A Database-Centric Virtual Chemistry System

Abstract

We describe an Oracle database application for general use within virtual chemistry. The application functions as a central hub and repository for chemical data with interfaces to external calculators. It deals with the general problems of merging data from disparate sources and with scheduling of computational tasks for parallel or sequential execution in a mixed environment. The central database is used for the storage of input, intermediary, and final data as well as for job control. A calculation job is split into distinct tasks, or units of work, which are put in a queue. Tasks are dequeued and handled by specialized calculators. These calculators are in-house or commercial programs for which adaptor modules for connection to the database must be written. Tasks are handled in a transactional fashion, so that uncompleted or failed tasks are left in the queue. This makes the system stable to many types of disturbances. Sorting, filtering, and merging operations are handled by the database itself. Usage is very general, but some specific examples are (1) as a back end for a chemical property calculator Web page, (2) in an automated quantitative structure-activity relationship system, and (3) in virtual screens.

Keywords

Computer scienceCalculatorDatabaseOracleQueueDatabase administratorData structureScheduling (production processes)Programming languageOperating system

Affiliated Institutions

Medivir (Sweden) SE

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Publication Info

Year: 2006
Type: article
Volume: 46
Issue: 3
Pages: 1034-1039
Citations: 8
Access: Closed

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APA Style

                            
                                    Peter Lind, 
                                
                                    Markus Alm
                                
                            (2006). 
                            A Database-Centric Virtual Chemistry System. 
                            Journal of Chemical Information and Modeling
                            , 46
                            (3)
                            , 1034-1039.
                            https://doi.org/10.1021/ci050360b

Identifiers

DOI: 10.1021/ci050360b