Design and Implementation of a Laboratory Information Management System (LIMS)

Dept of Pharmaceutical biosciences, Uppsala University
Genetta Soft AB, Uppsala
Background
The dept of pharmaceutical biosciences, div of pharmacology, is developing tools for rational drug design using a novel method called
Proteochemometrics. The aim is to predict interactions for drug
candidates with known receptors using computer models. The process
requires handling of large amounts of data, which today is done manually
using text-files.

The department wants to implement a high throughput information management system with databases, barcoded sample handling, automated
information exchange from laboratory instruments, and user-friendly
interfaces.

The project is a collaboration with Genetta Soft AB, a recently started
company specializing in software solutions for biological and
pharmacological research.
Depending of project progress and status at the end of the semester,there might be an opportunity for a summer job.

Objective
1. Design a general LIMS ¿ laboratory information management system
to store, manage, and retrieve information regarding the
resources, analyses, and results in a laboratory.
2. Configure and implement a LIMS for the dept of pharmaceutical
pharmacology. Interface against existing lab instruments.
3. Acquire and set up hardware (barcode readers, label writers,
computers etc)
4. Test the implemented system

2 positions are available
Due to the expected workload and crosscientific nature of the project we
require two persons; one with more biological/laboratory knowledge, and one with a background in computer science. However, it is one project and extensive collaboration between the two students will be a necessity. The two positions are described below.

1. Information management and database design
Prerequisites
- Database knowledge
- Some java knowledge
- Experience of laboratory work

2. Interface design and implementation
Prerequisites
- Experienced java skills
- Database knowledge
- Eclipse experience is an advantage

Operating system: We prefer Linux but Windows is also acceptable

Development tools
- Java
- Eclipse IDE
- Hibernate as OO-relational mapping
- Junit for testing
Other
- Ability to work independently with deadlines

References

LIMS
http://www.limsource.com/intro.html

Eclipse and RCP
http://www.eclipse.org/
http://dev.eclipse.org/viewcvs/index.cgi/~checkout~/platform-ui-home/rcp/index.html

Articles published at the department
http://www.farmbio.uu.se/upload/avd2/jarl/publ.html

Questions:
PhD student Ola Spjuth ([email protected]) tel: 018-471 4281
PhD student Martin Eklund ([email protected]) tel: 018-471 4281
Prof. Jarl S. Wikberg ([email protected]) tel: 018-471 4238