Copyright©2007 Antony Williams
Isaac Newton famously remarked “If I have seen a little further it is by standing on the shoulders of Giants.” We acknowledge that the guidance and input of an insightful and passionate advisory committee offers us the opportunity to create an offering via the ChemSpider website with the potential to cater to various type of chemists. Our advisory committee has gathered together a wide range of skill sets in chemistry including synthetic chemistry, pharmaceutical sciences and analytical sciences. They have been segregated into groups based on specific areas of focus. ChemSpider will have many types of users and we will be taking guidance from entire group but garnering their input based on their specific areas of interest. Below we introduce our present advisors. More will be added in the future as we expand the scope of the ChemSpider project.
Mike Lee has pioneered the application of new analytical methods in academic and industrial settings. He is passionate about the development of novel techniques that can be applied to medically relevant problems. During his career at Bristol-Myers Squibb, he led interdisciplinary teams that contributed to the Food & Drug Administration approval of Buspar, and Serzone, and the accelerated development and approval of Taxol. As president of Milestone Development Services, Mike has actively served all areas of analytical chemistry with consulting, workshops, symposia, and books. Mike has joined the ChemSpider Advisory Board to promote the awareness and use of chemical structure throughout the data generation-data analysis continuum.
John Shockcor has joined the ChemSpider Advisory Board in order to help expand the flow of important chemical knowledge. John’s experience in metabolic profiling has emphasized to him the need for a source of information on small biomolecules (metabolites) which collects all of our current knowledge in one place. John is currently working on several projects involving the application of metabolomics to disease diagnosis. John is presently the Business Development Manager for Metabolic Profiling at Waters Corporation.
Sean Ekins areas of interest are in vitro and computational ADME/Tox, Systems Biology, informatics and computer-aided drug discovery. Sean has joined the advisory board to promote the use of ChemSpider to pharmacologists, using the tool to inform SAR and drug discovery research. He has worked as a senior scientist at Pfizer, Lilly Research Laboratories, Concurrent Pharmaceuticals, Inc. and GeneGo. He is currently Adjunct Associate Professor, School of Pharmacy Department of Pharmaceutical Sciences, University of Maryland and Senior Vice President of Computational Biology at Arnold Consultancy and Technology LLC and Senior Consultant at Collaborations in Chemistry Inc. He is also on the scientific advisory board for Emiliem Inc. and the advisory board for Chemical Informatics at Indiana University.
Mark Bayliss (Mass Spectrometry)
Spectroscopy and software design are what interest Mark Bayliss professionally. In his words “Structures are such a powerful means of succinct communication and are so pervasive in chemistry driven industries and academia that, whether by passion or by need, much of our scientific lives in one way or another are focused in the pursuit of an understanding of structural space. This may come in the form of data driven extraction of structurally related information, elucidation or simply their usage. and thus being able to influence further applications of structure through the web is both an interesting and potentially powerful driver for future opportunities for much of the scientific community.” Mark Bayliss is the Director of Analytical Informatics at Advanced Chemistry Development Inc.
Gary Martin (NMR Spectroscopy)
Gary E. Martin has joined the ChemSpider Advisory Board in order to represent analytical chemists participating in impurities and degradants analysis as well as the study of natural products. Access to a large database of chemical structures offers an opportunity to shortcut the identification of unknowns by searching on elemental formulae/molecular masses and other appropriate meta data. ChemSpider offers him the opportunity to gain access to one of the largest aggregated datasets of diverse chemical structures available. Gary has extensive academic and industrial experience and is presently working in big pharma.
Academia and Public Chemistry Efforts
Jean-Claude Bradley is an Associate Professor of Chemistry and E-Learning Coordinator for the College of Arts and Sciences at Drexel University. He leads the UsefulChem project, an initiative started in the summer of 2005 to make the scientific process as transparent as possible by publishing all research work in real time to a collection of public blogs, wikis and other web pages. Jean-Claude coined the term Open Notebook Science to distinguish this approach from other more restricted forms of Open Science. The main chemistry objective of the UsefulChem project is currently the synthesis and testing of novel anti-malarial agents. The cheminformatics component aims to interface as much of the research work as possible with autonomous agents to automate the scientific process in novel ways. Jean-Claude has a Ph.D. in organic chemistry and has published and obtained patents in the areas of synthetic and mechanistic chemistry, gene therapy, nanotechnology and scientific knowledge management.
Martin Walker Martin A. Walker is an assistant professor of organic chemistry at the State University of New York at Potsdam. He previously worked in the fine chemicals industry for 12 years. His interests center on organic synthesis methodology, particularly green chemistry, as well as chemical information. He is active on Wikipedia, where he contributes to chemistry content and coordinates the Wikipedia 1.0 project, preparing offline releases of Wikipedia.
Barry A. Bunin works for Collaborative Drug Discovery www.collaborativedrug.com helping scientists in secure collaborative groups more rapidly develop drug candidates for commercial and humanitarian markets. He co-authored “Chemoinformatics: Theory, Practice, and Products”, a text that overviews modern chemoinformatics technologies and “The Combinatorial Index”, a widely used text on high-throughput chemical synthesis. Dr. Bunin was an Entrepreneur-in-Residence at Eli Lilly and the founding CEO, President, & CSO of Libraria. In the lab, Dr. Bunin did medicinal chemistry developing patented new chemotypes for protease inhibition at Axys Pharmaceuticals and RGD mimics to inhibit GP-IIbIIIa at Genentech. Dr. Bunin received his Ph.D. at Berkeley, where he synthesized and tested the initial 1,4-benzodiazepine libraries with Professor Jonathan Ellman.
John A. Meyers has joined the ChemSpider Advisory Board in order to represent analytical chemists in the Forensic community. Access to a large database of chemical structures offers the forensic chemists an enhanced opportunity to identify unknowns and unravel complex mixtures by searching on molecular masses and other collected data. ChemSpider offers him the opportunity to gain access to one of the largest aggregated datasets of diverse chemical structures available. John has extensive experience in forensic drug analysis having worked for the Drug Enforcement Administration (DEA) for over 35 years before retiring in 2006. He currently is providing training and consulting efforts in the forensic community and for First Responders.
Rich Apodaca is founder and CEO of Metamolecular, LLC, a company that builds collaborative Web applications and related tools for chemistry. Formerly at Johnson & Johnson, Rich has worked as a medicinal chemist on several drug discovery efforts. His research interests include all aspects of the interface between computers and chemistry. Rich joins the Advisory Group to help develop the ChemSpider Web API and access policies.
Steve Heller has worked with Open Standards for chemical structures and numeric data for decades – since the late 1960′s. He is currently a titular member of the IUPAC Division 8 and the former Chairman of JCAMP. Steve initiated the Open Source IUPAC InChI project in 2000 and is a member of the team that has created the InChI algorithm. Steve was the originator of the NIH/EPA/NIST Mass Spec database and the NIH/EPA CIS (Chemical Information System). Steve is a consultant and a well recognized expert in the area of chemical information, chemical structure searching, numeric databases who lectures regularly at domestic and international scientific meetings as well as consulting and lecturing at private companies throughout the world.
Joerg K. Wegner is a chemist and computer scientist working in the ‘Computational Virology and Chem/Bio-Informatics’ group of Tibotec (Johnson and Johnson). He is now supporting drug targets and projects on several levels and tries not to drown in the massive amount of information coming-in every single day. This is one reason why he believes that rational decisions are only possible; if enough ‘open standards’ exist to interconnect information from commercial and non-commercial sources. In his previous academic career he found some friends by sharing joelib.sf.net and communicating problem. Joerg has joined the ChemSpider Advisory Group to help resolve the issue identified here: “… these techniques (cheminformatics and modeling) have traditionally been considered the realms of scientists from different disciplines; differences in computer systems and terminology provide a barrier to effective communication. This is probably the single most challenging problem that chemoinformatics must solve.” [DOI 10.1016/S1367-5931(99)80057-X]
Open Source/Open Access Spectroscopy
Christoph Steinbeck is a lecturer, group leader and independent consultant in molecular informatics. His group develops the Chemistry Development Kit (CDK), a Java library for chemo- and bioinformatics as well as NMRShiftDB, an open content database for chemical structures and their NMR data. The group is further maintaining the SENECA system, a program suite for NMR-based computer-assisted structure elucidation. As a founding member of the Blue Obelisk Movement Christoph is an active evangelist promoting the creation and use of Open Data, Open Standards and Open Source in Chemistry and other molecular sciences. He is a lifetime member of the World Association of Theoretically Oriented Chemists (WATOC), chairman of the Computers-Information-Chemistry (CIC) division of the German Chemical Society and a trustee of the Chemical Structure Association (CSA) Trust.
Robert J. Lancashire has worked with Open Standards for many years. He is a member of the IUPAC Subcommittee on Electronic Data Standards (SEDS) that took over responsibility for the JCAMP-DX working group and is currently a titular member of the Committee on Printed and Electronic Publications (CPEP). He has been involved in the development of the AnIML protocol and CMLSpect, two XML approaches to Open Data Standards. He maintains the JAVA code for an Open Source Spectroscopy Viewer Project, JSpecView, which was released in March 2006.
William Griffiths has joined the ChemSpider advisory group to help bring to bear his skills regarding chemical literature searching. Will designed and built the ChemRefer search engine which indexes full text and freely available chemical literature. Full text searching brings with it enormous flexibility. While the vision for ChemSpider is to create a community for chemists around a structure centric database there will be a definite need for ChemSpider to continue to expand its text-based searching capabilities. Will’s development efforts around ChemRefer have been driven by his inherent belief that the type of information that a user can search for should not be defined or restricted by the service provider. Working to create an integrated chemical structure and text search engine will produce a more useful and relevant service to the chemical community.
Robin Y. Smith, has joined the ChemiSpider advisory board to bring a unique blend of enterprise software and synthetic chemistry experience to the organization. “This technology helps to unfold the complete landscape of information a bench scientist attempts to gather about a molecule”. Currently Mr. Smith is founder & CEO of ArtusLabs, a research data mining and management organization . Previous to that, Robin created Synthematix, and helped to pioneer a chemistry electronic lab notebook company and shepherded the organization to its acquisition by Symyx. Robin’s earlier experiences include a 10-year career in synthetic chemistry, initially with the synthetic work acceleration team (SWAT) labs at Burroughs Wellcome Co. (Glaxo-SmithKline), and Boron Biologicals. He later founded RYSCOR Science, a synthetic chemistry outsourcing company.
Egon Willighagen has joined the ChemSpider Advisory Board in order to help explore semantic solutions to improve the machine accessibility of the ChemSpider database. He received his MS degree in chemoinformatics in 2002 at the Radboud University Nijmegen, The Netherlands. His PhD research was in the field of chemometrics and focused on machine representations suitable for data mining, such as clustering/classification and property prediction, during which he also explored the semantic exchange of molecular data. In the following year he held a post-doc position in the group of Dr. Christoph Steinbeck during which he continued research on the opensource chemoinformatics Chemistry Development Kit and worked on Bioclipse as a rich client for chemo- and bioinformatics software, with computer-aided structure elucidation as his scientific interest. Currently, he is a post-doc within the Netherlands Metabolomics Centre working on plant metabolite identification based on GC/MS and LC/MS data. His advisory work for ChemSpider involves semantic markup languages such as the Chemical Markup Language and the Resource Description Framework..
Barrie has been involved in handling chemical data and structures on computers for many years. His career started with ICI Ltd (now Astra-Zeneca/Syngenta) where he moved from work as an organic research chemist into the field of chemical data, creating their corporate databases. For the last 14 years, he has worked as a consultant in which capacity he has created over 120 chemical databases working with many chemical companies, organisations and publishers. He conceived and developed CAOCI (Commercially Available Organic Chemical Intermediates) which was the basis for the ACD (Available Chemicals Database). He is a founding member of the Chemical Structure Association (CSA). His specialist interests concern pesticides, pharmaceuticals, fine chemicals, chiral intermediates, fluorine chemicals and flavour and fragrance chemicals, chemical nomenclature and presentation of structures.
John Blunt has worked on the isolation and characterisation of natural products for the past 40 years, mostly on bioactive compounds from marine organisms and more recently from novel fungal sources. He is the coordinating author for the annual review of Marine Natural Products for Natural Product Reports, and maintains the MarinLit database on the literature for marine natural products. A particular interest is in the development of MarinLit and its combination with AntiBase (AntiMarin) as tools for the rapid dereplication of marine and microbial natural products when used in conjunction with new NMR technologies that provide data from microgram quantities of compounds.
Chemical Informatics and Statistics Stan Young Stan Young has joined the ChemSpider Advisory Board to represent chemical informatics and statistics. He is the Assistant Director for Bioinformatics at the National Institute of Statistical Sciences and an adjunct professor of statistics at North Carolina State University, the University of Waterloo and the University of British Columbia, where he directs thesis work in data mining and statistics. He worked in the pharmaceutical industry on all phases of pre-clinical research, first at Eli Lilly and then at GlaxoSmithKline. He is a Fellow of the American Statistical Association and the American Association for the Advancement of Science.
Greg Pearl has joined the ChemSpider Advisory Board in order to represent computational chemistry, chemical informatics and statistics and to promote the use of ChemSpider as an open access tool/repository for model validation. During his career he has developed and validated computational and in vitro models for predicting ADME/Tox models at Bristol-Myers Squibb. He brings additional expertise in chemical informatics and software development expertise from his work at Oxford Molecular/Accelrys, IBM and ACD/Labs. He is currently the Physical Chemistry Product Manager at ACD/Labs.
Alexander Tropsha is professor and Chair in the Division of Medicinal Chemistry and Natural Products in the School of Pharmacy, UNC-Chapel Hill. He received his MS degree in chemical enzymology in 1982 and PhD in biochemistry and pharmacology in 1986, both from the Moscow State University, Moscow, Russia. Dr. Tropsha’s research interests are in the areas of Computer-Assisted Drug Design, Cheminformatics, and Structural Bioinformatics. Dr. Tropsha has authored more than 100 peer-reviewed publications and book chapters. The research in his group is supported by several grants from the National Institutes of Health, National Science Foundation, Environmental Protection Agency, and industry including a NIH RoadMap grant that helped establish the Carolina Center for Exploratory Cheminformatics Research. He is an elected member of the Board and vice-chair of the international Cheminformatics and QSAR Society.Stumble it!