Difference between revisions of "Website:Genome Browser Survey"
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Latest revision as of 14:42, 19 June 2014
Contents
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