Genome Browser Survey

Dear Cooperator,

The primary mission of MaizeGDB is to serve the maize community, and the MaizeGDB team is very fortunate that maize researchers are dedicated to guiding that mission.

A main goal for MaizeGDB is to facilitate access to the outcomes of maize research in an intuitive format. In that spirit, MaizeGDB is investigating the possibility of adopting and customizing a genome browser as the basis for displaying the annotated maize sequence as it becomes available. While it should be noted that MaizeGDB currently does not have the resources or expertise on staff to annotate the maize genome directly, displaying all available structural (gene model) and functional annotations simultaneously within the context of a genome browser is possible, as is making all relevant data available for download and off-site manipulation. If an outside group is funded to officially annotate the maize genome, MaizeGDB will pursue collaboration to house the official annotations long-term and will seek to create mechanisms for continued community annotation once the primary annotators' project has ended.

As you are probably aware, there are many different genome browsers, each having strengths and weaknesses. We are looking for maize researchers (students, postdocs, faculty, and others) who are willing to help choose a genome browser software for MaizeGDB by taking the following survey. Even if you don't have any experience with genome browsers, please give us a few minutes of your time to contribute your thoughts. You will be the ones using the genome browser regularly, so your input is of the utmost importance for planning purposes.

Feedback to the MaizeGDB team is very important for getting the genome browser software selection and implementation right. At the end of the survey you have the option to reveal your identity if you so desire. This would enable you to work with the team to make sure that the tools to be adopted and developed meet your needs.

Thanks very much for your time and interest,
The Maize Genetics Executive Committee


Please fill out as many of the questions below as you can. If you don't have an appropriate answer for a question, don't worry -- just continue to the next question.

How many hours per week do you personally access maize data from any web source?

Please list the websites you use most for your maize research. Please rank them in order of the most time spent, with #1 being the site you spend the most time on (e.g., ZmGDB, MaizeSequence.org, and MAGI, etc.).
1.
2.
3.
4.
5.
6.
7.

What types of genome browsers have you used? Please check the browsers below that you have experience with. Please write in any that are not listed (browsers for any species are welcome). Links open in a new window, so you won't lose the survey by clicking.
Ensembl (http://www.ensembl.org)
FlyBase (http://flybase.org/)
GBrowse (http://www.gmod.org/wiki/index.php/Gbrowse)
Gramene (http://www.gramene.org/)
JGI (http://www.jgi.doe.gov/)
MAGI (http://magi.plantgenomics.iastate.edu/)
MaizeSequence.org (http://www.maizesequence.org/)
NCBI Map Viewer (http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=4577)
PlantGDB (http://www.plantgdb.org/)
Pombe Browser (http://pombe.nci.nih.gov/genome/
Sigenae Contig Browser (http://public-contigbrowser.sigenae.org/)
SynBrowse (http://www.synbrowse.org/)
TAIR (http://www.arabidopsis.org/)
T-DNA Express (http://signal.salk.edu/cgi-bin/tdnaexpress)
TIGR (Craig Venter Institute) (http://www.tigr.org/)
UCSC Browser (http://genome.ucsc.edu/)
VEGA (http://vega.sanger.ac.uk/)
WormBase (http://www.wormbase.org/)
Others (please list: )

What genome browsers are or would be the most useful for your research? (You can give examples of web sites of other species you enjoy using.)

Which aspects of your favorite genome browser(s) do you like? Please rank them according to your preference (1 is the most important) and provide genome browser names as examples. If you don't see an aspect mentioned but you think it is important, please include them as the last rows of your response.
Speed (give examples, if any: )
Ease of use (give examples, if any: )
Visually informative (give examples, if any: )
Allows cross-species (or multiple inbred line) comparisons (give examples, if any: )
Ability to highlight or visualize multiple genes (give examples, if any: )
Distinction between experimental and computationally-derived data (give examples, if any: )
Links to Gene Ontology/Plant Ontology/etc. terms (give examples, if any: )
Other (give examples and/or comments, if any: )

Among these features, which ones are the most indispensable for your research?

What specific features would you like to see in a MaizeGDB Genome Browser? (even if the feature does not exist in currently available genome browsers)

Can you provide examples of features of genome browsers that are frustrating or not useful (please list the specific web sites)?
Name and/or Web Address Weakness

List here any other comments about genome browsers and your preferences. Please be as specific as you can.

Would you be willing to provide more feedback?

Would you be willing to serve on a guidance panel?

Would you be willing to be a beta tester?

If you answered "yes" to any of the last three questions, please provide:
your name:
your email:

This information will not be associated with your survey responses!