Gaining comparable experiment results is one aspect of the current work in the microarray community. The variety of parameters for microarray experiments asks for an optimal description of the complete microarray life cycle (see also MIAME).
Following steps identify this life cycle: production management (description of the microarray), sample description, the experiment itself with hybridization, image acquisition, image analysis and data mining. The tasks for which CLONDIAG is developing new microarray technologies require a management system which is open for new technologies (e.g. new detection systems, protein/antibody arrays) and ready to streamline the processes in a microarray facility.
The aim is to collect the minimum necessary information (MIAME) from experiments run under the same conditions delivering reproducible results. The main steps of the microarray life cycle are covered by tools and intuitive interfaces, which provide the database with all relevant information. Our system supports heterogeneous array platforms, process automation and MIAME compliance. Important considerations for the information management system: representation of the microarray production process; control and representation of the hybridization process; and distinction between facility and user of the micro array technology.
See the website of the system: http://www.clondiag.com/products/sw/partisan
Gene expression experiments can be clearly divided in discrete steps:
1. Scientific question (suitable for gene expression studies)
2. Then the following experimental steps:
Design of experiment
Array and experimental plan
Production of Arrays (or suitable of the shelf arrays)
Experiment
Visualization of the results (conversion in "numerical" values)
Analysis of the results
Repeat and compare (experimental work cycle)
3. Comparison with other (gene expression) experiments
The partisan arrayLIMS is build around the requirements needed for the precise documentation of array experiments. It allows the proper development of any type of array experiment from the initial scientific or diagnostic question to the complete management of the whole laboratory process. Starting at the design of the scientific experiment all information to build the array and to carry out the experiments can be collected in substance feature tables. These are combined with all sample features, the protocol information, the raw experimental results (images or others) and the results after analysis.
Template and real objects
One important feature of the system is the differentiation between templates and real objects. This concerns the objects "bioarray", "protocol" and "substance". Templates can be used as blue prints for real objects or as objects "ready to use" (like protocols). Real objects contain inherited information from the template, but also their own characteristics.
Substance libraries
The annotation of substances allows the use of predefined classes ( genes, oligonucleotides, PCR fragments, tissues etc. ) with specific attributes (sequences, accession numbers, modifications etc). Comprehensive hierarchies and networks can be built. The local administrator is able to define new local classes and attributes.
Search and sort functions
The program contains a powerful database query builder (hierarchical, class dependent). A special focus of the search is to keep track with the lifecycle of a work object. Example question: When was a specific design of a microarray realized in real microarrays and for which experiments were these microarrays used.
Multiuser environment
PARTISAN is designed as a multi-user-application. Multiple users are able to login and work in the database in parallel. Data can be easily shared and exchanged within teams. Thus, all partners can access all relevant information which is crucial for optimized data analysis and supervision of experimental quality. Also consistency of the data of each user is guaranteed.
Imaging tool IconoClust
This is a powerful image analysis application for microarrays.
It is a free-standing module of PARTISAN arrayLIMS. New bioarray technologies allow the generation of integrated microarrays in high quantities for HTS (high through put screening). Fast and efficient software systems are featured. IconoClust can accomplish the automated image analysis of slides and integrated arrays within minutes.
Standardized batch scripts
Running IconoClust in batch mode allows a high level standardization for the image analysis. The batch scripts adapt the image analysis process, data calculation and data output to the specific lab needs.
