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▄▄ ▀█▄ ▀▄▄ ▀▀▀▀▀▀▀ It goes AGAiN, AGAiN... ▀▀▀▀▀ ▄██▀ ▀▄▄██▀
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▓▓███▄ ▐█▌███▌ Acuity v4.0.0.60 ▄██ ▄▓▀ ▐██▄
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▀██████▄▄▄█▀ █▓▀ (c) Molecular Devices ▓▓██▄▀▓▄▄▄████▓▓▓
▄▄▄▀▀████▀▀ ▄▀ ▀▓█ ▀█▄▄▄██████▀
███ ▄▄▀ Cracker...: AGAiN 2006 ▀▄ ▀▀████▀▀▄▄▄
███▄ ▄▄██▀ Supplier..: AGAiN 2006 ▀▄▄ ███
▀███▀███▀ Packager..: AGAiN 2006 ▀██▄▄ ▄███
▄ ▄██▀ Tester....: AGAiN 2006 ▓███▀███▀
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▒ ▐██▌ OS..........: Windows ▐▌███
░ ▐██▌ Language....: English █ ███
███ Protection..: Dongle █ ▐██▌
▄ ▀██▄ Size........: 17 x 4.77mb ▐▌ ███
▄▓▄ ▀▀▀ Date........: 17/06/2006 ▄▀ ███
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▄▀ ▀███▓▄ R e l e a s e I n f o ▀▀▀▀▀▀▄▄▄▄▄▄▄▄▄▄▀▀▀
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▀█▄▄ Acuity ▀▀▄▄██▀▀
▄▄▀▀██▄▄ Enterprise microarray informatics software for data ▄█▀▀
▄██ ▀██ warehousing, advanced analysis, and visualization. █▓ █████▀
▓██▄ ▄▀ █▓ █▀████▄
▀▀████▄▄ Analysis ▀▄ ▄███▓▀
▄▀ ▀███▓▄ ▄▄████▀▀
█▓ █▄████▀ Normalization ▓██▀ ▀▄
█▓ █████▄ Acuity's Normalization Wizard can normalize an ▀██ ▄██
▀█▄▄ arbitrary number of microarrays with the click of a ▀▀▄▄██▀▀
▄▄▀▀██▄▄ 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. Once ▀▀▄▄██▀▀
▄▄▀▀██▄▄ 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 to ▀▀▄▄██▀▀
▄▄▀▀██▄▄ filter out noise from your data: filter on replicate ▄█▀▀
▄██ ▀██ statistics, on individual spot characteristics or on █▓ █████▀
▓██▄ ▄▀ many other quality measures. █▓ █▀████▄
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▄▀ ▀███▓▄ Once you have identified outliers, update their flag ▄▄████▀▀
█▓ █▄████▀ values in the database, or define your own custom flag ▓██▀ ▀▄
█▓ █████▄ values. ▀██ ▄██
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▄▄▀▀██▄▄ 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. ▀▀▄▄██▀▀
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▄██ ▀██ 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. ▀▀▄▄██▀▀
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▄██ ▀██ 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 can ▄█▀▀
▄██ ▀██ 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. ▀▀▄▄██▀▀
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▄██ ▀██ 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 amount of █▓ █████▀
▓██▄ ▄▀ computer memory available to Acuity, the clustering █▓ █▀████▄
▀▀████▄▄ algorithms partition the datasets and perform ▀▄ ▄███▓▀
▄▀ ▀███▓▄ calculations differently, so that Acuity is always ▄▄████▀▀
█▓ █▄████▀ working most efficiently. ▓██▀ ▀▄
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▀█▄▄ Analysis Audit Trail ▀▀▄▄██▀▀
▄▄▀▀██▄▄ All Acuity analysis operations and results are stored ▄█▀▀
▄██ ▀██ sequentially in the database as they are calculated, █▓ █████▀
▓██▄ ▄▀ 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. ▓██▀ ▀▄
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▀█▄▄ 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. █▓ █████▀
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▀▀████▄▄ 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 is █▓ █████▀
▓██▄ ▄▀ maximally flexible. █▓ █▀████▄
▀▀████▄▄ ▀▄ ▄███▓▀
▄▀ ▀███▓▄ ▄▄████▀▀
█▓ █▄████▀ Visualizations ▓██▀ ▀▄
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▀█▄▄ 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. ▀▀▄▄██▀▀
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▄██ ▀██ Expression Profiles █▓ █████▀
▓██▄ ▄▀ Clusters and other color-based visualizations do not █▓ █▀████▄
▀▀████▄▄ 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. ▀██ ▄██
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▄▄▀▀██▄▄ 3D Scatter Plots ▄█▀▀
▄██ ▀██ Some analyses, such as Principal Components Analysis, █▓ █████▀
▓██▄ ▄▀ are best displayed in three dimensions. Acuity's 3D █▓ █▀████▄
▀▀████▄▄ 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. ▀██ ▄██
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▄▄▀▀██▄▄ 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 KEGG █▓ █▀████▄
▀▀████▄▄ or BioCarta and display and interact with them in the ▀▄ ▄███▓▀
▄▀ ▀███▓▄ Acuity interface. ▄▄████▀▀
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█▓ █████▄ 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. ▄█▀▀
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▄██ ▀██ Unzip and unrar release, install it. xtract the █▓ █▀████▄
▓██▄ ▄▀ included patch into your app''s dir and run it. ▀▄ ▄███▓▀
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▄▀ ▀███▓▄ Enjoy. ▓██▀ ▀▄
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█▓ █████▄ Note that you need to have Microsoft SQL/MSDE or ▀▀▄▄██▀▀
▀█▄▄ Oracle 9 installed, or have remote access to it, in ▄█▀▀
▄▄▀▀██▄▄ order to use Acuity's database features. █▓ █████▀
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▓██▄ ▄▀ ▄▄▀ ▄█▀ - G r o u p ! - ▀▄ ▄███▓▀
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█▓ █▄████▀ There's the phoenix, immortality born with the flames, ▀██ ▄██
█▓ █████▄ strength rised from the ashes, mythical magnificence ▀▀▄▄██▀▀
▀█▄▄ resurrected from the sky - soul of the spiritual ▄█▀▀
▄▄▀▀██▄▄ being, intense excitement, cosmic fire the world began █▓ █████▀
▄██ ▀██ and will end in, death and rebirth regenerated. █▓ █▀████▄
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▀▀████▄▄ Things fade. Things die. He has been born again, he ▄▄████▀▀
▄▀ ▀███▓▄ lives again. WE LIVE AGAiN. Deathless inspiration. ▓██▀ ▀▄
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█▓ █████▄ [email protected] ▀▀▄▄██▀▀
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▄▀ ▀███▓▄ G r e e t i n g s ▓██▀ ▀▄
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█▓ █████▄ SSG - LND - SAC ▀▀▄▄██▀▀
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▄▄▄▄▄▄ ▄▄▀▀ ▄▄▄▄ sCr/strick9! ▀▀▀ ▀▀▀██████▄▄▄
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Ascii Header ▀▀▀▀▀ ▄▀▀▀▀▀█▄▄ ▀▀████▄█▄▄ ▄▄▄
and layout by Scour/SAC 2003. ▀██▄ ▀▀▀██████▄███▀
Ascii footer by Scour and Strick9. ▄ ▄██▀ ▀▀▀▀ ▄▓▄
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AGAiNST THE ODDS! ▀█▄
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