Mesa OpenEye OpenBabel CDK UNM Division of Biocomputing public web applications: Computational tools for cheminformatics and molecular discovery Jeremy Yang, Division of Biocomputing, University of New Mexico, Albuqueruqe, New Mexico, USA ChemAxon US User Group Meeting, Boston, September 13-15, 2010 ● Public web applications ● To benefit and engage the scientific community ● Cheminformatics and biomolecular discovery ● http://pasilla.health.unm.edu ● Employs diverse set of commercial, open- source and community-based components ● Limited bandwidth; etiquette essential WWW reigns! Now superpowered. Over the roughly 15 year history of the world wide web (WWW) the prevalence and usefulness of web applications has increased continuously. The “Web OS” paradigm is increasingly a reality, given tools such as GoogleDocs and Microsoft Office Web Apps, web services and cloud computing. Although web apps are not new per se, greatly enhanced capabilities are available via web apps now due to continual and dramatic improvements in (1) network bandwidth, (2) processor power, (3) web software development methods and (4) online data resources. In short, each year we can in practice do things with web apps we could not the year prior. What has not changed is the primary motivation for adoption of web apps: Deploying functionality via web apps is efficient and reliable for users, developers and managers. In addition and importantly (and this has changed somewhat as web UIs have become more complex), by virtue of their common features, web apps are generally easy to use. Web apps in cheminformatics In cheminformatics, the emergence of high quality programming toolkits, both commercial and community-based, has facilitated web app development with highly diverse aims and methods. Major software providers such as Daylight, Accelrys, ChemAxon and Chemical Computing Group have embraced web technologies, understanding their advantages and broad appeal. Web apps can vary from large scale enterprise tools (e.g. database access) to special purpose rapid prototypes for researching new algorithms. Diverse areas of research have been addressed with web apps, from toxicology prediction to 3D macromolecular visualization to quantum chemistry. Science enabled via WWW Web apps can also amount to a sort of scientific publishing. Whereas a journal article on computational methodology can leave many questions, and just as a picture can be “worth 1000 words”, arguably a functioning program might be worth 1000 pictures. In addition, agencies funding public research (such as NIH), where outcomes include computational methodology, quite reasonably and wisely require that such methodology and software be disseminated in effective, extensible, sustainable ways. Web apps developed with modern software engineering standards can well achieve these goals. Recently our app smartsfilter was used for a tuberculosis study1. ChemTattoo: colorized commonalities4 UNM Division of Biocomputing The UNM Division of Biocomputing is a multi-disciplinary research group within the Dept. of Biochemistry and Molecular Biology, in the UNM School of Medicine. Research areas include drug discovery, drug informatics, cheminformatics, bioinformatics, machine learning, QSAR, lead and probe identification. A major effort of the group is providing biomolecular screening informatics support for the UNM Center for Molecular Discovery (UNMCMD), an NIH Roadmap Molecular Libraries Programming screening center. As with UNMCMD, a long-term collaboration with Givaudan Flavors S&T has involved web apps and contributed to their development. These activities, and various other projects with collaborators who are geographically diverse, have motivated extensive use of web apps. ●Tudor I. Oprea (chief) ●Cristian Bologa ●Stephen Mathias ●Jerome Abear ●Oleg Ursu ●Gergely Zahoransky-Kohalmi ●Jeremy Yang Division of Biocomputing Personnel: Rapid prototyping enables research For scientific research web apps provide