Spotfire Tools, Guides, and Information Links

An overview of the Spotfire DecisionSite data analysis software.

We have extensive experience in the development of custom software modules within the Spotfire data analysis system.  Spotfire DecisionSite offers a wealth of sophisticated data visualization and analysis tools.  However, there are often needs for additional customization for particular applications.  The Spotfire system is very open, allowing customized software development on multiple fronts.  Most of our work has been with Spotfire DecisionSite client, with only limited work using the new TIBCO Spotfire product.

Example of custom Guides integrated with Spotfire DecisionSite

Guides

First, Spotfire offers the ability to capture difficult analysis workflows into a step-by-step "Guide" that can be executed by any user using their dataset.  We have developed many of these guides, for analyses involved in high-throughput screening, dose-response curve analysis, gene expresssion studies, etc.  These guides are made even more powerful by the inclusion of specific custom analysis tools (seel below).

Spotfire Information Links allow users to retrieve data from databases without needing to understand SQL.

Information Links

Secondly, the Spotfire Information Interaction Designer system offers a quite sophisticated way to link to one or more corporate databases.   The data can be exposed to the DecisionSite users as "folders", from which the users can pick which data they want to retrieve, and to be prompted for specific filtering criteria.  Furthermore, specific data retrievals can be pre-packaged into an Information Link, which allows even the least sophisticated users to retrieve real-time data directly from the database by simply selecting the link and answering some simple filtering questions.  All of the complicated data access code is automatically generated.  We have designed many of these Information Links; in some very complex situations we need to do a small amount of manual modification to get the desired result from the links.

Tools

Finally Spotfire allows the development of custom data analysis tools.  The default package has a great many tools.  However we have found some additional tools are required for certain circumstances.  The customs tools can be integrated directly into the DecisionSite's "Tools" menu.  Here are some examples of custom Tools that we have created:

Universal Data Importer tool

• Universal Data Importer:  A general tool for import of text-based data from instruments. For new instruments, an Excel template sheet is defined to harvest the desired data. Excel formulas can be used to pre-condition data before importing, as desired. User of tool can select multiple files, assigning to different groups if desired. Data files are read, extracted and transformed, and then transported into Spotfire automatically.

  Plate Layout Tool

• Ranking: A ranking column is created based upon sorting the dataset on columns selected by user. Ranking numbers can span entire dataset, or can be reset based on another column (for example, you could rank from 1…96 the response of the wells on each plate in your dataset).

• Plate Layout: A graphical interface to allow definition of well layout on microtiter plates. Allows user to define control wells, test wells, compound identifiers, concentrations. Special tools for quick definition of dose-response concentration gradients. If launched from within Spotfire, will send layout back into Spotfire. Also can save layout for future use in Spotfire without invoking tool.

• Custom Functions for "New Column from Expression" tool: Spotfire's standard "New Column from Expression" tool allows custom functions to be added. We have created many custom functions, including: Column counting based on matching desired values (CountEqual, CountNull)), Statistical functions (StDev across columns), Choose(), text search in columns (FindInAny, FindInAny_Count, FindInAny_Index ), Regular expression functions (RegExExtract, RegExReplace, RegExTest)

• Z/Z' Calculator: Computes the Z or Z' for each plate. Requires proper definition of control wells (i.e., plate layout).

  Flag Bad Data tool

• Flag Bad Data:  Floating window to allow user to quickly mark of bad records, using standard Spotfire marking techniques. Bad record selections are accumulated as the user proceeds with the data review. Many other tools in the BioAutomatix Spotfire tool suite offer the option to ignore records marked as bad in their calculations.

• New Column from Grouped Data:  This tool allows the aggregation of data from multiple related rows. A typical usage would be computing the Mean & StDev of a group of replicates. Supported functions include: Mean, StDev, Median, Sum, Max, Min, MAD. Special filters can be applied to limit the rows utilized for aggregation (for example, only Control wells).

  Curve Fitting tool

• Curve Fit: Automates the use of Excel Solver or GraphPad Prism functionality to perform curve-fitting of dose-response curves. Uses Sigmoid dose-response model, allows user to control fitting parameters. User can re-fit selected data. Additional curve models can be written if desired.

• Reset Ranges:  Under some conditions, selecting "Reset to All" does not again display all records. This tool ensures that all record filters are removed.

• Column Management:  Rename/delete/hide/show columns based upon wildcard matching (for example, hide all TimePoint query devices, which are typically not useful)

• Rename Pivoted/Normalized Columns:  After pivoting or normalizing, column names become ugly. This renames to more logical names.

Many of these tools can be made available at a fixed cost, because little or no additional customization may be necessary.  And of course, we are more than happy to develop completely new tools.  Almost any analysis tool that you can imagine can be added into the Spotifre system.  We write tool code in Javascript and VBScript, or VB.NET.  All code will be provided to allow you to further develop in the future, if required.  Note that all tools utilize the Spotfire Tool Automation model, which ensures the proper recording of the tool usage into Guides.