Friday, August 6, 2010

Framework


Taverna(Taverna: a tool for building and running workflows of services, http://www.taverna.org.uk/)

Pegasys(Pegasys: software for executing and integrating analyses of biological sequences, http://www.bioinformatics.ubc.ca/pegasys/)

WebLab(WebLab: a data-centric, knowledge-sharing bioinformatic platform, http://weblab.cbi.pku.edu.cn/srcDownload.do)

wEMBOSS(wEMBOSS: a web interface for EMBOSS, http://wemboss.sourceforge.net/)

GenePattern

To upload a directory structure to a module, your users would first create the directory structure locally, and then create a zip file to use as input to your module.
You would write a GP module which takes the zip file as an arg. Within the module, you would unzip as a first step and then call RNASeq.
The output files are stored in the server. The GP server allows users to browse the result files in a web browser, to download individual files, to launch subsequent analysis steps on those individual files, and to download all of the results as a zip file. There may be some problems with output files in nested directories. This has been dealt with in the past by writing a summary.html page as a result of the job. The summary page includes relative links to the nested job result files.

To summarize, the answers to your questions are:
1. no, GenePattern does not have the concept of a working space in the server. Although there are some workarounds, by writing helper modules which:
a) upload a file via the web browser and store it unaltered as a job result file
b) upload a zip file via the web browser and store it unzipped as a set of job results files
c) configuring the server to provide access to a subset of the server's file system. Write modules which accept a server file path (string arg) as the input.

2. Yes, you should be able to integrate RNASeq without changing the source code of GenePattern.

I would start by going through the tutorial and the other links which Michael sent.

Regards,

Peter




Requirement:


1. Account
user: register,login,logout,change password,
admin: create/modify/delete user, create/modify/delete group, change password,privilege.

2. Workspace
Workspace is like the home directory of a user. Each user has his own workspace.
Each group has a public workspace. The system has one workspace.
System's workspace are public to all members.
Group's workspace are public to members in this group.
User's workspace are public to him/her only.

User can create folders and files in his and group's workspace.

1. upload/create/modify/delete/share file
2. upload/create/modify/delete/share folder
3. upload/create/modify/delete/share workflow

workspace can be shared(read or read-write) with other groups or users.

3. Global job queue
1. First Come First Serve with priority
2. limited volume
3. queue management(submit, progress, runnung time, cancel, lower/upper priority)

4. History
track all operations and events
shows
expose the history to other user for re-use.

6. Workflow
A workflow is a combination and data and operations. It contains all the information to repeat a series of
operations by another user.

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