1) a light-weight, user-friendly database system and
2) a cross-platform analysis suite for microarray data.
The files used by "demo" account can be DOWNLOADED. Users that are logged into the guest account or any other account set up by the user can download the files to their local computers, unzip them, then upload them to practice the functions of WebArrayDB.
While people are encouraged to store their data on our repository and analyze them on our server, the program package is available for download by users to build their own databases and analysis platforms. The workflow of WebArrayDB is shown in the following chart:
1) WebArrayDB as a database system
- MIAME compatible Users are allowed to store information about project, arrays, samples, protocols and platforms, conforming to the requirements of Minimum Information About a Microarray Experiment (MIAME).
- User-defined features When filling information for arrays, platforms, projects, protocols and samples, users may define new fields(features) that are not avaiable in WebArrayDB yet.
- Key words are supported Key words can be added for arrays, platforms, projects, protocols and samples. Key words are indexed in database for fast searching.
- Supports data across different species and across microarray platforms
- Supports data from arrays of any number of channels
- Capability of multiple databases management Users (as administrators) are allowed to create multiple databases for different research purposes.
- Web interface and console interface While web interface is ideal for regular users to access the database, console interface can be used by computational biologists for data access or database maintenance management since SQL syntax is supported.
- Store data
- Edit data
- Browse/Search data
Steps for storing data:
- (optional) register/logon
- upload necessary files
- fill/submit online forms for a project
- check data status
2) WebArrayDB as an analysis platform
- Analysis based on databases Programs for analysis read data from WebArrayDB databases
- Full collection of algorithms for differential analysis The current implementation includes t-test, eBayes-moderated t-test (LIMMA), SAM, ANOVA / ANCOVA (both fixed-effect model and mixed-effect model), non-parametric tests (Friedman rank sum test / Kruskal-Wallis rank sum test / Wilcoxon rank sum test). All tests might be done with intensity data or paired data/ratio.
- Online computation Computation will be done on our server. Users just need a web browser to upload files, submit requests for analysis and to view results.
- Supports one-color and multiple-color data, compatible to many file formats Supports intensity data files of Affymetrix CEL format, Agilent, ArrayVision, Genepix, QuantArray, ImaGene, SMD, SPOT, user-defined format.
- Parallel computation WebArrayDB can use multiple CPU cores on SMP systems or Linux clusters. Multiple requests from users can therefore be responded to in parallel, and a single request can be completed much faster than running on single-CPU systems.
- Supports flexible experiment designs By creating groups from single channels, intensity-based analysis allow much flexible designs.
- Data alignment Data can be aligned across platforms by a variety of methods.
- Background subtraction Including "subtract", "half", "minimum", "movingmin", "edwards", "normexp" and "rma" - all the methods in LIMMA.
- Normalization For within-array normalization, methods cover "print-tip loess", "global loess", "median", "robust spline"; for between-array normalization, methods include "Aquantile", "Gquantile", "PCA", "Quantile", "Rquantile", "Scale" and "vsn"; for cross-platform normalization, in addition to those for between-array normalization, three more methods, "mrs", "qd" and "gq" are implemented.
- Differentical analysis across microarray platforms Aligned data can be used for analysis with algorithms list above.
Steps for analysis:
- (optional) logon/register
- search data from databases
- fill options for analysis and submit requests
- browse/download results