# 2008 GMOD Community Survey ### Date October 2008 The first annual GMOD Community Survey was taken in October 2008. We received 89 responses. All questions were optional. ### Table of Contents - [GMOD Components](#GMOD_Components) - [Apollo](#Apollo) - [Argos](#Argos) - [BioMart](#BioMart) - [Blast Graphic Viewer](#Blast_Graphic_Viewer) - [Caryoscope](#Caryoscope) - [Chado](#Chado) - [Chado::AutoDBI](#Chado::AutoDBI) - [CMap](#CMap) - [Ergatis](#Ergatis) - [Flash GViewer](#Flash_GViewer) - [GBrowse](#GBrowse) - [GBrowse_syn](#GBrowse_syn) - [GeneXplorer](#GeneXplorer) - [Genome Grid](#Genome_Grid) - [GMODTools](#GMODTools) - [GMODWeb](#GMODWeb) - [GO Graphic Viewer](#GO_Graphic_Viewer) - [InterMine](#InterMine) - [Java TreeView](#Java_TreeView) - [LuceGene](#LuceGene) - [MAKER](#MAKER) - [Modware](#Modware) - [Pathway Tools](#Pathway_Tools) - [Restriction Graphic Viewer](#Restriction_Graphic_Viewer) - [Sybil](#Sybil) - [SynBrowse](#SynBrowse) - [SynView](#SynView) - [Table Editor](#Table_Editor) - [Textpresso](#Textpresso) - [XORT](#XORT) - [GMOD Servers](#GMOD_Servers) - [GMOD Community Meetings](#GMOD_Community_Meetings) - [GMOD Project](#GMOD_Project) - [GMOD Help Desk](#GMOD_Help_Desk) - [About You](#About_You) - [Your Organization](#Your_Organization) - [Final Comments](#Final_Comments) ------------------------------------------------------------------------   ## GMOD Components   **Which GMOD components do you use and/or have feedback on?** You can provide additional feedback on any selected components.  
27
(30.3%)
Apollo  
0
(0.0%)
Argos  
19
(21.3%)
BioMart  
7
(7.9%)
BLAST Graphic Viewer  
0
(0.0%)
Caryoscope  
32
(36.0%)
Chado  
4
(5.3%)
Chado::AutoDBI  
9
(10.1%)
CMap  
5
(5.6%)
Ergatis  
5
(5.6%)
Flash GViewer  
63
(70.8%)
GBrowse  
4
(4.5%)
GBrowse_syn  
0
(0.0%)
GeneXplorer  
0
(0.0%)
Genome Grid  
9
(10.1%)
GMODTools  
5
(5.6%)
GMODWeb  
2
(2.2%)
GO Graphic Viewer  
9
(10.1%)
InterMine - Please select if you are *using or considering* InterMine  
2
(2.2%)
Java TreeView  
3
(3.4%)
LuceGene  
3
(3.4%)
MAKER  
1
(1.1%)
Modware  
12
(13.5%)
Pathway Tools  
0
(0.0%)
Restriction Graphic Viewer  
5
(5.6%)
Sybil  
5
(5.6%)
SynBrowse  
5
(5.6%)
SynView  
3
(3.4%)
Table Editor (MediaWiki)  
6
(6.7%)
Textpresso  
3
(3.4%)
XORT  
1
(3.1%)
Other  (Popup Balloons) ------------------------------------------------------------------------   ## Apollo   Which version of Apollo do you use?  
12
(44.4%)
CVS checkout since 1.9 release  
6
(22.2%)
1.9  
0
(0.0%)
1.8  
0
(0.0%)
1.7  
3
(11.1%)
1.6  
5
(18.5%)
Don't Know  
1
(3.7%)
Other  (We use 1.6 and up in my lab)  
 
Please rate Apollo using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.  
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
1
(3.7%)
8
(29.6%)
12
(44.4%)
3
(11.1%)
3
(11.1%)
Ease of installation/configuration
0
(0.0%)
3
(11.1%)
6
(22.2%)
6
(22.2%)
8
(29.6%)
4
(14.8%)
Support and documentation
2
(7.4%)
2
(7.4%)
9
(33.3%)
8
(29.6%)
2
(7.4%)
4
(14.8%)
  How do you load data into Apollo?  
7
(25.9%)
GAME XML  
5
(18.5%)
Chado XML  
11
(40.7%)
Chado JDBC  
15
(55.6%)
GFF Files  
2
(7.4%)
Ensembl DB (EnsJ)  
4
(14.8%)
GenBank  
2
(7.4%)
EMBL  
2
(7.4%)
Don't know  
6
(22.2%)
Other  (custom adapter,fasta,DAS,SOAP server,BSML,We usually convert GFF files to game xml for annotation)   How do you save annotations created in Apollo?  
8
(30.8%)
GAME XML  
3
(11.5%)
Chado XML  
6
(23.1%)
Chado JDBC with Triggers  
6
(23.1%)
Chado JDBC without Triggers  
11
(42.3%)
GFF Files  
1
(3.8%)
Ensembl DB (EnsJ)  
1
(3.8%)
GenBank Tabular  
3
(11.5%)
GenBank Human Readable  
2
(7.7%)
Don't know  
4
(15.4%)
Other  (TAIR,custom adapter,don't save,SOAP server)   Do you have any additional feedback or suggestions on Apollo   - it should continue to be supported/funded it would be great if more folks started using it - \- need better support for wiggle files - what about DAS? - Apollo needs to incorporate functional annotation! - It's very, very important that tooks like Apollo and Gbrowse explicitly define their usage conventions so other tools can follow suit! I think we're making progress here. - Apollo is a great product. I am happy to see it under current development again. I would definitely like to see increased flexibility in the glyphs that can be used. Either increase the types of glyphs or add more paramaters to describe glyph shapes. Apollo is currently not very good for drawing any type of Transposable Element structures. - Our genomics community is using Apollo for curating the gene structure. About 60 curator are saving their gene into our Chado database. It works well but few bug are still there (I have already sent a list to Ed, and working to add few other), and we would like to have few more feature, especially to add some other info in the annotation info editor (gene full nale, product) and a GO tree for functional annotation would be perfect. - very difficult to load data, loaders did not work - We're running Bio::DB::SeqFeature of GFF3 and tried the same GFF files with Apollo and had no luck loading it. Also any other gbrowse exported format except Genbank Human Readable (which worked partly) didn't load. I would find an example GFF3 file helpful! - Improve Apollo with GBOL (GMOD Bio Object Layer). Annotation of different genomic objects: protein coding genes with alternative splicing, non coding RNA genes, nested transposable elements, microsatellites (SSR). Improve annotation editor (author, comment, synonym, finish, is_problematic). Add functionnal editable annotation of protein coding genes with controlled vocabularies (e.g. gene name, product, gene ontology, ec_number). ------------------------------------------------------------------------   ## **Argos** No Argos users participated in the survey. ------------------------------------------------------------------------   ## BioMart  
 

Please rate BioMart using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
5
(26.3%)
8
(42.1%)
6
(31.6%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
6
(31.6%)
7
(36.8%)
4
(21.1%)
0
(0.0%)
2
(10.5%)
Support and documentation
2
(10.5%)
3
(15.8%)
3
(15.8%)
7
(36.8%)
2
(10.5%)
2
(10.5%)
  Do you have any additional feedback or suggestions on this component?   - Most of our users find the interface not very intuitive...it would be nice if that was easier to customize (in terms of th e workflow). Also, we'd like to be able to specify certain data fields as being in compressed format, so they could be expanded on the fly. - We have made several attempts to use Biomart with our Chado structured Postgres database and have been unsuccessful. While the email contacts have been responsive we have been unable to get this combination to work, We are using another simpler dabase with Biomart - BioMart is a wonderful tool. - Genuinely a remarkable tool, but laughably supported with the various setup and configuration tools which have opaque functionality and non-existent documentation. - I am just considering to use BioMart or InterMine on top of Chado. - The martView has a serious bug. When I attempt to retrieve some data which involves interpro attributes or gene ontology attributes (from uniprot17), the results are incorrect. For eg: if I choose the associated GO ID and GO Description as my attributes along with the UnirpotID for a given gene, say atoB in E. coli, I actually get a cross product of all the GO IDs against all the GO Descriptions. This is indeed a serious bug. Also, when I use the biomart-perl API, I found that not all elements that can be used as attributes can be used for defining filters. This is not like SQL where any field/column in a database table can be used either in the SELECT clause or in the WHERE clause. Apart from these two, Biomart is very useful especially for data federation. - Improve MartBuilder to optimize queries Allow optimized queries to cross between more than 2 datasets ------------------------------------------------------------------------   ## Blast Graphic Viewer  
 

Please rate Blast Graphic using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
2
(28.6%)
0
(0.0%)
4
(57.1%)
1
(14.3%)
0
(0.0%)
Ease of installation/configuration
1
(14.3%)
0
(0.0%)
1
(14.3%)
4
(57.1%)
1
(14.3%)
0
(0.0%)
Support and documentation
0
(0.0%)
1
(14.3%)
3
(42.9%)
1
(14.3%)
1
(14.3%)
1
(14.3%)
  Do you have any additional feedback or suggestions on this component?   - I had to do quite a few tweaks to get this to work and improve confiurability with multiple databases, but it's not a bad starting point. - A more modern look would be nice. ------------------------------------------------------------------------   ## Caryoscope No Caryoscope users participated in the survey. ------------------------------------------------------------------------   ## Chado   Which version of Chado do you use?  
7
(24.1%)
CVS checkout since 1.0 release  
12
(41.4%)
1.0  
3
(10.3%)
0.5  
4
(13.8%)
Don't know  
3
(10.3%)
Other  (0.5 with CVS update,0.003,FlyBase)  
 
Please rate Chado using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.  
 
  1 2 3 4 5 n/a
Functionality
1
(3.2%)
1
(3.2%)
4
(12.9%)
12
(38.7%)
10
(32.3%)
3
(9.7%)
Ease of installation/configuration
6
(19.4%)
4
(12.9%)
6
(19.4%)
10
(32.3%)
0
(0.0%)
5
(16.1%)
Support and documentation
3
(9.7%)
7
(22.6%)
7
(22.6%)
9
(29.0%)
3
(9.7%)
2
(6.5%)
  Which database management system do you use with Chado?  
25
(80.6%)
PostgreSQL  
3
(9.7%)
MySQL  
1
(3.2%)
Oracle  
0
(0.0%)
Sybase  
0
(0.0%)
DB2  
0
(0.0%)
Don't know  
5
(16.1%)
Other  (Several. PostgreSQL, MySQL, Oracle, Sybase,Would prefer to use MySQL over Postgres but willing to use with)   Which version/release of that DBMS is Chado running in?   Please indicate which Chado modules you use.  
26
(86.7%)
General - IDs and databases  
26
(86.7%)
Controlled Vocabulary (CV)  
27
(90.0%)
Seqeunce  
26
(86.7%)
Organism  
14
(46.7%)
Publication  
18
(60.0%)
Companalysis - Computational analysis results  
9
(30.0%)
Audit  
7
(23.3%)
Contact - people, groups, organizations  
7
(23.3%)
Expression - Non-microarry expression  
7
(23.3%)
Genetic  
4
(13.3%)
Library  
3
(10.0%)
Mage - Microarrays  
1
(3.3%)
Map - Non sequence maps  
10
(33.3%)
Phenotype  
3
(10.0%)
Phylogeny  
6
(20.0%)
Stock  
0
(0.0%)
WWW  
0
(0.0%)
Natural Diversity (pre-release)  
1
(3.3%)
Don't know  
0
(0.0%)
Other(s)      **Chado Middleware** Chado has a wide selection of middleware choices for accessing it and/or generating web sites that use it. Please indicate which middleware solutions you use to access Chado at your installation.  
1
(5.3%)
Modware  
3
(15.8%)
GMODWeb  
2
(10.5%)
Chado::AutoDBI (other than via GMODWeb)  
3
(15.8%)
XORT  
1
(5.3%)
Hibernate  
5
(26.3%)
Ibatis  
2
(10.5%)
Don't know  
7
(36.8%)
Other  (BioPython+Django ORM,GBOL,home made,Perl DBI,Coati/Prism,php,my own API (using Class::DBI))   Please provide any additional comments on middleware/website software in GMOD.   - It would be nice to have created_by, modified_by fields. The way I'm implementing it now is a separate table that stores the table, crud action, user(pointing to a Django user which is pointing to an LDAP user eventually), timetamps and a cvtype. Although it needs extra joins for some queries it won't break the chado schema and all old sql will work. - Be nice to see several API implementations for Chado in different languages. - We are very interesting in the development of Java middleware for creating gene report or other interface on top of Chado - Need for a common gene page based on GBOL (biojava) ? Need for a controller (view model controller)? Improve Modware GMODWeb is too difficult to install on Unix System Ibatis is used by Artemis   Please provide additional comments on Chado. For example, what changes or new modules would you like to see? What new functionality could you use? What documentation needs particular attention, ...   - Documentation and standardization of the Chado usage convention is an ongoing issue. Particularly with regard to genome annotation and comparative analyses. - Use a CV for companalysis terms. The documentation has improved immensely with the wiki. - Discussions or actions on incorporation of changes has been frustrating. The example I keep going back to is our suggestion of analysisfeature.type_id column a few years ago and at several meetings. Each time it seems to have been accepted among the group but nothing ever happens. This leads to different groups running different 'flavors' of Chado. - Need a way to store continuous (graph) data (e.g. wiggle) - organism module needs more attention - More specific documentation on preferred storage methods is needed to minimize divergence between user groups. - When we tried ~ a year a go (before V1) we had immense trouble resolving all dependencies under our 2.4 kernel CentOS4... In fact, we couldn't get it right - e.g. couldn't load the GFF3 we use with Bio::DB::SeqFeature. We will try again with the current version! - We would like to use the audit and the phylogeny modules ------------------------------------------------------------------------   ## Chado::AutoDBI  
 

Please rate BioMart using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
1
(25.0%)
0
(0.0%)
1
(25.0%)
0
(0.0%)
0
(0.0%)
2
(50.0%)
Ease of installation/configuration
1
(25.0%)
0
(0.0%)
1
(25.0%)
0
(0.0%)
0
(0.0%)
2
(50.0%)
Support and documentation
1
(25.0%)
0
(0.0%)
1
(25.0%)
0
(0.0%)
0
(0.0%)
2
(50.0%)
  Do you have any additional feedback or suggestions on this component?   - Clarify and improve Chado::AutoDBI, Modware, GMODWeb (Turnkey) and synchronize with GBOL ------------------------------------------------------------------------   ## CMap  
 

Please rate CMap using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
1
(10.0%)
8
(80.0%)
1
(10.0%)
0
(0.0%)
Ease of installation/configuration
1
(10.0%)
1
(10.0%)
3
(30.0%)
4
(40.0%)
1
(10.0%)
0
(0.0%)
Support and documentation
0
(0.0%)
0
(0.0%)
0
(0.0%)
6
(60.0%)
2
(20.0%)
2
(20.0%)
  Do you have any additional feedback or suggestions on this component?   - I hope that CMap documents could tell users how to break some default limitations and which function has limitations. Just like pictures scales and so on. - Perl dependencies are dreadful to install. Sometimes the dependences fail to install for various reasons. Perhaps versions and where you can download specific versions of the perl dependencies would be more helpful. - I think the support is much better than the documentation. I haven't yet upgraded from version 0.16. I seem to recall that the details for upgrading from version 0.12 to 0.14 and 0.14 to 0.16 were not as straightforward as they could be hence the reason I haven't upgraded to the latest version. - would be great if it works directly on Chado (may be it does already). - Add SVG for image format Improve zoom functionality Check indexes because there are errors (twice same name of index)
  ## Ergatis  
 

Please rate Ergatis using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
1
(20.0%)
2
(40.0%)
2
(40.0%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
1
(20.0%)
1
(20.0%)
2
(40.0%)
1
(20.0%)
0
(0.0%)
Support and documentation
0
(0.0%)
0
(0.0%)
4
(80.0%)
0
(0.0%)
1
(20.0%)
0
(0.0%)
  Do you have any additional feedback or suggestions on this component?   - We need a task manager, we would like to assess Ergatis and Galaxy. Futur of BSML ? ------------------------------------------------------------------------   ## Flash GViewer  
 

Please rate Flash GViewer using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
1
(20.0%)
3
(60.0%)
1
(20.0%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
2
(40.0%)
1
(20.0%)
2
(40.0%)
0
(0.0%)
Support and documentation
0
(0.0%)
0
(0.0%)
1
(20.0%)
4
(80.0%)
0
(0.0%)
0
(0.0%)
  Which version of Flash GViewer do you use?  
3
(60.0%)
0.5  
0
(0.0%)
0.4  
0
(0.0%)
0.2  
0
(0.0%)
0.1  
2
(40.0%)
Don't know  
0
(0.0%)
Other    Flash GViewer comes with genome maps for Human, Mouse and Rat. Which, it any, of these do you use and what other genome maps would you like to see available?  
1
(20.0%)
Human  
0
(0.0%)
Mouse  
0
(0.0%)
Rat  
4
(80.0%)
Others  (Rice Arabidopsis,Plants,TOMATO,malaria)   Flash GViewer allows you to visualize genome features aligned against the genome. On average, how many features do you display on Flash GViewer at a given time?  
1
(20.0%)
1-50  
4
(80.0%)
51-100  
2
(40.0%)
101-500  
1
(20.0%)
1001-5000  
0
(0.0%)
5000+   Flash GViewer has javascript connectivity, allowing you to send JavaScript messages to the GViewer from your web page to highlight specific features and access the Flash GViewer annotation data. Do you make use of these features?  
2
(40.0%)
Yes  
2
(40.0%)
No  
1
(20.0%)
Don't know   Do you have other feedback or suggestions for new features that you would like to see in Flash GViewer?   ------------------------------------------------------------------------   ## GBrowse   Which version of GBrowse do you use? By default, the version number is displayed at the bottom of every GBrowse page.  
2
(3.2%)
Don't use GBrowse, ignore the rest of this page.  
11
(17.5%)
CVS checkout since 1.69 release  
27
(42.9%)
1.69  
14
(22.2%)
1.68  
4
(6.3%)
Don't know  
7
(11.1%)
Other  (1.64,1.67,1.65,and 1.64,1.64)  
 
Please rate GBrowse using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.  
 
  1 2 3 4 5 n/a
Functionality
1
(1.6%)
0
(0.0%)
3
(4.9%)
26
(42.6%)
28
(45.9%)
3
(4.9%)
Ease of installation/configuration
1
(1.7%)
5
(8.3%)
11
(18.3%)
29
(48.3%)
10
(16.7%)
4
(6.7%)
Support and documentation
1
(1.7%)
4
(6.7%)
13
(21.7%)
24
(40.0%)
15
(25.0%)
3
(5.0%)
  Which GBrowse adaptor do you use? The adaptor and database for your GBrowse instance are found in the "GENERAL" stanza of your GBrowse configuration file.  
32
(53.3%)
Bio::DB::GFF  
15
(25.0%)
Bio::DB::SeqFeature::Store  
8
(13.3%)
Bio::DB::Das::Chado  
2
(3.3%)
Bio::DB::Das::BioSQL  
0
(0.0%)
FlatFile/Memory  
0
(0.0%)
LuceGene  
3
(5.0%)
Other  (Patched version of Bio::DB::Das::Chado working on oracle,DBI::mysql,?)   Which database management system, if any, do you use with GBrowse?  
40
(65.6%)
MySQL  
16
(26.2%)
PostgreSQL  
1
(1.6%)
Oracle  
0
(0.0%)
Sybase  
0
(0.0%)
DB2  
2
(3.3%)
None  
2
(3.3%)
Other  (informix,?)   If using a DBMS, what version/release of that DBMS is GBrowse using?   Do you have any additional feedback or suggestions on GBrowse?   General: - That's perfect good. - Congratulations - Outstanding compared to other choices - I'd like to download and start using it. - you are doing a great job! - Excellent! - I implemented a feature that allows users to show up/downstream regions (sequence) of a feature - useful if someone searches for regulatory elements.done with ajax. furthermore dna is translated into protein on the details page. And users can leave comments on the details page. finally i added a login page as our site is not public with a simple user management. - We're also interested in or potentially will use the LuceGene adaptor. Requests: - Installing GBrowse is made much harder due to having to installing a BioPerl nightly. - Would be good to bundle up a compatible version of BioPerl with each distro. Not haveing the 'correct' bioperl invariable causes headaches since modules are incompatible or missing. - Oracle port would be nice to have - We'd like to see a very big effort devoted to speeding up image generation. It is a huge bottleneck and makes the rendering of feature rich regions extremely slow (compared to, say UCSC). AJAX-ing the mouseovers helped a little bit, but the heavy-weight Sequence objects that need to be instatiated and then rendered make the drawing process far too slow. - Loading from GFF is currently a bit of a mess. Different scripts will result in loading supported by different adaptors but it's not completely clear what the benefits are of each or what features they provide. - GBrowse is difficult for cutomizing various functions. As an example, I'd like to freely work with perl script in configuration file (\*.conf). - try harder to make it generic. i.e test on a non linux box you do not have root on. document divorse it from bioperl, or at least have a known minimal cover set of libs (gbrowse only need about 5% of bioperl) document \*ALL\* other perl libs gbrowse needs and include them and cocument their versions. - it is sometimes slow on Chado. At least slower than Apollo - really looking forward to the AJAX enabled gbrowse - should be very impressive. The documentation is very helpful for the most part, but a few more case studies would be helpful (in particular for my application, dealing with partial assembled chromosomes/genomes) - I find the performance to be a bit less than stellar. I can see execute the queries against the remote mysql database and know that is not the problem. The problem is with gbrowse perl scripts themselves. I am running on a dual PIII 1GHz server with 2GB of memory. Also wish there was more documentation about the database queries/api. - The documentation is actually pretty good which is not reflected in the rating I gave. I was unhappy because the documentation appears not complete for all the glyphs and the scenarios where each of them can be used. For a biologist, the glyphs in action would be lot more attractive than a mere list of their names. Of course, this is totally a subjective opinion. In any case, thanks for such a wonderful tool. - Check the CDS frames because there are not coherent with those of Artemis ------------------------------------------------------------------------   ## GBrowse_syn  
 

Please rate GBrowse_syn using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
0
(0.0%)
2
(50.0%)
1
(25.0%)
1
(25.0%)
Ease of installation/configuration
0
(0.0%)
3
(75.0%)
0
(0.0%)
0
(0.0%)
1
(25.0%)
0
(0.0%)
Support and documentation
1
(25.0%)
1
(25.0%)
1
(25.0%)
1
(25.0%)
0
(0.0%)
0
(0.0%)
  Do you have any additional feedback or suggestions on this component?   - support is quick as usual with the mailinglist, but documentation could be better and more detailed. - We would like to assess GBrowse_syn, Sybil, Synview, SynBrowse. ------------------------------------------------------------------------   ## GeneXplorer No GeneXplorer users took the survey. ------------------------------------------------------------------------   ## Genome Grid No Genome Grid users took the survey. ------------------------------------------------------------------------   ## GMODTools  
 

Please rate GMODTools using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
3
(33.3%)
2
(22.2%)
2
(22.2%)
2
(22.2%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
2
(22.2%)
3
(33.3%)
2
(22.2%)
2
(22.2%)
Support and documentation
0
(0.0%)
0
(0.0%)
3
(33.3%)
2
(22.2%)
2
(22.2%)
2
(22.2%)
  Do you have any additional feedback or suggestions on this component?   - not really - assess the feasibility of developing a Fast bulk_loader for complete eukaryotic genomes: with an option to avoid integrity consistency check ------------------------------------------------------------------------   ## GMODWeb  
 

Please rate GMODWeb using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
1
(20.0%)
1
(20.0%)
0
(0.0%)
2
(40.0%)
1
(20.0%)
0
(0.0%)
Ease of installation/configuration
1
(20.0%)
4
(80.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
Support and documentation
0
(0.0%)
3
(60.0%)
2
(40.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
  Do you have any additional feedback or suggestions on this component?   - Needs more support... - I have try hard nut it never work on my side (RedHat) due to incompatibilities with MOD perl, Auto::DBI.It's a shame because it looks great. - GMODWeb is too difficult to install on Unix System. We do not think to use it.
  ## GO Graphic Veiwer  
 

Please rate the GO Graphic Viewer using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
1
(50.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(50.0%)
Ease of installation/configuration
1
(50.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(50.0%)
Support and documentation
0
(0.0%)
1
(50.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(50.0%)
  Do you have any additional feedback or suggestions on this component?   ------------------------------------------------------------------------   ## InterMine   Are you currently using or considering InterMine?  
2
(25.0%)
Yes  
5
(62.5%)
Hope to use it in the future  
1
(12.5%)
May use it, but I don't enough enough about it yet.  
0
(0.0%)
Not interested  
0
(0.0%)
Other   
 

Please rate InterMine using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
0
(0.0%)
3
(37.5%)
2
(25.0%)
3
(37.5%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
8
(100.0%)
Support and documentation
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
8
(100.0%)
  Which data types do/would you integrate? InterMine includes parsers for several standard biological data types/formats, which are most important for us to maintain:  
4
(57.1%)
Chado databases  
3
(42.9%)
Ensembl genomes  
5
(71.4%)
GFF3  
2
(28.6%)
Fasta  
1
(14.3%)
Genbank  
3
(42.9%)
UniProt XML (protein annotation)  
3
(42.9%)
Protein domains (*e.g.*, InterPro, PFam)  
2
(28.6%)
Protein structure (*e.g.*, PDB)  
5
(71.4%)
Orthologs (*e.g.*, InParanoid)  
0
(0.0%)
PSI XML (protein interactions)  
6
(85.7%)
GO annotation  
5
(71.4%)
OBO ontologies  
1
(14.3%)
KEGG pathways  
1
(14.3%)
Reactome pathways  
2
(28.6%)
Own data (please specify below)  
0
(0.0%)
Other (please specify below)   Please list any other data types of interest.   - chip seq Sequence/resequencing - Summary-level genotype data, allele/genotype frequencies Summary-level phenotype data Genome variation features   Which features do/would you find most useful?  
5
(100.0%)
Template queries  
3
(60.0%)
Report pages  
4
(80.0%)
QueryBuilder (design queries in web interface)  
4
(80.0%)
List upload (upload and resolve lists of IDs)  
3
(60.0%)
List analysis (graphical and statistical widgets)  
3
(60.0%)
Query by web service  
3
(60.0%)
Quick search  
4
(80.0%)
MyMine (account to save lists and queries)   Do you have any additional feedback or suggestions on InterMine?   - Compatability with Mart web service perhaps? Specifying (future) standardized data models & export/import RDF data representations. - not yet. - Intermine training done in Cambridge (30-31 october 2008 by Valentin Guignon)
  ## Java TreeView  
 

Please rate Java TreeView using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
1
(50.0%)
0
(0.0%)
1
(50.0%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
1
(50.0%)
0
(0.0%)
1
(50.0%)
0
(0.0%)
Support and documentation
0
(0.0%)
0
(0.0%)
1
(50.0%)
1
(50.0%)
0
(0.0%)
0
(0.0%)
  Do you have any additional feedback or suggestions on this component?   ------------------------------------------------------------------------   ## LuceGene  
 

Please rate LuceGene using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
2
(66.7%)
0
(0.0%)
0
(0.0%)
1
(33.3%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
1
(33.3%)
1
(33.3%)
0
(0.0%)
1
(33.3%)
Support and documentation
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(33.3%)
0
(0.0%)
2
(66.7%)
  Do you have any additional feedback or suggestions on this component?   - We've had to make local adaptations for the latest versions of the libraries. - We would like to use LuceGene for quick search on Chado but maybe Intermine will be enough ------------------------------------------------------------------------   ## MAKER  
 

Please rate MAKER using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(33.3%)
1
(33.3%)
1
(33.3%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(33.3%)
1
(33.3%)
1
(33.3%)
Support and documentation
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(33.3%)
1
(33.3%)
1
(33.3%)
  Do you have any additional feedback or suggestions on this component?   - We would like to assess Maker and to share annotation modules ------------------------------------------------------------------------   ## Modware  
 

Please rate Modware using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
1
(100.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
1
(100.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
Support and documentation
0
(0.0%)
1
(100.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
  Do you have any additional feedback or suggestions on this component?   ------------------------------------------------------------------------   ## Pathway Tools  
 

Please rate Pathway Tools using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
1
(9.1%)
2
(18.2%)
6
(54.5%)
1
(9.1%)
1
(9.1%)
Ease of installation/configuration
2
(18.2%)
2
(18.2%)
3
(27.3%)
2
(18.2%)
0
(0.0%)
2
(18.2%)
Support and documentation
1
(9.1%)
3
(27.3%)
3
(27.3%)
2
(18.2%)
0
(0.0%)
2
(18.2%)
  Do you have any additional feedback or suggestions on this component?   - Better API access to the back-end would be great (I guess dumping everything to Biowarehouse is a solution) - I find it rather disappointing that pw tools for the web creates the html pages at runtime. so it is impossible or hard to plug pw tools into an existing apache server without installing it onto the server directly and start it as www user (i work on a mulituser server and usually plug websites into the server with symlinks). - We would like to use pathway tools. How to connect Chado and a Pathway/Genome Databases (PGDBs)
  ## Restriction Graphic Viewer No restriction graphic users took the survey ------------------------------------------------------------------------   ## Sybil  
 

Please rate Sybil using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
1
(20.0%)
3
(60.0%)
1
(20.0%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
1
(20.0%)
4
(80.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
Support and documentation
0
(0.0%)
2
(40.0%)
2
(40.0%)
1
(20.0%)
0
(0.0%)
0
(0.0%)
  Do you have any additional feedback or suggestions on this component?   - We would like to have dynamic display with graphical object and not only SVG images. Futur of BSML ? ------------------------------------------------------------------------   ## SynBrowse  
 

Please rate SynBrowse using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
1
(20.0%)
2
(40.0%)
0
(0.0%)
1
(20.0%)
1
(20.0%)
Ease of installation/configuration
0
(0.0%)
4
(80.0%)
0
(0.0%)
0
(0.0%)
0
(0.0%)
1
(20.0%)
Support and documentation
1
(20.0%)
2
(40.0%)
1
(20.0%)
0
(0.0%)
0
(0.0%)
1
(20.0%)
  Do you have any additional feedback or suggestions on this component?   - This application needs more work. - What about SynBrowse2 ? ------------------------------------------------------------------------   ## SynView  
 

Please rate SynView using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
1
(25.0%)
2
(50.0%)
0
(0.0%)
1
(25.0%)
0
(0.0%)
Ease of installation/configuration
1
(25.0%)
1
(25.0%)
1
(25.0%)
0
(0.0%)
0
(0.0%)
1
(25.0%)
Support and documentation
1
(25.0%)
1
(25.0%)
1
(25.0%)
0
(0.0%)
0
(0.0%)
1
(25.0%)
  Do you have any additional feedback or suggestions on this component?   - We will not use SynView because It works only with GFF files. ------------------------------------------------------------------------   ## Table Editor (MediaWiki)  
 

Please rate Table Editor using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
2
(66.7%)
0
(0.0%)
1
(33.3%)
0
(0.0%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
1
(33.3%)
1
(33.3%)
0
(0.0%)
1
(33.3%)
Support and documentation
1
(33.3%)
0
(0.0%)
1
(33.3%)
0
(0.0%)
0
(0.0%)
1
(33.3%)
  Do you have any additional feedback or suggestions on this component?   - Interesting! Plan to use it for genome annotation! - Allow the round trips Chado / Table Editor ------------------------------------------------------------------------   ## Textpresso  
 

Please rate Textpresso using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
2
(33.3%)
0
(0.0%)
0
(0.0%)
3
(50.0%)
1
(16.7%)
Ease of installation/configuration
1
(16.7%)
0
(0.0%)
1
(16.7%)
0
(0.0%)
1
(16.7%)
3
(50.0%)
Support and documentation
1
(16.7%)
0
(0.0%)
1
(16.7%)
0
(0.0%)
1
(16.7%)
3
(50.0%)
  Do you have any additional feedback or suggestions on this component?   - actually we get our textpresso runs done for us by another group so I can't really comment (except that the output is apparently good enough for us at this time) ------------------------------------------------------------------------   ## XORT  
 

Please rate XORT using the following scale: 1 (poor) to 3 (average) to 5 (exceptional). Use n/a if you have no opinion.

 
 
  1 2 3 4 5 n/a
Functionality
0
(0.0%)
0
(0.0%)
1
(33.3%)
1
(33.3%)
1
(33.3%)
0
(0.0%)
Ease of installation/configuration
0
(0.0%)
0
(0.0%)
2
(66.7%)
0
(0.0%)
1
(33.3%)
0
(0.0%)
Support and documentation
1
(33.3%)
0
(0.0%)
1
(33.3%)
0
(0.0%)
1
(33.3%)
0
(0.0%)
  Do you have any additional feedback or suggestions on this component?   ------------------------------------------------------------------------   ## GMOD Server(s) Please describe the server(s) you run GMOD components on.   Which operating system does your server run? - You can leave this blank if you don't know, or provide as little (e.g. "Linux" or as much (e.g. "Ubuntu 7.10 (gutsy) Kernel Linux 2.6.22-14-generic") as you chose.   OS Summary: | \# | Operating System | |-----|------------------| | 55 | Linux | | 8 | Mac OS | | 6 | Solaris | | 2 | Windows | | 1 | Unspecified Unix | Detailed responses - Linux Mac OS X 10.5 Leopard - Red Hat Linux - Cent OS 5 - Unix - RHEL - CentOS 4 - Linux in both CentOS and Debian flavors - linux - Linux Fedora6 - Linux, Mac OS X - RedHat Enterprise 5 - Li,ux - linux, debian, etch - Ubuntu 8.04, RedHat 5 Enterprice Linux, Debian Stable - Linux - Ubuntu jeos - Apollo runs mainly on windows desktop systems (pentium 4 based single core processors) gbrowse runs on SunOS 5.10 Generic_118833-17 sun4u sparc SUNW,Sun-Fire-V240 Solaris - Mac OS X 10.5.5 - CentOS 2.6.18-92.1.10.el5 SMP x86_64 GNU/Linux - red hat linux fedora core 8 - Linux - Centos Linux 4 - Debian Linux - Linux-RedHat 4.0 64 bits - CentOS, currently 4.6 - RedHat 3.4.5 - FC8 - Ubuntu dapper - RH Linux ES - CENTOS 2.6.9-78.0.1.ELsmp - Linux Debian 4.0 (etch), kernel 2.6.18-6-686-bigmem - Ubuntu 8.04 - RHEL 5 - RedHat Enterprise - Solaris 10 - Linux (Debian Etch) - Fedora 6, Kernel 2.6.20-1 - Linux RHEL 5.0 - sun solaris - Mac OS X 10.5.x (Leopard) - Linux - 2.6.18-92.1.13.el5xen Centos 5.1 - OS X 10.5 - Mac OS X Server - LINUX 2.6.13-15.10-smp x86_64 x86_64 x86_64 GNU/Linux SunOS 5.10 Generic_118833-20 sun4u sparc SUNW,Ultra-4 - Ubuntu 7.10 - Windows - Solaris 2.8, Solaris 2.10 - Ubuntu 8.04 - Ubuntu 8.04 - Ubuntu 8.04 - linux - Ubuntu gutsy/hardy, Mac OS X 10.5 - OS X 10.5 - Linux (CentOS) - 64-bit RHEL5 - Solaris 9. soon to be Solaris 10 - Linux 2.6.9-22.0.1 RedHat - debian linux - MacOsX leopard I think? - Ubuntu 8.10rc server Linux 2.6.27-7-server on i686 - Linux web12 2.6.9-22.ELsmp - Debian Linux 2.6.17 - Linux - Linux myserver 2.6.16.60-0.21-bigsmp \#1 SMP Tue May 6 12:41:02 UTC 2008 i686 i686 i386 GNU/Linux - Mac OS X Tiger - solaris 10 - Ubuntu - CentOS 4 - Red Hat Enterprise Linux 4.0 64 bits   What hardware does your server have? - You can leave this blank if you don't know, or provide as little (e.g. "Intel" or as much (e.g. "Intel 2 Core Duo, 2.2 GHz, with 4MB level 2 cache, 4 GB memory, and a single 110 GB SATA 7200RPM drive.") information as as you want.   - Linux machine - ? Mac - Eight core Power Mac - 64Bit Intel - Amd Athlon 5000+, 4 GB memory, a single 320 GB SATA 7200 drive. - Mostly Intel, a couple of Sun SPARCs, mostly 8GB memory - 4 processor xeon machine - Opteron x86-64 1.6GHz to 2.8GHz - Dell Intel boxes - Intel - Intel IA 64 12GB Memory - sun - RHEL under VMware ESX server, 6GB Memory slice, 500GB disk 2 cores (2 x dualcore xeon 2.8Ghz in main VMware server) , Ubuntu native 64bit on a 2.2Ghz core2duo with 2 GB memory and 20 GB disk , Debian Stable native 32bit on a 2.0 Ghz Athlon with 1 GB Memory and 400 GB Disk - HP PAvillon dv5000 - apollo desktops= 1-2 GBs gbrowse server = 8 GBs (servers other applpications as well) - Intel Xeon 8 Core 64 bit 2.6 Ghz, 16 GB RAM, 4TB RAID 5 Intel Xeon 8 Core 64 bit 2.6 Ghz, 26 GB RAM, 2TB RAID10 (DB server) Intel Xeon 8 Core 64 bit 2.0 Ghz, 12 GB RAM, 300GB RAID 1 (Web server) - Intel Core Duo 2.2G ddr667 2G SATA 7200 240G - HP ProLiant DL580 G4 Server, 4 quadri-proc 7140M, 3.40GHz, 32GB memory - 64 bit dual core x86_64 - v40z Opteron, 4 CPu dual core, 16GB memory. We run two machines one for production and one for development. - Intel - Intel - Dual dual-core AMD Opteron 2216 6GB memory. Hardware RAID5 and RAID1 for data and system dirs respectively. - HP Proliant quad-Xeon CPU, 16GB RAM, SCSI + SATA disks both built-in and in external disk array, plus 2x near-identical but lesser spec servers. 5x slave nodes - Intel - Intel, multicore, NFS-mounted 16GB RAM blades - Intel - Intel(R) Xeon(TM) CPU 3.06GHz \* 4 2071076 kB memory 302260 kB cache 100GB Scsi \* 1 - Dual Xeon, 2 GB RAM - sun solaris - MacPro dual quad core Xeon ~2GHz, 13Gb RAM, 1.4Tb RAID5 - HP DL 145 Dual Processor with 4-8 GB of ram - Intel core 2 Duo - PowerPC G5 Dual 2GHz - Intel dual Core 2 Quad, 8GB RAM. - Bad - SunBlade 2.0 Gb RAM, 2x80Gb drives SunBlade 1.5 Gb RAM, 2x40Gb drives - AMD Athlon 1.8Ghz 2GB RAM - Intel - 2 Intel Xeon 4-core CPUs, 3.0 GHz, 16MB L2 Cache, 32 GB memory, 750GB SATA hard drive - Dual Pentium 2.2 GHz, 2GB memory - DL585, 4 x dual core cpus with 16GB RAM - 4 processor sparcv9 , 16G main memory - Sun v40z processors 64bits AMD Opteron 850 4GB RAM - Intel - Athlon 64 3200+, 1G ram, 1x20Gb IDE & 1x60Gb SATA HDD - Intel(R) Xeon(TM) CPU 3.20GHz MemTotal: 2074952 kB - 4 processors, 8GB memory - Intel(R) Pentium(R) Dual CPU E2180 @ 2.00GHz - Intel PIII 1GHz dual cpu, 2GB memory, CPU: L1 I cache: 16K, L1 D cache: 16K CPU: L2 cache: 256K mirrored system disk, SCSI scsi0 : IBM PCI ServeRAID 7.12.05 Build 761 \ Vendor: IBM Model: SERVERAID Rev: 1.00 Type: Direct-Access ANSI SCSI revision: 02 - Apple PowerMac, 8GB RAM, 4 x 2.5 GHz PowerPC G5 - i86 (amd i think), 8 dual core processors - AMD opteron quad 8GB 500GB RAID1 - HP ProLiant DL580 G4 4 quadriproc Xeon 3.40 GHz 32 GB memory and 1 To of hard drive   Is the server sufficient for your needs? If not, what would you change? - Faster or more CPUs, more disk, more memory, more servers, ...   A really approximate summary: | | | |-----|-------------------------------| | ~30 | Sufficient (at least for now) | | 8 | More Memory | | 8 | Faster/More CPUs/Servers | | 5 | Faster/More Disk | Details: - Yes - Yes - more memories. Just like CMap, when the database or map set has lots of features it takes long time to draw pictures. - Generally sufficient, always nice to have more CPUs - yes - faster disk i/o - yes - Yes - More Memory - more disk - the servers are currently performing on an average level, but soon we will switch to a more dedicated VMware esx server setup with 4 quad core xeons/32 GB and a SAN with 15000rpm SAS disks for the database volumes. - Sufficient. - apollo runs fine on our desktops, or at least, we don't believe the hardware is a limiting factor. Gbrowse we'd like to run on a separate machine from our main web application, but cpu speed may be a factor. - yes, for now. - more CPUs - yes it is sufficient - OK - Can get slow on deep databases (i.e. ones with lots of tracks). Often diffuclt to pinpoint exactly the bottleneck. I'd probably go with more memory, since that seems to fill up quickly! - Yes sufficient - Yes - Faster disk. DB writes are slow. More disk. More CPUs for better multi-use. - Sufficient. - Could always use more. - Yes - Disk space - it's enough - Yes - Utterly sufficient for in-house needs. If we open our setup (under discussion) we'd need more servers/CPUs. - Yes - yes - More processors and ram since we are using a virtualized environments. - More memory - yes - yes - Yes. - Need more memory and RAM - Faster cpu, more memory, more disk space - Yes - Faster with multiple core CPU and at least 8GB of RAM - I guess so. - faster and more CPUs - It is sufficient. - mor RAM - it is fine but we need more developnent servers so it will be replaced with a new T1 or somrthing to be determined - It gonna be faster in few months, we will have more servers - sufficient - it's fine - Just a test machine at present - ideally would like Core 2 Duo processor(s), lots more RAM and 500Gb+ 7200rpm SATA HDD - gbrowse_img is too slow - It's currently fine. - yes - dual cpus, each is 100%/0% utilized during browser refresh, I/O is negligible during these times, database is on remote machine - database is fast, network activity is negligible as well, system ping pongs from one cpu to another with one being 100% and the other 0%, memory is not the issue and there is no swapping during these times, it would be good to somehow parallelize the the perl script and/or make it somewhat more efficient - Runs a bit slow from text files, will try DB backend (Mysql) as soon as I find the appropriate documentation - yes - I think it is good enough for my purpose. - you always want to go faster, don't you? - separate computer cluster and DB and Web servers ------------------------------------------------------------------------   ## GMOD Community Meetings   GMOD holds community meetings every 6 to 12 months, usually co-located and immediately before or after large meetings like ISMB or Genome Informatics. Which, if any, GMOD meetings have you attended in the past?  
8
(36.4%)
2008 July (Toronto, before ISMB)  
9
(40.9%)
2007 November (Cold Spring Harbor, after Genome Informatics)  
6
(27.3%)
2007 January (San Diego, after Plant and Animal Genome)  
3
(13.6%)
2006 June (Durham NC at NESCent)  
9
(40.9%)
2005 October (Cold Spring Harbor, before Genome Informatics)  
3
(13.6%)
2005 May (Menlo Park, CA at SRI)  
7
(31.8%)
2004 and before   Do you expect to attend the January 2009 GMOD Community meeting? It will be held in San Diego, on January 15-16, immediately following the Plant and Animal Genome (PAG 2009) conference.  
5
(6.7%)
Yes 
14
(18.7%)
Probably 
17
(22.7%)
Probably not 
20
(26.7%)
No 
17
(22.7%)
Don't Know 
2
(2.7%)
n/a   
 
If you have attended GMOD meetings in the past, please rate the meeting(s) using the following scale: 1 (not at all) to 3 (reasonably) to 5 (exceptionally). Use n/a if you have no opinion.  
 
  1 2 3 4 5 n/a
Are meetings useful?
0
(0.0%)
1
(2.3%)
2
(4.7%)
17
(39.5%)
5
(11.6%)
18
(41.9%)
Are meetings well run and organized?
0
(0.0%)
2
(4.7%)
6
(14.0%)
10
(23.3%)
5
(11.6%)
20
(46.5%)
  If you have attended meetings in the past, please tell us what you found helpful at the meeting as well as any ways that meetings could be improved.   - Perhaps a more specific agenda with particular goals (i.e. deciding on SOPs for particular usage conventions) something where GMOD users/developers can lock themselves in a room and decide on usage conventions. Then perhaps have a way to rank the individual GMOD projects in terms of their adherence to the conventions. It would be nice to be able to pass around Chado instances to each other and actually be able to use them without major modifications. - Communication with other GMODers - Discussions on chado and data representation were good. Attempts to normalize usage and create validations could have gone a bit further. There were too many talks about tools people who were related to GMOD were working on. Didn't find many of these relevant. It was like they were advertising. - I found the meeting I attended very helpful. The only improvement I could suggest would be to tape it and put it on the net or provide slides and detailed summaries or the meeting for those who cannot make it. - Finding out what is the latest and greatest, and meeting the developers, both very important for us. - Meetings need to accomplish more than show-and-tell (which is nice) - but some sort of strategic planning needs to happen to better coordinate the project.s - Useful to get up to date on the status of the many different GMOD project. - I found all of the discussion about how gbrowse is used by others very interesting. - helpful -- meeting people. - i went to the workshop this year in durham and it was very useful and fun to meet people. - A more specific agenda available in advance would be useful. Show and tell only sometimes useful. Note: above attendance by various members of the group. - Try to clarify task priority, who is doing, what, when and where, and how collaborate   If you have not attended meetings in the past, please tell us why you did not attend and/or how the meetings could be changed so that you would consider attending.   Summary of popular reasons: | | | |-----|--------------------------------------------------| | 21 | Time, cost, distance | | 3 | Expected it not to be useful/appropriate for me. | | 2 | Didn't know about them. | Detailed responses: - Geographical location of GMOD meeting (time and money) and level of interest in the associated ISMB/Genome Informatics conference. If in Sweden at ISMB 2009 this looks possible. - Because I'm a Chinese user. It seems impossible to attend this meeting abroad. However, I hope one day such great meeting could be hold at China. - money and time ;) - -just wondering, if it can be useful for novice like me - Money talks - other member(s) of our staff attended or did not see a major reason to attend - too far - time mostly. Would be happy to contribute more by email/blog - I would attend a meeting in Germany or something close to it. - Time/money. Would attend a European based meeting. - Missed 2007 through ill-health Would be easier to attend if held in Europe. - I'd like to hold the meetings in Korea. - didn't have the time to travel due to other meetings I had to attend. The meetings at PAG are a good idea because it makes it easier to attend without additional traveling . - Not a developer. I was under the impression that it was for GMOD developers and contributors. - If the meeting is more geared to projects that use GMOD as a tool, instead of focusing the developments and progression of GMOD, it should attract more scientists from the field. - It's a very long and expensive trip from UK. - Too expensive as I am based in Australia - would something web based would be possible for overseas attendees? - Would be nice to have such meetings in Europe too :-) - I never used gmod before - No funding to travel - I woud certainly attend to a meeting in Europe. Why do not change each year as Genome Informatics. - too far away/expensive - closer to europe ;) - i didn't know about them. for example, this is the first I heard of the January 2009 meeting. - Geography - am in Australia - I have know GMOD only now, because I was searching for some Javascript Popup Balloons to use in my software. - Hadn't had the chance yet to attend one but will certainly consider it in the future. - i was never told of these meetings - Even though, I have been using GBrowse for more than 3 years as an end user, I actually got into the GBrowse configuration and usage of Biomart only during the last few months. So never thought about a GMOD conference before, but I guess, I would make it this time. - I just didn't have time yet! Would love to have one in Europe! - Try to do Gmod meeting in Europe ------------------------------------------------------------------------   ## GMOD Project   What aspects of the GMOD project are you most satisfied with?   Summary of popular responses: 23 GBrowse 17 Support and active community 8 Chado 8 Software tools quality, maintenance, breadth, and functionality 6 Open Source 6 Apollo Deatailed Responses: - GBrowse graphics - The Chado schema is a great schema to develop for (despite it's performance issues). - Open Source and good mailing-list support. GMOD's experts are really kind and patient for users' problems. They are great. - Apollo, XORT, Gbrowser - the software and the support - -open source community efforts -backed by the experienced people in genome databases -evolving - responsiveness of developer community - open source - wide variety of open source tools - the speed and quality of the support from both the helpdesk/website, mailing list and community (in both directions). - Excellent idea, chado has grown nicely. - apollo, gbrowse to a lesser extent - Gbrowse and the chado schema. The improvements in the documentation and the GMOD wiki. Good job on this. - Gbrowse - Apollo - The community is very active. - The quality of the software projects, and the helpfulness of the community. - GBrowse - Chado architecture. Gbrowse. Community. - Gbrowse is a fantastic centerpiece of the project. - GBrowse, easily. GBrowse karyotype also high there, Sheldon's done excellent work to make it usable to others and documented it well, so my hat is off to him. - Open and helpful community supporting valuable daily used softwares. - The community. - Continual update of GBrowse. - I really like the direction that Apollo is going in. I would like to see it be a lot easier to install Chado so that I can use it as a back end. I would also like to see chado be the most stable way to store data in apollo. It seems like xml is still the most stable way to serve apollo annotations. As it is now, I am using game.xml files on a samba server. This is not very satisfying, but it does the job. - GBrowse is great! also support for issue is pretty reasonable. - It's an impressive toolset for the relatively minor investment in time and resources to get it going. - Chado GBrowse the wiki documentation - It is open source and the community seems responsive. - Listserve support - genome browser - The aspect that satisfies me the most is the quick response to questions that users sent to the mailing list! - GBrowse - Gbrowse - GBrowse - Open Source generic and general purpose - gbrowse - Large spectrum of available tools to help with many different genomic needs. - Functionality - The best thing is the quick responses on the mailing list. - Our scientists love Gbrowse visualization of their data :-) - I will take the fifth. - GBrowse, Apollo Chado - chado - gbrowser - gbrowse - gbrowse, apolloo, synview - quality free software and documents - We're happy with Chado. User support has improved greatly in the past year. - Use gbrowse with yeast and soon with drosophila. - From what I have seen so far the GMOD project produces very high-quality output. - the fact that i can create my community with SDk and gmod - Finally some funding for tools - It's an excellent initiative! I fully support it and am very grateful for all the work that is made available for the community! It's really helpful also for small computational labs to get things done!! The mailinglists are very responsive and helpful! - GBrowse   What aspects of the GMOD project are you least satisfied with?   Summary of popular responses: | | | |-----|------------------------------------------| | 14 | Documentation | | 8 | Chado | | 7 | Difficult configuration and installation | | 5 | Integration and coordination | Detailed responses: - Instalation of server. Avability of pre configured server in VMware format (or compatible). - GMOD is probably better than nothing, but the lack of uniformity among groups still seems to be widespread and one wonders if it can truely be addressed for bioinformatics computing. - A clear understanding of what is GMOD. It seems to a newcomer that it is a mishmash of unconnected tools and competing middleware layers, some of which are low quality or virtually abandoned. The projects need to be unified under the GMOD name and the redundant and low quality stuff needs to be ditched from the GMOD umbrella. - synview - chaco - None really. Would be nice to get a definitive annotation method rather than 'clunky' Java editors. Hopefully AJAX GBrowse project will help this. - Support for GBrowse with BioSQL - I wish the developers of GMOD (myself included) had the time to document better our usage conventions and unify our efforts. - I find that the configuration of some of GMOD programs is a little complex. But I have to admit is the documentation is good to read and detailed. - the documentation and the fact that everything's in Perl - -documentation/tutorials - documentation - wide variety of open source tools - it is sometime hard to find relevant information on a subject as it might be in several places of the wiki. Maybe more best practices type of howto's. - Difficult to move things along. Requests about db schema changes don't happen. - Installation in general, it is quite confusing. Incoherent documentation. Highly tied to postgresql. - The lack of coordination. The sinking of effort into Chado without sufficient loading tools for the data from different sources to help projects that are bootstrapping, not those which are already established. - BioMart is still quite hard to configure, though I think the developers are working on an improved config-tool. Chado relational schema. More specifically the fact that Chado was very model organism oriented in terms of modeling genetic & phenotype data which did not match up well with my needs at the time for human genetic data. May have improved by now (this was a couple of years ago). - chado, since I have had so much problems trying to install it on the Mac. - Microarray - Gmod - tools integration - none - Somewhat steep learning curve (fine for me, but can be a bit daunting to a beginner). - Installation can be a chore; documentation sometimes lacking - none, it's all good. - documentation - GMOD Web, lack of web interface and reports. - BioPerl dependencies - for gbrowse, phasing out of Linkage Disequilibrium display, seems to have been taken over by haploview. - documentation, particularly: more advance worked example config/gff files, special cases etc. In particular, setup of low coverage genome browsers - Documentation could be better. - Documentation: the wiki is a good idea but it could be a bit more detailed. - NOTHING! - its not clear that GMOD solutions are best solutions, however, pressure is now becoming high from NIH to use GMOD whether or not it is a best solution. - Somethings could be better documented (which is hard to keep up with, I know). - Chado GMODTools Apollo GMODWeb Biomart - Some problem with integration of sub-projects. - 1\. Need to release genome browsers with Web 2.0. 2. Need to develop various moduls which are installed easly - Difficulty in installing chado. - I wish the many possible configurations (glyphs, to name one) and track setups were easier to sort out. Reverse engineering how HapMap works (to name one) isn't all that useful, as they have extensively customized their setup. - GMOD tools - the documentation is not very good, and many scripts have bugs - Some things just do not work, like GMODWeb. I see the need for a product like this, but I have had very little luck with it and I am considering other options.   What would you like to see GMOD work on in the next 12 to 18 months? - Better functionality in what we have, new functionality and tools, new types of data and tools, better integration, better documentation and training, ...   Some popular topics: | | | |----|----| | 18 | Documentation | | 14 | Integration | | 11 | GBrowse: testing, speed, Web 2.0, glyph documentation, features | | 5 | Chado: PostgreSQL 8.3 support, phenotypes, integration with Apollo, functional annotation | | 3 | Training | | 3 | Improve what we already have | Detailed Responses: - More Documentation ^^ - better documentation (and more extensive) for the newer core aspects of gbrowse (the SeqFeature version of the database schema for one thing), working on speeding up the load time for typtical gbrowse instances (GD may be a factor). - Conversion of the Chado schema to run on Pg 8.3 and the tools on perl 5.10. Better integration. - synview - Integration is always a biggie. As a minimum I would like solid ID resolution. As a long term aim - seamless GUI integration of the main biological datatypes - documentation, computational pipelines - Gbol - AJAX GBrowse for fast zooming and annotation More documentation on how to build your own glyphs. - Coherent documentation Clear specs about data loader, make them work out of the box. - Better integration and make what is already started being developed (GMOD-Web, Chado, Gbrowse) more stable and rock-solid and easy to install and populate with data. Better integration so that we can start to move towards a single solid data store that can be used to model the information and integrate it. - Keep churning out better and better GBrowse! Make InterMine more easy to install & configure (ongoing I believe) More effort into phenotype data & ontologies (Chris Mungall and friends at NCBO), if not already underway. - Testing GBrowse with BioSQL support - Unification of usage conventions would be nice, and perhaps a way of giving everyone a goal to get their projects to conform to the standards by a certain time. - I hope if possible provide users more demos and documentations. - Faster loading and update loading in GBrowse, better documentation is a must - -education and training - faster GBrowse!!! - online one hour live chat to help users - improve existing offerings - A 'Web 2.0' version of GBrowse. GBrowse has fallen behind with respect to ease of use and user experience. - Better integrate the different tools to have a GMOD recommended 'suite'. - I was very happy to see the GMOD Best Practices page and think we should really be working on getting that completely defined and as many tools as possible supporting it. - functions with ajax - Chado integration with apollo. Transposable element glyphs in apollo or the ability to easily generate my own glyphs. - better integration, better documentation and training - Better documentation, greater ease in integrating tracks and data sources than exists currently. Quicker 'cloud' access to allow for less local storage of public datasets. - definitely better documentation! also more integration with the plant community . e.g. The new iPlant collaborative does not seem to attempt to use the available GMOD features, which could really benefit all sides. - Need better integration between the various components and better documentation - better db searches from Gbrowse? - consolidating infrastructure is a very good thing. this includes documentation. - reports improvement of chado for the functional annotation - integration - Web2.0 gbrowser - documentation could probably be improved, just by watching someone trying to install things, and seeing what mistakes they make. i would love to be able to designate font size for features, for when my boss wants the gene symbols very large for a slide for example. Another idea to improve documentation might be to have sample browsers available showing features that someone might be interested in and links to the configuration files and gff files that they would use to get that display. For example, I don't know how to use wiggle and balloons. I can't figure out what would need to be changed in the configuration file for these features. - AJAX - and whatever other brilliant ideas you and your users come up with....I'm a just a noobie, and totally impressed with what I've seen so far. - More focus on fewer projects - better documentation, more efficient perl coding - Better documentation. - nothing i like it the way it is - Improving ease of integration of GMOD tools into non-GMOD environments. - GBol, controller, Common Gene Page, Apollo / Artemis Annotation history, update, reconciliation, checking of the annotation integrity Comparative Genomics Annotation training and jumboree GMOD hackaton - Stabilizing the tools making them production ready in some cases. Other cases, making the tools interoperable with other applications using web services. - Better documentation. - Would be nice to have a frontend management tool for Gbrowse servers. It's a very long load time if I make a mess of the mySQL database but I do direct surgery on it when small changes are required. - better integration documentation and training - adding even more functionality to gbrowse. What makes gbrowse so great is it's excellent documentation. Keep it updated, that is very important. - Design of middle layer that makes using different data sources (e.g. GFF3, Chado) transparent. ------------------------------------------------------------------------   ## GMOD Help Desk  
 
The GMOD Help Desk was created in 2007 to provide several services to the GMOD community.

Please rank the relative performance of the Help Desk in each area. Assign 1 to the task it does best at, 2 to the next best, and so on, down to 5 for the task it does least well. Use n/a if you have no opinion on a task.  
 
  1 2 3 4 5 n/a
Answering user questions - Providing useful and timely answers to user questions.
12
(15.6%)
2
(2.6%)
8
(10.4%)
12
(15.6%)
18
(23.4%)
25
(32.5%)
GMOD Web Site - Organizing and maintaining the GMOD web site and making it relevant to the GMOD community.
6
(7.6%)
13
(16.5%)
17
(21.5%)
23
(29.1%)
10
(12.7%)
10
(12.7%)
Education - Providing online and in person training about GMOD and GMOD components.
3
(3.9%)
6
(7.8%)
14
(18.2%)
18
(23.4%)
8
(10.4%)
28
(36.4%)
Outreach and Community Building - Getting the word out about GMOD and its capabilities and encouraging an active community of GMOD users and developers.
1
(1.3%)
9
(11.5%)
15
(19.2%)
18
(23.1%)
10
(12.8%)
25
(32.1%)
Developer Support - Polishing component documentation, and integration and beta testing services.
3
(3.8%)
13
(16.5%)
15
(19.0%)
16
(20.3%)
9
(11.4%)
23
(29.1%)
 
 
Please rank what the priorities of the Help Desk should be. Assign 1 to the most important task, 2 to the next most important, and so on.  
 
  1 2 3 4 5 n/a
Answering User Questions
28
(35.4%)
13
(16.5%)
14
(17.7%)
6
(7.6%)
10
(12.7%)
8
(10.1%)
GMOD Web Site
11
(14.1%)
17
(21.8%)
18
(23.1%)
14
(17.9%)
12
(15.4%)
6
(7.7%)
Education
6
(7.7%)
11
(14.1%)
24
(30.8%)
19
(24.4%)
9
(11.5%)
9
(11.5%)
Outreach and Community Building
2
(2.6%)
11
(14.1%)
17
(21.8%)
14
(17.9%)
23
(29.5%)
11
(14.1%)
Developer Support
13
(16.7%)
15
(19.2%)
12
(15.4%)
16
(20.5%)
13
(16.7%)
9
(11.5%)
  Are there other areas the Help Desk should allocate time to?   - Actually I think they are really good. - I don't really use the gmod helpdesk, but my answers above are mainly based on trying to get help for gbrowse from the gbrowse mailing lists (which I don't know if the gmod help desk gets copied on), which was spotty at best. But in general I think answering questions to the best of the ability of the help desk folks should be of paramount importance. - Getting to know some of the more fringe tools (or new tools) and learning/advising how they might better integrate into the overall software stack. - n/a - incorporating code and patches from users/developers. Many organizations have adapted GMOD code and have modified it for different usages. Encouraging submission of such code can benefit everyone in the community. - How about to set online classes? Or, How about to post the passed classes' materials, such as handouts, exercise questions, and answers onto website? The users like me who does not have time or money to attend a real class will like to pay for those e-learning materials. - If the tools were thoroughly tested, documented and maintained and the GMOD Web Site contained enough up-to-date information, wouldn't there be less need for the other tasks? - No - Sending me a mug? - n/a - none   GMOD offered a 2008 GMOD Summer School in North Carolina and will offer it again in 2009. The course covered Chado, GBrowse, Apollo, CMap, and the Community Annotation System. We are also considering offering a multi-day course elsewhere in 2009.   What training offerings would be most helpful to you or your colleagues?   - Configuration, Tips, Break Limitations. - GBrowse configuration (intermediate and advanced) - -training on basic schema to the novice -online tutorials...or webminaor....even in the informal ones will help -so that the complexity won't scare the new guys... - Chado/Postgres/Biomart - as far as technical people go (speaking from the technical side) I'm not convinced training for us is as important as basic support and documentation for specific, widely used packages. - GBrowse setup and configuration - Developing add on GBrowse tools and databases Galaxy integration Annotation - installation and management of gbrowse - Setting up chado, integration with apollo. - GBrowse - All of those (Chado, GBrowse, Apollo, CMap) - Tour of latest available tools, with hands-on demos on specific use-cases. - Gbrowse - On-line training modules - Apollo - Gbrowse - Chado - how to write a plugin - a web cast, for users outside the US - Pathway Tools user training - GBrowse and Apollo - learning how to code and create my own game or to script lua files - any course in Europe, especially Germany :-D - Community annotation system and genomic comparative   Would you be interested in attending a GMOD course in Europe in 2009? The course would likely cost a few hundred euros (or pounds) to cover costs.  
13
(16.7%)
Yes 
12
(15.4%)
Probably 
13
(16.7%)
Probably not 
23
(29.5%)
No 
14
(17.9%)
Don't know 
3
(3.8%)
n/a    We are currently considering 3 host countries for the GMOD Europe course. If you might attend, then which of these locations would work well for you?  
25
(56.8%)
France (several locations are under consideration)  
19
(43.2%)
The Netherlands (several locations are under consideration)  
27
(61.4%)
United Kingdom, Oxford  
21
(47.7%)
Other  (italy,Any,Australia,Germany,Korea,Dundee,Vienna,Spain,Cambridge/Hinxton,Ireland,Germany,India,Canada,United States,Germany)   Do you have a preferred location?  
8
(16.0%)
France  
3
(6.0%)
The Netherlands  
15
(30.0%)
United Kingdom  
11
(22.0%)
Other  
13
(26.0%)
Any   Would you be interested in attending a GMOD course in the Asia/Pacific area in 2009? The course would likely charge some tuition to cover costs.  
12
(16.0%)
Yes 
9
(12.0%)
Probably 
19
(25.3%)
Probably not 
23
(30.7%)
No 
8
(10.7%)
Don't know 
4
(5.3%)
n/a    If you are interested in a GMOD course in the Asia/Pacific area, where would you prefer it be held? What other locations could you make it too? Would you be willing to host the course, or do you have recommendations on who could host it?   Locations with more than 1 mention | | | |-----|------------| | 5 | Austrailia | | 5 | China | | 3 | Japan | | 3 | Singapore | | 2 | India | Detailed answers. - Beijing, China. - -ICGEB, New Delhi. It is in New Delhi, India. It was a WHO/TDR bioinformatics center for 4 years starting 2000 conducting 4 international bioinformatics workshops. It has a very nice computer lab and on campus lodging facilities... - Hong Kong / Singapore / Japan / Australia Hong Kong- HKU Faculty of Science / CUHK Faculty of Science - China - IRRI, Philippines - Daejeon in Korea. I recommend to contact director of Korean Bioinfomation Center, Jong Bhak. - China, Japan, Singapore - West Coast. - Somewhere in Australia Not sure re funding for next year - may have run out - China Tsinghua University - Australia - Hold the course in New Zealand, but I'v have no trouble attendinng if it was in Australia. My employer, AgResearch, would probably be interested in hosting or could co-host with CSIRO (Wes Barris's employers) - Singapore, Genome Institute of Singapore - Australia - major institutions to consider would be ANU (College of Science), CSIRO (Livestock Industries), Uni Melb/WEHI - Kazusa DNA Research Institute have enough equipment to held a cource/meeting and easy to reach from Tokyo and the International Air Port. - India. No idea about who could host it. ------------------------------------------------------------------------   ## About You!   Do you consider yourself to be a GMOD user, GMOD Developer, or both?  
35
(43.8%)
User  
6
(7.5%)
Developer  
34
(42.5%)
Both  
5
(6.3%)
Other  (Administrator,PI of database using GMOD components,First time user,3rd party developer,PI)   Can we list your name and email address on the GMOD web site as a contact person for your organization?  
47
(61.8%)
Yes  
29
(38.2%)
No   ------------------------------------------------------------------------   ## Your Organization Please provide us with information about your organization and its interests. **This information will be used to guide GMOD's future direction and to create a web-based directory of organizations using GMOD.**   What organism(s) or types of organisms is your web site / database about? - For example, arthropods, crustaceans, or *Daphnia pulex*.   - Oryza sativa, Arabidopsis thaliana, Musa acuminata, Sorghum bicolor - Paramecium - plants - We maintain and develop various labs GBrowse databases these include Human, Mouse, Arabidopsis and Bacterial instances. - Dictyostelium discoideum - Fungi - human - Populus - Large collection of prokaryotic, eukaryotic and metagenome projects. - Plants - Oryza sativa - human - Plants (Grape, Wheat, Rice, Arabidopsis ...) and crops bio-agressors (Fungi, insects) - Wheat, Maize are the organisms we are currently annotatiting, but this is not what our web site is about. - Human - Human - Solanaceae (tomato , potato, eggplant, pepper, tobacco, coffee) - Glycine max (soybean) - Brain tumor - Rattus norvegicus - Gossypium genome - Organisms involved in infectious diseases - Yeasts - Human, mouse - Mammals - Kangaroo (Macropus eugenii) - Cyanobacteria - Pathogens - yeast - current, drosophila - near future - We work with portals - plants, seleaginella, RNA - Bacteria - Physcomitrella patens, Selaginella moellendorfii, ... - South and tropical monocotyledones for Cirad, fungi, insects, wheat and grapevine - Prokaryotes - Soybean - Drosophila - arabidopsis thaliana - Plasmodium falciparum, Tripanosomes and Leishmania - Green Plants Metazoa - Drosophila - sheep mainly; has small amount of human, cattle and dog information - Cucumber - arthropods - Arabidopsis thaliana - Potato - Glycine max - Bos taurus - possumbase is for possums, but our internal sites are for sheep, cow, grasses and fungi. - zebrafish - acyrthosiphon pisum and lepidoptera (but this is not public yet) - mostly Drosophilids - echinoderms - Ascidian (Ciona intestinalis - plants and bacteria - Tomato - Arabidopsis thaliana - bacterial - Plants - mammals/vertebrates - paramecium - Bombyx mori   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.  
51
(71.8%)
Assembled sequence  
39
(54.9%)
Next generation sequences  
29
(40.8%)
Microarrays  
18
(25.4%)
Other expression  
22
(31.0%)
Phenotypes  
48
(67.6%)
Comparative genomics  
13
(18.3%)
Population genomics  
4
(5.6%)
Anatomy  
29
(40.8%)
Ontologies  
38
(53.5%)
Annotation pipelines  
43
(60.6%)
Manual genome annotation  
32
(45.1%)
Community annotation  
19
(26.8%)
Literature curation  
20
(28.2%)
Pathways  
18
(25.4%)
Workflow / Integration  
6
(8.5%)
Community directory  
24
(33.8%)
Mapping (genetic, physical, QTL, ...)  
10
(14.1%)
Phylogeny  
13
(18.3%)
Lines / Stocks  
6
(8.5%)
Other (please describe below)   If you checked "other", please describe other types of data that your organization is interested in and that you would like GMOD to support.   - 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. ------------------------------------------------------------------------   ## Finish   If you have any additional feedback, suggestions, criticism, or praise for us that wasn't captured by the preceding questions, please enter it here.   - Huge thanks to your developers. They really make wonderful work for bioinformatics research. - Thanks for developing this great stuff. We all here are excited about it. Thanks for all the support. - good job - good job!!! - GMOD Asia plz... I hope that Korea or Japan. - ParameciumDB would not exist without GMOD, which makes it possible for a very small team to maintain a state of the art model organism database. From my point of view, the GMOD project is 100% successful! - GBrowse is a fantastic tool and we have found the community and developers very friendly. Keep up the good work! - Thanks for all your hard work! - Please let me know if you have received my survey with all forms filling (I've tried to go previous page and it seems than some of the forms were empty) - Thank you, the GMOD team! - Please don't let GMOD go the EBI way (using training courses to hide the fact they can't write simple to use software). Leave out the pseudo-corporate babble and go for simple, robust, efficient software that does one thing well. Don't care about logo, but care about unit-tests. - You are doing a really great job! Thank you very much! - I really need this beautiful tee-shirt ! - Thanks for GMOD its a nice collection of very useful tools! - \*insert much praise here\* - GMOD is hugely impressive - well done!! - Thanks a lot - I'm very glad that the GMOD project exists. Well done on your achievements so far and best of luck for the future! - THANK YOU! - Thank you very much to the GMOD team for its amazing work and we hope to develop a fruitful collaborative work between our project and GMOD.   **Your feedback is very valuable to us and highly appreciated.**
--The GMOD Team