1. MATLAB DATABASE Configuration

2. 1st time use: Matlab ODBC Database A data source is a combination of:
Data we want to access
How to find the data
Data sources are accessed by ODBC drivers
Matlab
ODBC
Database
An ODBC driver is a standard Windows interface that enables communication between database management systems and SQL-based applications

3. Configuration: Open Matlab Click Start Toolboxes Database
Visual Query Builder

4. Query
 Define ODBC Data Source..

5. Click the Add button
Choose SQL Server and click Finish

6. Type in the data source name “gene_arch”, choose LIRANSRV for the server and click finish
Click OK

7. Now “gene_arch” is showing in the data sources list
Back in Matlab – a conn object of type database was added
Please notice that you receive a valid handle

8. 2nd time use and up:
Any other time after the first configuration just type
conn = database('gene_arch','','password')

9. Observing database structure
DB’s tables:
dbmeta = dmd(conn);
databasetables = tables(dbmeta, 'Gene-Architecture','dbo')
Table’s columns: dbmeta = dmd(conn);
tabcolumns = columns(dbmeta, 'Gene- Architecture','dbo',’TableName’)

10. MATLAB Data manipulation

11. Fetch data results= fetch(connection,select)
connection = the connection we established before
select = SQL select statement:
'select ColumnName1,…, ColumnNameN, from TableName‘
Example:
results= fetch(conn,'select Name, Details from Species');

12. fastinsert(conn,’TableName’,columnNames,data)
Insert data
fastinsert(conn,’TableName’,columnNames,data)
columnNames = {‘ColumnName1';’ColumnName2’; … ; ColumnNameN'};
data = either
cell array (i.e. {'A';'B'})
cell array in a structure (i.e. st.Names={'A';'B'},st.Details={'Apple';'Banana'})
Example:
fastinsert(conn,'Species`,
{'Name';'Details'}, data);

13. Update data Example: where = SQL where clause:
update(conn,’TableName’,columnNames,data,where)
where = SQL where clause:
{‘where ColumnName1 operator value1’; … ;
‘where ColumnName2 operator value2’}
operators: =, >, <, like, in,…
Example:
update(conn,‘Species‘,{‘Details’},data,{‘where Name like ‘’Anopheles gambiae’’’});

14. Execute general query query = Any SQL query. i.e.:
curs = exec(conn,query)
query = Any SQL query. i.e.:
'delete from Orthologous_db where idOrthologous_db=12’
curs = A cursor, an object which holds information about the transaction with the database
Why not to use exec?

15. Commit & Rollback
commit(conn)makes permanent changes made to the database connection since the last commit or rollback function was run
rollback(conn)reverses changes made to a database using fastinsert, insert, or update (and not to exec!) via the database connection
To use rollback, the AutoCommit flag for conn must be off
set(conn,'AutoCommit','off')

16. DB Preferences: setdbprefs ErrorHandling: store/report/…
Sets preferences for retrieval format, errors, NULLs, and more
ErrorHandling: store/report/…
DataReturnFormat: cellarray /numeric/structure
NullStringRead: NULL/’’/…
Example: s = setdbprefs; s.ErrorHandling = 'report‘; setdbprefs(s);

17. A good demo Can be found here
Combines tools from both bioinformatics and database matlab toolboxes
Note it uses insert instead of fastinsert (slower and older)
A “shlif” of functions can be found in the same folder (shlif.m)
Also, an example connection script (connecting.m)