Question: Web server to analyze sequence data
gravatar for becton
5.0 years ago by
becton10 wrote:

Hello,  my dept. Head gifted me with a nice hosting space in our institution new research cloud competing( 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 parametre1 parmaters2 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?

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by becton10

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.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Alex Paciorkowski3.3k
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