Ecosyste.ms: Issues

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GitHub / dondi/GRNsight issues and pull requests

#970 - D-pad and zoom control disappear from viewport when graph is loaded in beta 6.0.0

Issue - State: closed - Opened by kdahlquist over 2 years ago - 1 comment
Labels: bug, functionality, priority 0.5

#969 - Abstract for Yeast Genetics Meeting August 17-21, 2022

Issue - State: closed - Opened by kdahlquist almost 3 years ago

#966 - List of software needed to be installed in Seaver 120 and BIOL dept laptops

Issue - State: closed - Opened by kdahlquist almost 3 years ago
Labels: priority 0.5, logistics

#965 - Bug with Species Functionality in Top Toolbar in Master and Beta

Issue - State: closed - Opened by Onariaginosa almost 3 years ago - 2 comments
Labels: bug, invalid, functionality

#961 - Start working on documentation for database network loading scripts

Issue - State: closed - Opened by dondi almost 3 years ago - 5 comments
Labels: documentation, priority 0.5

#959 - Create and run GRNmap input workbooks with all Yeastract and SGD networks

Issue - State: closed - Opened by dondi almost 3 years ago - 21 comments
Labels: priority 0

#958 - Make networks for the Apweiler data from our own database

Issue - State: closed - Opened by dondi almost 3 years ago - 11 comments
Labels: priority 0

#957 - Consolidate existing web app API calls into an abstraction layer

Issue - State: closed - Opened by dondi almost 3 years ago - 2 comments
Labels: priority 0, review requested, refactor

#954 - Implement automatic updating of adjacency matrix data

Issue - State: open - Opened by dondi about 3 years ago - 1 comment
Labels: feature request, question, priority 2, database

#952 - Design and implement a user interface for accessing GRN data

Issue - State: closed - Opened by dondi about 3 years ago - 17 comments
Labels: feature request, priority 0.5, CMSI4072, database

#950 - Refactor existing database code into a genuine DAL module

Issue - State: closed - Opened by dondi about 3 years ago - 8 comments
Labels: priority 0.5, CMSI4072, refactor, database

#945 - Fit to window causes the graph to shrink to one node

Issue - State: closed - Opened by ahmad00m about 3 years ago - 26 comments
Labels: bug, priority 0, graph layout

#943 - Disabling node coloring will be enabled upon reload

Issue - State: closed - Opened by ahmad00m about 3 years ago - 20 comments
Labels: bug, priority 0, review requested

#937 - yeast expression data for database

Issue - State: closed - Opened by kdahlquist over 3 years ago - 43 comments
Labels: documentation, priority 0, review requested, for next release, database

#931 - Alexia and John are on the MS in CS webpage!

Issue - State: closed - Opened by kdahlquist over 3 years ago
Labels: web site, priority 0.5

#929 - Jade -> Pug Dependency Upgrade

Pull Request - State: closed - Opened by mihirsamdarshi over 3 years ago - 1 comment

#927 - Fix for #804

Pull Request - State: closed - Opened by igreen1 almost 4 years ago

#924 - Make Reload part of the Layout sidebar

Issue - State: closed - Opened by dondi almost 4 years ago - 1 comment
Labels: wontfix, priority 0.5, enhancement

#913 - Dependency issue regarding jsdom and canvg

Issue - State: closed - Opened by Onariaginosa almost 4 years ago - 10 comments

#912 - Security updates first wave

Pull Request - State: closed - Opened by dondi almost 4 years ago - 2 comments

#897 - Explore possible refactor to consolidate creation of new networks

Issue - State: closed - Opened by dondi about 4 years ago - 18 comments
Labels: priority 0, review requested, refactor

#887 - Corrected arrow direction

Pull Request - State: closed - Opened by luluriffic over 4 years ago

#872 - Revise GRNsight people page to match GRNmap layout more closely

Issue - State: open - Opened by dondi over 4 years ago - 2 comments
Labels: web site

#863 - Need indicator to user to differentiate between user-uploaded and Expression Database data

Issue - State: open - Opened by kdahlquist almost 5 years ago - 2 comments
Labels: question, functionality, priority 0.5, enhancement

#862 - Dahlquist data in Expression Database is redundant with demo files 1 and 2

Issue - State: closed - Opened by kdahlquist almost 5 years ago - 1 comment
Labels: functionality, backlog, enhancement

#858 - When clicking on links from gene page, each click should open a new tab, not overwrite tabs that are already open

Issue - State: closed - Opened by kdahlquist almost 5 years ago - 1 comment
Labels: feature request, functionality, backlog, gene page

#857 - Gene Page should only retrieve SGD data when yeast is selected as a species

Issue - State: closed - Opened by kdahlquist almost 5 years ago - 2 comments
Labels: bug, functionality, backlog, gene page

#854 - Fix demo files so that warning that no species chosen doesn't display

Issue - State: closed - Opened by kdahlquist almost 5 years ago - 2 comments
Labels: bug, functionality, testing, backlog, gene page

#853 - Gene Page display of GO information is disorganized with certain browser window sizes

Issue - State: closed - Opened by kdahlquist almost 5 years ago - 1 comment
Labels: bug, web site, functionality, backlog, gene page

#848 - 3-gene networks for six species to test gene page functionality

Issue - State: closed - Opened by kdahlquist almost 5 years ago - 22 comments
Labels: functionality, testing, backlog, gene page

#814 - Case-insensitivity for all worksheets in the Excel workbook

Issue - State: open - Opened by kdahlquist about 5 years ago - 2 comments
Labels: feature request, priority 1, functionality, enhancement

#808 - TypeError: strainData.data[gene] is undefined error for a particular workbook

Issue - State: closed - Opened by kdahlquist over 5 years ago - 3 comments
Labels: bug, functionality, backlog

#775 - Systematically check how large files can be before crashing server

Issue - State: closed - Opened by kdahlquist over 5 years ago - 1 comment
Labels: testing, backlog

#752 - When show all edge weights is checked, the edge weights might overlap

Issue - State: closed - Opened by kdahlquist over 5 years ago - 2 comments
Labels: functionality, backlog, enhancement

#720 - Read species name/taxon ID from GRNmap file and load into GRNstate

Issue - State: closed - Opened by dondi about 6 years ago - 34 comments
Labels: feature request, functionality, backlog, gene page

#682 - Investigate writing tests for gene pages using SinonJS framework

Issue - State: closed - Opened by kdahlquist over 6 years ago - 19 comments
Labels: testing, backlog, gene page

#675 - Create Documentation / Guidelines for GRNsight's Design

Issue - State: open - Opened by jlopez616 over 6 years ago - 1 comment
Labels: documentation, backlog

#674 - Security vulnerabilities in packages used by GRNsight

Issue - State: closed - Opened by mihirsamdarshi over 6 years ago - 8 comments
Labels: refactor

#666 - @kdahlquist to review colors for gene pages

Issue - State: closed - Opened by kdahlquist over 6 years ago - 3 comments
Labels: backlog, enhancement, gene page

#587 - Documentation needs to be written for new features in v3.0.0

Issue - State: closed - Opened by kdahlquist almost 7 years ago - 9 comments
Labels: documentation, priority 0.5

#575 - Add new features to client-side testing document

Issue - State: open - Opened by kdahlquist almost 7 years ago - 31 comments
Labels: ongoing, documentation, testing

#541 - Implement GraphML XSD validation

Issue - State: closed - Opened by dondi over 7 years ago - 12 comments
Labels: feature request, priority 1, testing

#540 - Catch missing < in GraphML node tags

Issue - State: closed - Opened by dondi over 7 years ago - 9 comments
Labels: testing, review requested

#507 - Add tooltips for new UI features

Issue - State: open - Opened by kdahlquist over 7 years ago - 3 comments
Labels: web site, priority 0.5, enhancement

#453 - We should allow GRNsight to be accessed at dondi.github.io/grnsight/

Issue - State: closed - Opened by NAnguiano almost 8 years ago - 6 comments
Labels: web site, backlog, logistics

#406 - Comment on this issue when beta is refreshed.

Issue - State: open - Opened by kdahlquist almost 8 years ago - 151 comments
Labels: ongoing, logistics

#400 - New papers to read

Issue - State: open - Opened by kdahlquist almost 8 years ago - 26 comments
Labels: ongoing, logistics

#351 - Loophole for number of nodes/edges warning vs. error

Issue - State: closed - Opened by kdahlquist about 8 years ago - 1 comment
Labels: bug, testing, backlog

#341 - Improve server-side logging to capture the filename that crashes it

Issue - State: closed - Opened by kdahlquist over 8 years ago - 2 comments
Labels: testing, backlog

#281 - Investigate influence of weights on force graph layout

Issue - State: closed - Opened by kdahlquist over 8 years ago - 1 comment
Labels: feature request, functionality, backlog, graph layout

#205 - Review library dependencies and confirm compatible/incompatible upgrades

Issue - State: open - Opened by dondi over 9 years ago - 15 comments
Labels: ongoing, functionality, documentation, logistics

#59 - Export vector image to pdf and/or svg in a format that can be read by Adobe Illustrator

Issue - State: open - Opened by kdahlquist over 10 years ago - 29 comments
Labels: feature request, functionality, priority 0.5