GeneNoteBook Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning

Unreleased

0.3.2

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

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

0.2.0 2020-01-22

Added

Mongodb logging
Verbosity toggle for gff parsing

Changed

Meteor version 1.10
Node.js version >12
MongoDB version 4.2
Fully migrated all react components to new hooks API
Upgraded to alanning:roles@3.2.0
BACKWARDS INCOMPATIBLE: Modified user permission schemas to comply with alanning:roles@3.2.0 for the following collections: users, genomeCollection, genomeSequenceCollection, ExperimentInfo, Transcriptomes. Existing servers attempt to fix this with automatic schema migration.

Fixed

Footer correctly displays version info on production builds
Plot tooltips can be closed by clicking anywhere on the screen, similar to dropdown menu
Various orthogroup loading fixes: results are properly returned to the cli and loading an orthogroup with an existing ID throws an error.

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

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

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

0.1.13 2018-11-29

Fixed

DB path folder creation

0.1.12 2018-11-29

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

0.1.11 2018-11-28

Fixed

Header logo and font loading when running production bundle on localhost

0.1.10 2018-11-25

Fixed

CLI executables logging
Header logo
Even more font loading fixes
Console logging and debugging

0.1.9 2018-11-21

Fixed

Font loading for icon fonts
Usage string for CLI scripts
BLAST url redirect when not logged in

Changed

Moved Docker files to separate repository

0.1.8 2018-11-15

Fixed

Several GFF3 parsing issues

0.1.7 2018-11-12

Fixed

Genetable correctly infers query from URL

Added

Spinner indicating that gene table query is loading

Changed

Switched to React Router v4
Transcriptome sample selection interface

0.1.6 2018-10-30

Fixed

Ability to set permission levels of transcriptome samples
Gene table column order

Added

Genome name column for gene table

0.1.5 2018-10-22

Fixed

Correctly set isPublic attribute during genome loading
Only admin and curator can edit genes

Changed

Updated meteor.js to v1.8.0
Cleanup package.json

0.1.4 2018-10-03

Added

Ability to change passwords
Cancel filter option to GeneTable dropdown menu

Fixed

Orthogroup tip labels correctly show on firefox and safari

Changed

Color orthogroup tip nodes by organism

0.1.3 2018-09-29

Added

Protein domain popovers
Gene attributes with multiple values can be toggled to display more or less values
Option to download primary transcripts only
Add kallisto tsv files from command line

Fixed

Parsing newick formatted orthogroup trees and linking genes on gene ID / transcript ID
Adding Interproscan gff3 (genenotebook add interproscan)
Downloads no longer save empty files

Changed

Parsing genome annotation gff3 more efficiently fetches genomic regions and skips (with warning) unrecognized features

0.1.2 2018-08-29

Added

Popovers for genemodels

Fixed

Searching and dropdown queries no longer conflict

Changed

Orthogroup trees are now stored as text and parsed into an object in the browser, since some trees are too big to fit into MongoDB as objects.
During the adding of annotations, corresponding sequences are loaded one-by-one in stead of all at once. This fixes memory issues for large genomes.

0.1.1 2018-08-02

Added

Executable to add Orthofinder phylogenetic trees (genenotebook add orthogroups)

Fixed

Ability to unselect default gene attribute columns in GeneTable view
Scanning gene attributes in the admin section now also removes old/unused attributes

0.1.0 - 2018-07-25

Added

First GeneNoteBook version ready for use