Real time PCR - European Pharmaceutical Review

HIGH CONTENT SCREENING ISSUE 2009
HC/DC
The architecture of HC/DC was
designed based mostly on eclipse
plugin framework and Eclipse-KNIME
data workflow system. HC/DC is a
functional node set, working together
with package KNIME and ImageJ
presented. A plug-in for opening and
processing proprietary HCS files
(library, numeric results and images)
was developed within the KNIME
environment. All those open source
components (Eclipse environment,
KNIME, R-Project, Weka and ImageJ)
were chosen for its platformindependence,
openness, simplicity,
■
single image. Software supports
all image types which are
supported by ImageJ and ImageJ
plug-ins
Computation: Dataflow pipelines
dictate that each processor be
executed as soon as its data
inputs are available, and
processors that have no data
dependencies amongst each other
can be executed concurrently.
They are used for integrating data
from different sources, data
capture, preparation and analysis
pipelines, and populating scientific
models or data warehouses.
■
■
automatically reacting to changed
environmental circumstances
Modularity: Processing units and
containers should not depend on
each other in order to enable easy
distribution of computation and
allow for independent
development of different image
processing algorithms
Easy expandability: In HC/DC, like
in Knime, it is easy to add a new
microscope, data analysis, image
processing software nodes or
views and distribute them through
a simple plug-in mechanism
without the need for complicated
install/reinstall procedures. In
order to achieve this, a data
processing consists of a pipeline
of nodes, connected by edges that
transport data.
Figure 3 on page 19 shows in schematic
way an example of HCS data analysis
flow and corresponding nodes.
Figure 4: Workflow Projects manager and export/import possibilities from submenu.
and portability. They are also the
fastest pure Java image, dataprocessing
programs currently
available. The programs have built-in
command recorder, editor, and Java
compiler; therefore, it is easily
extensible through custom plug-ins.
The pipeline model of HC/DC
describes the exact behaviour of the
workflow when it is executed. The
nodes of HC/DC are designed with
main principles:
■ Resource type: The source of data
can be collection high level
images familiar to the user or
■
■
Control flows directly dictate the
flow of process execution, using
loops, decision points etc
Interactivity: Nodes execution
could be wholly automatic or
interactively steered by the user.
Data flows are combined by simple
drag&drop from a variety of
processing units. Customised
applications can be modeled
through individual data subpipelines
Adaptivity: The nodes and
workflow design or instantiation
can be dynamically adapted “in
flight” by the user or by
Workflow Projects
Workflow Projects manager shows all
currently defined workflow projects in
HC/DC. The context menu of the
project manager allows you to create
new projects, import existing
workflows into the workbench and
export own workflows (see Figure 4).
Each project is saved in the
workspace. The workspace is located
in your HC/DC installation directory
by default (see below how to change
this). On the file system a workflow
project consist of several files and
folders to store the current status of a
flow; this structure is not visible in the
Workflow Projects Manager as it
represents internal information not
intended to be changed manually.
HCS nodes
Workflows in HC/DC (based on
KNIME) are essentially graphs
connecting nodes, or more formally, a
direct acyclic graph (DAG). The
Workflow Manager allows to insert
new nodes and to add directed edges
(connections) between two nodes. It
also keeps track of the status of
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