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BxArraytm
| 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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Icon Table
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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Task Table
Icon Table
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