2009 GMOD Community Survey

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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.
How long it takes to process and load data into backing databases.
 31%   33%   29%   2%   4% 
Browser install and setup Script
The GBrowse NetInstaller is an example.
 20%   31%   29%   4%   16% 
Graphical user interface for administering the browser.
Update configuration, add tracks, load data, ... through a GUI.
 24%   24%   28%   7%   7% 
Configuration file checker with helpful error messages.  31%   51%   9%   0%   9% 
User management
Allow users to login. This would enable other functionality.
 27%   29%   24%   4%   16% 
Community annotation
Support users adding annotation to individual features and/or uploading features or tracks for sharing with others.
 38%   40%   18%   2%   2% 
Package browser software within a ready-to-install virtual machine that includes several other commonly used GMOD components.
For example, see the community Annotation System.
 16%   33%   24%   11%   16% 
Make browser instance metadata available via web services
See this page for an explanation of how this might be done in GBrowse.
 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), ...
GBrowse.org is a step in this direction.
 29%   44%   20%   0%   7% 
Extensibility
Support for plugins and user defined glyphs
 27%   38%   24%   0%   11% 
Individual feature display customization
Allow browser admin to write their own code to adjust how a feature is shown (height, color, border, ...), based on the feature's attributes. (This is done with Perl callbacks in GBrowse.)
 42%   36%   16%   2%   4% 
Individual base display customization
Allow browser admin to write their own code to adjust how an individual base is shown (height, color, border, ...) at run time, based on the base's attributes. This could show the alignment quality, or coverage, or ... for next generation sequencing data.
 22%   36%   27%   4%   11% 
Admin control of browser layout.
The browser admin configuration of what sections (e.g., search box, instructions, etc.) appear and where, what text appears and where, and so on. GBrowse allows admins to control some aspects of the layout.
 20%   42%   24%   4%   9% 
Hierarchical listing of available tracks.
GBrowse already supports this.
 31%   29%   22%   0%   18% 
Show multiple regions simultaneously
Select and then show multiple regions of the genome.
 29%   40%   18%   0%   13% 
Comparing two or more genomes.
GBrowse_syn, for example, does this.
 49%   24%   7%   2%   18% 
Whole genome/chromosome browsing
e.g., GBrowse karyotype
 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.
Visualize the NGS short reads themselves, showing items like read quality for individual bases.
 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
i.e., wiggle_density tracks
 53%   20%   11%   2%   13% 
Quantitative data shown on an x-y graph
i.e., wiggle_xyplot tracks
 49%   22%   11%   2%   16% 
Log scaling for quantitative data  36%   20%   16%   2%   27% 
Show multiple datasets in a single quantitative track.
Data in color intensity tracks (wiggle_density) could be stacked; data in x-y tracks (wiggle-xyplot) could be superimposed (may be require multiple scales), or stacked.
 42%   18%   20%   2%   18% 
Aggregation functions for quantitative data
e.g., show mean, max, min, across all data or sliding windows.
 44%   9%   22%   2%   22% 
Alignment tracks.
Showing insertions, deletions, ...
 33%   33%   9%   4%   20% 
Geolocation data
how things like genotype and allele frequencies phenotypes, environment, ... by geolocation.
 11%   11%   29%   13%   36%