Changes to the GEP Web Framework - Sep. 2008

Change log for the Genomics Education Partnership Web Framework
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Changes to the GEP Web Framework - Sep. 2008

Post by wleung » Mon Sep 01, 2008 5:15 pm

Hello Everyone,

Based on technical support questions we have received during the past year and constructive criticisms we have received from the alumni workshop, we have made some changes to the GEP web framework. As the fall semester begins, I would like to take this opportunity to review some of these changes and also briefly mention some of new tools we have developed for finishing and annotation.

1. Project Management System
a.) Changes to the basic architecture
- Redesign the Project Management System to make it platform and browser independent (now works on Internet Explorer 7, Safari 3 and Firefox 2). We have also made additional performance improvements and bug fixes to improve the system.

- Changed the project names in the claim system so that they match the project names on the UCSC Browser mirror at the gander server (

For example:
refers to the contig1 in the Aug. 2006 assembly for D. erecta

- Projects can now be claimed unlimited number of times. A project will disappear from the claim list only if the project has been submitted twice. However, projects claimed three times or more are highlighted in red in the claim table.

- Added new section to allow faculty members to review the projects they have claimed and submitted.

b.) Annotation
- The number of claimed D. erecta projects have been reset based on the number of submitted projects that have annotations for all isoforms. (Note: more D. erecta dot chromosome projects now available to be claimed, so please claim these projects first).

- The difficulty scores for all the D. erecta projects have been revised to give additional emphasis on the number of predicted genes your students will annotate.

- Annotation projects are compressed using the zip format instead of the tgz format. zip files can be open on MS Windows, Mac OS X and Linux systems by default and do not require you to install additional software.

- Claimed table includes direct links to the corresponding genome browser on the gander server so faculty members can assess the projects prior to claiming the projects.

- In addition to the Project Claim System, you can download the project packages through the GEP Data Repository (under Projects in the main navigation bar).

- We anticipate that additional changes will be made to the annotation project submission system to ensure that students have annotated all isoforms for all the genes in a given project (e.g. an annotation checklist).

c.) Finishing
- The Drosophila mojavensis projects, additional sequencing results and digest data are available for download through the GEP Data Repository.

- The finishing portion of the Project Management System is being redesigned in preparation for the D. grimshawi finishing project next spring. Links to the following sections have been disabled: claiming and submitting finishing projects, reaction orders and student accounts.

2. GEP Live CD
- The GEP Live CD allows you to run phred/phrap/consed without configuring and installing the software yourself. Using the Live CD image, you can run phred/phrap/consed on MS Windows, Mac OS X and Linux systems.

- Two sequence improvement training projects are included in the Live CD image (Intro to Consed and Using Consed Graphically).

- You can burn the LiveCD image as a bootable CD or launch a virtual appliance with the Live CD image inside a virtual machine.

- The Live CD image and instructions for installing the image on the Sun Microsystems' VirtualBox virtual machine software is available at the 'Projects Under Development' section on the GEP homepage ( The Live CD image has been tested under a variety of virtual machines and environments including:
* MS Virtual PC, VirutalBox, VMware Player on Microsoft Windows XP SP2
* Parallels, VirtualBox on Mac OS 10.4 (intel)
* VirtualBox should work under most Linux distributions as well but we have not yet tested this setup.

- The Live CD is ready for public alpha testing. Due to Consed's licensing restrictions, the Live CD image is password-protected. If you would like to help us test the Live CD, please use the following username and password to download the image:
username: gep06
password: dna53

3. New Annotation Tools
a.) EMBOSS Tools
- A suite of web based tools for manipulating sequences (e.g. extract sequence, translate sequence, etc). Please use the following username and password to access the tools:
username: geptools
password: gep2007

b.) Gene Record Finder
- Identify the set of unique exons for all isoforms in a given gene. This tool can be used to substantially decrease the amount of work required to annotate all isoforms of a gene since many isoforms share the same exons.

- Documentation for the Gene Record Finder is available under 'Help -> Documentations' on the GEP main page.

c.) BLAST Viewer Generator
- Generate a web-based graphical output viewer from a plain-text BLAST output. You can use the viewer to examination and interpret complex BLAST results (e.g. annotation homework #2).

- Documentation for the BLAST Viewer Generator is not yet available. Once the documentation is complete, you can access the file through the 'Help -> Documentations' section on the GEP main page.

d.) GEP Data Repository
- Allow you to access all the annotation and finishing project files without using the Project Management System.

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