Genenotebook v0.3.2

this release also includes changes from 0.3.1

0.3.2 2022-11-04

Added

• Support for additional InterproScan file formats (tsv, gff, xml)
• EggNog annotations
• BLAST/diamond alignment reading/visualizing

Changed

• Meteor version 2.8.0

0.3.1 2021-01-28

Added

• User accounts can be added/changed/removed from the CLI
• Bulk operations for user account management through CLI
• --dbStartupTimeout option to genenotebook run to allow specifying how long to wait for the mongo daemon to start
• --dbCacheSizeGB option to genenotebook run to allow specifying how many GBs of RAM can be used for mongodb cache.

Changed

• Removed settings.json
• Phylogenetic tree now made with react-bio-viz
• Meteor version 2.5.6

Fixed

• Once again fixed version display
• Popover menus

Genenotebook v0.3.1

Added

• User accounts can be added/changed/removed from the CLI
• Bulk operations for user account management through CLI
• --dbStartupTimeout option to genenotebook run to allow specifying how long to wait for the mongo daemon to start
• --dbCacheSizeGB option to genenotebook run to allow specifying how many GBs of RAM can be used for mongodb cache.

Changed

• Removed settings.json
• Phylogenetic tree now made with react-bio-viz
• Meteor version 2.5.6

Fixed

• Once again fixed version display
• Popover menus

Genenotebook v0.3.0

[0.3.0] 2021-09-17

Added

• External links and descriptions on GO terms and INTERPRO ids
• Make the list of default user accounts configurable using settings.json configuration file
• Ability to upload genome sequence through the browser

Changed

• Meteor version 2.4
• Node.js version 14

Fixed

• Option parsing for CLI
• Version display in browser

GeneNoteBook v0.2.0

0.2.0 2020-01-22

Added

• Mongodb logging
• Verbosity toggle for gff parsing

Changed

• Meteor version 1.9
• Node.js version >12
• Fully migrated all react components to new hooks API
• Upgraded to alanning:roles@3.2.0
• Modified user permission schemas to comply with alanning:roles@3.2.0 for the following collections: users, genomeCollection, genomeSequenceCollection, ExperimentInfo, Transcriptomes

Fixed

• Footer correctly displays version info on production builds
• Plot tooltips can be closed by clicking anywhere on the screen, similar to dropdown menu

GeneNoteBook v0.1.16

[0.1.16] 2019-05-02

Added

• Working 404 page
• Multiline queries in gene table

Changed

• Meteor version 1.8.1

Fixed

• Base url of download links
• BLAST result options menu
• Downloads for users that are not logged in
• Trim whitespace search string
• Genome selection menu

GeneNoteBook v0.1.15

[0.1.15] 2019-03-26

Added

• Download options for annotations and gene expression

Changed

• Download loading indicators

Fixed

• Downloading no longer requires user to be logged in

GeneNoteBook v0.1.14

[0.1.14] 2019-03-21

Added

• Loading indicator for expression plots
• View gene expression and protein domains of BLAST hits
• Link BLAST hits to Gene Table
• Footer that displays running GeneNoteBook version and links to documentation
• Warning indicating absence of BLAST databases
• Set BLAST Parameters
• Display original input and used parameters of finished BLAST jobs

Changed

• Orientation of gene expression x-axis to maximize space use

Fixed

• Expression plots now display scroll on overflow
• Executables read version info from package.json instead of being hardcoded
• BLAST databases no longer mysteriously disappear

GeneNoteBook v0.1.13

[0.1.13] 2018-11-29

Fixed

• DB path folder creation

GeneNoteBook v0.1.12

Added

• --db-path option for genenotebook run to specify location of MongoDB datafiles when letting GeneNoteBook handle the MongoDB daemon.

Changed

• GeneNoteBook now runs a MongoDB daemon under the hood by default, so having a running MongoDB daemon is no longer a requirement. It is still possible by specifying --mongo-url when executing genenotebook run.
• Updated to Meteor 1.8.0.1

GeneNoteBook v0.1.11

Fixed

• Header logo and font loading when running production bundle on localhost