Acuity. 4.0 Enterprise Microarray Informatics
Acuity is a complete microarray database, data min
and visualization package that has been designed and
optimized for Windows.
Analysis
Normalization
Acuity's Normalization Wizard can normalize an
arbitrary number of microarrays with the click of
button. Choose to normalize on all spots, control
spots, negative controls or any other subset of spots
that you can specify with a fully general database
query. Normalize groups of microarrays to a time point
or a sample. Choose linear ratio-based methods or
non-linear lowess methods, including print-tip groups.
Normalizations are easy to apply and remove so that
you can experiment freely with different methods.
you are finished, unnormalized and normalized data are
displayed side-by-side in the Normalization Viewer.
Filtering
Establishing data quality is paramount in microarray
experiments, as unbiological outliers can skew
downstream analyses. Acuity has a large number of
analytical and statistical tools that you can use
filter out noise from your data: filter on replicate
statistics, on individual spot characteristics or on
many other quality measures.
Once you have identified outliers, update their flag
values in the database, or define your own custom flag
values.
Replicate Analysis
Tracking replicate substances and microarrays is
intrinsic to Acuity analyses. Replicate substances are
automatically combined, and can be filtered by
standard deviation, coefficient of variation and many
other measures. Replicate microarrays can be easily
combined to construct representative data points from
each time or for each tissue in an experiment.
Find Matching Expression
Use Acuity's Match Expression function to investigate
the behaviour of individual substances in your
experiment. Choose from nine different similarity
metrics to find the substances that are most highly
correlated with a single profile or to an average
profile built from a class of substances.
Many Clustering Methods
There is no single analysis technique that can be used
for all types of data, so Acuity has a suite of
advanced analysis methods, among them Hierarchical
Clustering, Self-Organizing Maps, K-Means and
K-Medians, Gap Statistic, Principal Components
Analysis, Gene Shaving and more. Each algorithm offers
a large choice of similarity metrics, so that you
use the analysis that is appropriate for your data.
Use the output of one algorithm as input to the next.
For example, you can optimally order the branches in a
dendrogram from a hierarchical cluster, with the order
derived from a Self-Organizing Map or a Principal
Components Analysis.
Performance Optimization
All Acuity analyses have been optimized for speed and
memory use on very large data sets so that a standard
desktop computer can be used to cluster hundreds of
microarrays. Clustering and other processor-intensive
tasks are implemented as background processes, so that
you can queue and execute multiple analysis tasks
while continuing to work on other tasks in Acuity.
Depending on the size of the dataset and the amoun
computer memory available to Acuity, the clustering
algorithms partition the datasets and perform
calculations differently, so that Acuity is always
working most efficiently.
Analysis Audit Trail
All Acuity analysis operations and results are stored
sequentially in the database as they are calculate
so an audit trail is maintained automatically and
displayed in the Acuity project tree for each data
set. You can easily reproduce an analysis, or remove
data transformations from microarrays or datasets.
Substance and Microarray Lists (Quicklists)
Acuity Quicklists are a powerful method of saving
lists of interesting substances, microarrays or
annotations. With the click of the mouse you can save
all selected substances as a quicklist, either
globally or with a dataset. Each list can be assigned
a color. Together with the ability to apply a list to
the current view of the data, so that the substances
and microarrays are colored appropriately, colored
quicklists give you the ability to track multiple sets
of substances through all Acuity visualizations.
Reports and Scripting
Like GenePix Pro, Acuity supports standard scripting
languages such as VBScript and JavaScript, as well as
any other scripting languages supported by Internet
Explorer, such as PerlScript and PythonScript. Extract
data via script, write custom analyses through ActiveX
objects, generate HTML reports: Acuity scripting i
maximally flexible.
Visualizations
Clear and Interactive
Acuity's clear and interactive display of analyzed
data can reveal subtle structure and relationships in
the data that are not apparent from less elegant
visualizations. Acuity displays clustering results in
many different ways, uses smooth interactive 3-D plots
of principal components data (exportable as AVI
animations), and synchronizes all views so that
substances and their annotations selected in one view
are automatically grouped in all other views.
Color Tables
The Color Table is the central data view in Acuity.
Microarrays are organized into columns, with
substances in rows. The table is colored automatically
based on user-specified thresholds, and these colors
are propagated throughout Acuity.
Expression Profiles
Clusters and other color-based visualizations do n
always demonstrate the co-expression of a set of
substances as effectively as a simple line plot.
Examine the expression profiles of groups of
substances easily with the Acuity Graph tab.
3D Scatter Plots
Some analyses, such as Principal Components Analysis,
are best displayed in three dimensions. Acuity's 3
display is fast, smooth and fully interactive, so that
you can easily rotate, zoom and select points of
interest. You can also export rotating animations as
AVI for display on web sites.
Microarray and Substance Summaries
Display dataset, microarray or substance summaries at
any time.
Single Microarray View
You always have access to your original raw data in
Acuity, including GenePix analysis images. View your
raw data at any time, linked to images, and draw
scatter plots of raw data columns. This is an
essential tool for microarray quality control.
Web Links
With Acuity's web links functionality you are only
ever a click away from looking up a substance in any
web-based database. Define as many web links as you
like, and look up substances based on any identifier.
Pathways
Link directly to web-based pathway sites such as K
SPA or BioCarta and display and interact with them in
the Acuity interface.
Save As PDF
Easily generate publication-quality graphics in
Portable Document Format (PDF) from all your Acuity
analysis visualizations. PDF files are compact enough
to send as email attachments but retain layout and
font information, as well as preserving the resolution
and quality of graphs and images. PDF files are text
searchable and seamlessly import into publishing
software packages such as Adobe Photoshop or
Illustrator as vector graphics, so that they can be
resized without loss of quality.
Data Management
A Scaleable Relational Database
Data management is the essence of bioinformatics: it
is pointless having good data if you cannot store it,
access it and share it with colleagues and
collaborators. Central to Acuity is its powerful and
scaleable relational database that can effortlessly
store and retrieve terabytes of data. Acuity users
connect to a central Acuity server from home, from
another lab or from the other side of the world. All
configurations are as simple as double-clicking on the
Acuity icon.
Manage Multiple Users
Acuity now has additional tools for managing multiple
users at the enterprise level: set permissions for
users and groups on a folder-by-folder basis, show and
hide folders from users and groups. Enterprise
microarray informatics has never been easier or more
affordable.
Full Integration with GenePix Pro
GenePix scanners, GenePix Pro and Acuity form a
single, integrated system. Perform acquisition,
first-pass analysis and advanced analysis all within
the one environment. Save your data directly from
GenePix Pro to the Acuity database with the GenePix
Pro "Save To Acuity" command. At the enterprise level,
use the Acuity database as a centralized repository
for GenePix data.
Acuity imports normalized GenePix Pro files in their
normalized state, so that they can be unnormalized
renormalized in Acuity using the same normalization
method that was used in GenePix Pro. Acuity recognizes
GenePix Pro flagged features, so that when you select
features on the image in the Acuity Results tab, the
GenePix flags are displayed (see below).
Familiar Interface
The Acuity Project Tree is a high-level view of th
Acuity database. Import thousands of microarrays and
organize them with a Windows Explorer-like tree.
The Tree behaves like any other Windows tree. You can
cut, copy, paste, drag and drop, rename and delete
microarrays, folders, datasets and quicklists in the
familiar way, as well as assigning access and
permissions to users.
Full Database Queries
Construct datasets with fully general queries across
the entire database with the Query Wizard. The Query
Wizard allows you to build complex database queries by
combining a series of simple, step-by-step conditions.
MAGE-ML Export
Export microarrays in MAGE-ML format for upload to
web-based databases such as ArrayExpress. A growing
number of journals, such as Nature, are requiring that
microarray data is made available in MAGE-ML format as
part of publication. Acuity gives you the ability to
export data in this format. Acuity has on-the-fly
compression during export to minimize file sizes.
Track Microarrays
Manage all the properties of your microarrays, from
slide production through scanning and analysis, and
store them in the database, where they can be searched
or used to filter data. Acuity can be an indispensable
part of your laboratory information management system,
as all your microarray experimental data is recorded,
stored, analyzed and displayed in the one place.
Annotation Management
The Acuity database manages annotations automatically.
Once annotations are imported, they are displayed
whenever a substance is displayed. You can annotate
substances using an unlimited number of properties,
and link directly to an unlimited number of
web-accessible databases. Acuity includes a tool to
build standard ontologies (biological process,
cellular component, molecular function) automatically
from your annotations.
Universal Text File Import
Acuity imports tab-delimited text files from any
source, including Affymetrix CHP files. Import
microarray data files, experiment descriptions,
substance annotations or any other data in
tab-delimited files.
Advanced Database Management Tools
As well as tools to manage users, groups and
permissions, Acuity has advanced tools to manage your
database at a very low level. Add and delete fields,
re-build table indexes to optimise database
performance, and create new ODBC connections all f
the Acuity client.
Easy To Use
Acuity makes enterprise microarray informatics
accessible to everyone. From installing and
maintaining the database, to managing users and groups
through to filtering and analyzing your data, Axon
put every effort into giving Acuity an intuitive
interface. Common tasks are all accessible through
small wizards on a toolbar, so that novices can get
started on real work quickly.
Optimized for Windows
Microarray datasets are large, and are only going
get larger. Because Acuity has been designed and
optimized for Windows, it effortlessly manages large
datasets, many simultaneous users, and multiple
concurrent analyses and visualizations. There are no
bottlenecks to accessing, searching, filtering or
analyzing your data. If you work on Windows platforms,
it makes sense to use software that has been designed
and optimized for Windows.
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