Web server to analyze sequence data

Question

[becton]

Hello, my dept. Head gifted me with a nice hosting space in our institution new research cloud computing (12 core and I think 16 RAM size). I built a basic web app that will analyze a genomic data and print the results to user, I used Java related web technologies JSF etc, ( because my old work was in java ) the web app works fine with a small # of sequences,however it crashes when I try large sequence files. I'm beginner when it comes to web technologies, going the wrong direction will cost me valuable time. I would like to hear your advices, Ideas about how I should tackle this project, keeping in mind that I already have the java code written in old fashion way (console filename parameter1 parameter2 outputfile) etc

Here is the some of my concern and questions

1. What are the most popular web technologies used by big institution bioinformatics tools? Is there a state of art Java implementation in this area?
2. Does including a database in the implementation have bad effect "performance wise"? (in my current implementation, the sequences first stored in db before executing the analysis)
3. In a local environment, a researcher will leave his PC running for days. In server side environment I need queries service when the submitted data require long processing time, I need resources to do this kind of implementation in java/JSF
4. Finally my old work written in single threaded java code, as workaround I overclocked my cpu, my recent work mostly multi threaded. How does the threading enhance the performance of the web application?

[Alex Paciorkowski]

I can't answer most of your questions because I have no idea what some of your parameters are. When you say "the web app works fine with a small # of sequences" -- what number is small? "Large sequence files" - what number is large? What exactly do you mean by "it crashes" -- do you get an out of memory error and the job is killed? When you say you built a "basic web app that will analyze genomic data" -- do you mean you wrote a new mapper, variant caller, etc -- or that you have used Java to connect things like BWA, GATK, etc into a web interface?

You might want to take a look at the Galaxy project. Some places use this as a web-based GUI to analyze genomic data.