|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 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
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
|Process Flow Tasks
||This application provides a central controller for accessing
information and launching tasks.
||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.
||This application manages all samples using unique IDs and
stores provided information. It also allows establishing a collection of
samples through grouping IDs.
||This application provides the ability to design custom
experiments using proprietary algorithms. It provides output data for
||Sample preparation involves all steps that prepare the
samples for assaying. It uses output data from the Designer.
||Raw assay measurement data is stored and linked together
using the sample IDs and barcodes.
||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
|Process Flow Icons
||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
||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
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