Projects

hupo-kupp-lims

An initial LIMS system for the HUPO Kidney and Urine Proteome Project.About this applicationThe simple LIMS system handles Spectrum Mill output, and relies on a specific folder structure to recognize identifications coming from single 1D gel bands, or 1D gel bands after prior IEF separation. It ... [More] obtains all the identified proteins, their supporting peptides and the corresponding MS/MS spectra from the Spectrum Mill output folders, and stores this information in a relational database. Installing the applicationInstalling the application is deceptively easy. Simply create a new folder somewhere, and download the two files indicated on the right of this page to that folder. These files constitute the program itself ('hkupp-lims-x.y.jar' -- 'x.y' stands for the version) and the libraries it depends on ('lib.zip'). You'll have to unzip the 'lib.zip' file in the folder you created for the application to work. After unzipping, a new 'lib' folder should appear. Double-clicking the 'hkupp-lims-x.y.jar' file will then start up the application. Software requirementsYou need a Java Virtual Machine (VM) version 5 (also known as 1.5) or higher. Java is a programming language developed by Sun Microsystems. You can download a free Java VM for your machine from www.java.com if it doesn't have one installed already. About the files available hereThe RDBMS folder contains a relational schema in 'DBDesigner4 (fork)' file format and a MySQL creation script. The Java source provides a GUI tool to import Spectrum Mill output and spectra into this database schema recursively from a top level folder. It also includes a set of (generated) table accessors and derived classes that might come in handy when you want to develop additional code around the database. Find these in the 'org.hkupp.db' package. The whole project is managed by Maven2 and you can easily and quickly build it from scratch that way. Relational database schema imageThe relational database schema of the HUPO-KUPP-LIMS. Right-click to save image locally. [Less]