This tutorial will show you how to create a CellBase instance. First, you will download a set of raw files from several data sources. These raw files shall contain the core data that will populate the Cellbase knowledgebase. Then, you will build the JSON documents that should be loaded into the Cellbase knowledgebase.
You do not need to install CellBase to run queries. See Using CellBase for information how to run queries.
Building a CellBase instance has three stages:
Stage
Description
Download **
Downloads the data files for the specified data sets
Build **
Parses the downloaded data files, generates JSON objects, e.g. gene.json
Load
Loads the generated JSON objects into the Mongo database
These three stages are described in detail below.
** We have already downloaded and processed these data, and the resulting JSON documents are available through our FTP server. For those users who wish to skip these two sections, directly download json documents from http://bioinfo.hpc.cam.ac.uk/downloads/cellbase/v4/homo_sapiens_grch37/mongodb/ and jump to the [[Load Data Models]] section.
Step 1 - Configuring the Server
Hardware
Which sort of hardware you need depends on how much data you need, query load, etc. A full CellBase instance is 1 TB of data, but loading only genomic data is XXX GB. Also loading and querying data is very resource intensive, we recommend at least XXX GB of RAM.
Software Dependencies
Below are the software dependencies required by CellBase.
