This workflow uses one or more services that
are deprecated as of 31st December 2012
(almost 12 years ago), and may no longer function.
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Drug Re-Purposing Workflow
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This workflow will not work for anyone outside the Newcastle University domain, and may not even work past Spring 2011 due to Microbase webservices. It takes in two GI numbers and Blasts in the Cloud using Microbase, compares the results to the target proteome, and returns any proteins that are unique to the target strain.
- Needs to be 3 files on the user’s computer: source_proteins.txt, target_proteins.txt, blast_results.txt. These can be empty; they need to exist for Taverna to write to.
- Need a Tomcat server on the computer. Make sure the host has a semi-public address: in the tomcat/conf/server.xml file, change all references to “localhost” to your machine name, e.g. “cypher001.ncl.ac.uk”.
- Create and compile the two Java files: HelloWorldExample and RequestInfoExample. Change the file paths to the location of the source_proteins.txt and target_proteins.txt files respectively. They will need server-api.jar on their classpath (get it from the Tomcat lib)
- Drop the class files into tomcat/webapps/examples/WEB-INF/classes.
- Restart the Tomcat server
- The two Servlets are available from these addresses (depending on your machine name):
- Modify the get_target_url and get_source_url to point to the links above, as appropriate for your machine.
- Run with the paths of the three files from part 1, and the GI ids of two different species.
HelloWorldExample.java:
import java.io.*;
import javax.servlet.*;
import javax.servlet.http.*;
public class HelloWorldExample extends HttpServlet {
public void doGet(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException {
// output an HTML page
res.setContentType("text/html");
// load a configuration parameter (you must set this yourself)
String root = getInitParameter("root");
// print some html
ServletOutputStream out = res.getOutputStream();
// print the file
InputStream in = null;
try {
in = new BufferedInputStream
(new FileInputStream("D:\\Workflows\\Ours\\source_proteins.txt") );
int ch;
while ((ch = in.read()) !=-1) {
out.print((char)ch);
}
}
finally {
if (in != null) in.close(); // very important
}
}
}
RequestInfoExample.java:
import java.io.*;
import javax.servlet.*;
import javax.servlet.http.*;
public class RequestInfoExample extends HttpServlet {
public void doGet(HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException {
// output an HTML page
res.setContentType("text/html");
// load a configuration parameter (you must set this yourself)
String root = getInitParameter("root");
// print some html
ServletOutputStream out = res.getOutputStream();
// print the file
InputStream in = null;
try {
in = new BufferedInputStream
(new FileInputStream("D:\\Workflows\\Ours\\target_proteins.txt") );
int ch;
while ((ch = in.read()) !=-1) {
out.print((char)ch);
}
}
finally {
if (in != null) in.close(); // very important
}
}
}
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Created: 2011-03-30 | Last updated: 2011-04-01
Credits:
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