Activity

From 01/21/2014 to 02/19/2014

02/19/2014

11:19 am Bug #165 (Closed): browser frozen when panning of BAM tracks
* Thanks for fixing! Daofeng Li
11:07 am Bug #165 (Resolved): browser frozen when panning of BAM tracks
Fixed in v32.1.8! Xin Zhou
10:15 am Bug #165 (Closed): browser frozen when panning of BAM tracks
* using this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli/C... Daofeng Li
10:13 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub
Daofeng Li
10:11 am Bug #164 (Resolved): UI frozen when click 'remove all' from json hub
Fixed in v32.1.7. Thanks! Xin Zhou
09:58 am Bug #164 (Closed): UI frozen when click 'remove all' from json hub
* loading this hub: http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://cgs.wustl.edu/~dli... Daofeng Li

02/18/2014

03:39 pm Bug #163 (New): long responsive time while track missed in hub
* see Junchen's hub at http://remc.wustl.edu/jgu/human/remc/methylomes/methylomes_all_hub.json
* apache error log sh...
Daofeng Li
08:02 am Feature #162 (Resolved): Tooltip information
Implemented in v32.1.4. Thanks! Xin Zhou

02/15/2014

01:09 pm Bug #160 (Resolved): Custom PE BAM files unstable
Fixed in v32.1.4
http://epigenomegateway.wustl.edu/browser/?genome=danRer7&custombam=xx,http://cgs.wustl.edu/~rlow...
Xin Zhou
08:00 am Bug #153: track information display error
Missing GEO accession has been fixed. Xin Zhou

02/14/2014

10:18 pm Bug #147 (Closed): crash when track file not exist in json hub
fixed. Daofeng Li
10:17 pm Bug #153: track information display error
GEO links also could not be recovered? Daofeng Li
04:46 pm Bug #159 (Closed): Session not saving
Xin Zhou
04:45 pm Bug #155: browser url parameter for coordinate not working
Use the "native_track" keyword and add gene track to your JSON datahub.
Find example in this hub:
http://vizhub...
Xin Zhou
04:43 pm Bug #155: browser url parameter for coordinate not working
OK. I see.
Then how do I include the gene annotation track by default with my own data? When I uploaded my own tr...
Junchen Gu
04:43 pm Bug #157: refSeq gene position didn't keep in session
refSeq is a "native track". Current design only keeps order of custom tracks. Native tracks are all piled to the bottom. Xin Zhou
04:29 pm Bug #155 (Rejected): browser url parameter for coordinate not working
When the "session" and "statusId" parameters are in use, the "coordinate" parameter is disregarded, since the view ra... Xin Zhou
04:25 pm Bug #153 (Resolved): track information display error
Fixed in v32.1.3, but the track details from previous saved sessions cannot be recovered. Xin Zhou
03:58 pm Bug #147 (Resolved): crash when track file not exist in json hub
can you try again with the new code? Xin Zhou
03:31 pm Feature #162 (Closed): Tooltip information
Would be great if the tooltip could include per-read CIGAR strings, mapping quality scores, and maybe insert size inf... Rebecca Lowdon

02/13/2014

05:59 pm Feature #158: wrapping for tooltip read information
good suggestion :) Daofeng Li
05:58 pm Bug #159: Session not saving
my bad, wrong permission for the session folder. Should be fixed now. Please let me know if problem still exists. Daofeng Li
03:32 pm Feature #161 (New): Include scaffolds on genome snapshot
Would be nice to view scaffolds and unassigned chromosome fragments (in danRer7 referred to as "NA###") in the "genom... Rebecca Lowdon
03:27 pm Bug #160 (Closed): Custom PE BAM files unstable
BAM tracks of paired-end alignments appear unstable on the browser. Relocating or zooming in/out causes reads to "mov... Rebecca Lowdon
03:20 pm Bug #159 (Closed): Session not saving
Was trying to save a session to send you another bug ... but sessions not working on danRer7! Rebecca Lowdon
03:18 pm Feature #158 (New): wrapping for tooltip read information
Would be nice if information in tooltip would automatically wrap to display all information. For example, I want to v... Rebecca Lowdon

02/11/2014

10:52 pm Bug #123 (Closed): embedded browser cannot handle hidden tracks
Daofeng Li
10:52 pm Feature #145 (Closed): loose format requirement for coordinates format
* yes, it works great! Daofeng Li
10:52 pm Bug #152 (Closed): clicking "zoom in" button makes browser unresponsive
Daofeng Li
10:51 pm Bug #148 (Closed): add geneset to genome snapshot error
Daofeng Li
10:50 pm Bug #157 (New): refSeq gene position didn't keep in session
* move refSeq gene to top of canvas
* same session, load, the refSeq gene goes to bottom
Daofeng Li

02/07/2014

11:45 pm washugb v32 release
* We have released v32 of WashU EpiGenome Browser.
h2. Updates
* shared metadata, for details please see: http:...
Daofeng Li
11:32 pm Complete Epigenome Browser Bug #156 (New): WUGB popup link get blocked
* the popup being blocked seems are default behavior of most modern browsers
Daofeng Li
04:11 pm Bug #155 (Rejected): browser url parameter for coordinate not working
Xin,
If you go to my Feb. 2014 wiki and on Feb. 6-7, I have a table of regions and in the last column there are brow...
Junchen Gu

02/06/2014

02:11 pm Bug #154 (Resolved): Cannot search for gene in embedded browser
Fixed in v32.0.7.
See this example: http://cgs.wustl.edu/~xzhou/embed/1.html
Xin Zhou
02:04 pm Bug #154 (Closed): Cannot search for gene in embedded browser
If the embedded browser only imports "base.js" it can't search and jump to a gene, this error will be given:
Objec...
Xin Zhou

02/05/2014

12:31 pm Bug #153 (Closed): track information display error
* same a session, load it with the link generated
* right click a track, choose Information, you will see some infor...
Daofeng Li
10:32 am Bug #152 (Resolved): clicking "zoom in" button makes browser unresponsive
Fixed in v32.0.3 on public browser
The bug is still there on test server for you to check out.
Xin Zhou
10:31 am Bug #152 (Closed): clicking "zoom in" button makes browser unresponsive
CLick the "+" (zoom in) button multiple times until getting this message:
At finest level, cannot zoom in
And t...
Xin Zhou

02/01/2014

08:35 am Feature #145 (Resolved): loose format requirement for coordinates format
Fixed in v32.0.1. Try these coordinates with multiple spaces separating fields:
chr7 55418829 55419003
chr7...
Xin Zhou

01/31/2014

08:41 am Bug #119 (Closed): fixedscale and track height probem in json hub
Daofeng Li
08:40 am Bug #144 (Closed): mouse over event for meta data header ( in track table ) disappear
Daofeng Li
08:40 am Bug #150 (Closed): js error and clickable 'None yet'
Daofeng Li
08:31 am Bug #150 (Resolved): js error and clickable 'None yet'
Fixed, thanks for finding out this tricky problem! Xin Zhou
12:19 am Bug #150 (Closed): js error and clickable 'None yet'
* the js errors in the console seems happened when open 2nd panel, while no crash happens
* the 'None yet' in 'custo...
Daofeng Li

01/30/2014

06:50 am Bug #149 (Rejected): possible coordinate issue
Xin Zhou
06:50 am Bug #149: possible coordinate issue
Thanks for reporting this. This is because our browser's coordinates are 0-offset, they all start from 0. But in UCSC... Xin Zhou
01:09 am Bug #149 (Rejected): possible coordinate issue
I was looking at a SNP (chr16:89986117-89986117) which is a C shown on UCSC browser (see attached image) but it's a G... Junchen Gu

01/28/2014

07:20 am Bug #148 (Resolved): add geneset to genome snapshot error
Fixed, thanks! Xin Zhou

01/27/2014

05:22 pm Bug #148 (Closed): add geneset to genome snapshot error
* submit a list of coordinates to gene set
* looks like browser didn't give a default name for the list, when you cl...
Daofeng Li
03:11 pm Bug #147 (Closed): crash when track file not exist in json hub
* I found if I renamed a file in my hub, loading the hub without updating it, browser will throw 'Json syntax error' Daofeng Li

01/24/2014

05:21 pm Support #136 (Closed): Collecting new Hi-C data sets
Daofeng Li
05:07 pm Support #136: Collecting new Hi-C data sets
* processed the data, but found the data was already in our browser.... Daofeng Li

01/23/2014

11:58 am Bug #140 (Resolved): error with tracks of same file URL
Fixed in v31.0.8
Load a hub with duplicated track URLs:
http://epigenomegateway.wustl.edu/browser/?genome=hg19&...
Xin Zhou
11:57 am Bug #144 (Resolved): mouse over event for meta data header ( in track table ) disappear
Fixed in v31.0.8 Xin Zhou
11:56 am Feature #139 (Resolved): metadata heatmap compatibility between data hubs
A mechanism for sharing metadata vocabulary among hubs is now available in v31.0.8
Example: a pair of hubs sharing...
Xin Zhou
08:35 am Bug #144: mouse over event for meta data header ( in track table ) disappear
I will put it back then! Xin Zhou
08:33 am Bug #144: mouse over event for meta data header ( in track table ) disappear
ok...at least Bo and I think it's pretty useful and convenient... Daofeng Li
08:32 am Feature #145: loose format requirement for coordinates format
how about not limit to 1 space delimited? People usually view DMRs copied from terminal may have multiple space betw... Daofeng Li
07:37 am Bug #146 (New): Session cannot save more than 1 custom metadata vocabularies
If 2 or more custom metadata vocabularies are loaded, only 1st one can be saved in session. Xin Zhou
07:08 am Feature #145: loose format requirement for coordinates format
what other formats do you suggest? Xin Zhou
07:06 am Bug #144: mouse over event for meta data header ( in track table ) disappear
No I removed this feature. Xin Zhou

01/22/2014

10:28 pm Feature #145 (Closed): loose format requirement for coordinates format
* in current version of browser, the format for coordinates have to be exactly same as 'chr:start-end' or 'chr start ... Daofeng Li
10:22 pm Bug #144 (Closed): mouse over event for meta data header ( in track table ) disappear
* on public site, when mouse over the meta data headers, no 'Select all' function appears like before
* attached is ...
Daofeng Li
12:41 pm Bug #143 (Resolved): error when switching from intra- to inter-chromosomal display
Fixed in v31.0.7 Xin Zhou
09:38 am Bug #143 (Closed): error when switching from intra- to inter-chromosomal display
Load the browser and show some tracks in intra-chromosomal region (e.g. the default location, only within one chromos... Xin Zhou
08:46 am washugb v31 release
* We have released v31 of WashU EpiGenome Browser.
h2. Updates
* Improved user interface, for details please se...
Daofeng Li
08:37 am Bug #142 (Closed): typo "Unselect All"
Daofeng Li
07:51 am Bug #142 (Resolved): typo "Unselect All"
Fixed, it was changed into "Deselect" instead of "Unselect" Xin Zhou

01/21/2014

10:30 pm Bug #142 (Closed): typo "Unselect All"
Daofeng Li
08:44 am Bug #141 (Resolved): improper view range in session-restored gene set view
Fixed in v31.0.5 Xin Zhou
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