2013 GMOD Survey

About You

What is your relationship to GMOD?

Relationship N respondents
User 27
Developer of GMOD components 3
Sys admin (installing/configuring/maintaining, etc., GMOD tools) 7
User, developer 6
User, developer, sys admin 8
User, sys admin 14
Developer, sys admin 0
None of the above 1

Where are you located?

See the GMODgeosurveyome map.

Your GMOD Usage

How do you use GMOD?

How do you use GMOD?
GMOD usage N respondents
Currently use (or provide for users) one or more GMOD components 58
Planning to use (or provide) GMOD components 5
Assessing GMOD and other software to see what fits our use cases best 3

What type(s) of biological data do you use or plan to use GMOD tools to manage, visualize, or annotate?

Data type Frequency
Assembled sequence 52
Next generation sequences 52
Comparative genomics 38
Annotation pipelines 27
Other expression data 25
Manual genome annotation 25
Ontologies 24
Community annotation 20
Phenotypes 19
Microarrays 15
Population genomics 14
Mapping (physical, QTL, genetic, etc.) 14
Pathways 13
Workflow / Integration 13
Literature curation 12
Phylogeny 8
Lines or stocks 8
Proteomics 5
Anatomy 5
Community directory 0

Other

  • ChIP-Seq data on histone modifications
  • Fly stock data
  • Genotype data (marker alleles)
  • Natural diversity data [localities, collectors, environmental measurements]
  • RNAi
  • phenotypes, genotypes

What do you find most valuable about the GMOD project and/or its components?

  • The community (developers and users) : 12
  • Open source : 11
  • GBrowse : 9
  • ease of use : 7
  • ease of set up : 6
  • It's free : 6
  • helpful, active mailing lists : 5
  • active development : 5
  • Chado : 4
  • code maturity : 4
  • customizable, flexible tools : 4
  • integrated, interoperable components : 4
  • the tools have already been developed : 3
  • annotation visualization : 2
  • components are modular and easy to extend : 2
  • ease of configuration : 2
  • Galaxy : 2
  • great support : 3
  • knowledgable help desk : 2
  • online tools : 2
  • stable, long-lived project : 2
  • standard data formats : 2
  • well documented : 2
  • Apollo : 1
  • JBrowse : 1
  • genome annotation curation tools : 1
  • ontology-driven : 1
  • can contribute code for others to use : 1
  • range of organisms and organizations using it : 1
  • the components are generic : 1
  • the project is directed by user needs : 1
  • the range of tools : 1

What aspects of the GMOD project are you least satisfied with? How could we make GMOD and its components more useful or easier to use?

  • Documentation quality is variable : 11
    • improve AWS documentation : 1
    • create more tutorials : 1
    • more biologist-friendly tutorials : 1
    • improve Chado genetic module docs : 1
    • documentation is hard to find : 1
    • GBrowse installation docs are out of date, incomplete : 1
    • tutorials lag behind software : 1
    • get users/devs more involved in wikis - topics recur on gbrowse mailing list, should be consolidated on wiki : 1
    • need more best practices to aid newbies : 1
  • Tool administration : 8
    • configuration is difficult : 3
    • dependencies make installing/upgrading difficult : 2
    • BioPerl makes installing/upgrading difficult : 2
    • GBrowse install is time-consuming : 1
    • there should be installation webinars : 1
  • Tools should be more interoperable/interlinked : 5
    • GBrowse and Tripal : 1
    • there should be a proper website to link all data and tools : 1
    • all tools should support Chado : 1
    • make it easier for users of one MOD to use another MOD : 1
  • Scope
    • GFF3/Chado need a SOFA-compliant prokaryotic gene model : 2
    • support for circular molecules in Chado, GBrowse : 2
    • better phylogenetic support in Chado - phenotype schema seems to be biased towards flies : 1
    • representation of phenotypes, anatomies : 1
    • support for prok genomes in Chado, GBrowse : 1
    • transposable element model curation (WebApollo) support : 1
    • transposable element model support in GFF3 : 1
    • transposable element model support in ontologies : 1
    • transposable element model visualization support : 1
  • Tool-related
    • more performance optimization : 2
    • synteny browsing is problematic : 2
    • unmaintained/unsupported projects (e.g. CMap) : 2
    • code quality - bug fix releases often break other things : 1
    • it is difficult to extract sequence and annotation data : 1
    • GBrowse configuration files should be more modular and reusable : 1
    • GBrowse/JBrowse - better instance management, particularly single instance for multiple projects : 1
    • provide VMs with current version of tool : 1
  • discontinuation of Wormmart and unstable biomarts : 1
  • queues waiting for job to be done (Galaxy) : 1
  • response on mailing lists can be slow : 1
  • user friendly formats for bulk data DL (e.g. from BLAST) : 1

Are there any tools or functionality that you think are missing from GMOD?

  • More breeder resources : 2
    • breeders: marker-assisted breeding techniques : 1
    • breeders: pedigree management, phenotype : 1
  • Tool-related:
    • assembly tools : 1
    • better multiple genome visualization : 1
    • blast server : 1
    • cloud services : 1
    • command-line workflow management tool : 1
    • data curation system (e.g. delete artefacts via GUI/tool, not from GFF3) : 1
    • general purpose genome annotation library for use with GMOD-based data : 1
    • interactive visualisations : 1
    • comparative and phylogenetic tools : 1
    • literature curation pipelines (beyond Textpresso) : 1
    • more NGS tools : 1
    • tools to represent gene regulatory networks : 1
  • Expanding GMOD's scope:
    • Chado : 2
      • natural diversity module needs more development and support : 1
      • publication module needs development and documentation : 1
    • support for embryo anatomies, phenotypes : 1
    • LIMS (laboratory information management system) : 1
    • storing RNAi experiments in Tripal : 1
    • support for genome features other than genes (transposable elements!) : 1
    • systems biology/systems genetics - network biology module for Tripal : 1
    • variant (SNPs) annotation, integration with protein structure : 1
  • Integration:
    • integration with R : 1
    • pipelines for common tools (e.g. Galaxy/Chado integration) : 1
    • shared sign on via SAML2 btwn Tripal, GBrowse : 1
    • transparent connectivity btwn tools (e.g. GBrowse/CMap) : 1
  • better comparisons of RNAseq/gene expression differences : 1
  • characterizn of gene lists : 1
  • show BLAST hits in GBrowse : 1
  • permission management (GBrowse, Chado) : 1
  • allow relational data queries : 1
  • support for Chado ontologies in custom content types (cck) in Tripal : 1

What would you like to see GMOD work on in 2013 and 2014?

  • Documentation : 5
    • guidelines on best practices : 1
    • installation, functionality, troubleshooting : 1
    • tools on the wiki : 3
      • clean up tool list on wiki (clearly mark tools as not currently maintained, etc.) : 2
      • comparison charts between tools with similar functionality : 1
      • non-wiki website w/ clear tool pages that are easier to navigate : 1
    • more examples, detail in GBrowse docs : 1
    • update and clean up wiki : 1
  • Comparative genomics : 4
    • gene family and synteny comparisons : 1
    • ortholog cluster information : 1
  • Tool integration : 4
    • create a fully integrated genome annotation, curation, visulation pipeline - like GitC but with MAKER, Apollo, GBrowse, Tripal all reading and writing to the same Chado DB : 2
    • Chado backend for WebApollo : 1
    • integrate GBrowse and CMap : 1
    • integrate GMOD and Galaxy - like UCSC tracks : 1
  • make the best, most beautiful genome/seq browser : 1
  • JBrowse : 3
    • data set size : 1
    • track management, subtracks : 1
  • GBrowse : 2
    • increase speed, performance : 2
    • more support for population genomics, data visualization : 1
    • make it more interactive, responsive : 1
  • Galaxy : 1
  • WebApollo : 1
  • Tool-related
    • circular genome browsers : 1
    • connect genomics data w/ structural data : 1
    • easy deployment of Chado and tools to server : 1
    • encourage users to make Chado instances available to the public, esp those w/ whole genomes : 1
    • literature curation pipelines : 1
    • NGS visualisation tools : 1
    • NGS-related development and add-ons : 1
    • sequencing data visualisation (inc. improving performance data/speed) : 1
    • support for NGS data formats (BAM, VCF, gene expr) : 1
    • mobile device support : 1
  • Chado
    • extend Chado/Tripal, e.g. store RNAi expts : 1
    • metadata: how to capture metadata to make easier to share across projects : 1
    • natural diversity module : 1
    • organism module - current Chado organism table is not good for comparative genomics, communities of organisms, and documenting relationships between species : 1
  • extend GMOD to non-model organisms : 1
  • more pre-release cross-platform tests : 1
Tagxedo image map!

GMOD Help Desk

Please rate the performance of the GMOD Help Desk in the following areas.

Mean
Answering user questions: providing helpful and timely answers to help queries 0 0 9 23 11 4.05
GMOD website: maintaining the GMOD website and making it useful and relevant for the GMOD community 0 1 11 32 6 3.86
Education: providing online and in person training on GMOD and components 0 2 10 24 8 3.86
Outreach and community building: spreading the words about GMOD; encouraging an active community of GMOD developers and users 0 3 11 26 7 3.79
Developer support: enhancing documentation, integration and beta testing services; bridging the developer-user gap 0 7 19 14 6 3.41

Which of these help desk activities is most important to you?

Mean
Answering user questions 3 0 5 19 25 4.21
GMOD website 1 3 13 21 16 3.89
Education 2 10 11 17 11 3.49
Outreach and community building 3 8 18 12 9 3.32
Developer support 2 3 7 17 23 4.08

Are there other areas that the GMOD Help Desk should spend time on or allocate resources to?

  • GMOD does a wonderful job with meetings and summer schools where folks get together in person. But I don't get the sense that people feel more than a "developer" or a "user" of GMOD. Perhaps if GMOD could transition into more a professional society with memberships, newsletters, etc. More "remote" activities so that people feel like they belong even if they can't attend meetings or they only go to a single GMOD Summer school as a student. I also feel like some tools are explored by folks but then dropped because the user can't quite get it working, or are just exploring and they don't reach out for help. Can the help desk try to get folks more engaged so that they are more willing to pick up a tool again they may have tried before. I think membership may do that. It may make folks more loyal and more willing to stick with some of the tools which they may have troubles with.
    Perhaps memberships could even require a small fee. Can GMOD receive revenue? Could it transition into a non-profit? Can it offer services such as on-site training and help with installation of GMOD tools? Can it put out books on its tools (e.g. GMOD for Dummies)... To do these kinds of things there would need to be more help desk staff, and more money coming in.
  • Add questions asked on the mailing lists to an FAQ list
  • online demos of all GMOD tools
  • industry partnering on collaborative development
  • customised tools for users

Training

See the Training and Outreach section on the GMOD wiki for GMOD tutorials and training opportunities.

Have you used the tutorials and training materials on the GMOD website?

  • No, I have not needed them : 12
  • No, I could not find them : 2
  • Yes, but they were inadequate : 6
  • Yes, and they were adequate : 34
  • Yes, and they were fantastic : 8

If you found the tutorials and training materials inadequate, how could we improve them?

  • check material is not out of date, works with current software, and is relevant : 4
  • needs an overview of how projects fit together
  • more tutorials aimed at users (not developers)
  • more video tutorials
  • prerequisites should be clearly stated
  • ensure that any differences between OSs are covered
  • documentation and tutorials are of variable quality
    • Galaxy tutorials are great! Make them all that good.
    • Chado documentation is uneven
    • some GBrowse documentation needs review (e.g. glyphs, plugins, options)
    • BioMart docs are impenetrable
    • Chado tutorials are difficult to replicate on different OSs

What training courses would be most useful for you and your colleages?

  • Basics for end users : 3
    • e.g. how can GBrowse help me in my research?
  • All aspects of the tools:
    • CMap : 1
    • Galaxy : 2
    • GBrowse : 1
    • JBrowse : 1
    • WebApollo : 2
  • Usage:
    • Apollo : 1
    • Pathway Tools : 1
    • SOBA : 1
    • Sybil : 1
  • Development of extensions/plugins:
    • Chado : 1
    • Galaxy : 1
    • GBrowse : 2
      • GBrowse - customising pop ups
      • GBrowse plugins - Excel dumper
    • Tripal : 1
  • Installation/configuration:
    • Apollo/WebApollo : 1
    • Chado : 2
    • Galaxy : 1
    • GBrowse : 3
    • Tripal : 1
  • Use cases : 2
  • Annotation : 1
  • Assembly : 1
  • Courses on basic bioinformatics for biologists : 1
  • Genome comparison : 1
  • Methods/conventions for integrating hi-thruput data in GMOD tools (storage in Chado, display in GBrowse) : 1
  • NGS data analysis : 1
  • Updates on new features : 1
  • Using gene annotation pipelines : 1

Would you be interested in attending a live online tutorial?

  • Yes : 28
  • Yes, depending on timing / software requirements : 21
  • No : 14
  • No response : 3

Would you be interested in attending a training course in your geographic region?
Note that GMOD would need to charge attendees a fee to cover the instructors' travel and accommodation costs.

  • Yes : 26
  • Yes, depending on distance / cost / timing : 21
  • No : 15
  • No response : 4

GMOD Community Meetings

Do you intend to attend the 2013 GMOD meeting in Cambridge on April 5-6, to be held in conjunction with Biocurator?

  • Yes : 8
  • No : 46
  • Unsure : 12

If future meetings offered an audio or video feed, or the option to attend remotely, would you be interested in participating?

  • Yes, I'd like to attend remotely (i.e. be able to ask questions and participate) : 33
  • Yes, I'd listen to audio / watch video but not participate : 21
  • No, I am happy to read the meeting minutes : 11

Have you attended GMOD meetings in the past?

  • Yes, multiple meetings : 14
  • Yes, one meeting : 14
  • No : 37

If you have attended GMOD meetings, please rate the following aspects:

Mean
How well organized was the meeting? 0 0 7 13 9 4.07
How useful was the meeting? 0 0 5 11 12 4.25

What aspects of the GMOD meetings are most useful?

  • The Social Network : 14
    • Talking to developers : 10
    • Talking to other users : 7
  • Discussing future directions : 3
  • Seeing new GMOD tools : 3
  • Demos and hands-on sessions : 2
  • Getting an overview of tools : 2
  • Seeing new technologies : 2
  • Talks : 2
  • Discussing developmental practices and goals : 1
  • Tool updates : 1

What aspects of the meetings could be improved?

  • A hackathon or live hands-on event : 4
  • Make meetings more accessible : 2
  • Discussion of how to integrate GMOD components : 1
  • Food : 1
  • Keep things moving : 1
  • More specific agenda and goals : 1
  • Parallel track for advanced users : 1
  • Post-meeting training : 1
  • Regional GMOD workshops to make attendance easier, with meetings about specific components : 1
  • Targeted working groups for areas that need attention - e.g. prokaryotic genomes in GFF3/Chado/GBrowse : 1

If you have not attended a GMOD meeting, what are your reasons?

  • lack of money : 5
  • lack of time : 3
  • schedule conflicts : 2
  • didn't know about them : 2
  • not necessary : 2
  • not relevant : 1
  • developer-oriented : 1

GBrowse and JBrowse

JBrowse is a JavaScript-based reimplementation of the genome browser GBrowse, optimised for speed and usability.

If you are a current GBrowse user or provider, have you considered switching to JBrowse? What, if anything, is JBrowse missing that would help you make the switch?

  • I prefer the GBrowse UI : 6
  • JBrowse is not as feature-rich : 4
  • Don't have time to test, migrate server : 3
  • less (easily) configurable : 2
  • JBrowse is limited in # of scaffolds that can be loaded : 2
  • JBrowse needs a Chado backend : 2
  • I don't know enough about JBrowse : 2
  • JBrowse needs improved glyphs for more data types : 2
  • JBrowse is not as flexible : 1
  • JBrowse set up and installation needs smoothing : 1
  • JBrowse needs better support for track management, including subtracks : 1
  • JBrowse should support bigbed and other file types : 1
  • JBrowse needs UI controls for displaying XYplot data from BAM, bigwig files : 1
  • JBrowse needs track sharing : 1

GMOD in the Cloud

GMOD in the Cloud is an Amazon Machine Image (AMI) with a set of GMOD components installed on it. Users can launch their own AMI, upload their data, and have their own server for data access and analysis. More GMOD in the Cloud information is available on the GMOD wiki.

Have you used GMOD in the Cloud?

  • Yes, in a full-time production environment : 0
  • Yes, in an on-demand production environment (e.g. annotation jamboree; teaching course) : 1
  • Yes, in a testing or development environment : 7
  • No, but I plan to use it : 15
  • No. : 36
  • What is GMOD in the Cloud? : 1

Are there any components that should be added to GMOD in the Cloud?

The current GMOD in the Cloud AMI has the following components: Apollo; a Chado database; GBrowse; GBrowse_syn synteny browser; JBrowse; and Tripal. WebApollo will shortly be added to GMOD in the Cloud.

Do you have any other comments or suggestions about GMOD in the Cloud?

  • Great project
  • Provide a raw image for other private clouds
  • The documentation needs improvement

GMOD Components

Which of the following GMOD components do you use or provide for users?

For users of GMOD components, please indicate your usage or awareness of each GMOD component.

For those who provide GMOD components, please indicate whether you provide the component, and if not, whether you are aware of it.

  • Now: you use or provide it now;
  • Past: you have used or provided it;
  • Future: you plan on (or are considering) using or providing it;
  • Aware: you are aware of the component but have not used/provided it;
  • Unaware: you do not know about the component.

There were 64 responses to this question.

Click on a table header to sort by that column.

Component Unaware Aware Past Present Future Awareness Current and future usage
Apollo / WebApollo18 28.1323 35.946 9.3813 20.314 6.2546 71.8817 26.56
Argos55 85.947 10.941 1.561 1.560 09 14.061 1.56
Bio::Chado::Schema27 42.1917 26.564 6.2513 20.313 4.6937 57.8116 25
BioMart21 32.8118 28.135 7.8115 23.445 7.8143 67.1920 31.25
Blast Graphic Viewer47 73.4410 15.631 1.564 6.252 3.1317 26.566 9.38
Caryoscope57 89.064 6.250 03 4.690 07 10.943 4.69
Chado16 2513 20.317 10.9423 35.945 7.8148 7528 43.75
Chado::AutoDBI46 71.8811 17.194 6.253 4.690 018 28.133 4.69
CMap38 59.3813 20.312 3.139 14.062 3.1326 40.6311 17.19
DIYA56 87.56 9.380 01 1.561 1.568 12.52 3.13
Ergatis50 78.1311 17.193 4.690 00 014 21.880 0
Flash GViewer58 90.634 6.251 1.560 01 1.566 9.381 1.56
Galaxy15 23.449 14.064 6.2528 43.758 12.549 76.5636 56.25
GBrowse7 10.944 6.257 10.9443 67.193 4.6957 89.0646 71.88
GBrowse Synteny Viewer (GBrowse_syn)22 34.3821 32.811 1.566 9.3814 21.8842 65.6320 31.25
GeneXplorer59 92.195 7.810 00 00 05 7.810 0
Genome Grid63 98.441 1.560 00 00 01 1.560 0
GMOD Tools37 57.8111 17.196 9.3810 15.630 027 42.1910 15.63
GO Graphic Viewer48 758 12.52 3.132 3.134 6.2516 256 9.38
InterMine37 57.8113 20.315 7.814 6.255 7.8127 42.199 14.06
ISGA59 92.192 3.133 4.690 00 05 7.810 0
JBrowse18 28.1319 29.697 10.947 10.9413 20.3146 71.8820 31.25
LuceGene55 85.948 12.50 00 01 1.569 14.061 1.56
MAKER27 42.1916 251 1.5612 18.758 12.537 57.8120 31.25
Modware53 82.8111 17.190 00 00 011 17.190 0
Pathway Tools41 64.0611 17.193 4.698 12.51 1.5623 35.949 14.06
SOBA50 78.137 10.943 4.694 6.250 014 21.884 6.25
Sybil50 78.1310 15.631 1.561 1.562 3.1314 21.883 4.69
SynBrowse43 67.1914 21.882 3.130 05 7.8121 32.815 7.81
SynView48 7510 15.631 1.560 05 7.8116 255 7.81
TableEdit (wiki extension)53 82.817 10.942 3.131 1.561 1.5611 17.192 3.13
Textpresso37 57.8116 254 6.255 7.812 3.1327 42.197 10.94
Tripal39 60.9410 15.633 4.698 12.54 6.2525 39.0612 18.75
WebGBrowse45 70.3113 20.314 6.252 3.130 019 29.692 3.13
XORT56 87.54 6.252 3.132 3.130 08 12.52 3.13

The top fifteen GMOD components, ranked by how aware respondents were of the component (including those who had used, currently use, or plan to use the tool). The figure indicates the number or percentage of the 64 respondents.

Tool Awareness Percentage
GBrowseGBrowse5789.06
GalaxyGalaxy4976.56
ChadoChado4875
ApolloApollo4671.88
JBrowseJBrowse4671.88
BioMartBioMart4367.19
GBrowse syn GBrowse Synteny Viewer (GBrowse_syn)4265.63
Bio::Chado::SchemaBio::Chado::Schema3757.81
MAKERMAKER3757.81
GMOD ToolsGMOD Tools2742.19
TextpressoTextpresso2742.19
InterMineInterMine2742.19
CMapCMap2640.63
TripalTripal2539.06
Pathway ToolsPathway Tools2335.94

The top fifteen GMOD components, ranked by current usage. The figure indicates the number or percentage of the 64 respondents who use the tool.

Tool Usage: now Percentage
GBrowseGBrowse4367.19
GalaxyGalaxy2843.75
ChadoChado2335.94
BioMartBioMart1523.44
ApolloApollo1320.31
Bio::Chado::SchemaBio::Chado::Schema1320.31
MAKERMAKER1218.75
GMOD ToolsGMOD Tools1015.63
CMapCMap914.06
TripalTripal812.5
Pathway ToolsPathway Tools812.5
JBrowseJBrowse710.94
GBrowse synGBrowse Synteny Viewer (GBrowse_syn)69.38
TextpressoTextpresso57.81
InterMineInterMine46.25

The top fifteen GMOD components, ranked by how current and future usage. The figure indicates the number or percentage of the 64 respondents who currently use or who plan to use the component.

Tool Usage: now and future Percentage
GBrowseGBrowse4671.88
GalaxyGalaxy3656.25
ChadoChado2843.75
BioMartBioMart2031.25
MAKERMAKER2031.25
JBrowseJBrowse2031.25
GBrowse synGBrowse Synteny Viewer (GBrowse_syn)2031.25
ApolloApollo1726.56
Bio::Chado::SchemaBio::Chado::Schema1625
TripalTripal1218.75
CMapCMap1117.19
GMOD ToolsGMOD Tools1015.63
Pathway ToolsPathway Tools914.06
InterMineInterMine914.06
TextpressoTextpresso710.94

Individual Tool Ratings

Apollo

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 1 3 3 1 3.5 8
Ease of installation/configuration 1 1 3 2 2 3.333 9
Functionality 0 2 2 3 2 3.556 9
Support 0 0 3 2 3 4 8

Bio::Chado::Schema

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 1 0 1 2 0 3 4
Ease of installation/configuration 0 1 1 2 0 3.25 4
Functionality 0 0 2 2 0 3.5 4
Support 0 0 2 2 0 3.5 4

BioMart

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 1 1 0 4 0 3.167 6
Ease of installation/configuration 0 1 2 1 0 3 4
Functionality 0 1 0 5 2 4 8
Support 0 1 0 3 0 3.5 4

Chado

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 1 3 5 1 3 3.154 13
Ease of installation/configuration 0 5 6 1 2 3 14
Functionality 0 0 4 6 4 4 14
Support 0 4 3 2 3 3.333 12

Chado::AutoDBI

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 1 1 0 3.5 2
Ease of installation/configuration 0 0 1 1 0 3.5 2
Functionality 0 0 1 1 0 3.5 2
Support 0 0 1 1 0 3.5 2

CMap

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 1 0 3 1 0 2.8 5
Ease of installation/configuration 0 1 2 2 0 3.2 5
Functionality 0 0 3 2 0 3.4 5
Support 2 1 1 1 0 2.2 5

DIYA

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 1 0 0 3 1
Ease of installation/configuration 0 0 1 0 0 3 1
Functionality 0 0 1 0 0 3 1
Support 0 0 1 0 0 3 1

Ergatis

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 1 0 0 0 2 1
Ease of installation/configuration 1 0 0 0 0 1 1
Functionality 0 0 1 0 0 3 1
Support 0 0 1 0 0 3 1

Galaxy

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 2 9 5 4.188 16
Ease of installation/configuration 0 0 2 6 6 4.286 14
Functionality 0 1 1 6 8 4.313 16
Support 0 0 1 8 7 4.375 16

GBrowse

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 1 3 15 3 3.909 22
Ease of installation/configuration 2 2 8 6 3 3.286 21
Functionality 0 0 1 10 11 4.455 22
Support 0 0 7 6 9 4.091 22

GBrowse syn

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 1 1 0 0 2.5 2
Ease of installation/configuration 1 1 0 0 0 1.5 2
Functionality 0 0 2 0 0 3.0 2
Support 0 0 2 0 0 3.0 2

GMOD Tools

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 1 0 0 1 3.5 2
Ease of installation/configuration 0 0 1 0 1 4 2
Functionality 0 0 1 0 1 4 2
Support 0 1 0 0 1 3.5 2

InterMine

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 2 0 0 3 2
Ease of installation/configuration 0 0 0 0 0 N/A 0
Functionality 0 0 0 2 0 4 2
Support 0 0 0 1 0 4 1

JBrowse

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 4 0 0 3 4
Ease of installation/configuration 0 1 2 2 0 3.2 5
Functionality 0 1 1 3 0 3.4 5
Support 0 0 1 2 0 3.667 3

LuceGene

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 1 0 0 0 0 1 1
Ease of installation/configuration 0 0 0 1 0 4 1
Functionality 0 1 0 0 0 2 1
Support 1 0 0 0 0 1 1

MAKER

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 1 1 0 2 3.75 4
Ease of installation/configuration 0 0 2 1 1 3.75 4
Functionality 0 0 0 1 3 4.75 4
Support 0 0 1 0 3 4.5 4

Pathway Tools

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 0 1 1 4.5 2
Ease of installation/configuration 0 0 2 0 0 3 2
Functionality 0 0 0 2 0 4 2
Support 0 0 1 1 0 3.5 2

SOBA

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 1 1 0 3.5 2
Ease of installation/configuration 0 0 0 2 0 4 2
Functionality 0 1 1 0 0 2.5 2
Support 0 0 1 1 0 3.5 2

Textpresso

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 1 1 1 0 3 3
Ease of installation/configuration 0 0 1 1 0 3.5 2
Functionality 0 1 1 2 0 3.25 4
Support 0 1 0 1 0 3 2

Tripal

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 2 4 0 3.667 6
Ease of installation/configuration 0 1 1 3 1 3.667 6
Functionality 0 0 2 3 1 3.833 6
Support 0 0 1 4 1 4 6

Web Apollo

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 1 1 0 3.5 2
Ease of installation/configuration 0 1 0 1 0 3 2
Functionality 0 0 0 2 0 4 2
Support 0 0 0 2 0 4 2

WebGBrowse

Rated on a scale of 1 (very poor) - 5 (very good); 5 is best.

Rating1
(very poor)		2
(poor)		3
(average)		4
(good)		5
(very good)		MeanN ratings
Documentation 0 0 0 1 0 4 1
Ease of installation/configuration 0 0 0 0 1 5 1
Functionality 0 0 0 0 1 5 1
Support 0 0 0 1 0 4 1