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My Personal Excitement Regarding our Involvement in the Chemical Database Service Project

20 Dec

For whatever reason, at the end of the year I get kind of thoughtful regarding what I have done over the past year and what is coming in the year ahead. I’ll hopefully get some time to review what’s gone past in 2012 but in reality I will likely be spending a lot of my spare time over the holidays working with my colleagues on the Chemical Database Project that RSC has been funded to deliver by EPSRC.

The first page is up already here (http://cds.rsc.org) and declares what we intend to deliver on January 2nd 2013. At that time we will have been working in the initial delivery for about 5 weeks only and will, in my experience, have gone through some of the best team experiences I have gone through in many a year. We will have negotiated prices and reviewed contracts, integrated a series of commercial databases and some of our own resources, built out an infrastructure to host the system and navigated many challenges around timeliness, delivery of heterogeneous software platforms and databases, debugging of many tens of thousands of lines of code and working across multiple time zones within our team. I have the privilege of working with some great people committed to getting it done!

The vision of the project, as we see it now, is outlined at a very basic level on the Chemical Database Service blog so I will not reiterate it here. Suffice to say we have outlined a project and future for the CDS that was appropriate to have us be awarded the tender. It includes not only the integration of a series of commercial databases and prediction services but also the development of a data repository for UK chemists that will allow embargo-based storage of user-defined licensed data at a personal, group and institutional level. The repository, as it is built out, will include storage of chemicals, syntheses, analytical data, property data etc. The project is still being scoped out and will engage the community of users and collaborators in defining how it should be implemented and the priority of development to deliver greatest value as the project progresses. We have five years of development ahead. It’s going to be challenging, entertaining, motivating and important. It’s going to be a tiring holiday season to meet the January 2nd deadline but that is just the start. Next year the fun really starts!

 

About tony

Antony (Tony) J. Williams received his BSc in 1985 from the University of Liverpool (UK) and PhD in 1988 from the University of London (UK). His PhD research interests were in studying the effects of high pressure on molecular motions within lubricant related systems using Nuclear Magnetic Resonance. He moved to Ottawa, Canada to work for the National Research Council performing fundamental research on the electron paramagnetic resonance of radicals trapped in single crystals. Following his postdoctoral position he became the NMR Facility Manager for Ottawa University. Tony joined the Eastman Kodak Company in Rochester, New York as their NMR Technology Leader. He led the laboratory to develop quality control across multiple spectroscopy labs and helped establish walk-up laboratories providing NMR, LC-MS and other forms of spectroscopy to hundreds of chemists across multiple sites. This included the delivery of spectroscopic data to the desktop, automated processing and his initial interests in computer-assisted structure elucidation (CASE) systems. He also worked with a team to develop the worlds’ first web-based LIMS system, WIMS, capable of allowing chemical structure searching and spectral display. With his developing cheminformatic skills and passion for data management he left corporate America to join a small start-up company working out of Toronto, Canada. He joined ACD/Labs as their NMR Product Manager and various roles, including Chief Science Officer, during his 10 years with the company. His responsibilities included managing over 50 products at one time prior to developing a product management team, managing sales, marketing, technical support and technical services. ACD/Labs was one of Canada’s Fast 50 Tech Companies, and Forbes Fast 500 companies in 2001. His primary passions during his tenure with ACD/Labs was the continued adoption of web-based technologies and developing automated structure verification and elucidation platforms. While at ACD/Labs he suggested the possibility of developing a public resource for chemists attempting to integrate internet available chemical data. He finally pursued this vision with some close friends as a hobby project in the evenings and the result was the ChemSpider database (www.chemspider.com). Even while running out of a basement on hand built servers the website developed a large community following that eventually culminated in the acquisition of the website by the Royal Society of Chemistry (RSC) based in Cambridge, United Kingdom. Tony joined the organization, together with some of the other ChemSpider team, and became their Vice President of Strategic Development. At RSC he continued to develop cheminformatics tools, specifically ChemSpider, and was the technical lead for the chemistry aspects of the Open PHACTS project (http://www.openphacts.org), a project focused on the delivery of open data, open source and open systems to support the pharmaceutical sciences. He was also the technical lead for the UK National Chemical Database Service (http://cds.rsc.org/) and the RSC lead for the PharmaSea project (http://www.pharma-sea.eu/) attempting to identify novel natural products from the ocean. He left RSC in 2015 to become a Computational Chemist in the National Center of Computational Toxicology at the Environmental Protection Agency where he is bringing his skills to bear working with a team on the delivery of a new software architecture for the management and delivery of data, algorithms and visualization tools. The “Chemistry Dashboard” was released on April 1st, no fooling, at https://comptox.epa.gov, and provides access to over 700,000 chemicals, experimental and predicted properties and a developing link network to support the environmental sciences. Tony remains passionate about computer-assisted structure elucidation and verification approaches and continues to publish in this area. He is also passionate about teaching scientists to benefit from the developing array of social networking tools for scientists and is known as the ChemConnector on the networks. Over the years he has had adjunct roles at a number of institutions and presently enjoys working with scientists at both UNC Chapel Hill and NC State University. He is widely published with over 200 papers and book chapters and was the recipient of the Jim Gray Award for eScience in 2012. In 2016 he was awarded the North Carolina ACS Distinguished Speaker Award.
1 Comment

Posted by on December 20, 2012 in Chemical Database Service

 

One Response to My Personal Excitement Regarding our Involvement in the Chemical Database Service Project

  1. Jeffrey Harris

    December 26, 2012 at 5:23 pm

    Tony,
    I want to thank you for demonstrating the possibilities for meaningful collaboration, research and design in human society. As you know, I take your work and frequently extend your processes to other industries. In my work we call this translation; where a noted process or experimental outcome intuitively shows value in other aspects of medicine; and when broadened in scope often brings rewards quickly to other scientific interests.

    Then-or course- I like to connect science with humanity to place an emotional reward to your style of thinking – often by providing you with closed-loop feedback on how your work improves my life.

    Readers who do not know me should benefit from a brief introduction. My name is Jeffrey Harris, I have retired recently from a 33 year in healthcare with 18 years dedicated to guiding clinical teams on establishing care-models for patients with chronic lung and heart disease and the last 15 years learning to embed a formulas for human wellness into web-native care coordination systems which harnessed multiple data sources from different industry sectors to provide decision support to doctors, social workers, nurses and families: selecting the best care, for the right patient, delivered by the correct professional at the right time. The work has been exhilarating since it provides such a beautiful representation of how fragile and dynamic human well-being is when influenced by a rapidly evolving social-science.

    With the development of ChemSpyder, I noticed a dedicated team of professionals driven by several frustrations in their work. The overwhelming volume of data relating to the properties of chemical compounds and excruciating time to retrieve answers to research questions relating to any given list of compounds created an extensive barrier to rapid-cycle product development in pharmaceuticals. Beyond that, the same scientists were frustrated by the lack of reproducible data between manufacturers creating many concern as to the quality of the data.

    In-stead of ‘boiling the ocean’ and assuming a academic arrogance that would require you to launch into fifty years of untangling the errors in the databases, you assembled a technology allowing scientific minds and others to define their search criteria and compare the results within a nanosecond or two. The outcome…decreases cost of rapid cycle development and I am sure creattes more opportunities for products in the future to treat us patients.

    Your team’s work recently to define the needs of the market to return a product to the industry combining core elements with substantial value added features in less than six months is fantastic .Your team realized that the work needed to be done to support your colleagues so they could continue their work and grow their capacity. This is true customer-centered behavior as opposed to the classic scenario in my industry of Healthcare where we flood the users with concepts of products that can never be defined due to the nebulous nature of the ‘market probing’ requirements for the “next big thing”. I hope someone writes a Harvard Business Review Case Study. I can imagine the article having a title such as: “Sometimes Business Is Personal”.

    I am retiring at a time when American Healthcare is now decades into the design, deployment and societal education surrounding our healthcare information systems. Our own free-market economy has driven us to a grave inefficiency that can actually be calculated as lost quality life years and increased accident rates, morbidity and mortality. I chose to write this today because I have been ill for the last week with a flare-up of Chronic Regional Pain Syndrome. This coupled with 45 years of diabetes ruined my families Christmas. After spending three hours looking for details on my disease to see if any new treatments were available I gave up. You see, none of my physicians is knowledgeable of modern therapy or even pathological theory and every time I came upon an interesting paper the publisher wanted me to purchase the article got $40.00.

    Great work my friend!
    Jeff Harris

     

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