GIPSY: A Problem-Solving Environment for Bioinformatics Applications - Parallel Computing for Bioinformatics and Computational Biology - page 632

Query Builder Module The user parameter initialization module (Query Builder)
is the heart of PSE as it is responsible for the following tasks:

Creating user input;

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Input confirmation (it helps user in viewing the input, editing, and saving input);

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Creating files required during run time for the program execution;

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Building the query string that will be used to run the shell script;

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Building the shell script dynamically.

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The creation of input can be done in two ways:

1. Uploading the input file;
2. Building the input file interactively query with the Web interface.

The user parameter initialization module uses the several bean components, the
functions of which are described in detail in Table 25.1.

Job Execution Module The execution module is designed to submit a job to the
job manager, which could be a loadleveler or PBS (portable batch system) or a simple
fork. In this implementation, IBM loadleveler has been used for job submission. The
Execute bean component accepts the query string produced by Query Builder Bean
component and executes the shell script to submit a particular job through loadleveler.

Job Management Module The loadleveler manages both serial and parallel jobs
over a cluster of servers. On PARAM Padma, under loadleveler, there is a pool of IBM
P630 / P690 processors for performing batch jobs. Jobs are allocated to machines in

TABLE 25.1 Bean Components Used in Query Builder

Component Name Function

File Writer Bean To write the user input in a particular format based on the application;

this bean is also responsible for creating files required for the
program execution

Input Confirmation Bean Users can view / edit the input file created dynamically; if the user

edits the input file, the changes made will be saved with the help
of the JSP

Upload File Bean Users can upload the input file from client machine to the

server; after uploading, the JSP uses Input Confirmation Bean
to view / update the uploaded input file

Query Builder Bean Formulates the Query String and the shell script that will

be submitted to job manager on the server