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Call for participants: ChemAxon European UGM - Budapest, Hungary, May 17-18.
by Alex Allardyce 08 Apr '11

08 Apr '11

Excuse cross postings: We are announcing the program and calling for participants for ChemAxon's 7th European User Group Meeting (E-UGM) which will take place on May 17-18th in Budapest, Hungary. Highlights of the event: 1. Program is launched with presentations from industry users including; Abbott Laboratories, Astra Zeneca, Digital Science, Elsevier, Evotec, GlaxoSmithKline, Roche and Thomson Reuters. Full presentation titles below. Program: http://www.chemaxon.com/events/2011_eugm/#program 2. As usual the UGM is preceded by a training day with two different tracks: one for developers and the other for end users. 3. On the morning of the 19th of May we'll host a dedicated Markush Forum, sponsored by Thomson Reuters, discussing the development of our Markush IP tools. 4. Following the training day we will have our traditional one to one sessions from 5.30 pm at ChemAxon offices where you interact on your issues with ChemAxon developers and management. 5. Gala dinner for this year is quite opulent as we enjoy one of Budapest's most famous bath-houses, the Szechenyi Bath, do bring your swimwear! 6. We are using two linked hotels this year to help with late booking availability - chose your style! Useful links: Program: http://www.chemaxon.com/events/2011_eugm/#program More information: http://www.chemaxon.com/events/2011_eugm/ Registration: http://www.chemaxon.com/ugm.php Developer training details: http://www.chemaxon.com/events/2011_eugm/#training--developer End user training details: http://www.chemaxon.com/events/2011_eugm/#training--application-focus UGM archives: http://www.chemaxon.com/library/ugm-presentations/ Program: Presentation titles 01 The challenges facing the modern large pharma R&D manager, an exchange of views 02 Migrating to ChemAxon - the good, the bad & the ugly 03 A sneak peek at the ChemAxon Registration Service 04 Structure Checker - in silico surgery for molecules 05 Reliably converting names to structures with ChemAxon tools 06 Benchmarking ChemAxon's Name-to-Structure batch tool on patent text 07 Automated spelling correction to improve recall rates of name-to-structure tools for chemical text mining 08 Seeing structures and their properties online: chemicalize.org 09 JChem enters Formula 1 (and formula enters JChem) 10 Advanced searching chemical structures in patents 11 Patent Space Exploration: an application of Markush structure enumeration and search 12 Analyzing search hits with ChemAxon's Markush Enumeration tool 13 Perspiration, Inspiration, and Happenstance in Scientific Discoveries 14 DrugPredict: Online drug discovery service using polypharmacology-based interaction profiling 15 Blobs of hope and other flights of fancy 16 Computational toxicology - in silico assessment of the hERG channel inhibition potential for the early drug cardiotoxicity testing 17 JChem for SharePoint 18 Cheminformatics in SharePoint 19 Enterprise structure search in Sharepoint 20 Interactive structure standardization 21 Reactor - switching on the manual gear 22 Using Knime to provide desktop tools to chemists 23 Instant JChem - more ways to see your data 24 The chemistry Excel add-in game 25 SAR analysis in Excel using Helium and JChem 26 7 Years of ChemAxon at Evotec - choices and possibilities 27 Marvin 5.4 - A new generation of structure indexing at Elsevier 28 Utilizing Marvin in rich internet applications using Microsoft Silverlight Hope to see you here in May. ChemAxon -- *Alex Allardyce* Marketing Dir. *ChemAxon**Ltd*. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Tel: +361 453 0435 Fax: +361 4532659 mailto:aa@chemaxon.com

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Three reports
by Wendy Warr 02 Mar '11

02 Mar '11

Two free reports Report on JCIM 50th Anniversary Symposium and Celebrating the history of chemical information are freely accessible at http://www.warr.com. On a larger scale, the latest issue of our ACS report is going to press right now: Chemical Information and Computation 2010, Number Two 240th ACS National Meeting and Exposition: Boston, MA, August 22-26, 2010 Our 36th ACS report has transcripts of: * papers from the 50th anniversary symposium of the Journal of Chemical Information and Modeling * some of the papers in Tony Hopfinger's Herman Skolnik Award symposium on molecular simulation, modelling and QSAR * papers on data-intensive drug design * papers on recent progress in chemical structure representation. plus six months' worth of news from about 75 companies. Contents list and order form at http://www.warr.com. Half price to academia and government. Commercial organizations will find the multi-site license beneficial. 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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Events listing
by Wendy Warr 11 Jan '11

11 Jan '11

(Apologies for duplicate postings.) May we draw your attention to our 2011 events page at http://warr.com/meetings.html. If your favorite meeting is missing please use the form at http://warr.com/form.html to alert us. We advertise a fairly eclectic mix: broadly speaking, meetings that will interest computational chemists in drug discovery, research information specialists, and library and information professionals. 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<mailto:wendy@warr.com> http://www.warr.com<http://www.warr.com/>

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Multimedia and Visualization Innovations for Science
by Wendy Warr 05 Jan '11

05 Jan '11

Below is a description of a February 8 workshop in Redmond, WA, titled "Multimedia and Visualization Innovations for Science" that the DOE Office of Scientific and Technical Information (OSTI) has been heavily involved in organizing. At the workshop, OSTI will launch its latest product, ScienceCinema, a tool for multimedia search and retrieval in the sciences. Multimedia and Visualization Innovations for Science A One-Day Workshop Hosted Jointly By the International Council for Scientific and Technical Information And Microsoft Corporation Venue Microsoft Research, One Microsoft Way, Building 99, Redmond, WA 98502, USA Tuesday 8 February 2011 - 9.00am to 5.30pm (Check-in and breakfast from 8.15am) Why attend Multimedia and visualization tools and technology offer tremendous opportunity for accelerating scientific discovery. Where science was once limited to text and two-dimensional graphs and charts for communications purposes, multiple factors have contributed to a rise in the use and availability of multimedia and visualization as tools to augment and enhance more rapid uptake of science. This workshop will feature leading-edge innovations in science-oriented web multimedia, large-scale data exploration and visualization, speech and object recognition, image indexing and analysis, human/computer interaction and virtual environments, among other topics. Presentations will be made by technology, science, and information professionals across the broad spectrum of academia, government, business, and industry. Confirmed Speakers and Topics * Peter Tu, GE Global Research, "Video Analytics and its Application to Science and Technology." * Behrooz Chitsaz, Microsoft Research, and Lorrie Apple Johnson, U.S. Department of Energy Office of Scientific and Technical Information, "ScienceCinema: Multimedia Search and Retrieval in the Sciences." * Wilmot Li, Adobe Systems, "Explaining Complex 3D Objects with Interactive Illustrations." * Tim Smith, CERN (The European Organization for Nuclear Research), "Communications from the Particle Frontier." * Michael Ackerman, National Library of Medicine, "Interactive Multimedia Scientific Publishing." * Alexander Waibel, Carnegie Mellon University, "Speech Processing Applications in Quaero (European Multimedia Search Engine)." * Robert M. Hanson, St. Olaf College, "Delivering Interactive 3D Molecular Structure - The Jmol Solution." * Rafael Sidi, Elsevier, "The Impact of Visualization on Search and Discovery" * Curtis Wong, Microsoft Research, "Telling Stories in the Cloud" * Peter Fox, Tetherless World Constellation, Rensselaer Polytechnic Institute, "Semantics for Innovation in Visualization and Multimedia; Smarter Information Science." * Jennifer Lin, Microsoft Corporation, "PivotViewer: A Living Infographic for Your Data." * Mike Frame, U.S. Geological Survey, "Visualization and Indexing of Ecological/Biological Data." Registration: Because seats are limited, advance registration is required. The registration fee, which includes continental breakfast, lunch and refreshment breaks, is $250/295 (before/after 12 January) for ICSTI members, $300/395 (before/after 12 January) for non-members and $150/195 (before/after 12 January) for students. Members of ALPSP, NFAIS, GreyNet, and CENDI are eligible for the member rate for this event, as are members of ICSU's scientific unions and CODATA. Check the ICSTI website URL http://www.icsti.org/ for a registration form. For more information, contact the organizers Brian Hitson, US Department of Energy, hitsonb(a)osti.gov<mailto:hitsonb@osti.gov<mailto:hitsonb@osti.gov%3cmailto:hitsonb@osti.gov>>, Tony Llewellyn, ICSTI Executive Director, aj.llewellyn(a)btinternet.com<mailto:aj.llewellyn@btinternet.com<mailto:aj.llewellyn@btinternet.com%3cmailto:aj.llewellyn@btinternet.com>>, or the ICSTI Secretariat. ICSTI Secretariat: 33, rue de Naples - 75008 Paris - France Email : icsti(a)voila.fr<mailto:icsti@voila.fr<mailto:icsti@voila.fr%3cmailto:icsti@voila.fr>> Tel: +33 (0)6 14 65 16 57 <http://www.icsti.org/> 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<mailto:wendy@warr.com> http://www.warr.com<http://www.warr.com/>

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Multimedia and Visualization Innovations for Science
by Wendy Warr 15 Dec '10

15 Dec '10

RESERVE THE DATE - 8 FEBRUARY 2011 Multimedia and Visualization Innovations for Science A One-Day Workshop hosted by Microsoft venue Microsoft Research, One Microsoft Way, Building 99, Redmond, WA 98502, USA Tuesday 8 February 2011 - 9.00am to 5.30pm (Check-in and breakfast from 8.15am) why attend Multimedia and visualization tools and technology offer tremendous opportunity for accelerating scientific discovery. Where science was once limited to text and two-dimensional graphs and charts for communications purposes, multiple factors have contributed to a rise in the use and availability of multimedia and visualization as tools to augment and enhance more rapid uptake of science. This workshop will feature leading-edge innovations in science-oriented web multimedia, large-scale data exploration and visualization, speech and object recognition, image indexing and analysis, human/computer interaction and virtual environments, among other topics. Presentations will be made by technology, science, and information professionals across the broad spectrum of academia, government, business, and industry. confirmed Speakers and Topics * Peter Tu, GE Global Research, "Video Analytics and its Application to Science and Technology." * Behrooz Chitsaz, Microsoft Research, and Lorrie Apple Johnson, U.S. Department of Energy Office of Scientific and Technical Information, "ScienceCinema: Multimedia Search and Retrieval in the Sciences." * Wilmot Li, Adobe Systems, "Explaining Complex 3D Objects with Interactive Illustrations." * Tim Smith, CERN (The European Organization for Nuclear Research), "Communications from the Particle Frontier." * Michael Ackerman, National Library of Medicine, "Interactive Multimedia Scientific Publishing." * Alexander Waibel, Carnegie Mellon University, "Speech Processing Applications in Quaero (European Multimedia Search Engine)." * Robert M. Hanson, St. Olaf College, "Delivering Interactive 3D Molecular Structure - The Jmol Solution." * Rafael Sidi, Elsevier, "The Impact of Visualization on Search and Discovery" * Curtis Wong, Microsoft Research, "Telling Stories in the Cloud" * Peter Fox, Tetherless World Constellation, Rensselaer Polytechnic Institute, "Semantics for Innovation in Visualization and Multimedia; Smarter Information Science." * Jennifer Lin, Microsoft Corporation, "PivotViewer: A Living Infographic for Your Data." * Mike Frame, U.S. Geological Survey, "Visualization and Indexing of Ecological/Biological Data." REGISTRATION OPEN FROM NOVEMBER 2, 2010 Registration: Because seats are limited, advance registration is required. The registration fee, which includes continental breakfast, lunch and refreshment breaks, is $250/295 (before/after 5 January) for ICSTI members, $300/395 (before/after 5 January) for non-members and $150/195 (before/after 5 January) for students. Members of ALPSP, NFAIS, GreyNet, and CENDI are eligible for the member rate for this event, as are members of ICSU's scientific unions and CODATA. Check the ICSTI website URL http://www.icsti.org/ for updates, including additional speakers, final program content and registration form. *****************************************************************************************************************For more information, contact the organizers Brian Hitson, US Department of Energy, hitsonb(a)osti.gov<mailto:hitsonb@osti.gov>, 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)voila.fr<mailto:icsti@voila.fr> Tel: +33 (0)6 14 65 16 57

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JCIM 50th Anniversary Symposium
by Wendy Warr 16 Nov '10

16 Nov '10

Please excuse duplicate postings. A report on the ACS symposium celebrating the 50th Anniversary of J. Chem. Inf. Model. is available free on the Web at http://www.warr.com/JCIM50th2.pdf. The site has also been updated with other items - see http://www.warr.com. We will be reviving our events/meetings pages next. 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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Multimedia and Visualization Innovations for Scence
by Wendy Warr 05 Nov '10

05 Nov '10

Posted on behalf of ICSTI RESERVE THE DATE - 8 FEBRUARY 2011 Multimedia and Visualization Innovations for Science A One-Day Workshop hosted by Microsoft venue Microsoft Research, One Microsoft Way, Building 99, Redmond, WA 98502, USA Tuesday 8 February 2011 - 9.00am to 5.30pm (Check-in and breakfast from 8.15am) why attend Multimedia and visualization tools and technology offer tremendous opportunity for accelerating scientific discovery. Where science was once limited to text and two-dimensional graphs and charts for communications purposes, multiple factors have contributed to a rise in the use and availability of multimedia and visualization as tools to augment and enhance more rapid uptake of science. This workshop will feature leading-edge innovations in science-oriented web multimedia, large-scale data exploration and visualization, speech and object recognition, image indexing and analysis, human/computer interaction and virtual environments, among other topics. Presentations will be made by technology, science, and information professionals across the broad spectrum of academia, government, business, and industry. confirmed Speakers and Topics * Peter Tu, GE Global Research, "Video Analytics and its Application to Science and Technology." * Behrooz Chitsaz, Microsoft Research, and Lorrie Apple Johnson, U.S. Department of Energy Office of Scientific and Technical Information, "ScienceCinema: Multimedia Search and Retrieval in the Sciences." * Wilmot Li, Adobe Systems, "Explaining Complex 3D Objects with Interactive Illustrations." * Tim Smith, CERN (The European Organization for Nuclear Research), "Communications from the Particle Frontier." * Michael Ackerman, National Library of Medicine, "Interactive Multimedia Scientific Publishing." * Alexander Waibel, Carnegie Mellon University, "Speech Processing Applications in Quaero (European Multimedia Search Engine)." * Robert M. Hanson, St. Olaf College, "Delivering Interactive 3D Molecular Structure - The Jmol Solution." * Rafael Sidi, Elsevier, "The Impact of Visualization on Search and Discovery" * Curtis Wong, Microsoft Research, "Telling Stories in the Cloud" * Peter Fox, Tetherless World Constellation, Rensselaer Polytechnic Institute, "Semantics for Innovation in Visualization and Multimedia; Smarter Information Science." * Brett Brewer, Microsoft Live Labs. * Mike Frame, U.S. Geological Survey, "Visualization and Indexing of Ecological/Biological Data." REGISTRATION OPEN FROM NOVEMBER 2, 2010 Registration: Because seats are limited, advance registration is required. The registration fee, which includes continental breakfast, lunch and refreshment breaks, is $250/295 (before/after 5 January) for ICSTI members, $300/395 (before/after 5 January) for non-members and $150/195 (before/after 5 January) for students. Members of ALPSP, NFAIS, GreyNet, and CENDI are eligible for the member rate for this event, as are members of ICSU's scientific unions and CODATA. Check the ICSTI website URL http://www.icsti.org/ for updates, including additional speakers, final program content and registration form. *****************************************************************************************************************For more information, contact the organizers Brian Hitson, US Department of Energy, hitsonb(a)osti.gov<mailto:hitsonb@osti.gov>, 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)voila.fr<mailto:icsti@voila.fr> Tel: +33 (0)6 14 65 16 57 Wendy

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InChI Trust Documentation RFP
by Wendy Warr 16 Oct '10

16 Oct '10

(Posted on behalf of Steve Heller.) Under a contract from the InChI Trust (http://www.inchi-trust.org<http://www.inchi-trust.org/>), Digital Chemistry has prepared a detailed report and specifications for high level documentation of the InChI algorithm and related software. The Trust now wishes to contract to undertake this documentation effort. The following provides the background/summary for the work. Details and the full RFP can be obtained from Steve Heller. Individuals and organizations are encouraged to submit bids for this work,. The deadline for submission of bids is 12 November 2010. All responses to this RFP will be evaluated by a technical panel from the IUPAC Division VIII InChI subcommittee, the group responsible for the InChI standard. Steve Heller Project Director InChI Trust Summary: Though a substantial amount of documentation for users of InChIs and the InChI Software is available, detailed technical documentation of the algorithms used, and of the program code itself, is incomplete and somewhat scattered. Documentation is required both to rigorously describe the process of creating an InChI so that it can in principle be re-implemented de novo, and to describe the way in which that process is implemented in the existing InChI program code. To a considerable extent the current definition of the InChI-generation process is the existing program itself, and we therefore recommend that the appropriate sections of the existing Technical Manual be expanded to give full program documentation with references to the program code. Though the original code authors are likely to be able to produce appropriate documentation in the shortest time, an independent documentation writer is likely to be able to document it more comprehensively We estimate that an independent writer would need around 20 days for the task. Steve Heller Project Director InChI Trust steve(a)inchi-trust.org<mailto:steve@inchi-trust.org>

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ACS Copyright changes
by Wendy Warr 08 Oct '10

08 Oct '10

New ACS Journal Publishing Agreement expands author rights and clarifies responsibilities Media Contact Michael Bernstein 202-872-6042 m_bernstein(a)acs.org<mailto:m_bernstein@acs.org> Michael Woods 202-872-6293 m_woods(a)acs.org<mailto:m_woods@acs.org> WASHINGTON, Oct. 6, 2010 - The American Chemical Society's (ACS) Publications Division will begin rolling out a new publishing agreement in mid-October that expands author rights and clarifies author responsibilities. The ACS Journal Publishing Agreement (JPA) is a result of ACS' ongoing efforts to provide the best possible publishing experience for authors of ACS' suite of 38 peer-reviewed journals, including its flagship Journal of the American Chemical Society. That experience includes efficient online manuscript submission; rapid, responsible peer review and publication; global distribution; the award-winning ACS Web Editions Platform; and now, extended author use rights. The JPA replaces the previous ACS Copyright Status Form. It gives ACS authors a number of new rights regarding the use of their manuscripts and outlines certain behaviors that are expected of ACS authors. There are several key differences between the new JPA<http://pubs.acs.org/userimages/ContentEditor/1285231362937/jpa_user_guide.p…> and the old ACS Copyright Status Form: * The new agreement specifically addresses what authors can do with the different versions of their manuscript - e.g. use in theses and collections, teaching and training, conference presentations, sharing with colleagues, and posting on websites and repositories. The terms under which these uses can occur are clearly identified to prevent misunderstandings that could jeopardize final publication of a manuscript. * The new agreement clarifies that the transfer of copyright in Supporting Information is nonexclusive. Authors may use or authorize the use of Supporting Information in which they hold copyright for any purpose and in any format. * The new agreement extends key terms of use to an author's previously published work with ACS - as long as the same conditions of use are met. * Behaviors expected of ACS authors are more fully addressed throughout the agreement. The JPA shines a spotlight on two current ACS programs. The first is ACS AuthorChoice<http://pubs.acs.org/page/policy/authorchoice/index.html>, which provides authors or their funding agencies the opportunity to sponsor immediate, unrestricted online access to their final published article. The other is ACS Articles on Request<http://pubs.acs.org/page/policy/articlesonrequest/index.html>, which permits convenient, free distribution of journal article reprints online via author-directed links provided to the author when their article is published online. The JPA is a direct result of the extensive review and consultation process undertaken by a task force consisting of ACS journal authors, editors, librarians, governance members, and legal counsel who identified activities in which today's authors typically engage, or would like to engage. The JPA incorporates the task force's recommendations and more clearly communicates ACS Publications' policies regarding the use of submitted, accepted and published works. Wendy Dr. Wendy A. Warr Associate Editor, J. Chem. Inf. Model. 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./fax +44 (0)1477 533837 jcim(a)warr.com

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Report on Spring ACS Meeting
by Wendy Warr 07 Sep '10

07 Sep '10

Apologies for the delay in mailing copies of our latest report; one of the speakers has still not checked the transcript of his talk. Nevertheless, we intend to release the report this week. This report, the 35th issue in our ACS report series, has 40 transcripts of papers on visual analysis of chemical data, the future of scholarly communication, chemical entity extraction, biochemical pathways and retrobiosynthesis, and finding synthetic methods, plus six months' worth of news from about 70 companies. The two and a half day symposium on the future of scholarly communication is of particular interest to publishers and information professionals. You can choose to buy one electronic copy for yourself, or, at little more than the price of two copies, you can license the report for your whole organization. Contents list and order form at http://www.warr.com. Note that the report itself will not be on the Web. 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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