Difference between revisions of "Website:Genome Browser Survey"
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== Worm Community Survey == | == Worm Community Survey == | ||
− | This questionnaire will be send to the worm community via SurveyMonkey. | + | 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. | '''Q:''' This questionnaire is anonymous, but please provide some context on your background. | ||
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* I am a Master/Bachelor student | * I am a Master/Bachelor student | ||
* other: ''text field'' | * 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? | '''Q:''' How frequent do you use the WormBase genome browser? | ||
Line 24: | Line 37: | ||
* for downloading sequences of genomic features | * for downloading sequences of genomic features | ||
* other: ''text field'' | * other: ''text field'' | ||
+ | |||
+ | === WormBase GBrowse Experience === | ||
'''Q:''' Which aspect do you find most annoying about the WormBase genome browser? | '''Q:''' Which aspect do you find most annoying about the WormBase genome browser? | ||
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* visualization is more important than functionality | * visualization is more important than functionality | ||
* both functionality and visualization are important to me | * 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? | '''Q:''' How much do you customize the appearance of track displays? | ||
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* alignments | * alignments | ||
* decorated FASTA file | * decorated FASTA file | ||
+ | * Genbank format | ||
* track data as GFF3 | * track data as GFF3 | ||
+ | * never downloaded any data using the genome browser | ||
* other: ''text field'' | * 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 | * never downloaded any data using the genome browser | ||
+ | * other: ''text field'' | ||
'''Q:''' How do you share tracks in the WormBase genome browser? | '''Q:''' How do you share tracks in the WormBase genome browser? | ||
Line 97: | Line 128: | ||
* never used it, but consider using it in the future | * never used it, but consider using it in the future | ||
* never used it and I will not use this feature in the foreseeable 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'' | ||
+ | |||
+ | [[Category:GBrowse (Web Dev)]] |
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