Published by Oxford University Press on behalf of Nucleic Acids Research. Web server availability: opal2/dashboard?command= serviceList. We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application.
#Opal viewer lite software
Chimera uses Opal, a toolkit for wrapping scientific applications as web services, to provide scalable and transparent access to several popular software packages. By streamlining access to web services, including the entire job submission, monitoring and retrieval process, Chimera makes it simpler for users to focus on their science projects rather than data manipulation. We describe how we have enhanced UCSF Chimera (), a program for the interactive visualization and analysis of molecular structures and related data, through the addition of several web services (). Integrating access to web services with desktop applications allows for an expanded set of application features, including performing computationally intensive tasks and convenient searches of databases. Huang, Conrad C Meng, Elaine C Morris, John H Pettersen, Eric F Ferrin, Thomas E PMID:24861624Įnhancing UCSF Chimera through web services. Įnhancing UCSF Chimera through web services
It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. The Opal-enabled service model is useful for a wide range of applications. The number of successfully executed jobs more than doubled from 205 to 411 per day between 20. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs.
In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. 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. Opal allows both web forms-based access and programmatic access of all our applications.
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. 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. Towards this end, we built a production web server () in August 2007 to support the bioinformatics application called MEME. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces.
The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Ren, Jingyuan Williams, Nadya Clementi, Luca Krishnan, Sriram Li, Wilfred Wīiomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. Opal web services for biomedical applications.
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