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The overall architecture of a distributed and integrated process flow for a microarray (e.g. DNA, SNP, Protein, ...)  laboratory (BxArraytm ) is illustrated in the following diagram. The Process Flow tables below describe each Task and Icon in the illustration.


This illustration conveys typical tasks (rounded corner rectangles) and how they are connected together in a Microarray experiment. The red lines indicate that distributed tasks and databases are linked together through a network.  This means that tasks are usually performed in different laboratories or work areas and information is stored/retrieved for each task through database applications over a network. Databases are divided into Laboratory Information Management System (LIMS)  and Knowledge data storage components. The LIMS component can be viewed as storing information related to Microarray experiments  while the Knowledge component contains additional information used in analyzing and interpreting experimental results. The Knowledge component is discussed in more detail in the BxKnowledgetm Process Flow section. The green arrows indicate a typical beginning to end, step by step process for an experiment.  The black lines with arrows indicate the physical movement of material such as probes, slides and samples that are managed using unique barcodes.  These barcodes provide unique identifiers for associating information, tracking steps in the process, linking to analysis results and reporting status.

An important design concept is that all databases are designed to be integrated together to facilitate different methods of analysis,  data mining and report generation scenarios. The Laboratory Information Management System (LIMS) component is not just a database that records data along the process, but it is designed to be linked to expression results and to information in the Knowledge databases.  Conversely, Knowledge databases are designed to link back to LIMS data; for example, sample information and chip information. This provides for seamless integration and synergy of all databases.


Table Describing Process Flow Tasks

Process Flow Tasks Description
Coordinator This application provides a central controller for accessing information and launching tasks.
Administrator This application provides capability for entering Principal Investigators, users, clients, contracts/grants, collaborators and other laboratory information associated with microarray experiments. It also allows for assigning of privileges and security access levels.
Librarian This application manages all probes, slides/chips and samples using unique IDs for each and stores provided information about each. It also allows establishing a collection of probes, slides or samples through grouping IDs.
Designer This application provides the ability to design custom slide/chip probe patterns using proprietary algorithms for mapping probes onto slides/chips. It provides output data to control an Arrayer.
Arrayer The Arrayer is a combination of a software control module and an instrument used to produce custom slides from probes and chemically prepared slides. This system is provided by third party vendors.

BioXing will interface to Arrayers by customizing the output from the Designer Task for input into the Arraying software.

Hybridization Process This application provides for the use of and development of standard protocols for hybridizing samples to arrayed slides. The protocol and all parameters are stored in the database.
Scanner The scanner is a combination of a software control module and an instrument that reads multi-channel emissions from the hybridized slide and creates raw image data for each channel. This system is obtained from third party vendors.

BioXing will provide interface software between the Scanner system and the BxArray databases.

Image Analyzer This application processes image files and creates normalized expression values with confidence values. Summarized values can also be calculated.

BioXing will provide interface software that links BxArray databases and third party image analysis software together.

Data Mining Applications These are applications that utilize data contained in the Laboratory Information Management System (LIMS) and Knowledge databases for analyzing and interpreting results;  for example,  correlations and biomarkers. They also generate custom reports and help design the next set of experiments.
Knowledge Database Process Flow This represents the seamless integration of the Knowledge Database Process Flow data that are used in analysis and interpretation of results and report generation.

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Table Describing Process Flow Icons

Process Flow Icons Description
This represents a relational database containing all information inputted and generated during the BxArraytm process flow. This database can grow to terabytes in size mainly depending upon the size of images and results files. It can also be distributed across multiple hardware servers.
This represents the collection of knowledge databases created using BxKnowledgetm Process Flow.
   Probes This represents the set of microtitre plates containing the probes and controls that are arrayed onto slides using patterns created using the Designer.  A more general model is that the icon represents a source for cDNA or oligos. Each microtitre plate has a unique barcode which is used to track  the content data for each well in the Laboratory Information Management System (LIMS) DB.
        Samples                  This represents the samples that are used during the hybridization process. Each samples has a barcode which is used to track the source data stored in the Laboratory Information Management System (LIMS) DB.
This represents a set of coated or prepared slides/chips with unique barcodes. This barcode is used to link Probes, Samples, Hybridization protocols, images and analysis results.
This represents a set of slides/chips that have gone through the arraying process and thus contains a pattern of bound probes.
This represents a set of slides/chips that have gone through the hybridization process and thus contains samples bound to probes.
This represents all of the different types of reports that can be generated. Examples are expression levels with confidence values, status reports, analysis reports, 2D and 3D plots of differences.


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Last modified: December 22, 2014