Design and Implementation of Bioinformatics Databases
 BINF 8211/BINF 6211
 UNCC
 Spring 2008

Software Links
Discussed in Class
The following links pertain to some of the software that will be discussed in this class.


UPDATE: Visio
  • Visio Professional 2003 or Visio Professional 2007



RDMS:   PostgreSQL          http://www.postgresql.org/     
  • Windows: download the binary from postgres.org
  •  Linux:  look for a distribution before compiling from source.  Postgres supports Fedora and RedHat and provides distributions.  SUSE often comes bundled with postgres using the SUSE distribution with SUSE Linux is reccomended rather than installing from source.  Debian allows apt-get installation of the proper packages.
  •  MAC OS:  you will have to aqcuire the proper package for your version of the OS they exist and I would start by looking at the following.  http://www.postgresqlformac.com/


GUI Administration Tool for PostgreSQL:   PGAdminIII       http://www.pgadmin.org/    
  • Windows:  (Don't need to download or install already incluced in the binary package)
  • Linux:  Install the appropriate package from pgadmin.org
  • MAC:  Install the appropriate package from pgadmin.org


Scripting Language:  Python     
http://www.python.org/
Use a version of python 2.5  (Do not use the 3.0!!!!)                  
  • Windows:  Download the installer
  • Linux:  Often included with the OS. If not present check for rpm or compiled package via flavors distribution update tool before installing from source.
  • MAC:  Download the installer (works for PPC and Intel)

      
DBC Driver Postgres and Python:   psycopg2     http://www.initd.org/tracker/psycopg/wiki/PsycopgTwo
Use a version for python 2.5 and the correct version of Postgres                 
       A good help link for using psycopg2 is: http://www.devx.com/opensource/Article/29071



GUI Building Tool:      PyQT4   http://www.riverbankcomputing.co.uk/pyqt/

PyQT is a easy to learn GUI building tool that interfaces well with most relational database systems.  PyQT is a python wrapper that has been placed around Trolltech's QT package. QT is C++ based and is rapidly gaining popularity in software development circles, both academic and industry.  I have found lots of help is available in the opensource package of QT via the QTAssitant tool and the examples that are provided.

You may find it worthwhile to look at QT which is available under the opensource license.

Acceptable alternatives to what is discussed in class
Although we will focus on the tools above.  Below is a short list of alternatives that are acceptable for use in the class.  We are not going to cover these in class.  You are welcome to use them for your projects.
 RDMS
  MySQL   http://www.mysql.com/
GUI Admin Tools
  (Any that work with your choice of RDMS)
Scripting Languages   C++, Java, Perl
Drivers
 ( Any that will connect, an example good alternative for python and postgres) PyGreSQL http://www.pygresql.org/
GUI Building Tools
 (Any such as php, Tkinter, Tcl/Tk, java)  No MSFoundation classes. Try and stay platform independent
Course Schedule
Course Readings

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