Proteomics LIMS

Bioinformatics Fox Chase Cancer Center

ProteomicsLIMS


Importance of Infrastructure

Abel Wolman and Linn Enslow perfect the Chlorination of Drinking Water

In one year, the death rate from typhoid dropped over 90% in the United States


LIMS

• caLIMS– Large LIMS built around Java RMI– Inventory Control, Storage Location

• Domain Specific Information– Need to add tables– Don’t want to mangle caLIMS structure


Sample Data Flow


Proteomics LIMS

Business Tier Data TierPresentation Tier

protLIMS

Struts framework

(Servlets, JSP pages, HTML,

XML)

caLIMS+

protLIMS tables

Database

Flat files

JDBC

FTP

caLIMSLogic Objects

+protLIMS Logic

Objects

(Projects, samples, adapters etc)

protLIMSEJB

RMI

Data/File Access Objects


Added Tables


Prototype Interface




Design Principles• ProtLIMS keeps all caLIMS

architectural features:• N-Tiered structure• Extensibility• OS Portability• Compatibility with other

caLIMS systems

• ProtLIMS uses all major caLIMS technologies:

• Java Programming Language

• Java Server Pages, Java Servlets

• LDAP – Lightweight Directory Access Protocol

• Java RMI – Remote Method Invocation

• JDBC – Java Database Connectivity

• ProtLIMS also uses following technologies:

• Struts framework• J2EE architecture

approcah


FGDP

• Automated, multiple, simultaneous analyses of functional genomics data

• Java based using RMI for distribution

• Integrated through JDBC to microarray LIMS

• Plan to use for QA/QC as well as data analysis for Proteomics LIMS


Models Data Flow

Parsing/Image Analysis

Normalization

Statistical Analysis

Filtering

Pattern Recognition

Image Generation

Output Parsing

Documents

Proteomics LIMS