Where are you located? See the [GMODgeosurveyome map](mapping.html).

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- improve Chado genetic module docs : **1** - documentation is hard to find : **1** - GBrowse installation docs are out of date, incomplete : **1** - tutorials lag behind software : **1** - get users/devs more involved in wikis - topics recur on gbrowse mailing list, should be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**

What other bioinformatics tools do you use in your day-to-day work?

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

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**

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**

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**

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. - BioMART - InterMine - MAKER - Orthology search tools (eg. [Ortholuge](http://www.pathogenomics.ca/ortholuge/), [OrthoMCL](http://www.orthomcl.org/)) - WebApollo

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