemical Sciences Birkbeck University of London 10.30 - 11.00 Use of Reaxys in synthetic chemistry research Dr. Jonathan Goodman, Reader in Chemistry, University of Cambridge, Department of Chemistry 11.00 - 11.15 Break 11.15 - 12.00 Innovations in Chemistry: An Elsevier Perspective Karel Nederveen, Publishing Director Chemistry, Elsevier 12.00 - 12.45 Maximising the Synthetic Chemistry Research Workflow: Reaxys David Evans, Director R&D Reaxys, Elsevier 12.45 - 13.15 30min Moderated Question & Answers and Closing Remarks Karel Nederveen 13.15 Lunch Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./Fax +44 (0)1477 533837 <mailto:wendy@warr.com> wendy(a)warr.com <http://www.warr.com/> http://www.warr.com

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Report on ACS Meeting in Salt Lake City
by Wendy Anne Warr 06 Aug '09

06 Aug '09

Chemical Information and Computation 2009, Number One; ACS National Meeting and Exposition, Salt Lake City, UT, March, 2009 Now going to press. Visit http://www.warr.com/ Text mining, cheminformatics, library design, fragment-based drug design, drug discovery, virtual screening, QSAR, pharmacophore elucidation, use of InChI, and more; plus news from more than 70 companies. New format, more detail, more graphics, more readable layout, greater value... Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./fax +44 (0)1477 533837 <mailto:wendy@warr.com> wendy(a)warr.com <http://www.warr.com> http://www.warr.com

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InChI Trust
by Wendy Warr 22 Jul '09

22 Jul '09

DISTRIBUTED BY NATURE PUBLISHING GROUP ON BEHALF OF THE INCHI TRUST 21 July 2009 Contact: Grace Baynes Corporate Public Relations, Nature Publishing Group T:+44 (0)20 7014 4063 g.baynes(a)nature.com The InChI Trust, a not-for-profit organisation to expand and develop the InChI Open Source chemical structure representation algorithm, is formally launched this week. Originally developed by the International Union of Pure and Applied Chemistry (IUPAC), the IUPAC International Chemical Identifier (InChI) is an alpha-numeric character string generated by an algorithm. The InChI was developed as a new, non-proprietary, international standard to represent chemical structures. The Trust aims to develop and improve on the current InChI standard, further enabling the interlinking of chemistry and chemical structures on the web. The connection with IUPAC is maintained through IUPAC's InChI Subcommittee. The InChI algorithm turns chemical structures into machine-readable strings of information. InChIs are unique to the compound they describe and can encode absolute stereochemistry Machine-readable, the InChI allows chemistry and chemical structures to be navigable and discoverable. A simple analogy is that InChI is the bar-code for chemistry and chemical structures. The InChI format and algorithm are non-proprietary and the software is open source, with ongoing development done by the community. "The goal of the InChI Trust", says Project Director Stephen Heller "is to continue to develop the InChI and InChIKey, the condensed machine-searchable version, as a tool to enable widescale linking of chemical information." The InChI Trust was formally incorporated in the UK in May 2009, and now has 6 charter members: The Royal Society of Chemistry, Nature Publishing Group, FIZ-Chemie Berlin, Symyx Technologies, Taylor & Francis and OpenEye. Further organizations and publishers are in the process of joining the InChI Trust. "Nature Publishing Group is delighted to be a charter member of the InChI Trust", says Jason Wilde, Publisher for the Physical Sciences, Nature Publishing Group."We view the ongoing maintenance of the InChI algorithm, and the resulting adoption of InChI, as important for the development of chemistry communication. The interlinking that the InChI offers between journal content and databases ensures that chemistry is the first truly web-enabled scientific discipline." "The InChI has already gained a wide user base," says Richard Kidd, Informatics Manager at the Royal Society of Chemistry, "and the Trust will ensure continuing development and support for this key standard, helping to link together chemical resources across the internet. The RSC is proud to support the InChI Trust." Since the introduction of the InChI in 2005, there has been widespread take-up of InChI standards by public databases and journals. Today, there are more than 100 million InChIs in scientific literature and products. To date, numerous databases, journals, and chemical structure drawing programs have incorporated the InChI algorithm. These include the NIST WebBook and mass spectral databases, the NIH/NCBI PubChem database, the NIH/NCI database, the EBI chemistry database, ChemSpider, Symyx Draw and many others. The initiative serves chemists, publishers, chemical software companies, chemical structure drawing vendors, librarians, and intermediaries by creating an international standard to represent defined chemical structures. This provides a consistent, credible and compatible way for databases of chemical structures to be linked together for the benefit of users of chemical information around the world. -ENDS- For further information, please contact: Project Director, Dr. Stephen Heller at steve(a)inchi-trust.org Background notes: The InChI project was initially undertaken by IUPAC with the cooperation of National Institute for Standards and Technology (NIST). In 2009, a standard version of InChI and the InChIKey were released. Members of the InChI Trust will pay annual dues to support the continued development of InChI, and maintainance of the InChI algorithm. This income will be used exclusively for InChI algorithm development, maintenance, outreach, and educational activities associated with the project Details of the up-take by many chemical database providers, software developers, and educational activities associated with the project Details of the up-take by many chemical database providers, software developers, and journal publishers are available at www.iupac.org/inchi/adopters.html Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England +44 (0)1477 533837 <mailto:wendy@warr.com> wendy(a)warr.com <http://www.warr.com/> http://www.warr.com

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ChemAxon launches Marvin and JChem version 5.2: Web Services, native .NET API, homology groups, 3D Alignment and Structural frameworks.
by aa 15 Apr '09

15 Apr '09

Please excuse cross postings. ChemAxon launches Marvin and JChem version 5.2; Web Services, native .NET API, homology groups, 3D Alignment and Structural frameworks. BUDAPEST, Hungary, April 15, 2009 -- ChemAxon, a software solutions provider for cheminformatics today announced the launch of version 5.2 of their cheminformatics toolkits, Marvin & JChem. The release sees many new functionalities added, new integration options and improvements in search performance. Marvin & JChem is a software suite of application programming interfaces (API’s) and graphic user interfaces (GUI’s) used by life science informatics architects and developers to build chemically aware, platform independent and web ready enterprise informatics systems. Marvin includes structure and reaction editing, visualization and structure based property prediction; JChem includes structure management and search, library enumeration and library profiling. For structure based calculation new Calculator Plugins are added: Flexible 3D Alignment Plugin builds on our 3D expertise allowing multiple molecules to be aligned to each other and the Structural frameworks Plugin provides clustering capabilities, using various ring models and Bemis-Murcko. All Calculator Plugins are integrated and available throughout the JChem suite. For developers we launch new integration interfaces: JChem Web Services provide SOAP access to JChem, extending the environments that can integrate JChem (C#, .NET, Javascript, Perl, Python, etc). A new native .NET API is made available for direct (bridgeless) access to the JChem API from .NET. In the patent space we introduce new features for drawing and searching Markush structures, including support for homology groups and repeating units. Our Markush project works toward robust support for Chemical IP, including identification of overlap of Markush libraries without enumeration. Developments of core search features include a new chemical hashed fingerprint to improve search performance and added support for polymer storage and search. To freely evaluate ChemAxon's Marvin, JChem and Instant JChem or access our free academic package, please visit our website. Alex Alex Allardyce Marketing Dir. ChemAxon Ltd. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce

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Program announcement and call for participants: ChemAxon's European UGM: 3-4 June, Budapest, Hungary
by aa 15 Apr '09

15 Apr '09

Please excuse cross postings. The program is now available for ChemAxon's 2009 European User Group Meeting which will be held on Wednesday and Thursday, June 3-4 at the Danubius Health Spa Resort on Margit Island in Budapest, Hungary. The meeting will preceded by a training day on June 2nd. Program: http://www.chemaxon.com/UGM/09/program.html The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development. Preceding the meeting will be an end user and developer training day on June 2nd, for beginner to advanced level users to become familiar with ChemAxon's toolkits and end user applications. As usual, we will have extensive social events for attendees to mix and enjoy. To find out more about the meeting and training day, register or submit a poster abstract (open until May 22nd) and view the program, please visit: http://www.chemaxon.com/UGM/09/ , for training day topics see: http://www.chemaxon.com/training/UGM0609.html . We look forward to welcoming you here. Alex *Confirmed presenters:* Ian Berry, Evotec Michael Dippolito, DeltaSoft Dimitar Hristozov, Eli Lilly László Molnár, Gedeon Richter Andy Mott, Contur Sorel Muresan, AstraZeneca Catherine Reisser, Evotec Josef Scheiber, Novartis Pharma Gert Thijs, Silicos Lutz Weber, OntoChem ChemAxon Partners participants (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html -- *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce

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Program announced for ICIC Meeting in October
by Wendy Warr 07 Apr '09

07 Apr '09

The 2009 ICIC meeting will take place in Sitges (Barcelona), 18-21 October 2009 >From the Web site http://www.infonortics.eu/chemical/index.html : "Habitual attendees tell us that ours is the meeting to which they go to spot the trends, as well as the meeting that provides unparalleled opportunities for networking. Trends and networking will be high on the Sitges agenda in October 2009. The ICIC meeting covers trends in the field of scientific and professional information with an impressive line-up of significant figures in the information world. Among the topics that will be covered and discussed by the 22+ speakers are: Tools for Competitive Intelligence (e.g., mining tools, visualisation, analysis tools, etc) Challenges for the information community over the next five years Changes in the information environment for patents, innovation and intellectual property Trends in Search Engines and Information Retrieval Case Studies in Data and Content Integration" Full program is at http://www.infonortics.eu/chemical/ch09/09chempro.html Wendy Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England wendy(a)warr.com http://www.warr.com

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ACS report
by Wendy Warr 11 Mar '09

11 Mar '09

Chemical Information and Computation 2008, Number Two 236th ACS National Meeting and Exposition Philadelphia, PA, August 17-21, 2008 The contents list is on the Web at http://www.warr.com/morepubs.html. A 12-page extract is available free at http://www.warr.com/phillyacs08.pdf. The report includes: 1. news from more than 70 companies (including some not exhibiting) 2. condensed press releases for the last six months of 2008 3. accurate transcripts of presentations, complete with color figures and literature references, with the following themes: Herman Skolnik Award Symposium, awardee Gerry Maggiora data mining and text mining approaches to drug discovery ADME informatics, converting raw data to useful knowledge for drug discovery predictive properties a retrosynthesis search engine working with IUPAC names open meetings of the ACS committees on ACS Publications and CAS Contact me by email for further details. 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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