v6.0.7

GRNsight v6.0.7 includes the following new features and bug fixes:

• The back-end database was updated.
  • Refreshed the network database on the production database. (#1022, #1025)
  • Renamed Backend Database to appropriately reflect the data contained within. (#1020, #1025)
• The language of the file names in the menu bar was clarified.
  • When generating a network from the database it will display "GRN (data source; X genes Y edges)". (#1023, #1025)
• Dependency Version Update::
  • Updated from pg v8.0.0 to v8.0.3 (#1026)
• Bug Fixes:
  • Export to Excel now exports the specified sheets when exporting. (#1018, #1019)
  • Fixed the graph to display the edges of the network. (#1024, #1025)

v6.0.4

GRNsight v6.0.4 includes the following new features and bug fixes:

• The back-end database was updated

  • Apweiler data is uploaded to backend expression database. (#937, #971, #988)

• The language of the export to excel menu was clarified and the functionality expanded (#978, #985, #996)

  • GRNsight can now export additional sheets (i.e: production_rates, optimization_parameters, etc).
  • GRNsight allows users to choose which specific sheets they would like to include in their exported workbook.

• The language of the Load from Database modal was clarified (#982)

• The GRNsight API module and the GRNsight DAL were refactored and expanded

  • Removed residual hard-coded database information and replaced them with database calls. (#1003, #1004)
  • Transitioned remaining "bare" network calls to the API module. (#993, #1007)

• The Documentation for loading a local copy of GRNsight's databases was completed (#988, #961, #985)

• Bug Fixes:

  • Yeast genes with irregular naming patterns are now allowed in the load from database function. (#989, #966)
  • If a demo is chosen from the sidebar dropdown menu, the UI will update consistently. (#976, #985)
  • If a network is generated from the database and no relations are observed, GRNsight will work as intended. (#990, #985)
  • Node menu is active after generating a network from the database. (#977, #985, #984, #996)
  • Generating a network from the database correctly counts all of the edges in the assigned workbook name. (#972, #985)
  • Updated database to store timestamp values in UTC. (#995, #996)
  • Export to Excel modal acts appropriately when you cancel out of it and go back in. (#981)

v6.0.0

GRNsight v6.0.0 includes the following new features and bug fixes:

• A new gene regulatory network backend database was implemented and menu and panels were re-organized to reflect the new feature. (#949, #950, #952, #960)
  • In the Network menu, users can select one of the four demo networks, upload a network from a file, or (new) load a network from the database. The database contains regulation information from the Saccharomyces Genome Database (SGD) obtained via Yeastmine.(#949, #952)
  • The user selects genes to include in the network and GRNsight generated the connected network according to SGD data. (#952)
  • An Export menu now hold the Export functions. (#952)
• Bug Fix: If node coloring is disabled, it will remain disabled upon reload of the graph (#943)

v5.1.0

GRNsight v5.1.0 includes the following new features and bug fixes:

• New Expression Database

  • Refactored the Expression Database to take into account multiple species, and added appropriate data types to data stored within the database. #938
  • Connected Expression Database to the export to excel functionality, so that users can export data from the Expression Database. #938
  • Fixed bugs within the expression data selection. #941

• New Export to excel functionality

  • GRNsight can export workbooks using a modal selector to determine the data in the exported workbook.
    • Users can select between weighted and unweighted graphs, what expression data source (either the original expression data, or sources from the Expression Database), and which particular expression data sheets to export. #935 #938

• Documentation update

  • Updated Export to Excel instructions to reflect the new Export to Excel feature's functionality.

v5.0.0

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

v4.0.0

GRNsight v4.0.0 includes the following new features and bug fixes:

• GRNsight now follows a strict Model-View-Controller paradigm for its basic architecture. Except for the graphs, all elements displayed in the iframe (the main GRNsight functionality) now follow this architecture. These changes have occurred "under the hood" and will not be noticeable to users, except that it has made GRNsight more robust and has facilitated fixing many bugs caused by the interactions of new features introduced in previous versions. (#576, #735)
  • Force Graph Parameter slider values are saved when a graph is uploaded. (#760)
  • The File > Reload menu option reloads the graph in the layout configuration it was previously in. (#600)
  • Reset and Undo Reset Buttons are now grayed out when the Force Graph Parameter sliders are locked. (#245)
  • Various bugs that arose from the refactor are now fixed. (#592, #598, #610, #687, #736, #753, #758, #769, #772, #774, #778, #779)
• The Gene Page feature was improved both in its layout and "under the hood" to make database API calls and queries more robust. Changes were made to eventually enable the retrieval of gene information for genes from species other than Saccharomyces cerevisiae. (#621, #644, #654, #655, #658, #665, #676, #679, #680, #681, #689, #690, #691, #694, #695, #696, #697, #698, #701, #704, #709, #718, #722, #723, #730, #737)
  • Gene page variables are also now a part of GRNstate in the Model-View-Controller paradigm. (#719)
• Zoom levels remain consistent despite any user-defined parameter changes. (#561, #751)
• A bug was fixed in the automatic selection of the edge weight normalization factor. GRNsight now correctly uses the highest magnitude weight value for the default normalization factor, disregarding the sign of the weight. (#708)
• Gray edges now only have one thickness. (#437)
• GRNsight now returns an error when a file is too large. (#747, #766)
• The dropdown menu and sidebar menu viewport sizes now initialize to the same values. (#599)
• The Log Fold Change Max Value field will only accept positive values, and the allowable range has been set to 0.01 - 100. (#759)
• GRNsight is now wholly served over HTTPS. (#327, #688)
• GRNsight libraries and documentation were updated. (#715, #717)

v3.1.3

This is a small bug-fix release that addresses loose ends from v3.1.0. Please refer to that release for details.

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)