Opal web services for biomedical applications

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal’s programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239 814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

[1]  Edward A. Lee,et al.  CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper. 2000; 00:1–7 Prepared using cpeauth.cls [Version: 2002/09/19 v2.02] Taverna: Lessons in creating , 2022 .

[2]  Kim K. Baldridge,et al.  Opal: SimpleWeb Services Wrappers for Scientific Applications , 2006, 2006 IEEE International Conference on Web Services (ICWS'06).

[3]  Nathan A. Baker,et al.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations , 2004, Nucleic Acids Res..

[4]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[5]  Edward A. Lee,et al.  Scientific workflow management and the Kepler system , 2006, Concurr. Comput. Pract. Exp..

[6]  Philip E. Bourne,et al.  A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites , 2007, BMC Bioinformatics.

[7]  Zsolt Bikádi,et al.  Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock , 2009, J. Cheminformatics.

[8]  Gerhard Klebe,et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations , 2007, Nucleic Acids Res..

[9]  Lei Xie,et al.  Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments , 2008, Proceedings of the National Academy of Sciences.

[10]  Cláudio T. Silva,et al.  VisTrails: enabling interactive multiple-view visualizations , 2005, VIS 05. IEEE Visualization, 2005..

[11]  Philip E. Bourne,et al.  A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery , 2009, Bioinform..

[12]  Carole A. Goble,et al.  Taverna: a tool for building and running workflows of services , 2006, Nucleic Acids Res..

[13]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[14]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Michel F. Sanner,et al.  ViPEr , a Visual programming Environment for Python , 2001 .

[16]  Michael M. Mysinger,et al.  Automated Docking Screens: A Feasibility Study , 2009, Journal of medicinal chemistry.

[17]  Philip E. Bourne,et al.  SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison , 2010, Nucleic Acids Res..

[18]  Matthias Stein,et al.  webPIPSA: a web server for the comparison of protein interaction properties , 2008, Nucleic Acids Res..

[19]  M F Sanner,et al.  Python: a programming language for software integration and development. , 1999, Journal of molecular graphics & modelling.

[20]  Brian K. Shoichet,et al.  ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..

[21]  Rommie E. Amaro,et al.  Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase , 2008, Journal of medicinal chemistry.

[22]  Sriram Krishnan,et al.  Design and Evaluation of Opal2: A Toolkit for Scientific Software as a Service , 2009, 2009 Congress on Services - I.

[23]  Liwei Li,et al.  BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome , 2009, Nucleic Acids Res..

[24]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[25]  G. Church,et al.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.

[26]  Wei Zhang,et al.  Impact of the 1000 genomes project on the next wave of pharmacogenomic discovery. , 2010, Pharmacogenomics.

[27]  David Abramson,et al.  Nimrod/K: Towards massively parallel dynamic Grid workflows , 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

[28]  Xiaohui Wei,et al.  Providing Dynamic Virtualized Access to Grid Resources via the Web 2.0 Paradigm , 2007, GCE 2007.