This release has identical code to v7.4.0 but has some updated documentation. It was also created to address a synchronization problem with Zenodo.

Full Changelog: v7.4.0...v7.4.1

v7.4.0 contains enhancements and bug fixes in these areas of functionality:

• Clarification of functionality and user indicator for the GRN vs. PPI network mode
• Graph display bugs were fixed
• UI consistency between sidebar panels and top menus
• Node coloring behavior and UI
• Clarification of options and interface for Export Data to Excel
• Port Network Database loading scripts to AllianceMine from Yeastmine
• Update scripts for appending additional degradation and production rates to the Expression Database
• Dev Ops
  • Rename the master branch to main
  • Update library requirements, including to Node 18.x
  • Implement GitHub Actions

What's Changed

• #1082: Fixed Fit to Window Functionality by @ceciliazaragoza in #1168
• Updating database [Cecilia's PR] by @ntran18 in #1175
• #1173 Change Protein-Protein-Physical Interaction Network to PPI Netw… by @ntran18 in #1182
• #1150 updated solution to align with the existing structure by @Amelie1253 in #1178
• #863 separated options into User-Uploaded and Expression Database by @Amelie1253 in #1181
• Updating scripts to download data from AllianceMine by @ntran18 in #1176
• Beta hotfix to avoid using export keyword by @ceciliazaragoza in #1183
• Improving upon #1183 hotfix by @ceciliazaragoza in #1184
• #1120 #1164 Fix for updating data by @ntran18 in #1185
• Parameter Order Fixed and Console Log Removed by @ceciliazaragoza in #1186
• #1180 change the class of averageDataBottomMenu from viewport to nodeColoring by @ntran18 in #1187
• Adding back old schemas for GRN and PPI by @ntran18 in #1188
• #1173 Rename the PPI file name from PPI Network to PPI by @ntran18 in #1190
• #1148 include test coverage in actions by @akaiap in #1170
• #1169: Network Mode is Informational in Navbar and Sidebar by @ceciliazaragoza in #1194
• #1192 Adding warnings when missing degradation rates or production r… by @ntran18 in #1195
• #1169: Network Mode In Side Panel by @ceciliazaragoza in #1200
• Updating coverage link by @akaiap in #1197
• Fixing genes' orders in network sheet for ppi and grn by @ntran18 in #1196
• Amelie milka 863 by @Amelie1253 in #1199
• Update .gitignore to ignore pycache files by @ntran18 in #1207
• Prettier Configuration by @akaiap in #1198
• Fixing schemas of genes tables to include time_stamp as key to prevent duplicate key issue when updating data by @ntran18 in #1220
• Switching from Object.keys to Object.entries to preserve order of genes by @ntran18 in #1225
• #1192 Adding warning when importing a workbook with degradation/production rate sheet with empty data and exporting that workbook with empty degradation/production rate by @ntran18 in #1230
• #1231 adding overflow: auto to warning models and error models by @ntran18 in #1232
• #1224 Only show warnings model when there are 1 or more warnings by @ntran18 in #1233
• Cosmetic Change for Expression Database Dropdown - Issue #863 by @MilkaZek in #1236
• Displaying Expression Database Opt Groups in Top Menu - for Issue #1211 by @MilkaZek in #1237
• #1241 Change spelling on function "showWarningsModel" to "showWarningsModal" by @ntran18 in #1242
• #1192 Modify the export warning message to desired message by @ntran18 in #1243
• Opt Groups Cosmetic Change - for Issue #1211 by @MilkaZek in #1245
• Removed Unused Import for Issue #1208 by @MilkaZek in #1246
• Disabled Grid Layout button/menu item when no graph is loaded for issue #1214 by @MilkaZek in #1247
• #1227: Renaming web-client to web-client-classic and downgrading npm packages by @ceciliazaragoza in #1234
• Improve the script to get data from AllianceMine by @ntran18 in #1249
• #1226: Create frontend in React by @ceciliazaragoza in #1251
• #1239: Establish how the React app will invoke the existing API by @ceciliazaragoza in #1255
• #1239: Fix for beta server config by @ceciliazaragoza in #1259
• Fixed PPI print functionality on updated branch for issue #1213 by @MilkaZek in #1261
• Fixed menu bar over-expanding issue and added side scrolling for issue #1172 by @MilkaZek in #1262
• 1266: React Prettier Config by @ceciliazaragoza in #1274
• #1120 Remove the constraint on feature type ORF for all tables and modified the logic of how to detect unique PPI by @ntran18 in #1268
• Fix for double downloading when exporting to excel and changing different expression sources by @ntran18 in #1281
• #1270 Modify preprocessing and loader scripts for expression tables to easily preprocessing and update different tables by @ntran18 in #1280
• Disable option to export a "network_optimized_weights" sheet for an unweighted network by @ntran18 in #1282
• #1174 Expansion/correction of export expression options and corresponding UI (pre-selection and deselection) by @Amelie1253 in #1285
• Added wrap-around styling for demo name in export to excel window by @MilkaZek in #1263
• #1212: Unweighted GraphML option properly grayed out by @Amelie1253 in #1288
• #1240: Basic Graph Implementation by @ceciliazaragoza in #1287
• #1265: Configure Prod React App to Access Server by @ceciliazaragoza in #1279
• Update expression database loader script to do staging + upsert for all tables except production/degradation rates by @ntran18 in #1297
• v7.4.0 release by @dondi in #1298

New Contributors

• @Amelie1253 made their first contribution in #1178
• @MilkaZek made their first contribution in #1236

Full Changelog: v7.2.0...v7.4.0

What's Changed

• Remove testing schema that I forgot to delete by @ntran18 in #1123
• #1106 Allowing query for any gene in gene table even if it's not in network table by @ntran18 in #1124
• #1080: Display warning when node coloring enabled for PPIs by @ceciliazaragoza in #1125
• #1102 Adding tests and errors message for uploading mixed type relati… by @ntran18 in #1127
• #1055 Make the node coloring menu for top bar and side bar to be cons… by @ntran18 in #1128
• 1080: Node Coloring Navbar and Sidebar synced and PPI warning displays less by @ceciliazaragoza in #1129
• #1130. Fixed path containing NaN and BOUNDARY_MARGIN warning by @ceciliazaragoza in #1131
• #1059 and #1093 Fixed issue for exporting SVG modify the graph itself. by @ntran18 in #1132
• #1107 Modify alpha value on optimization_parameters from 0.002 to 0.02 by @ntran18 in #1136
• #1098 Fixing file selector appears twice after importing wrong file by @ntran18 in #1133
• #1068 Allow node coloring for PPI by matching the gene name (MERGE #1080 first) by @ntran18 in #1134
• #1108 When export, making network and network_weights sheets to be id… by @ntran18 in #1137
• #1053 fixing p.length error by @ntran18 in #1138
• #59 Improve current export images (png and pdf) by @ntran18 in #1141
• Addition fix to previous fix for #1093 by @ntran18 in #1140
• Issue 1118 GitHub actions by @akaiap in #1135
• #1142: Warning String Displays Correctly by @ceciliazaragoza in #1143
• #1030 Change environment variable name by @ntran18 in #1154
• #1147 include npm lint by @akaiap in #1149
• #1145 gain compatibility with node 20.x by @akaiap in #1155
• #1146 syncing GitHub actions to badge by @akaiap in #1156
• #1144 Disable node coloring when uploading file with no expression by @ntran18 in #1153

New Contributors

• @akaiap made their first contribution in #1135

Full Changelog: v7.1.2...v7.2.0

This release is identical to v7.1.1 but has been created to address a synchronization problem with Zenodo.

GRNsight v7.1.1 includes the following new features and bug fixes:

• Features:
  • Lock Force Parameters are available for both Force Graph and Grid Layout. (#1016)
  • Protein Protein Physical Interactions Database and UI (#1028, #1020)
  • Adding Protein-protein interaction (PPI) demo (#1065)
  • Restrict to Viewport is enabled for D-pad and Zoom (#1083)
• Enhancements:
  • Change order of Yeastmine versions in generate GRN modal (#1035)
  • Filename and display nomenclature for YeastMine-generated Networks (#983)
• Bug Fixes:
  • Remove the checks from Force Graph and Grid Layout options from the menu. (#1016)
  • The current state of the Force Graph/ Grid Layout is reflected consistently between the menu and the side panel. (#1016)
  • Selected dataset is centralized to an internal state value, allowing the menu and the side panel to choose and display the same dataset. (#1033)
  • Fixed the button "Restrict Graph to Viewport" from the menu to work correctly (#1034, #1119)
  • Fixed the modals not to close when clicking or dragging the modal window with the mouse (#1029)
  • Fixed Node Coloring Top Menu Options from disappearing when uncheck "node coloring" box on side panel (#1081)
• Documentation:
  • Database setup in Initial Setup wiki (#1011)
  • Database update instructions (#1113)

GRNsight v7.1.0 includes the following new features and bug fixes:

• Features:
  • Lock Force Parameters are available for both Force Graph and Grid Layout. (#1016)
  • Protein Protein Physical Interactions Database and UI (#1028, #1020)
  • Adding Protein-protein interaction (PPI) demo (#1065)
  • Restrict to Viewport is enabled for D-pad and Zoom (#1083)
• Enhancements:
  • Change order of Yeastmine versions in generate GRN modal (#1035)
  • Filename and display nomenclature for YeastMine-generated Networks (#983)
• Bug Fixes:
  • Remove the checks from Force Graph and Grid Layout options from the menu. (#1016)
  • The current state of the Force Graph/ Grid Layout is reflected consistently between the menu and the side panel. (#1016)
  • Selected dataset is centralized to an internal state value, allowing the menu and the side panel to choose and display the same dataset. (#1033)
  • Fixed the button "Restrict Graph to Viewport" from the menu to work correctly (#1034)
  • Fixed the modals not to close when clicking or dragging the modal window with the mouse (#1029)
  • Fixed Node Coloring Top Menu Options from disappearing when uncheck "node coloring" box on side panel (#1081)
• Documentation:
  • Database setup in Initial Setup wiki (#1011)
  • Database update instruction (#1113)

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)

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)

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)

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.