v3.1.0

GRNsight v3.1.0 includes the following new features and bug fixes:

• Added new gene information page feature
  • A dynamic gene information webpage now opens when a user right-clicks on a node in the graph. The page sends a series of Asynchronous JavaScript and XML (AJAX) data requests, written using the jQuery JavaScript library, to the JASPAR, NCBI Gene, UniProt, Ensembl, and Saccharomyces Genome Databases. The webpage is then populated with data returned regarding the gene’s description, protein sequence, DNA binding motif frequency matrix and sequence logo, and Gene Ontology terms. (#573, #603 , #604 , #606, #607, #620, #621, #638, #641, #642, #643, #645, #653)
• Began a refactor to consolidate state management into a single controller for user selected options
  • The front end has now started to follow a Model-View-Controller Architecture (MVC), and has a combination of new files to reflect that change (#576)
• Numbers can now be used as node labels (#438)
• Various bug fixes and UI enhancements
  • The option to Default to black edges has been reworded to be consistent with node coloring, and the behavior has been changed to reload the graph upon selection (#591, #627)
  • The print modal does not load twice when trying to print (#365)
  • Graph is now centered on the page when printing (#629)
  • The viewport "Fit to window" option now functions properly (#461)
  • Weight value font now shows up properly (#625)
  • The check box for dashed edges has been moved underneath the gray threshold slider

v3.0.0

GRNsight v3.0.0 includes the following new features and bug fixes:

• Node coloring feature was added to visualize gene expression data

  • GRNsight's Excel spreadsheet controller was expanded to process data from entire GRNmap input or output workbook, including expression and meta data (#241)
  • Node coloring feature was implemented (#566)
  • Demo Files 1 and 2 were updated to be in the correct format for node coloring (#585)

• Grid Layout option was added (#558)

• Gray edges options were improved

  • Gray edge threshold value was changed to percent scale (0 - 100%) (#518)
  • Option to show gray edges as dashed was added to increase accessibility for color-blind users (#568)

• User Interface was updated with new features

  • Dropdown menu options were expanded to duplicate all functions available in the sidebar menu (#462)
  • State variables for user selected options were consolidated (#576)
  • New features were added to the client-side testing document (#575)

• Documentation on GRNsight website was updated with new features (#587)

• Security Vulnerability with "qs" package was resolved (#564)

• Webpack module bundler added to GRNsight (#577)

v2.3.0

GRNsight v2.3.0 includes the following new features and bug fixes:

• d3 visualization library was updated to v4

  • It was determined that the move from v3 to v4 was feasible (#520)
  • Transitioned GRNsight to d3 v4 (#523)
    • Removed sliders for "Charge Distance" and "Gravity" since the combination of "Link Distance" and "Charge" sliders accomplishes the same functionality.

• ESLint correctly applied to code base

  • Found that ESLint was inconsistent between Mac and Windows developers (#535)
  • Linting errors were fixed (#538)

• Bug relating to edge weights were fixed

  • Minimum weights have been normalize to zero instead of the smallest weight in the worksheet (#515)
  • Edges that have the same weight value now render as thickest instead of thinnest edge thickness (#513)

• Additional tests were added

  • Syntactic tests for malformed GraphML XML (.graphml) files were completed which return errors to the user if an incorrectly formatted GraphML XML file is imported into GRNsight (#363)

• Developer-related issues were resolved

  • npm start procedure was fixed for Windows users (#521)

v2.1.11

GRNsight v2.1.11 includes the following new features and bug fixes:

• Improvements were made to the zoom functionality (#465), including:
  • Zoom now originates from the center of the graph #468
  • Zoom factor is now annotated on zoom slider #485
  • A vertical bar on the zoom slider indicates where the 100% zoom level is #484
  • Mousewheel zoom was disabled #473
  • Various bugs were fixed #479, #480, #508
• The user can now customize the normalization factor which controls how the thicknesses of the edges are determined based on the weight values #264 or reset it back to the default value for that graph #506
  • The user can also set the threshold upon which a weighted edge is colored gray using a slider
• Additional tests were added:
  • Syntactic tests for malformed Simple Interaction Format (.sif) files were completed which return errors to the user if an incorrectly formatted SIF file is imported into GRNsight #362
  • The routine that checks for syntactic errors in SIF and GraphML files was integrated with the semantic checker routine that looks for error common to all file formats that GRNsight supports #386
  • Tests for incorrectly named Excel worksheets were added #355
  • GRNsight now returns an error if a blank Excel, SIF , or GraphML file is uploaded #428
• An automatic client-side test generator was created that generates a document that can be followed by a user to systematically test specific combinations of user interface functions #326
• Additional bugs were fixed #491, #510
• Code quality was improved by the use of ESLint #503

v2.0.20

GRNsight v2.0.20 includes the following new features and bug fixes:

• When a weighted graph is loaded, the user now has the options to show weights upon mouseover of an edge, always show weights, or never show weights #285
• The bounding box and viewport for the graph have been separated allowing for the following new features:
  • The bounding box can now be fixed to the size of the viewport or adapted to the size of the graph #396, #398
  • The viewport size can be selected from among small, medium, and large options #159, #397
  • The best viewport size is automatically detected from the browser #395
  • The viewport can be fit to the size of the browser window #411
  • Zooming and scrolling have been enabled and refined #345, #399, #465, #467, #469, #470
• Improvements to visuals have been made, including:
  • Reducing the white space on either side of a node label for long labels #333
  • Setting the minimum size of a node #333
  • Making the pointed arrowhead larger for the thinnest edges #392
  • Minor adjustments to the placement and centering of edge end-markers #188
• The use of special characters (except for "-" and "_") in node labels are no longer supported due to integration of cytoscape.js code into GRNsight for future implementation of graph statistics feature #343
• "Under the hood":
  • The versions of package dependencies have been standardized and documented in the package.json file #334, #383
  • Code has been ported to version v0.7.2 of Node-xlsx #204
  • Testing suite has been refactored into semantic and syntactic tests #300, #335, #386
  • Additional syntactic tests have been written for SIF (#362) format
  • A catch-all syntactic error has been implemented for ill-formed GraphML files so that the server doesn't crash upon loading (#363)
  • A cap has been placed on the number of errors returned according to a tunable strictness parameter #339
• Numerous bugs have been fixed #335, #337, #340, #347, #364, #408, #419, #450, #451, #454, #479, #443

v1.18

GRNsight v1.18 includes the following new features and bug fixes:

• Implemented import of weighted and unweighted network data from Simple Interaction Format (SIF, *.sif) format #287, #301, #305, #306, #309
• Implemented export of weighted and unweighted network data to Simple Interaction Format (SIF, *.sif) format #288, #301, #309
• Implemented import of weighted and unweighted network data from GraphML (*.graphml) format #287, #306, #312, #314, #321
• Implemented export of weighted and unweighted network data to GraphML (*.graphml) format #288, #310, #311, #314
• Menu items for features that are not yet implemented are hidden #302
• The true filenames of the demo files now display in the menu bar #308
• Fixed bug where weights were not displaying upon edge mouseover by new implementation of the feature #284

v1.12

• The node and edge count is now displayed in the green menu bar #200
• The tooltips that display the weight values of edges were disabled for unweighted networks #194
• Most libraries that GRNsight uses have been updated to the most current version. See this wiki page for a list of libraries and versions: https://github.com/dondi/GRNsight/wiki/Library-Requirements, #177
• The test suite, test.js, was refactored to make unit tests more concise #207, #206
• Two warning messages were created to address potential formatting problems with input Excel spreadsheets:
  • Extraneous data outside of the adjacency matrix #189
  • NaN's found in the adjacency matrix #211, #212

v1.10.4

• Made edges gradually turn straight when nodes get close enough to each other. (#101)
• Implemented an upload counter for Google Analytics. (#116)
• Implemented additional test cases for the unit testing framework. (#144, #179, #180, #181)

v1.10.0

• Implementation of unit testing framework to facilitate test-driven development (TDD) (issue #144).
• Adjusted and refined space between repressor bars and their attached nodes (issue #101).
• Added page counter to the bottom of each webpage based on data collected through Google Analytics (issue #134).

v1.8.2

• Fix reset button before graph is loaded #173
• Bounding box constraints on nodes and self-referential edges #81