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dondi/GRNsight: v5.0.0

Mihir Samdarshi; dondi; Nicole Anguiano; Anindita Varshneya; John Lopez; Alexia; Britain Southwick; Ian; Onariaginosa; Kam Dahlquist; Kevin; Blair Hamilton; Edward Bachoura; ArashLari; Eddie Azinge; Justin Kyle Torres; ZACH VAN YSSELDYK; Ahmad Mersaghian; luluriffic; B.J. Johnson; Qiyue

GRNsight v5.0.0 includes the following new features and bug fixes:

  • Created Client-Side testing documents for testing User Interface

    • It gives a set of instructions for a human to perform the tests because automated testing requires data analysis of the graph state to determine whether the desired feature has been achieved.
    • The tests are generated for a subset of features by permuting all possible combinations of feature states, which creates steps for the user to follow.
    • Each feature is given a unique static ID that is used to reference it easily.
    • The generator script can include features based on an activation state in the features JSON, by command line arguments, or by a separate JSON file created by the tester.
    • The client-side testing document was updated so that the features include their ID, and the wiki was updated. (#909)
  • Improved Import and Export functionality

    • GRNsight expanded its testing capabilities to check sheets that are not necessary to display a gene regulatory network model but are used in the GRNmap MATLAB software.
    • Error and warning messages became more descriptive and pinpointed which sheet the issue was found in, and the row/column or cell that the error was located. (#886, #896, #919, #920, #907)
  • Refactored existing GRNsight import test, and expanded export tests

    • Refactored existing GRNsight code to consolidate error and warning messages, as well as adding new tests for additional sheets in a GRNsight workbook. (#895, #894, #892, #898, #901, #915)
    • Updated tests to reflect additional features that GRNsight recently developed. (#850, #900, #902)
    • Expanded export tests to increase user visibility on possible errors that occurred during the import process.
    • Fixed bugs within the existing GRNsight export functionality and created a system to automatically fix minor issues within a workbook, alert a user of issues within a file that they must fix, or send an error message that something went wrong with the export process. (#874, #734, #918, #917)
  • Graph visualization was refined

    • Improved edge detection for nodes, eliminating issues with nodes going out of the viewport. (#803, #880)
    • Grey edge threshold was fixed to properly gray out all edges at 100% threshold. (#832, #876, #881)
    • Toggle buttons were fixed so that all buttons properly represent the state of the program. (#906, #910, #922)
    • Viewport resizing was modified to account for window resizing. (#926 , #923)
  • Export to excel feature

    • GRNsight can import data in a variety of formats including Excel workbook, SIF, and GraphML and can export to SIF and GraphML.
    • Added an element to the user interface that gives the user the option to export GRNsight data to an Excel workbook.
  • Gene information from Public Databases when a user selects a node (#841, #843, #844)

    • Application Processing Interfaces (APIs) allow GRNsight to gather data from public databases for display on gene pages. (#846)
    • Databases include Saccharomyces Genome Database (SGD), NCBI gene database, UniProt, JASPAR.
  • Documentation update

    • Updated wiki layout
    • New documentation
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