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2008 GMOD Community Survey

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The first ever GMOD Community Survey was conducted in the last half of October 2008. Almost 100 people participated in the survey, providing feedback and suggestions on everything from GMOD Components to GMOD Meetings to hardware to research interests.

This survey provides the first comprehensive view of the GMOD user community, what it is using and happy with, as well as what needs improvement and what priorities for the future are.


Note: See the 2009 GMOD Community Survey for the following year's survey, which focused on genome and comparative genomics visualization.


Survey Links

Highlights of the survey are on this page. The complete report summarizing all multiple choice questions and free text answers is also available.

To see the detailed section for any question in the survey, click on the link in this list.


GMOD Components

The survey asked participants which GMOD Components they used. Here were the most popular responses:

 % Using Component
70.8% GBrowse
36.0% Chado
30.3% Apollo
21.3% BioMart
13.5% Pathway Tools
10.1% CMap
10.1% GMODTools
10.1% InterMine


Popular Combinations

From the 89 responses we received, how often are the 5 most popular components used at the same site? The cutoff for inclusion in the table was 9 responses.

Components and Combinations # Responses
GBrowse 63
Chado 32
Apollo 27
Chado GBrowse 25
Apollo GBrowse 22
Apollo Chado 21
BioMart 19
Apollo Chado GBrowse 18
BioMart GBrowse 18
Pathway Tools 12
GBrowse Pathway Tools 11
Apollo BioMart 10
Apollo BioMart GBrowse 9
BioMart Chado 9

GMOD Servers

The survey also asked several questions about the servers GMOD components are running on.

See Computing Requirements for recommendations.

Operating System

Operating systems in use had a definite skew towards Unix based systems:

# Responses Operating System
55 Linux
8 Mac OS X
6 Solaris
2 Windows
1 Unspecified Unix

Current Server Sufficient?

We also asked users to describe their current server hardware (not summarized here, but available in the survey), and whether or not their servers were sufficient to meet their current needs. Responses to the latter question are summarized here.

# Responses Answer
~30 Sufficient (at least for now)
8 Need more memory
8 Faster/More CPUs/Servers
5 Faster/More disk

GMOD Meetings

The survey included a section on GMOD Meetings.

  • 24 of 25 respondents thought meetings were reasonably to exceptionally useful.
  • 21 of 23 respondents thought meetings were reasonably to exceptionally well run and organized
  • 21 of 31 respondents who have not attended meetings cited time, cost and/or distance as a reason for not attending.

See Meetings for a summary of past and upcoming meetings.

GMOD Project

The survey asked several questions about the project overall.

Most Satisfied With

There were 59 responses to the question:

What aspects of the GMOD project are you most satisfied with?

Popular responses were:

# Responses Aspect / Component
23 GBrowse
17 Support and active community
8 Chado
8 Software tools quality, maintenance, breadth and functionality
6 Open Source
6 Apollo

Least Satisfied With

There were 44 responses to the question:

What aspects of the GMOD project are you least satisfied with?

Recurring responses were:

# Responses Aspect / Component
14 Documentation
8 Chado
7 Difficult configuration and installation
5 Integration and coordination
3 None

Next 12 to 18 Months

There were 47 responses to the question:

What would you like to see GMOD work on in the next 12 to 18 months?

Recurring responses were:

# Responses Task
18 Documentation
14 Integration
11 GBrowse: testing, speed, Web 2.0, glyph documentation, features
5 Chado: Chado: PostgreSQL 8.3 support, phenotypes, integration with Apollo, functional annotation
3 Training
3 Improve what we already have.


GMOD Help Desk

The survey asked several questions about the GMOD Help Desk.

Questions asked included:

  • Please rank the relative performance of the Help Desk in each of 5 areas.
  • Please rank what the priorities of the Help Desk should be in each of those 5 areas (responses summarized below)
  • Are there other areas the Help Desk should allocate time to?
  • What training offerings would be most helpful to you or your colleagues?
  • Several questions about holding a GMOD Course in Europe and Asia/Pacific. (responses summarized below).

Help Desk Priorities

The question:

Please rank what the priorities of the Help Desk should be.

resulted in this priority ranking for these 5 areas:

  1. Answering User Questions
  2. GMOD Web Site
  3. Developer Support
  4. Education
  5. Outreach and Community Building

GMOD Course in Europe

  • 25 respondents were definitely or probably interested in attending a GMOD course in Europe in 2009.
  • Of three possible locations given (UK, France, Netherlands), the UK was the preferred location for a course.

Note: We are moving forward with plans to hold a GMOD Course in Oxford, UK in 2009. Watch the website for details.

GMOD Course in Asia/Pacific

21 respondents were definitely or probably interested in attending a GMOD course in Asia/Pacific in 2009.

When asked what locations respondents could make it to, these locations had more than one response:

# Responses Location
5 Austrailia
5 China
3 Japan
3 Singapore
2 India

Note: We will investigate possible locations and interest in a GMOD Course in Asia/Pacific during the last half of 2009 and during 2010.


Survey Participants and Organizations

The survey a number of questions about survey respondents and their organizations.


Questions included:

  • Do you consider yourself to be a GMOD user, GMOD Developer, or both? (Summarized below)
  • What organism(s) or types of organisms is your web site / database about?
  • Please indicate what types of biological data your database/website is about or that you are interested in now or in the near future, and that you are planning or hoping to use GMOD to manage, visualize, or annotate. (Summarized below)


User or Developer

80 participants answered the question:

Do you consider yourself to be a GMOD user, GMOD Developer, or both?
# Responses Response
35 User
6 Developer
34 Both
5 Other

Interests

Finally, the survey asked:

Please indicate what types of biological data your database/website is about or that you are interested in now or in the near future, and that you are planning or hoping to use GMOD to manage, visualize, or annotate.

Respondents were given a list of choices along with Other

# Responses Interest
51 Assembled sequence
48 Comparative Genomics
43 Manual genome annotation
39 Next generation sequence
38 Annotation pipelines
32 Community annotation
29 Microarrays
29 Ontologies
24 Mapping (genetic, physical, QTL, ...)
22 Phenotypes
20 Pathways
19 Literature curation
18 Other expression (besides microarrays)
18 Workflow / Integration
13 Lines / Stocks
13 Population genomics
10 Phylogeny
6 Community directory
6 Other
4 Anatomy

Responses under Other included:

  • research materials such as cDNA and genomic arrayed libraries
  • proteomics
  • More support for time course data in GBrowse
  • Metagenomics
  • binding sites of proteins.
  • SNPs, Genome Wide Association (GWA) study results
  • portals
  • We don't have any data (we are not a molecular biology lab). But currently we are simulating the Assembled Sequence data and Microarray data in order to test our systems. E. coli is our model organism and we extract the data from NCBI and ASAP. Once the system gets ready, we are envisioning the biologists to populate their own data.