Difference between revisions of "2009 GMOD Community Survey"
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+ | === 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 |
Revision as of 20:20, 5 October 2009
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.
Contents
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.
|
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% | |
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