gmod / gmod-web

Issues with or about, and tools for the GMOD website (currently a wiki)

gmod-web

Issues with or about, and tools for the GMOD website (currently a MediaWiki wiki).

gmod-web's Issues

GMOD Member Directory

As noted by @tnabtaf:

It would be nice to have a member directory on the web site, that listed organizations who use GMOD. I picture this as a giant table listing organizations, urls, descriptions, components used, contact information, ...

This would give people an idea of who uses what combination of components. It's also a good way to highlight that lots of different sites use it.

A problem here is how to get people to contribute, and still make the information easy to access.

A couple of options:

1. Use TableEdit. A template could be used so that when people click on "add row" they get some help with each column. See below for an example template.
2. Use another form-based extension (I have no idea which one). This could somehow aggregate the information into a table.

Approach 2 might bear some investigating, but I'm betting approach 1 is the way to go for many reasons.

Here's a draft TableEdit template that could be used with a member table:

<headings>
Database / Resource||database|text
Supporting Institution(s)||institution|text
Description||description
GMOD Components Used||components|something_modeled_on_go_annotation|Apollo|Argos|Bio::Chado::Scehma|BioMart|Blast Graphic Viewer|Caryoscope|Chado|Chado::AutoDBI|CMap|DIYA|Ergatis|Flash GViewer|Galaxy|GBrowse|GBrowse_syn|GeneXplorer|Genome Grid|GMODTools|GMODWeb|GO Graphic Viewer|InterMine|Java TreeView|LuceGene|MAKER|Modware|Pathway Tools|Restriction Graphic Viewer|Sybil|SynBrowse|SynView|Table Edit|Textpresso|XORT 
GMOD Page(s)||gmodpage
Contact(s)||contact
</headings>

What exists meanwhile is not exactly a member directory, but a collection of logos of GMOD members.

GMOD sourceforge.com project needs to be updated

The GMOD sourceforge site is outdated. Updating should presumably include putting a redirection link to the Github organization.

Establish clear default Creative Commons By (CC-By) License for uploads

This should appear for file uploads. (You may need to be logged in for the example link to work.)

GMOD.org Scrapbook / Contrib Infrastructure

As noted by @tnabtaf:

The GMOD mailing lists contain lots of little code snippets and scripts that aren't important/widely useful enough to include in any GMOD distribution, but that are interesting nonetheless.

I'd like to create infrastructure in the gmod.org website to encourage people to record these snippets / scripts in a way that makes them both easy to find, and easily identifiable as contributed.

The code could be anything from GBrowse callbacks (short perl subroutines) to scripts for converting from one format to another.

Issues to work out/investigate:

1. The best way to handle complete scripts. Should these be inlined, or should we link to a repository somewhere?
2. MediaWiki support: What extensions would help with this? Should we use a namespace and category tags? Just category tags?

This case is related to, and complements issue #9.

GMOD.org libgd page

As noted by @tnabtaf:

libgd problems are one of the more common sources of woe for people install GMOD tools, particularly GBrowse. Should Document common problems and workarounds.

Transfer repo into gmod organization on Github

This repo belongs to the @GMOD on Github. I'm just creating it here in advance so I can start populating issues on the tracker.

GBrowse 2 and GBrowse 1 doc reorganization

As noted by @tnabtaf:

GBrowse 2 was released in early 2010. However, GBrowse 1.x continues, and will continue, to have hundreds of installations.

Need to better document GBrowse 2 from it's current ad-hoc organization. Also need to reorganize all GBrowse implementation so it's clear what applies to 1, 2, or both.

There's now Category:GBrowse_2, but still seems to need considerably more work.

GBrowse WIG, BIGWIG, XYplot, and density Documentation

As noted by @tnabtaf:

WIG and BIGWIG files, and xyplots and density (intensity) glyphs are used in GBrowse to show quantitative data. They are quite popular. Unfortunately:

1. there are a number of edge cases on how to use them
2. several key, not too well documented features
3. they have been buggy and are subject to significant, periodic reimplimentation

These items are a constant source of problems and subsequent email traffic.

We need better comprehensive documentation on how to use them. This would be generated by mining email threads and experimentation.

GMOD.org User Log/Experience Infrastructure

As noted by @tnabtaf:

Some users take copious notes of what they went through to get something installed or to get a particular feature to work. A few people have already created pages on GMOD.org that describe their experience.

I'd like to create an infrastructure on the web site that

1. Encourages people to record their experiences on a wiki page, where others can find it.
2. Helps people locate these logs when they are trying do similar things.

Having this would help people know that when they are using Ubuntu 8 they will need to install package X, whereas in Ubuntu 9 package X has been folded into Package Y, which is already installed.

I'm not sure how to do this yet. It could just be a separate namespace with category tags, or maybe just category tags. There might be extensions that could help with this.

Self Documenting GBrowse Glyphs

As noted by @tnabtaf:

At the January 2009 GMOD Meeting, @rbuels suggested that support be added to GBrowse glyphs to enable them to be self-documenting. That is, to make it possible to programmatically ask a glyph what it can do and how to interact with it.

@lstein liked the idea and started to implement it. He added other things like also generating MediaWiki documentation and example images, but only got halfway through the glyphs. This case is about following this work through to completion.

ProcessCite / References plugin on GMOD wiki yields error

The error is evident for example from the Publications page. Even though the References section is currently commented out because it would otherwise list as many errors as there are references, the error can still be seen for the example in Adding Citations:

Cite error: <ref> tags exist, but no <references/> tag was found

Chado ER diagrams on Web Site

Of the Chado Module pages, many don't have Entity-Relationship diagrams:

• Chado modules lacking Entity-Relationship diagrams
• Existing entity-relationship diagrams for Chado modules

Documentation about dealing with having two Perls installed

As noted by @tnabtaf:

The problem of having two perls installed comes up frequently. Need to document how to avoid it and how to detect it.