Laboratory Information Management
Multi-tier architectures have become the prevalent building block to
develop laboratory information management systems (LIMS). The
increasing prevalence of automated experimental techniques has allowed
life-science researchers to dramatically increase the amount of data
processed over the course of a typical scientific experiment. Such
large volumes of data must be reliably stored, and processed for
monitoring and data mining purposes. Therefore, many research groups
maintain LIMS that keep track of the experiments conducted, record
which ingredients and instruments are used, and any observations and
results achieved.
Our research group has been working with two bioinformatics groups at
the NRC (Macromolecular Structure Group at Biotechnology Research
Center) and McGill (Biomedical Engineering, Center for Bioinformatics)
in order to better understand the open problems asscociated with LIMS.
From there, we have built Exp-DB, a framework for the development of
LIMS. We put particular focus on access control and workflow support.
- As the groups collaborate with each other, they want to give
their partners access to their LIMS, however, with very specific
restrictions. We have developed a fine-grained access control mechanism
based on role-based access control that allows the plug-in of arbitrary
rules that can then be implemented in the form of programs. We use
aspect-oriented programming which allows us to inject access control
wherever it is needed in the application code without changing the code
itself.
- Another open problem for life-science researchers is to
appropriately control their scientific experiments and automatically
link the data to be fed to and retrieved from their wet labs with the
LIMS in place. Existing workflow management systems, however, are often
very difficult to integrate with the existing LIMS infrastructure of
the labs. Thus, we have developed a workflow management system that is
loosely coupled with the LIMS via aspect-oriented programming. It
observes whenever data is entered or changed and triggers the start of
new experiments whenever needed. It can communicate with robots and
external agents via a distributed infrastructure.
Students:
- Brian Gabor
- Xueli Li
- Nomair Naeem
- Stefan Schmidlin
- Hesheng Chen
Related Papers:
Exp-WF: Workflow Support for
Laboratory
Information Systems. B. Gabor, B. Kemme. IEEE Workshop on Workflow
and Data Flow for Scientific Applications (SciFlow'06), co-located with
Int. Conf. on Data Engineering, Atlanta, Georgia, April 2006.
Fine-Granularity Access Control in
3-tier
Laboratory Information Systems. X. Li, N. A. Naee, B. Kemme. IDEAS
Conf. Montreal, Canada, July 2005.
Exp-DB: Fast Development of
Information Systems for Experiment Tracking. N. A. Naeem,
S. Raymond, A. Poupon,
M. Cygler,
B. Kemme. Conference on Advanced Information Systems Engineering (CAiSE
'03),
Klagenfurt/Velden, Austria, June, 2003, CAiSE Forum, Short Paper
Proceedings.