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ßßÛÛÜ ßßßßßÛÜÜÜÜÜ ÜÜÜÜÜÜÛÛÛß ÛÛÝ
ÜÜ ßÛÜ ßÜÜ ßßßßßßß AGAiN is proud to present.. ßßßßß ÜÛÛß ßÜÜÛÛß
ÜÛÛÝ ß²Ü ÛÛÜ ÜÛß ÜÛß ÜÜ
²²ÛÛÛÜ ÞÛÝÛÛÛÝ Acuity v4.0.0.49 ÜÛÛ Ü²ß ÞÛÛÜ
²²²ÛÛÛÛÜÜܲßÜÛÛ²² (c) Axon Laboratory ÞÛÛÛÞÛÝ ÜÛÛÛ²²
ßÛÛÛÛÛÛÜÜÜÛß Û²ß ²²ÛÛÜß²ÜÜÜÛÛÛÛ²²²
ÜÜÜßßÛÛÛÛßß Üß Cracker...: AGAiN tEAM! ß²Û ßÛÜÜÜÛÛÛÛÛÛß
ÛÛÛ ÜÜß Supplier..: AGAiN tEAM! ßÜ ßßÛÛÛÛßßÜÜÜ
ÛÛÛÜ ÜÜÛÛß Packager..: AGAiN tEAM! ßÜÜ ÛÛÛ
ßÛÛÛßÛÛÛß Tester....: AGAiN tEAM! ßÛÛÜÜ ÜÛÛÛ
ÜÛÛß ßÛÛÛßÛÛÛß
ÛÛÛ² Protection..: Dongle ßÛÛÜ
ßÛÛÜ Size........: 14 x 4.77mb ÜÜß ²ÛÛÛ
ßßß Date........: 02/02/2005 ÜÛÛ ÜÛÛß
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ÜÜÜÛÛÛÛÛÛÛÛÛÛÜÜ ßÛ²ÜÜ ÞÛÜ ßß²²ÛÛßß
ÜÜÛÛßßÜÛÛßß ßßßÛÛÜ ßÜßÛßÜÜÜ ÜÜß ßßÜÜ
ÜÛÛÛÛÜ ÛÛÛß ÞÛÛ ßÛÜÜ ÞÝ ßÜÜßßÛ²²ÜÜÜÜÜÜÜÜÜÛÛßß ÞÝ ßßßßÜÜÜÜ
ß ÜÜßßßÛÛÛÛÜ ßÛÛÜÜ Ü ÜÛß ßß ÜÜß ÛßßÛÜÜßßßßßßßßß Üß ÜÜÜßßß
ÜÛÛ ßßÛÛÜÜ ßßÛÛÛÛÜÜÜÜÜÛÛÛÛÛÛÛÛßß ÜÛ ßßÛÜÜÜ ÜÜÜßß ÜÛß
²ÛÛÜ Üß ßßßÛÜÜÜÜÛÛÛ²²²ßßßßß ÜÜßß ßßÜÜ ßßßßßßß ßÛÜ
ßßÛÛÛÛÜÜ ÞÛÜÜÜÜßßß ßßßÜÜÜÜ ÜÜß
Üß ßÛÛÛ²Ü R e l e a s e I n f o ßßßßßßÜÜÜÜÜÜÜÜÜÜßßß
Û² ÛÜÛÛÛÛß ÜÜÜ ßÜ
Û² ÛÛÛÛÛÜ Acuity® 4.0 Enterprise Microarray Informatics ßÛÛ ÜÛÛ
ßÛÜÜ ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Acuity is a complete microarray database, data mining, ÜÛßß
ÜÛÛ ßÛÛ and visualization package that has been designed and Û² ÛÛÛÛÛß
²ÛÛÜ Üß optimized for Windows. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Analysis ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Normalization ßÛÛ ÜÛÛ
ßÛÜÜ Acuity's Normalization Wizard can normalize an ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ arbitrary number of microarrays with the click of a ÜÛßß
ÜÛÛ ßÛÛ button. Choose to normalize on all spots, control Û² ÛÛÛÛÛß
²ÛÛÜ Üß spots, negative controls or any other subset of spots Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ that you can specify with a fully general database ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü query. Normalize groups of microarrays to a time point ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß or a sample. Choose linear ratio-based methods or ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ non-linear lowess methods, including print-tip groups. ßÛÛ ÜÛÛ
ßÛÜÜ Normalizations are easy to apply and remove so that ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ you can experiment freely with different methods. Once ÜÛßß
ÜÛÛ ßÛÛ you are finished, unnormalized and normalized data are Û² ÛÛÛÛÛß
²ÛÛÜ Üß displayed side-by-side in the Normalization Viewer. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Filtering ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß Establishing data quality is paramount in microarray ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ experiments, as unbiological outliers can skew ßÛÛ ÜÛÛ
ßÛÜÜ downstream analyses. Acuity has a large number of ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ analytical and statistical tools that you can use to ÜÛßß
ÜÛÛ ßÛÛ filter out noise from your data: filter on replicate Û² ÛÛÛÛÛß
²ÛÛÜ Üß statistics, on individual spot characteristics or on Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ many other quality measures. ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Once you have identified outliers, update their flag ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß values in the database, or define your own custom flag ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ values. ßÛÛ ÜÛÛ
ßÛÜÜ ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Replicate Analysis ÜÛßß
ÜÛÛ ßÛÛ Tracking replicate substances and microarrays is Û² ÛÛÛÛÛß
²ÛÛÜ Üß intrinsic to Acuity analyses. Replicate substances are Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ automatically combined, and can be filtered by ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü standard deviation, coefficient of variation and many ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß other measures. Replicate microarrays can be easily ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ combined to construct representative data points from ßÛÛ ÜÛÛ
ßÛÜÜ each time or for each tissue in an experiment. ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ ÜÛßß
ÜÛÛ ßÛÛ Find Matching Expression Û² ÛÛÛÛÛß
²ÛÛÜ Üß Use Acuity's Match Expression function to investigate Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ the behaviour of individual substances in your ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü experiment. Choose from nine different similarity ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß metrics to find the substances that are most highly ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ correlated with a single profile or to an average ßÛÛ ÜÛÛ
ßÛÜÜ profile built from a class of substances. ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ ÜÛßß
ÜÛÛ ßÛÛ Many Clustering Methods Û² ÛÛÛÛÛß
²ÛÛÜ Üß There is no single analysis technique that can be used Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ for all types of data, so Acuity has a suite of ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü advanced analysis methods, among them Hierarchical ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß Clustering, Self-Organizing Maps, K-Means and ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ K-Medians, Gap Statistic, Principal Components ßÛÛ ÜÛÛ
ßÛÜÜ Analysis, Gene Shaving and more. Each algorithm offers ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ a large choice of similarity metrics, so that you can ÜÛßß
ÜÛÛ ßÛÛ use the analysis that is appropriate for your data. Û² ÛÛÛÛÛß
²ÛÛÜ Üß Use the output of one algorithm as input to the next. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ For example, you can optimally order the branches in a ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü dendrogram from a hierarchical cluster, with the order ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß derived from a Self-Organizing Map or a Principal ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Components Analysis. ßÛÛ ÜÛÛ
ßÛÜÜ ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Performance Optimization ÜÛßß
ÜÛÛ ßÛÛ All Acuity analyses have been optimized for speed and Û² ÛÛÛÛÛß
²ÛÛÜ Üß memory use on very large data sets so that a standard Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ desktop computer can be used to cluster hundreds of ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü microarrays. Clustering and other processor-intensive ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß tasks are implemented as background processes, so that ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ you can queue and execute multiple analysis tasks ßÛÛ ÜÛÛ
ßÛÜÜ while continuing to work on other tasks in Acuity. ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Depending on the size of the dataset and the amount of ÜÛßß
ÜÛÛ ßÛÛ computer memory available to Acuity, the clustering Û² ÛÛÛÛÛß
²ÛÛÜ Üß algorithms partition the datasets and perform Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ calculations differently, so that Acuity is always ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü working most efficiently. ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Analysis Audit Trail ßÛÛ ÜÛÛ
ßÛÜÜ All Acuity analysis operations and results are stored ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ sequentially in the database as they are calculated, ÜÛßß
ÜÛÛ ßÛÛ so an audit trail is maintained automatically and Û² ÛÛÛÛÛß
²ÛÛÜ Üß displayed in the Acuity project tree for each data Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ set. You can easily reproduce an analysis, or remove ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü data transformations from microarrays or datasets. ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Substance and Microarray Lists (Quicklists) ßÛÛ ÜÛÛ
ßÛÜÜ Acuity Quicklists are a powerful method of saving ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ lists of interesting substances, microarrays or ÜÛßß
ÜÛÛ ßÛÛ annotations. With the click of the mouse you can save Û² ÛÛÛÛÛß
²ÛÛÜ Üß all selected substances as a quicklist, either Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ globally or with a dataset. Each list can be assigned ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü a color. Together with the ability to apply a list to ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß the current view of the data, so that the substances ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ and microarrays are colored appropriately, colored ßÛÛ ÜÛÛ
ßÛÜÜ quicklists give you the ability to track multiple sets ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ of substances through all Acuity visualizations. ÜÛßß
ÜÛÛ ßÛÛ Û² ÛÛÛÛÛß
²ÛÛÜ Üß Reports and Scripting Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ Like GenePix Pro, Acuity supports standard scripting ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü languages such as VBScript and JavaScript, as well as ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß any other scripting languages supported by Internet ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Explorer, such as PerlScript and PythonScript. Extract ßÛÛ ÜÛÛ
ßÛÜÜ data via script, write custom analyses through ActiveX ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ objects, generate HTML reports: Acuity scripting is ÜÛßß
ÜÛÛ ßÛÛ maximally flexible. Û² ÛÛÛÛÛß
²ÛÛÜ Üß Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ Visualizations ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß Clear and Interactive ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Acuity's clear and interactive display of analyzed ßÛÛ ÜÛÛ
ßÛÜÜ data can reveal subtle structure and relationships in ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ the data that are not apparent from less elegant ÜÛßß
ÜÛÛ ßÛÛ visualizations. Acuity displays clustering results in Û² ÛÛÛÛÛß
²ÛÛÜ Üß many different ways, uses smooth interactive 3-D plots Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ of principal components data (exportable as AVI ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü animations), and synchronizes all views so that ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß substances and their annotations selected in one view ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ are automatically grouped in all other views. ßÛÛ ÜÛÛ
ßÛÜÜ ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Color Tables ÜÛßß
ÜÛÛ ßÛÛ The Color Table is the central data view in Acuity. Û² ÛÛÛÛÛß
²ÛÛÜ Üß Microarrays are organized into columns, with Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ substances in rows. The table is colored automatically ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü based on user-specified thresholds, and these colors ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß are propagated throughout Acuity. ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ ßÛÛ ÜÛÛ
ßÛÜÜ Expression Profiles ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Clusters and other color-based visualizations do not ÜÛßß
ÜÛÛ ßÛÛ always demonstrate the co-expression of a set of Û² ÛÛÛÛÛß
²ÛÛÜ Üß substances as effectively as a simple line plot. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ Examine the expression profiles of groups of ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü substances easily with the Acuity Graph tab. ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ 3D Scatter Plots ßÛÛ ÜÛÛ
ßÛÜÜ Some analyses, such as Principal Components Analysis, ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ are best displayed in three dimensions. Acuity's 3D ÜÛßß
ÜÛÛ ßÛÛ display is fast, smooth and fully interactive, so that Û² ÛÛÛÛÛß
²ÛÛÜ Üß you can easily rotate, zoom and select points of Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ interest. You can also export rotating animations as ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü AVI for display on web sites. ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Microarray and Substance Summaries ßÛÛ ÜÛÛ
ßÛÜÜ Display dataset, microarray or substance summaries at ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ any time. ÜÛßß
ÜÛÛ ßÛÛ Û² ÛÛÛÛÛß
²ÛÛÜ Üß Single Microarray View Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ You always have access to your original raw data in ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Acuity, including GenePix analysis images. View your ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß raw data at any time, linked to images, and draw ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ scatter plots of raw data columns. This is an ßÛÛ ÜÛÛ
ßÛÜÜ essential tool for microarray quality control. ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ ÜÛßß
ÜÛÛ ßÛÛ Web Links Û² ÛÛÛÛÛß
²ÛÛÜ Üß With Acuity's web links functionality you are only Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ ever a click away from looking up a substance in any ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü web-based database. Define as many web links as you ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß like, and look up substances based on any identifier. ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ ßÛÛ ÜÛÛ
ßÛÜÜ Pathways ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Link directly to web-based pathway sites such as KEGG, ÜÛßß
ÜÛÛ ßÛÛ SPA or BioCarta and display and interact with them in Û² ÛÛÛÛÛß
²ÛÛÜ Üß the Acuity interface. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Save As PDF ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß Easily generate publication-quality graphics in ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Portable Document Format (PDF) from all your Acuity ßÛÛ ÜÛÛ
ßÛÜÜ analysis visualizations. PDF files are compact enough ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ to send as email attachments but retain layout and ÜÛßß
ÜÛÛ ßÛÛ font information, as well as preserving the resolution Û² ÛÛÛÛÛß
²ÛÛÜ Üß and quality of graphs and images. PDF files are text Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ searchable and seamlessly import into publishing ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü software packages such as Adobe Photoshop or ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß Illustrator as vector graphics, so that they can be ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ resized without loss of quality. ßÛÛ ÜÛÛ
ßÛÜÜ ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Data Management ÜÛßß
ÜÛÛ ßÛÛ Û² ÛÛÛÛÛß
²ÛÛÜ Üß A Scaleable Relational Database Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ Data management is the essence of bioinformatics: it ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü is pointless having good data if you cannot store it, ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß access it and share it with colleagues and ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ collaborators. Central to Acuity is its powerful and ßÛÛ ÜÛÛ
ßÛÜÜ scaleable relational database that can effortlessly ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ store and retrieve terabytes of data. Acuity users can ÜÛßß
ÜÛÛ ßÛÛ connect to a central Acuity server from home, from Û² ÛÛÛÛÛß
²ÛÛÜ Üß another lab or from the other side of the world. All Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ configurations are as simple as double-clicking on the ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Acuity icon. ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Manage Multiple Users ßÛÛ ÜÛÛ
ßÛÜÜ Acuity now has additional tools for managing multiple ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ users at the enterprise level: set permissions for ÜÛßß
ÜÛÛ ßÛÛ users and groups on a folder-by-folder basis, show and Û² ÛÛÛÛÛß
²ÛÛÜ Üß hide folders from users and groups. Enterprise Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ microarray informatics has never been easier or more ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü affordable. ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Full Integration with GenePix Pro ßÛÛ ÜÛÛ
ßÛÜÜ GenePix scanners, GenePix Pro and Acuity form a ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ single, integrated system. Perform acquisition, ÜÛßß
ÜÛÛ ßÛÛ first-pass analysis and advanced analysis all within Û² ÛÛÛÛÛß
²ÛÛÜ Üß the one environment. Save your data directly from Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ GenePix Pro to the Acuity database with the GenePix ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Pro "Save To Acuity" command. At the enterprise level, ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß use the Acuity database as a centralized repository ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ for GenePix data. ßÛÛ ÜÛÛ
ßÛÜÜ Acuity imports normalized GenePix Pro files in their ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ normalized state, so that they can be unnormalized or ÜÛßß
ÜÛÛ ßÛÛ renormalized in Acuity using the same normalization Û² ÛÛÛÛÛß
²ÛÛÜ Üß method that was used in GenePix Pro. Acuity recognizes Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ GenePix Pro flagged features, so that when you select ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü features on the image in the Acuity Results tab, the ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß GenePix flags are displayed (see below). ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ ßÛÛ ÜÛÛ
ßÛÜÜ Familiar Interface ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ The Acuity Project Tree is a high-level view of the ÜÛßß
ÜÛÛ ßÛÛ Acuity database. Import thousands of microarrays and Û² ÛÛÛÛÛß
²ÛÛÜ Üß organize them with a Windows Explorer-like tree. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ The Tree behaves like any other Windows tree. You can ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü cut, copy, paste, drag and drop, rename and delete ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß microarrays, folders, datasets and quicklists in the ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ familiar way, as well as assigning access and ßÛÛ ÜÛÛ
ßÛÜÜ permissions to users. ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ ÜÛßß
ÜÛÛ ßÛÛ Full Database Queries Û² ÛÛÛÛÛß
²ÛÛÜ Üß Construct datasets with fully general queries across Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ the entire database with the Query Wizard. The Query ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Wizard allows you to build complex database queries by ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß combining a series of simple, step-by-step conditions. ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ ßÛÛ ÜÛÛ
ßÛÜÜ MAGE-ML Export ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Export microarrays in MAGE-ML format for upload to ÜÛßß
ÜÛÛ ßÛÛ web-based databases such as ArrayExpress. A growing Û² ÛÛÛÛÛß
²ÛÛÜ Üß number of journals, such as Nature, are requiring that Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ microarray data is made available in MAGE-ML format as ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü part of publication. Acuity gives you the ability to ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß export data in this format. Acuity has on-the-fly ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ compression during export to minimize file sizes. ßÛÛ ÜÛÛ
ßÛÜÜ ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Track Microarrays ÜÛßß
ÜÛÛ ßÛÛ Manage all the properties of your microarrays, from Û² ÛÛÛÛÛß
²ÛÛÜ Üß slide production through scanning and analysis, and Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ store them in the database, where they can be searched ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü or used to filter data. Acuity can be an indispensable ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß part of your laboratory information management system, ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ as all your microarray experimental data is recorded, ßÛÛ ÜÛÛ
ßÛÜÜ stored, analyzed and displayed in the one place. ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ ÜÛßß
ÜÛÛ ßÛÛ Annotation Management Û² ÛÛÛÛÛß
²ÛÛÜ Üß The Acuity database manages annotations automatically. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ Once annotations are imported, they are displayed ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü whenever a substance is displayed. You can annotate ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß substances using an unlimited number of properties, ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ and link directly to an unlimited number of ßÛÛ ÜÛÛ
ßÛÜÜ web-accessible databases. Acuity includes a tool to ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ build standard ontologies (biological process, ÜÛßß
ÜÛÛ ßÛÛ cellular component, molecular function) automatically Û² ÛÛÛÛÛß
²ÛÛÜ Üß from your annotations. Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü Universal Text File Import ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß Acuity imports tab-delimited text files from any ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ source, including Affymetrix CHP files. Import ßÛÛ ÜÛÛ
ßÛÜÜ microarray data files, experiment descriptions, ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ substance annotations or any other data in ÜÛßß
ÜÛÛ ßÛÛ tab-delimited files. Û² ÛÛÛÛÛß
²ÛÛÜ Üß Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ Advanced Database Management Tools ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü As well as tools to manage users, groups and ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß permissions, Acuity has advanced tools to manage your ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ database at a very low level. Add and delete fields, ßÛÛ ÜÛÛ
ßÛÜÜ re-build table indexes to optimise database ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ performance, and create new ODBC connections all from ÜÛßß
ÜÛÛ ßÛÛ the Acuity client. Û² ÛÛÛÛÛß
²ÛÛÜ Üß Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ Easy To Use ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß Acuity makes enterprise microarray informatics ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ accessible to everyone. From installing and ßÛÛ ÜÛÛ
ßÛÜÜ maintaining the database, to managing users and groups ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ through to filtering and analyzing your data, Axon has ÜÛßß
ÜÛÛ ßÛÛ put every effort into giving Acuity an intuitive Û² ÛÛÛÛÛß
²ÛÛÜ Üß interface. Common tasks are all accessible through Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ small wizards on a toolbar, so that novices can get ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü started on real work quickly. ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ Optimized for Windows ßÛÛ ÜÛÛ
ßÛÜÜ ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ Microarray datasets are large, and are only going to ÜÛßß
ÜÛÛ ßÛÛ get larger. Because Acuity has been designed and Û² ÛÛÛÛÛß
²ÛÛÜ Üß optimized for Windows, it effortlessly manages large Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ datasets, many simultaneous users, and multiple ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü concurrent analyses and visualizations. There are no ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß bottlenecks to accessing, searching, filtering or ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ analyzing your data. If you work on Windows platforms, ßÛÛ ÜÛÛ
ßÛÜÜ it makes sense to use software that has been designed ßßÜÜÛÛßß
ÜÜßßÛÛÜÜ and optimized for Windows. ÜÛßß
ÜÛÛ ßÛÛ Û² ÛÛÛÛÛß
²ÛÛÜ Üß Û² ÛßÛÛÛÛÜ
ßßÛÛÛÛÜÜ ßÜ ÜÛÛÛ²ß
Üß ßÛÛÛ²Ü ÜÜÛÛÛÛßß
Û² ÛÜÛÛÛÛß ²ÛÛß ßÜ
Û² ÛÛÛÛÛÜ ßÛÛ ÜÛÛ
ßÛÛÜÜ ßßÜÜÛÛßß
ßÜÛÛßÛÜÜÜÜ ÜÛßß
ßßßÜÜÜÜßßßßßßßßÜÜÜÜÜÜ Û² ÜÜÜ
Üß ßßßßßßÜÜÜÜÜÜ ßßßßßÜÜ ÜÜÛßßßÛÜÜ ÜÜÜ Û² ß ßßÜ
Û² ßßßßßÜÜ ßÜ ÛÛÛÛÛ²²²²²Û ÜÛÛß ÜÛß ßÜ ÞÝ
Û² I n s t a l l I n f o Û Üß ÛÛÛÛÛÛÛ²²²Û ÛÛÛ ÛßÛ ÜÜß ßßÜÜÜÜß
ßÛÜÜ ÜÜÛßß ßßÛÛÛÛÛßß ßÛÛÜÜ ÜÜß ßßßß Üß
ÜÜßßÛÛÜÜ ßßßß Û² ÛÛÛÛÛß
ÜÛÛ ßÛÛ Unzip, unrar and install the application. Û² ÛßÛÛÛÛÜ
²ÛÛÜ Üß Extract the included patch into your app''s dir and ßÜ ÜÛÛÛ²ß
ßßÛÛÛÛÜÜ run it. ÜÜÛÛÛÛßß
Üß ßÛÛÛ²Ü Note that you need to have Microsoft SQL/MSDE or ²ÛÛß ßÜ
Û² ÛÜÛÛÛÛß Oracle 9 installed, or have remote access to it, in ßÛÛ ÜÛÛ
Û² ÛÛÛÛÛÜ order to use Acuity's database features. ßßÜÜÛÛßß
ßÛÜÜ ÜÛßß
ÜÜßßÛÛÜÜ Enjoy. Û² ÛÛÛÛÛß
ÜÛÛ ßÛÛ Û² ÛßÛÛÛÛÜ
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ßßÛÛÛÛÜÜ ÜÜÛÛÛÛßß
Üß ßÛÛÛ²Ü ²ÛÛß ßÜ
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ßÛÜÜ ßÜÜ Üß ßßÜ ßÜßßÜÜ ÜÜÛÛÜÜ ÜÜ ÜÜÜÛÛ²²²²ÜÜÜ ÜÛßß
ÜÜßßÛÛÜÜ ßßß Üß Û ßßÜ ß ßÛÜ ß²²ß ß ßßÜ Û² ÛÛÛÛÛß
ÜÛÛ ßÛÛ ßßßÜÜÜÜß ÞÝ ÛÛ ßÛ² ÛßÛÛÛÛÜ
²ÛÛÜ Üß ÜÜß ÜÛß - J o i n U s ! - ßÜ ÜÛÛÛ²ß
ßßÛÛÛÛÜÜ ßßÜÜÜÜÜÛßß ÜÜÛÛÛÛßß
Üß ßÛÛÛ²Ü ²ÛÛß ßÜ
Û² ÛÜÛÛÛÛß Here we are AGAiN! Our team is based on talented and ßÛÛ ÜÛÛ
Û² ÛÛÛÛÛÜ experienced people from different known groups which ßßÜÜÛÛßß
ßÛÜÜ capabilities connected together can do something ÜÛßß
ÜÜßßÛÛÜÜ outstanding. If you are interested in joining Û² ÛÛÛÛÛß
ÜÛÛ ßÛÛ us and if you think we might need you then get in Û² ÛßÛÛÛÛÜ
²ÛÛÜ Üß touch with us at: team-again@hush.com ßÜ ÜÛÛÛ²ß
ßßÛÛÛÛÜÜ ÜÜÛÛÛÛßß
Üß ßÛÛÛ²Ü Experienced crackers, coders, software/hardware ²ÛÛß ßÜ
Û² ÛÜÛÛÛÛß suppliers, shell owners, are currently the ones we are ßÛÛ ÜÛÛ
Û² ÛÛÛÛÛÜ mostly looking for. ßßÜÜÛÛßß
ßÛÜÜ ÜÜÜÜß ÜÜÜÜ ÜÛßß
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ÜÛÛ ßÛÛßßÜÜÜÜÜÜÜÜ ßÜß ßÜ Üß ßÜß ÜÜÜÜÜÜÜÜßßÛ² ÛßÛÛÛÛÜ
²ÛÛÜ ÜßÜßß ßÛÛÛ Üß ßÛÜÜÜÜÜÛß ßÜ ÛÛÛß ßßÜßÜ ÜÛÛÛ²ß
ßßÛÛÛÛÜÜ ÜÛÛÜÜÜßß ßßß ßßÜÜÜÛÛÜ ÜÜÛÛÛÛßß
Üß ßÛÛÛ²Ü G r e e t i n g s ²ÛÛß ßÜ
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ßÜÜ ßßßßßßßßßßßßßßßßßßßßßßßßß ÛÛßßßßßßßßßßßßßßßß ÛÛßßßßßßßßßß Ûßß ²ÛÛ ßßßÛÛÛ
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