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The overall architecture of a process flow for building generic (e.g. 2D Gel) Laboratory databases (BxLabtm )  is illustrated in the following diagram. The tables below describe the Tasks and Icons in the illustration.


This illustration conveys typical tasks (rounded corner rectangles) and how they are connected together in a generic 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 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 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 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 assay 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 experiments. It also allows for assigning of privileges and security access levels.
Librarian This application manages all samples using unique IDs and stores provided information. It also allows establishing a collection of samples through grouping IDs.
Designer This application provides the ability to design custom experiments using proprietary algorithms.  It provides output data for sample preparation.
Sample Preparation Sample preparation involves all steps that prepare the samples for assaying. It uses output data from the Designer.
Assay Raw assay measurement data is stored and linked together using the sample IDs and barcodes.
Analyzer This application processes raw measurement data and creates results with confidence values. Summarized values can also be calculated.
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 BxLabtm process flow. This database can grow to terabytes in size mainly depending upon the size of raw assay measurement data and results files. It can also be distributed across multiple hardware servers.
This represents the collection of knowledge databases created using BxKnowledgetm Process Flow.
   Samples This represents the set of microtitre plates containing the samples that are prepared for assaying using the output from the Designer.  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.
This represents all of the different types of reports that can be generated. Examples are processed values  with confidence values, status reports, analysis reports, 2D and 3D plots of differences.

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Last modified: December 22, 2014