Cytoscape Wiki|
← Revision 4 as of 2007-10-24 22:20:29
Size: 3709
Comment:
|
← Revision 5 as of 2007-10-24 22:27:25 →
Size: 3783
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 19: | Line 19: |
| 1. You and I are molecular biologists investigating cardiovascular disease. We work in different labs in different institutions. I have been using Cytoscape for two years, as a standalone application. You have never heard of Cytoscape and generally try to avoid installing and learning complicated new software. You use the web daily for literature searches, email. We both use microarrays and statistical data analysis programs. I have done a study into Atherosclerosis and have identified some genes that may be putative targets. In particular, I have found a couple of genes that are not themselves highly differentially regulated but are highly connected in Cytoscape networks | 1. You and I are molecular biologists investigating cardiovascular disease. We work in different labs in different institutions. I have been using Cytoscape for two years, as a standalone application. You have never heard of Cytoscape and generally try to avoid installing and learning complicated new software. You use the web daily for literature searches, email. We both use microarrays and statistical data analysis programs. My microarray studies have focused on similiarities to Huntington's Disease, while yours have focused on the role of the ERK5 protein in Neuronal Development. I have done a study into schizophrenia and have identified some genes that may be putative targets. These genes are highly connected in regions of genes which show |
RFC Name : Web Front End (proof of principle) |
Editor(s): Sarah Killcoyne, Allan Kuchinsky |
Date: October 24, 2007 |
Status: draft |
Proposal
Cytoscape offers a lot of functionality for a desktop user, but more and more scientific work and collaboration is done via the web. Many popular applications also offer both a web and desktop version.Biologists find the web browser user interface an intuitive way to get things done. Since they are already familiar with the web user interface, there is less of a learning curve that the user needs to climb before being able to use the application. In order to allow Cytoscape users to use the web for their work, a basic web front end can be added to Cytoscape after relayering of the core has been finished to provide simple access to the model and to parts of the core.
Background
This is a proof of principle project that will be done after the relayering of Cytoscape ([:CytoscapeLayerRefactor: RFC 46]). Some aspects of the design of the project, e.g. learning about and deciding upon a choice of alternative web-based graphical rendering packages (e.g. AJAX, GWT, Flash), can be done concurrently with the relayering of Cytoscape.
Use Cases
- Institution wide server version of Cytoscape, encouraging wider usage
- Facilitate collaboration through simple sharing of networks and data
- Basic network functions available to new users
Simplify collaborator usage, such as http://t1dbase.org or http://www.reactome.org
Scenario 1: collaboration via simple sharing of networks and data.
1. You and I are molecular biologists investigating cardiovascular disease. We work in different labs in different institutions. I have been using Cytoscape for two years, as a standalone application. You have never heard of Cytoscape and generally try to avoid installing and learning complicated new software. You use the web daily for literature searches, email. We both use microarrays and statistical data analysis programs. My microarray studies have focused on similiarities to Huntington's Disease, while yours have focused on the role of the ERK5 protein in Neuronal Development. I have done a study into schizophrenia and have identified some genes that may be putative targets. These genes are highly connected in regions of genes which show
Implementation Plan
The view and application layers of Cytoscape can be swapped out to provide a web front end through use of web technologies including Tomcat, SVG and/or the [http://code.google.com/webtoolkit/ Google web toolkit].
Project Management
Project Timeline
It is estimated that a basic implementation could be provided in 4 weeks after relayering has been done. After a prototype has been worked out a release version could be done in 6-8 weeks time. An actual timeline can be worked when the relayering gets to a point that the correct hooks are available for Views/Applications to be added.
Tasks and Milestones
- Prototype web front end (est 4 weeks)
- Write new RFC describing project (est 1 week)
Related RFCs
[:CytoscapeLayerRefactor: RFC 46 - Cytoscape Refactor]
Issues
Comments
How to Comment
Edit the page and add your comments under the provided header. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.