Website:Genome Browser Survey

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Worm Community Survey

This questionnaire will be send to the worm community via SurveyMonkey. Envisaged publication date: 3rd September or later (after US Labour Day)

Todd might contact PIs, so that they can distribute the questionnaire to their lab members.

Background

Q: This questionnaire is anonymous, but please provide some context on your background.

  • I am a PI
  • I am a researcher (Research Associate, Scientific Associate, etc.)
  • I am a postdoc
  • I am a PhD student
  • I am a Master/Bachelor student
  • other: text field

Q: What is your educational background?

  • bioinformatician by training
  • biologist by training
  • chemist by training
  • computer scientist by training
  • other: text field

WormBase GBrowse Usage

Q: How frequent do you use the WormBase genome browser?

  • every day
  • multiple times a week
  • once a week
  • once a month
  • never used it (if this is your choice, please still complete the survey with random answers -- thank you)

Q: For which primary purpose do you use the WormBase genome browser?

  • to support my research
  • as a quick lookup tool
  • for visualization aspects during presentations (screenshot or live demonstration)
  • for downloading sequences of genomic features
  • other: text field

WormBase GBrowse Experience

Q: Which aspect do you find most annoying about the WormBase genome browser?

  • it is slow
  • it is not customizable
  • it is hard to use
  • it visualizes data badly
  • no complaints; it is just fine

Q: How to you approach the genome browser?

  • functionality is more important than visualization
  • visualization is more important than functionality
  • both functionality and visualization are important to me

WormBase GBrowse Utilization

Q: How many tracks do you usually view at the same time?

  • 1-3
  • 4-6
  • 7-9
  • 10 or more

Q: How much do you customize the appearance of track displays?

  • most track displays have been customized by me
  • I customize specific tracks only
  • I once customized a track display and found it useful at the time
  • I once customized a track display, but the benefits were not outstanding
  • never customized a track display

Q: Do you download data using the WormBase genome browser? (multiple choice)

  • alignments
  • decorated FASTA file
  • Genbank format
  • track data as GFF3
  • never downloaded any data using the genome browser
  • other: text field

Q: If you download data using the genome browser, which regions do you download?

  • only the genomic region spanning the genomic feature I am interested in
  • a larger continuous region of a chromosome
  • the whole chromosome
  • never downloaded any data using the genome browser
  • other: text field

Q: How do you share tracks in the WormBase genome browser?

  • via e-mail; sending a link of the genome browser view
  • other; sending the data so that the other person can upload the data themselves
  • never shared tracks

Q: How important are track permissions to you?

  • very important: uploaded data should in some cases only be visible to me only and should not be visible to collaborators
  • very important: uploaded data should in some cases only be visible to me and collaborators
  • important: uploaded data should only be accessible to people who know the track name, but there is no need for an explicit login requirement
  • unimporant; always share more data publicly

Q: Which data/protocol standards do you use when importing data into the genome browser? (multiple choice)

  • BAM
  • BED
  • BedGraph
  • bigBed
  • bigWig
  • CBS
  • CN
  • DAS
  • FASTA
  • genePred
  • GFF2
  • GFF3
  • GISTIC
  • Goby
  • GTF
  • GVF
  • GWAS
  • LOH
  • MAF
  • PSL
  • RES
  • SAM
  • SEG
  • SNP
  • VCF
  • WIG
  • other: text field

Q: How often do you make use of the WormBase GBrowse REST API?

  • every day
  • once a week
  • every now and then; as needed
  • never used it, but consider using it in the future
  • never used it and I will not use this feature in the foreseeable future

Q: Do you use GBrowse Image (gbrowse_img)?

  • yes, frequently
  • yes, occasionally
  • yes, I used it once
  • no, I have not application for it
  • no, I do not know what it is

Awareness and Utilization

Q: Which desktop genome browsers are you familiar with? (multiple choice)

  • Apollo
  • Argos
  • Artemis
  • Gaggle
  • IGB
  • IGV
  • Savant
  • other: text field
  • none; I only use web-based genome browsers

Q: Which genome browsing experience do you prefer?

  • desktop application genome browsers
  • web based genome browsers
  • no preference
  • not applicable

Q: Which web-based genome browsers are you familiar with? (multiple choice)

  • Dalliance
  • Ensembl
  • GBrowse
  • Genome Maps
  • JBrowse
  • UCSC
  • other: text field
  • none

Q: Which is your favourite web-based genome browser?

  • Dalliance
  • Ensembl
  • GBrowse
  • Genome Maps
  • JBrowse
  • UCSC
  • other: text field

WormBase Data Content

Q: Have you used modEncode data at WormBase?

  • yes, I mostly work with modEncode data
  • yes, I use all kind of WormBase data and modEncode data is part of it
  • yes, I have used modEncode data at WormBase a few times
  • no, and I will not use the modEncode data in the foreseeable future
  • no, I am unaware of what modEncode data is

Q: What are your favourite WormBase tracks?

  • gene tracks
  • modEncode tracks
  • phenotype and expression tracks
  • sequence similarity tracks
  • other: text field

Q: Do you think we are missing your favourite WormBase GBrowse track?

  • no, WormBase GBrowse tracks are feature complete for my use cases
  • yes, you are missing: text field