The <display:*> tag library

BioSilico is a web-based database system that provides integrated access to public metabolic databases available. An integrated data structure and a variety of querying logics are developed to allow easy and efficient retrieval of various data in the metabolic network. The system is installed on the IBM RS/6000 server running the IBM AIX 5.0L operating system, and run on Java Virtual Machine of JDK 1.4.0. The generated codes are written in Java, MySQL (version 3.23.47), and JavaServer Pages (JSP). Two Marvin Java applets (MarvinSketch and MarvinView) and JChem libraries from ChemAxon, Inc are also part of the system. Thus, two databases, the BioSilico and a database of chemical structures (Chem DB) support the system, and its web pages are dynamically generated through JSP scripts.

A simple and robust MVC-architecture of BioSilico

BioSilico adopts simple JSP applications (JSP-pages and JavaBeans) in Model-View-Controller (MVC) to manage the complexity in developing the large web-DB site. The MVC is a commonly used and powerful architecture for GUIs; the logic, presentation and program flow of BioSilico can be separated as follows:

Model: coding a set of JavaBeans for handling the database access (or access to other external resources), i.e., BioSilico and Chem DB. Display tag library is also used to provide high-level web-presentation patterns.

View: coding a view for presenting the data fetched by the beans.

Controller: coding a controller for examining the requests from the user, invoking JavaBeans, and controlling error handling and module flow.

The interaction between the BioSilico and the Chem DB

Using a web browser, the user enters a structure into MarvinSketch. A custom JSP script for substructure/similarity searching is activated, which connects to a database through JDBC, searches in a table containing structures, and creates a list containing the ID numbers of found structures. The JSP script retrieves mixed structural and non-structural data by SQL SELECT statements, using the list of hits and tables or views in the Chem DB. The JSP script also creates the page that displays the retrieved data in the client's browser using MarvinView.

UML modeling of BioSilico

Class diagrams are the backbone of almost every object-oriented method including UML. They describe the static structure of a system. For more detailed information, go to the UML modeling page.

Example source code

<%@ include file="Init.jsp" %>  
<div id="header">
	<h1>List compound(s): with 'compound whose name contains' option</h1>
</div>
<%
String path = request.getContextPath();
String basePath = "http://"+request.getServerName()+":"+request.getServerPort()+path+"/";
String compound = request.getParameter("compound");
String lClass = "mars"; //or isis, mars, simple, report, mark
%>
<% include file="inc/header.jsp" %>
<% request.setAttribute( "list_compound", new ListTableListCompound(con, compound) ); %>
<h2><a href="./Search.jsp">Back to the Search Page</a> > LIST compound(s) whose name <%= "'" + compound + "'"%> contains.</h2>
<display:table name="list_compound" id="parent" class="<%=lClass%>">
  <display:column title="LIGAND COMPOUND">
  	<display:table name="<%="list_compound.item[" + (parent_rowNum.intValue() -1)+ "].subListLCompound"%>" id="child" class="simple sublist" defaultsort="1" >
			<display:column property="id" title="ID" sortable="true" headerClass="sortable"/>
			<display:column property="common_name" title="COMMON NAME" sortable="true" headerClass="sortable"/>
			<display:column property="synonyms" title="SYNONYMS" sortable="true" headerClass="sortable"/>
	 </display:table> 
   </display:column>
 </display:table>

<display:table name="list_compound" id="parent" class="<%=lClass%>">
  <display:column title="EcoCyc/MetaCyc COMPOUND">
  	<display:table name="<%="list_compound.item[" + (parent_rowNum.intValue() -1)+ "].subListPgCompound"%>" id="child" class="simple sublist" defaultsort="1">
			<display:column property="id2" title="ID" sortable="true" headerClass="sortable"/>
			<display:column property="common_name2" title="COMMON NAME" sortable="true" headerClass="sortable"/>
			<display:column property="synonyms2" title="SYNONYMS" sortable="true" headerClass="sortable"/>
	 </display:table> 
   </display:column>
 </display:table>

<% include file="inc/footer.jsp" %>

System Architecture