Activity
From 10/31/2013 to 11/29/2013
11/29/2013
- 11:11 pm Feature #118 (New): search auto completion by right clicking from gene tracks
- * Is it possible or useful to implement auto completion when we do gene name searching from right clicking of gene/SN...
- 11:10 pm Feature #117 (New): add track name to genome snapshot
- * I think it would be useful if the track name could be display when generating genome snapshot
11/24/2013
- 09:17 pm Bug #112 (Closed): bam display as 'density' when specified as 'full' in UCSC hub
- 09:13 pm Bug #113 (Closed): retrieve session which contains USCS hub error
- fixed and closed
- 09:12 pm Bug #116: chromHMM tracks cannot be found by "chromhmm" keyword
- * that's a useful update
* tested worked.
* so the search will perform against not just track name, also meta data ... - 05:15 pm washugb v29 release
- * We have released v29 of WashU EpiGenome Browser.
h2. Updates:
* access HTTPS resources, including Dropbox, fo... - 03:44 pm Bug #114: Cannot read property 'cigar' of undefined
- no clue...
- 03:42 pm Bug #113 (Resolved): retrieve session which contains USCS hub error
- fixed on public server
- 03:25 pm Bug #111: Tracks disappear when using config panel
- Sorry I just figured out the trouble. You must have used this in declaring the track in your hub:
height:"20",
... - 01:47 pm Bug #112 (Resolved): bam display as 'density' when specified as 'full' in UCSC hub
- fixed on public server
- 11:55 am Bug #116 (Resolved): chromHMM tracks cannot be found by "chromhmm" keyword
- fixed in v29 on public browser
- 11:55 am Bug #116: chromHMM tracks cannot be found by "chromhmm" keyword
- fixed in v29 on public browser
- 10:22 am Bug #116 (Closed): chromHMM tracks cannot be found by "chromhmm" keyword
- in hg19, search tracks by keyword "chromhmm" and found nothing
"chromhmm" should match a metadata term and should tu...
11/23/2013
- 04:19 pm Bug #115: tracks do not relocate and some disappear in GSV
- When I load a new browser session (not from a saved session ID, but start over completely), then load the gene list, ...
- 04:07 pm Bug #115 (New): tracks do not relocate and some disappear in GSV
- Loaded my browser session ID: L607cgtoI3
Then loaded attached regions into GSV via copy-paste.
Adjust to view "gen...
11/22/2013
- 09:31 pm Bug #114 (Rejected): Cannot read property 'cigar' of undefined
- * use the UCSC hub: http://vizhub.wustl.edu/hubSample/hg19/hg19/trackDb.txt
* open a 2nd panel
* switch to full
* ... - 09:24 pm Bug #113 (Closed): retrieve session which contains USCS hub error
- * session id: LvPDnsxtlZ (public hg19)
* use the UCSC hub mentioned before, save session, retrieve, an error happene... - 09:20 pm Bug #112 (Closed): bam display as 'density' when specified as 'full' in UCSC hub
- * minor issue
* when submit an UCSC hub, I have define the bam tracks display as 'full' mode
* the browser actually...
11/21/2013
- 11:17 am Bug #111 (New): Tracks disappear when using config panel
- Tried adding three new tracks via Facet browser from my data hub. When I load them they appear with a huge track heig...
- 12:08 am Bug #90 (Closed): long range track display runs into error
- * tested the long range tracks and could be displayed well.
* Closed and could re-opened if we found this issue again.
11/20/2013
- 03:13 pm Feature #110 (New): hub check button
- * I think it would be great to add a 'check hub' button to the hub submission panel
* users could check the hub firs... - 10:28 am Bug #109: Problem saving session
- Saving session with many tracks and a large gene set will run into this error
mysql rejects a very long query by s...
11/19/2013
- 05:13 pm Bug #109 (Closed): Problem saving session
- Tried to save my session (for the second time) but get an error.
- 05:13 pm washugb v28 release
- h2. updates
* multiple track selection, for details please see: http://washugb.blogspot.com/2013/11/v28-1-of-2-mul... - 08:06 am Feature #108 (New): compute pearson correlation in scatterplot
- as requested by a user from MIT
11/18/2013
- 10:33 pm Bug #87 (Closed): SNP track showing all SNPs to be on reverse strand
- * could observer SNPs in reverse strand!
- 10:28 pm Bug #82 (Closed): crashed when restoring session
- * cool fix
- 10:27 pm Bug #74 (Closed): circlet plot generates wrong graph
- * tested zoom in the circlet view, Fixed!
- 10:22 pm Bug #71 (Closed): cannot handle irregularity in custom metadata
- * cool error message!
- 10:17 pm Feature #60 (Closed): "file type" category for custom facet table
- * nice feature!
- 10:15 pm Bug #66 (Closed): Save custom metadata vocabulary into session
- * closed
- 10:06 pm Bug #65 (Closed): Error rendering RRBS track
- *fixed!
- 10:01 pm Bug #73 (Closed): bam track in json hub set to show cause syntax error
- fixed
- 10:00 pm Feature #67 (Closed): change background color
- Feature completed!
- 09:59 pm Bug #88 (Closed): gene tracks are omitted in restored sessions
- * closed
- 09:58 pm Bug #91 (Closed): crashed when loading bam track
- * tested loading custom bam file, works! Closed!
- 09:56 pm Bug #92 (Closed): configuration of category track not 'apply to all' and 'apply background'
- * nicely solved
- 09:55 pm Bug #94 (Closed): Crashed when creating gene set on mm9
- works well and closed
- 09:54 pm Bug #95 (Closed): crashed when loading a hub with wrong metadata vocabulary
- fixed and closed
- 09:53 pm Feature #98 (Closed): multiple selection of tracks
- * feature completed!
- 09:51 pm Bug #102 (Closed): problem loading a datahub with no tracks shown by default
- fixed and closed!
- 09:51 pm Bug #104 (Closed): configuration of long range track missing height adjustment
- nicely solved!
- 09:49 pm Bug #107: handling of hub file errors
- * this is cool
* how about adding an UCSC option for datahub type for loading UCSC hubs? - 09:47 pm Bug #106 (Closed): gencodeV17 track cannot be saved in session
- fixed and closed!
- 12:05 pm Bug #59 (Closed): error filling contents for facet table of 2nd datahub
- 12:04 pm Bug #69 (Rejected): track name in svg
- I may not be able to solve it soon, but user can either turn off track name on SVG output, or increase the track name...
- 12:03 pm Bug #73 (Resolved): bam track in json hub set to show cause syntax error
- Fixed in v27.3 on test browser
In the datahub, if a bam track is set to "show", it will be shown as a read density... - 11:58 am Bug #92 (Resolved): configuration of category track not 'apply to all' and 'apply background'
- Fixed in v27.3, on test browser
Both options "apply to all" and "background color" are now available for categoric... - 11:57 am Bug #104 (Resolved): configuration of long range track missing height adjustment
- Fixed in v27.3, on test browser
If the long range track is in heatmap mode, the height option will appear, otherwi... - 11:54 am Bug #106 (Resolved): gencodeV17 track cannot be saved in session
- Fixed in v27.3, on test browser
- 11:54 am Bug #107 (Resolved): handling of hub file errors
- Fixed in v27.3, on test browser
- 11:53 am Bug #107 (Closed): handling of hub file errors
- errors include:
non-existent hub file, e.g. http://vizhub.wustl.edu/hubSample/hg19/hub.missing
file with wrong ... - 11:50 am Bug #102 (Resolved): problem loading a datahub with no tracks shown by default
- Fixed in v27.3 on test browser
- 10:19 am Bug #106 (Closed): gencodeV17 track cannot be saved in session
- found by Rebecca on hg19, public browser
- 07:25 am Bug #105 (Rejected): 'Remove all' button in Facet of public hub was not working
- that's not an issue, that's a feature
One REMOVE ALL button controls the native tracks and will remove all native ... - 07:19 am Bug #103 (Rejected): taking screen shot of genome snapshot
- Don't know what you mean. The "screenshot" button IS DISABLED when you click it.
- 07:17 am Feature #98: multiple selection of tracks
- when you have multiple-selected some tracks, and then you right click on a new one that's not selected, the selection...
11/17/2013
- 09:23 pm Bug #105 (Rejected): 'Remove all' button in Facet of public hub was not working
- * after loading one the public hub
* try to remove all tracks (native or tacks from hub)
* the two 'Remove all' but... - 07:45 pm Bug #104 (Closed): configuration of long range track missing height adjustment
- * seems the configuration of long track was not normal
** missing height adjustment
** adding font change like gene... - 07:34 pm Bug #103 (Rejected): taking screen shot of genome snapshot
- * Is it possisble to make this 'screenshot' button gray (not usable) after clicking it, now this button could always ...
- 07:24 pm Feature #98: multiple selection of tracks
- * few minor issues:
** after multiple selection, sometimes the yellow background of track name would disappear (like... - 02:20 pm Bug #102 (Closed): problem loading a datahub with no tracks shown by default
- Load a datahub (json) with all tracks set to "hide"
the loading GIF image never disappears, making it impossible f...
11/15/2013
- 10:59 pm Feature #98: multiple selection of tracks
- * I tested the multiple selection on PC works pretty well
* might use check box instead of keyboard events would bri...
11/13/2013
- 10:03 am Bug #101: json syntax error when retrieving session
- sorry for missing those info, hg19 on public server.
- 09:49 am Bug #101: json syntax error when retrieving session
- genome and server?
- 09:48 am Bug #101 (Closed): json syntax error when retrieving session
- * I have this session id: m4doLKKJHz with many status, only one of the status (id: 954222367) will give me 'Syntax er...
11/11/2013
- 10:27 am washugb v27 release
- * We have released v27 of WashU EpiGenome Browser.
h2. Updates:
* GENCODE V17 track for the human genome, for d...
11/10/2013
- 12:08 am Bug #100 (Closed): geneplot (lines plot) error
- Fixed and closed.
11/09/2013
- 07:37 am Bug #100 (Resolved): geneplot (lines plot) error
- Fixed, thanks!
- 12:05 am Bug #93 (Closed): new genecode v17 track not work with genome snapshot
- * fixed
11/08/2013
- 11:59 pm Bug #100 (Closed): geneplot (lines plot) error
- * happened both at public and test server
* choose lines plot from geneplot panel, see screeshot for error message - 06:46 am Bug #96 (Rejected): location jumping was not accurate
- 06:46 am Bug #96: location jumping was not accurate
- reported in #46
11/07/2013
- 05:36 pm Feature #99 (New): function that move track(s) to top or bottom
- * Is it useful to add a function that move track(s) to top or bottom of canvas?
- 05:36 pm Feature #98 (Closed): multiple selection of tracks
- * Is it possible to support multiple selection of tracks? Like I want to select 2 tracks from different samples or as...
- 05:33 pm Feature #97 (New): user defined track color
- * when changing track colors, is it possible to use other colors? Such as using RGB values or HEX values.
- 05:32 pm Bug #96 (Rejected): location jumping was not accurate
- * in the browser, if I want to jump to a location for example chr1:89443114-89943027
* the browser will give me chr1... - 02:01 pm Bug #95 (Resolved): crashed when loading a hub with wrong metadata vocabulary
- Fixed on public browser. The "Age" term which appears both as parent and child will be rejected. An error message wil...
- 02:00 pm Bug #95 (Closed): crashed when loading a hub with wrong metadata vocabulary
- the vocabulary contains following:
"Age":{
"Age":["1 year", "2 year"],
...
} - 09:32 am Bug #94 (Resolved): Crashed when creating gene set on mm9
- Fixed on public browser.
text descriptions of above items contain quote marks that need to be dealt with. - 09:30 am Bug #94 (Closed): Crashed when creating gene set on mm9
- With following text input:
Mir7675
Mir6387
Mir3066
Mir6937
Mir680
Mir5099
Mir1938
Mir5627
Mir1843a
Mir306... - 08:26 am Bug #92: configuration of category track not 'apply to all' and 'apply background'
- yes.
- 07:34 am Bug #92: configuration of category track not 'apply to all' and 'apply background'
- Do you mean the options "apply to all" and "apply background" are not available for categorical track?
11/06/2013
- 09:43 pm Bug #93 (Closed): new genecode v17 track not work with genome snapshot
- * an error "Uncaught TypeError: Cannot read property 'chr1' of undefined "
- 09:30 pm Bug #92 (Closed): configuration of category track not 'apply to all' and 'apply background'
- * not sure this was a bug or specific design though
11/05/2013
- 07:29 pm Bug #91 (Resolved): crashed when loading bam track
- Fixed in v26.2 on PUBLIC browser, still there on the test for you to see it
the error was because the code was try... - 07:28 pm Bug #91 (Closed): crashed when loading bam track
- try loading a bam track from submission panel, crashes
- 06:26 pm Bug #90 (Resolved): long range track display runs into error
- fixed in v26.2 on PUBLIC browser. Still there on test browser
it's the max score-calculating part that's causing t... - 06:21 pm Bug #90 (Closed): long range track display runs into error
- display a long range track. The track may not be able to show at all, or crashes when turning its display mode.
- 01:26 pm Bug #89: mCRF tracks not recognized
- Did a quick fix and added the error-reporting function, see this:
http://epgg-test.wustl.edu/browser/?genome=hg19&... - 11:53 am Bug #89 (Resolved): mCRF tracks not recognized
- Thanks for the report, following issues have been fixed.
* numerical hub tracks (bigwig or bedgraph) will be show... - 11:16 am Bug #89 (Closed): mCRF tracks not recognized
- When I load my dataHub, some of the mCRF tracks are not recognized by the browser. They are set to mode:"full" to app...
- 07:41 am Bug #88 (Resolved): gene tracks are omitted in restored sessions
- Fixed on public browser. This problem still exists on test browser for you to see it.
BE SURE TO FULLY TEST THE BR... - 07:40 am Bug #88 (Closed): gene tracks are omitted in restored sessions
- save a session with numerical tracks and gene track
restore this session
the gene track is absent from tracks resto...
11/04/2013
- 10:04 pm Bug #86: 2nd panel didn't align top with main panel
- * happens on the iMAC i am using, not on PC
11/01/2013
- 11:05 am washugb v26 release
- We have applied v26 source code to our public servers.
h2. updates:
* SNP information is a long-desired feature...
10/31/2013
- 10:46 am Bug #87 (Resolved): SNP track showing all SNPs to be on reverse strand
- Fixed on public server, still visible on test server
Problem is that SNP track use +/- to indicate SNPs while the br... - 10:44 am Bug #87 (Closed): SNP track showing all SNPs to be on reverse strand
- happens to all SNPs in hg19 SNP track
- 09:39 am Bug #86 (Closed): 2nd panel didn't align top with main panel
- * minor display issue
* see screenshot - 09:35 am Bug #84 (Closed): background in 2nd panel didn't apply to main panel automatically
- Fixed!
- 09:35 am Bug #85 (Closed): rmsk track configuration not available for subfamily tracks
- Fixed
- 08:52 am Bug #84 (Resolved): background in 2nd panel didn't apply to main panel automatically
- Fixed in v25.5, thanks!
- 08:51 am Bug #85 (Resolved): rmsk track configuration not available for subfamily tracks
- fixed on test
in fact they are family-tracks, not subfamilies. Their parent tracks are TE classes.
the bug was be...
Also available in: Atom