# Working with a mySQL database

When running large-scale *hctsa* computations, it can be useful to set up a *mySQL* database for time series, operations, and the computation results, and have many Matlab instances (running on different nodes of a compute cluster, for example) communicate directly with the database.

The *hctsa* software comes with this (optional) functionality, allowing a more powerful, distributed way to compute and store results of a large-scale computation.

This chapter outlines the steps involved in setting up, and running *hctsa* computations using a linked *mySQL* database.

## Installing the *hctsa* code package to work with a *mySQL* database

The *hctsa* package requires some preliminary set up to work with a *mySQL* database, described [here](/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/setup_mysql_database.md):

1. Installation of *mySQL*, either locally, or on an accessible server.
2. Setting up Matlab with a *mySQL* java connector (done by running the `install_jconnector` script in the **Database** directory, and then restarting Matlab).

After the database is set up, and the packages required by *hctsa* are installed (by running the `install` script), linking to a *mySQL* database can be done by running the `install_database` script, which:

1. Sets up Matlab to be able to communicate with the *mySQL* server and creates a new database to store Matlab calculations in, described [here](/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/setup_mysql_database.md).
2. Populates the database with our default library of master operations and operations, as described [here](/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/populating.md). (NB: a description of the terminology of 'master operations': a set of input arguments to an analysis function, and 'operations': a single time-series feature, is [here](/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/populating.md)).

This section contains additional details about each of these steps.

Note that the above steps are one-off installation steps; once the software is installed and compiled, a typical workflow will simply involve opening Matlab, running the `startup` script (which adds all paths required for the *hctsa* software), and then working within Matlab from any desired directory.

### Adding a time-series dataset

Once installed using our default library of operations, the typical next step is to [add a dataset of time series](/hctsa-manual/installing-and-using-hctsa/overview_mysql_database/adding_time_series.md) to the database using the `SQL_Add` command. Custom [master operations](https://github.com/benfulcher/hctsaDocumentation/tree/71794292cac125d96004eacd0c1934c6feacd36b/adding_master_operations.md) and [operations](https://github.com/benfulcher/hctsaDocumentation/tree/71794292cac125d96004eacd0c1934c6feacd36b/adding_operations.md) can also be added, if required.

### Computation, processing, and analysis

After installing the software and importing a time-series dataset to a *mySQL* database, the process by which data is retrieved from the database to local Matlab files (using `SQL_Retrieve`), feature sets computed within Matlab (using `TS_Compute`), and computed data stored back in the database (`SQL_store`) is described in detail [here](/hctsa-manual/installing-and-using-hctsa/calculating.md).

After the computation is complete for a time-series dataset, a range of processing, analysis, and plotting functions are also provided with the software, as described [here](/hctsa-manual/installing-and-using-hctsa/analyzing_visualizing.md).


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