FlyData/Activity/Phase1
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FlyData project - Phase 1
- Start date
- 14-Sep-2007
- Target effort
- 20 man-days
- Target duration
- 2-3 months
Goal
The high-level goal of this phase is to create an initial system that displays locally created Affymetrix gene expression data with corresponding data from www.flyatlas.org (Drosophila adult gene expression atlas, University of Glasgow).
Outline plan
The key element of this development is to create a local web server that will combine information from a local Affymetrix data file and related data obtained from FlyAtlas. This will involve investigating the file formats and choosing an appropriate level of data selection. Possibly, we will wish to devise a mechanism for cacheing FlyAtlas data on the local server.
A secondary element of the development will be the creation of a shared, semi-controlled (or at least organized) web-accessible data area that can be used for holding local data files. (Cf. possible future link with proposed SABRE project.)
From a development standpoint, the phase will create an initial infrastructure for ongoing deployment of the FlyData system (which will be delivered via a web server with a browser-based user interface).
Tasks
See:
1. Technical infrastructure setup (some of this is predicated on completion of current research group infrastructure development)
- 1.1 Establish SVN repository for the project
- 1.2 Establish and organize local storage area from which local data is accessed (WebDAV?)
- 1.3 Establish regular backup for local data
- 1.4 Establish a ticketing system
2. Functional requirements detail clarification
- 2.1 Clarify range and selection criteria of gene expression and related data to be displayed
- 2.2 Determine how to get required data from FlyAtlas
3. Testing framework
- 3.1 Create test code to access FlyAtlas - this will be used to confirm that future deployments of FlyAtlas are still behaving as expected
- 3.2 Create mock FlyAtlas server
- 3.3 Outline test cases based on: (a) presumed data from FlyAtlas; (b) mock FlyAtlas server; (c) sample of local data; (d) expected web display
- 3.4 Write test case code based on scripted HTTP client, to run against FlyData server and mock FlyAtlas server
4. Implementation and testing
- 4.1 Implement FlyData server to satisfy test cases. Ideally, the actual development will be a pair-programmed exercise - training for Jun?
- 4.2 Test system with real browser
- 4.3 If necessary, update test cases and repeat from 4.1
5. User acceptance
- 5.1 Demonstrate system to Helen's team; ask them to evaluate it; record feedback
- 5.2 For shortcomings in meeting immediate goals, update test cases and repeat from 4.1
- 5.3 Add new requirements to the ticketing system
- 5.4 Work with Helen's team to select requirements for next phase
Test case outline
- Demonstrate web page of local Affymetrix data - test that page is successfully displayed
- Demonstrate web page of FlyAtlas data - test that page is successfully displayed
- Demonstrate web page of combined data - test that page is successfully displayed with some expected content from each source.
Links
- http://www.flyatlas.org/ - FlyAtlas: the Drosophila adult gene expression atlas, University of Glasgow.
- http://dx.doi.org/doi:10.1038/ng2049 - FlyAtlas citation URI
- http://130.209.132.177/atlas/data.html - FlyAtlas Affymetrix data page, also has notes on interpretation of the data files
- Sample CEL data file - this is a tab-delimited file of Affymetrix data, which can be interpretted with reference to the Affymetrix chip annotation file (e.g. http://flyatlas.org/drosophila_2.na23.annot.csv).
- http://www.affymetrix.com/ - Affymetrix
- http://www.affymetrix.com/support/technical/byproduct.affx?product=fly-20 - Affymetrix support page for drosophila_2 microarray
- http://www.affymetrix.com/Auth/analysis/downloads/na23/ivt/Drosophila_2.na23.annot.csv.zip - annotation file at Affymetrix web site
