JBrowse & GMOD users, 2016

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This survey is aimed at users (and potential users) of GMOD genome databases, especially the JBrowse genome browser. It will directly inform the priorities for renewal of the R01 that funds JBrowse software development and the GMOD helpdesk, and your time in filling it out is GREATLY appreciated.

The first part of the survey deals with JBrowse software development; the second part with the GMOD helpdesk position.

Please start by telling us your name and email address (totally optional, of course):

And what genome project do you work on?

What web-facing genome browser are you currently using for your project?

GBrowse

JBrowse

UCSC

Biodalliance

Other:

Clear selection

Does your genome browser have limitations for your users? If so, what?

How many species do you host browsable genome annotations for?

2-9

10-99

100 or more

Clear selection

How many builds/versions per species do you deal with?

One or two

Three or four

Five or more

Clear selection

How many different kinds of annotation track do you host (per species)?

1-10

11-20

21-50

Over 50

Clear selection

How do you organize your tracks? What categories or metadata do you include?

Do you have any specialized track types: ontology/orthology tracks, etc.? If so, what?

What are your essential core tracks and what additional tracks would your community like to see?

Is there any genome browser functionality integrated into other pages in your site, outside of the standard browser interface?

Yes

Clear selection

Do you integrate high throughput data in your genome browser?

Yes

Clear selection

If you do have high-throughput data, how do you deal with the issues that arise - e.g. finding relevant tracks, prioritization/selection/filtering of datasets, display?

What do YOU think JBrowse should prioritize?

Top priority

High priority

Medium priority

Low priority

Comparative genomics and synteny views (e.g. multiple JBrowse panes in the same page, relationships between genomes, Mauve-style ribbon views)

Structural rearrangement views (e.g. duplicated features or segments, Circos-style circular views)

Population genomics views (richer visualization of variants, population structure, haplotypes)

Graphical configuration and customization of tracks over the web (as opposed to editing JSON files)

Dynamic interactive filtering of track data (e.g. using slider or other controls to select subsets of features by score, length, etc)

Ability to upload, manage and delete new tracks via the web (as opposed to writing files on the server)

Integration with server applications and content frameworks (e.g. Galaxy, Chado, Tripal, Maker...)

Integration with client-side components to make web "dashboards" (alignment viewers, tree viewers, PDB viewers, ontology browsers, BioJS components, geographic maps)

General improvements to the user interface (e.g. resizing track heights, moving track labels, flip forward/reverse strands, subtracks)

Scalability (improved search; better handling of large track databases, large genomes, large numbers of reference sequences, multiple genomes, deep-coverage sequencing tracks)

More features for sharing and collaboration (Google Maps-style markup: ability to stick "pins" in the genome and share these overlays, commenting, chat, collaborative editing and annotation)

General improvements to the data back-end (understanding more file formats like CRAM, VCF4.2, more efficient bigbed/bigwig access)

More data of relevance to human genomics (e.g. a reference JBrowse instance with pre-loaded datasets for UCSC, ENCODE, HapMap, 1000 genomes, etc; easier cross-linking of model organisms to human orthologs/pathways)

Tools aimed at genome editing and bioengineering (e.g. CRISPR guide & primer design, confirming edits by resequencing)

Tools aimed at cancer informatics