Hi all,
Recently I got a question about the possibility to display a DNA sequence from the web portal using webstart. I think it would be nice to share.
Background
The current implementation of Artemis, was designed to run as client application. When you work on web clients (Webport) that's not possible.
Solution
This component, bundled as package, allows you to display and interact with your sequence using Artemis from a web protocol using Java Web start. Because all resources are resolved within the pipeline pilot server installation, it should work behind a firewall on company networks.
It works on single sequences generating a button like icon:
For multiple sequences it displays a table were sequences are represented with their accession number and clicking on each accession number. They will open a new session of Artemis with the selected sequence.
Package Description:
Name: Artemis Web Viewer
Author: Pedro Gomez Fabre
Version: 1.0.3
Created: 04/2011
Purpose: Display incoming nucleotide sequence from a web interface using Artemis.
Requirements: Pipeline Pilot 8.0 (or later), JRE (Java Runtime Environment)
O/S: PP Server Windows and Linux
Client: PP client Windows, Web port
Limitations: Not known.
Keywords: JNLP, JAR, ARTEMIS, WEB, SEQUENCE VIEWER, DNA
Installation:
1) Copy the ArtemisWeb.zip into the \\\$(scitegicRoot)/apps folder
2) Unzip the file. If scitegicforum folder already exist, it will add the content to it. If not a new folder called scitegicforum will be created.
3) Windows: open a cmd window and navigate to \\\$(scitegicRoot)/bin and type:
pkgutil -i scitegicforum/bioutils
Linux: Navigate to \\\$(scitegicRoot)/linux_bin and type:
\\\$ source ppvars.sh; ./pkgutil -i scitegicforum/bioutils
This will create an Accelrys Forum folder in components and protocols. An example protocol is located at:
“ProtocolsWeb ServicesAccelrys ForumBioUtilitiesDisplay Sequence on Web (Artemis)”
and the Artemis component can be found at “ComponentsAccelrys ForumBioUtilitiesReportingArtemis Web”
You need to reboot the apache service to apply the final configurations to the package. Otherwise the resulting jnlp file will be seen as Text.
Feeback on bug/suggestions/ideas welcome
Pedro
