Modern biology confront scientists with the daunting challenge of storing heterogeneous
data in a structured and organized way. Among the available data management solutions there
is no intuitively usable system which covers the complete work flow of microscopy experiments.
Therefore we have developed the web application iLAP (Laboratory data management, Analysis
and Protocol development) which combines experimental protocol development, wizard-based data
acquisition and high-throughput data analysis into one single, integrated system.
A unique feature of iLAP is that it supports the experimental design phase. The working protocols
that scientists develop for wet lab experiments can be stored and modified within iLAP.
Eventually, these protocols lead to the acquisition of image data. iLAP then provides a data
acquisition wizard to assist the scientist in associating the acquired image data with steps in
the protocol. Standardization initiatives, such as MISFISHIE[1] for DNA fluorescence in situ
hybridization, can be supported by enforcing the input of required parameters during this data
acquisition. Further processing and analysis of the raw image data can be performed either with
analysis modules developed specifically within iLAP or with external third party programs. Interesting
visual observations can be documented as notes at any place.
We have realized iLAP as a standard three tier business application using state-of-the-art JEE
(Java Platform, Enterprise Edition 5) software technologies. Due to this flexible software architecture
we were able to develop an intuitive web interface as well as a generic SOAP (Simple
Object Access Protocol)- based programming interface. This platform independent programming
interface allows external image processing applications like ImageJ[2] to access the files
stored in iLAP. Computationally intensive tasks like three-dimensional deconvolution of image
stacks[3] are transparently distributed on high-performance computing infrastructure, and
results are stored within the underlying relational database management system. These results
are associated automatically with the original experiment data. To facilitate ease of use, this
complexity of data management and IT infrastructure is completely hidden from the user.
iLAP is an open source project which is freely available for the microscopy community. It
has been tested extensively in our in-house microscopy facility and continuous user feedback
has led to improvements in functionality, usability and responsiveness. A distinctive virtue of
iLAP is that it inherently leads to structured recording of experiments, conserving the complete
experimental context of data records throughout the history of the research project.
[1] E.W. Deutsch et al., Development of the Minimum Information Specification for In Situ
Hybridization and Immunohistochemistry Experiments (MISFISHIE), OMICS, Vol. 10, 205-
208 (2006)
[2] M.D. Abramoff et al., Image Processing with ImageJ, Biophotonics International, Vol 11
Issue 7, 36-42 (2004)
[3] J.G. McNally et al., Three-dimensional imaging by deconvolution microscopy, Methods,
Vol 19, 373-385 (1999)
Citation
Stocker G, Fischer M, Rieder D, Bindea G, Kainz S, Oberstolz M, McNally JG and Trajanoski Z
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis, BMC Bioinformatics,
2009 Nov 10(6) iLAP PMID: 19941647