A list of usefull classes and tools which come with BinBase

All these tools need to be build from the source code! So please check the latest svn version out and build the binbase! If you don't know how todo this, please look under Building and testing BinBase

Create DB Tools

a simple tool which is used to add a database to an existing BinBase installations.

This tool can be found in the svn and comes with a simple to gui to create a database to an existing binbase instance. The user (which equals the databasename) needs to exist on the database server and needs to have create privileges. He also needs to have the same password which was configured in the initial BinBase installation.

Aquire the tool

check out the source code and build the binbase
go into binbase/binbase-core/target
the tool is here located

Basically all what the tool does is:

create the schema in the database
create the tables and views in the database
create the indexes
calculates the correct values for all the sequences

we are working on the script and try to provide the possibility to create users and privileges in the future. But did not do this so far since this is a security issue and most database admins are not very happy if people create users without there knowledge.

Executing the tool

execute this command and follow the instructions. It's pretty simple!

java -jar create-db.jar

Statistical Tools

The BinBase system comes with several statistical tool. This is a small overview of them. All these tools can be found under

binbase/binbase-core/binbase/binbase-client

And you need to build them from the source code.

ExportBinSpeciesTable

this tool generates a report over all bins and all species. Basically it gives you an overview how often each bin is found in each species.

You can start it with

java -jar ExportBinSpeciesTable.jar

and it requires 4 arguments

application server (127.0.0.1)
database name (my database)
private key (my private key)
output files (result.xls)

ExportSpeciesAnotationCountTable

this tool will generate a table which gives you the possibility to calculate the average number of named bins or unnamed bins for each species.

You can start it with

java -jar ExportSpeciesAnotationCountTable.jar

and it requires 4 arguments

application server (127.0.0.1)
database name (my database)
private key (my private key)
output files (result.xls)