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.

Features are listed in the order they appeared in the survey.

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% 

Expansion / Clarification

If you want to explain/expand any of your answers above, please do so here. 

  • Geolocation within genomic space would be interesting but not so interested in ecological applications quite yet.
  • I think basic elements like speed to load a region in GBrowse and documentation of track configuration and additional data type adding are core requirements that could be made better. Although I haven't used gbrowse 2 it sounds like the performance element is being addressed.
  • User GBrowse v2 Tutorial?
  • "part of my job takes place on an academic expression platform. I have to deal with expression microarray analyzes comming from 2 colors arrays and also from RNA-Seq and ChIP-Seq experiments. We use to give our users text files (in the time of small format arrays) but now, with tiling arrays, our users, who are big fans of bioinformatics skills, they cannot open their files with conventional text tools. we intend to give them gff3 files so that they can visualize the data on Gbrowse locally or on our platform. The problem is that we have to ensure the confidentiality of their data. That's the reason I am very interested in a better User management.
  • Perl callbacks are not difficult to use when well documented. It's the major problem of bioperl to me. There are many modules but not enough documentation with concrete examples. So a big YES for ""Allow browser admin to write their own code to adjust how a feature is shown"" with better doc."
  • It would be great to merge two of the questions: the comparison feature but with single NGS reads. It might be something like AMOS' hawkeye, but by web! I think the current engine can be adapted to support this, and it would be great to be able to manually curate some sequence with weird features (for example, an unexpected stop codon) based in both the summarised quality (already supported by quantitative tracks) and the original reads.
  • no


Other High Priority Features

Are there other high priority features you would like to see that are not in the list above?

  • Ability to curate features that are not genes. The majority of genomes are not composed of genes, and the weakness of most browsers is their inability to display features that are not genes. I would especially like better support for the display and curation of of Transposable Elements.
  • Support for displaying/summarizing alignments in BAM format.
  • About 'support next generation sequencing individual reads', it is beautiful if SAM (or other format) has got an 'attributes' field.
  • bridging interface between the different tools, (common data format?)
  • Improve the chado examples for different use cases.
  • More customization of data tracks by end user, not just by the admin. For example, in GBrowse (v1.69) XY data plots, generic track attributes may be adjusted by the end user, but not specific XY plot attributes, such as min and max values, etc.
  • The previous answer also counts for this one. The previous answer was:
    • It would be great to merge two of the questions: the comparison feature but with single NGS reads. It might be something like AMOS' hawkeye, but by web! I think the current engine can be adapted to support this, and it would be great to be able to manually curate some sequence with weird features (for example, an unexpected stop codon) based in both the summarised quality (already supported by quantitative tracks) and the original reads.
  • not really


Other Medium Priority Features

Are there other medium priority features you would like to see that are not in the list above?

  • Ability to generate heatmap color bin from a set of different algorithms (equal interval, quantiles ..).
  • Native chado database connection instead of adapter type chado connection (although the latter may be more flexible, speed is an issue)
  • A much more difficult one, but nice enough to mention: sequence and/or annotation editing capabilities.
  • not really


Are there other Low priority features you would like to see that are not in the list above? 

  • Conquer the world, but with very low priority, first science.
  • not really