I have a web application that I have been developing for a small group within my company over the past few years, using Pipeline Pilot (plus jQuery and Python scripting) for web development and back-end computation, and Oracle 10g for my RDBMS. Users upload experimental genomic data, which is parsed into a database, and made available for querying, transformation, and reporting.
Experimental data sets are large and have many layers of metadata. A given experimental data record might have a foreign key relationship with a table that describes this data point's assay. Assays can cover multiple genes, which can have multiple transcript, which can have multiple mutations, which can affect multiple signaling pathways, etc. Users need to approach this data from any point in those layers in the metadata. Since all data sets for a given data type can run over a billion rows, this results in some large, dynamic queries that are hard to predict.
New data sets are added on a weekly basis (~1GB per set). Experimental data is never updated, but the associated metadata can be updated weekly for a few records and yearly for most others. For every data set insert the system sees, there will be between 10 and 100 selects run against it and associated data. It is okay for updates and inserts to run slow, so long as queries run quick and are as up-to-date as possible.
The application continues to grow in size and scope and is already starting to run slower than I like. I am worried that we have about outgrown Pipeline Pilot, and perhaps Oracle (as the sole database). Would a NoSQL database or an OLAP system be appropriate here? What web application frameworks work well with systems like this? I'd like the solution to be something scalable, portable and supportable X-years down the road.
Here is the current state of the application:
- Web Server/Data Processing: Pipeline Pilot on Windows Server + IIS
- Database: Oracle 10g, ~1TB of data, ~180 tables with several billion-plus row tables
- Network Storage: Isilon, ~50TB of low-priority raw data