2009 GMOD Community Survey
From GMOD
The 2009 GMOD Community Survey focused on genome and comparative genomics visualization. The survey was open for 10 days in September 2009 and got 45 responses.
Which components have you used?
GMOD has a wealth of genome and comparative genomics browsers. Which of the following have you used?
Component | % | |
---|---|---|
GBrowse | 87% | |
CMap | 31% | |
JBrowse | 29% | |
GBrowse_syn | 29% | |
Apollo's synteny viewer | 13% | |
BLAST Graphic Viewer | 13% | |
SynBrowse | 7% | |
GBrowse karyotype | 7% | |
SynView | 4% | |
Sybil | 2% | |
Documentation
How satisfied are you with the documentation for these components?
Administration Documentation
- e.g. GBrowse Configuration HOWTO, GBrowse_syn Tutorial, ...
% | ||
---|---|---|
Very | 50% | |
Average | 35% | |
Not at all | 5% | |
No Opinioin | 10% | |
End user Documentation
- e.g. GBrowse User Tutorial, CMap Tutorial, ...
% | ||
---|---|---|
Very | 45% | |
Average | 33% | |
Not at all | 3% | |
No Opinioin | 20% | |
Overview Documentation
- e.g. Comparative Genomics, Overview, ...
% | ||
---|---|---|
Very | 23% | |
Average | 40% | |
Not at all | 0% | |
No Opinioin | 38% | |
Features
This section asked participants to prioritize features in browsers.
- For each feature, please indicate that feature's importance to you. Please try to classify no more than 1/3 of the features as high importance.
Please rank the importance of each feature.
Key: | High | Medium | Low | Not at all | No opinion |
---|
Feature | ||||||
---|---|---|---|---|---|---|
Browser response time (speed!) | 71% | 22% | 4% | 2% | 0% | |
Data loading speed.
|
31% | 33% | 29% | 2% | 4% | |
Browser install and setup Script
|
20% | 31% | 29% | 4% | 16% | |
Graphical user interface for administering the browser.
|
24% | 24% | 28% | 7% | 7% | |
Configuration file checker with helpful error messages. | 31% | 51% | 9% | 0% | 9% | |
User management
|
27% | 29% | 24% | 4% | 16% | |
Community annotation
|
38% | 40% | 18% | 2% | 2% | |
Package browser software within a ready-to-install virtual machine that includes several other commonly used GMOD components.
|
16% | 33% | 24% | 11% | 16% | |
Make browser instance metadata available via web services | 13% | 36% | 20% | 7% | 24% | |
A public repository of browser-ready reference genomes, including example annotations such as gene models, NGS data, quantitative data (wiggle), ...
|
29% | 44% | 20% | 0% | 7% | |
Extensibility
|
27% | 38% | 24% | 0% | 11% | |
Individual feature display customization
|
42% | 36% | 16% | 2% | 4% | |
Individual base display customization
|
22% | 36% | 27% | 4% | 11% | |
Admin control of browser layout.
|
20% | 42% | 24% | 4% | 9% | |
Hierarchical listing of available tracks.
|
31% | 29% | 22% | 0% | 18% | |
Show multiple regions simultaneously
|
29% | 40% | 18% | 0% | 13% | |
Comparing two or more genomes.
|
49% | 24% | 7% | 2% | 18% | |
Whole genome/chromosome browsing
|
22% | 38% | 13% | 4% | 22% | |
Browsing on mobile devices
|
4% | 7% | 16% | 44% | 29% | |
Semantic zooming | 22% | 27% | 27% | 0% | 24% | |
Autocomletion of Search Terms | 18% | 40% | 18% | 11% | 13% | |
Popup Balloons | 20% | 36% | 24% | 7% | 13% | |
Rubber Band Selection | 27% | 40% | 16% | 0% | 18% | |
Linkage disequilibrium tracks | 20% | 18% | 18% | 4% | 40% | |
Support next generation sequencing individual reads.
|
53% | 24% | 11% | 0% | 11% | |
Display markers from CMap in the genome browser.
See this page for an explanation of how this might be done in GBrowse. |
22% | 18% | 20% | 2% | 38% | |
Quantitative data shown with color intensity
|
53% | 20% | 11% | 2% | 13% | |
Quantitative data shown on an x-y graph
|
49% | 22% | 11% | 2% | 16% | |
Log scaling for quantitative data | 36% | 20% | 16% | 2% | 27% | |
Show multiple datasets in a single quantitative track.
|
42% | 18% | 20% | 2% | 18% | |
Aggregation functions for quantitative data
|
44% | 9% | 22% | 2% | 22% | |
Alignment tracks.
|
33% | 33% | 9% | 4% | 20% | |
Geolocation data
|
11% | 11% | 29% | 13% | 36% | |