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| | + | == By Function == |
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| | + | GMOD is a collection of software applications (components) aimed at providing the functionality that is needed by all organism databases. The table below classifies GMOD components according to their functional categories. |
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| − | GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by all model organism databases. The applications are linked together by their use of a common database schema known as Chado. | + | See [[:Category:External]] for software mentioned in the GMOD web site (and possibly used by GMOD components) that is not part of the GMOD project. |
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| − | This diagram represents a model organism database (MOD) and its typical components. The "top ten" types of functionality are represented in the top row of the diagram as a set of interfaces. The "Vis" prefix on the end of each interface is an abbreviation of "Visualization", and should be interpreted literally -- an alignment visualization interface should not merely allow users to passively view pre-existing alignments, but should also to user interaction to create and visualize alignments of their own.
| + | Read the [[GMOD_Membership#Software | requirements for software to be considered a GMOD component]]. |
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| − | <center><br />[[<br />[[Image:roadmap25.jpg]]]<br />]<br /></center>
| + | {{GMODComponents}} |
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| − | [http://www.gmod.org/?q=node/99 Key to diagram]
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| − | GMOD components fulfilling the requirements of an interface are linked to the interface, as well as to the Chado schema modules if they are known to interact with Chado. The requirements of an interface, as well as the components that implement a given interface are described in the documents linked at the end of this document.
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| | + | ==Architecture Diagram== |
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| − | ---- | + | The diagram below represents a model organism database (MOD) and its typical components. The ''top ten'' types of functionality are represented in the top row of the diagram as a set of interfaces. The ''Vis'' prefix on the end of each interface is an abbreviation of ''Visualization'', and should be interpreted literally -- an alignment visualization interface should not merely allow users to passively view pre-existing alignments, but should also to user interaction to create and visualize alignments of their own. |
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| − | While this book (hierarchical set of web pages) is largely intended to replace the software matrix that was on the old GMOD website, I have received some requests for the old [[software matrix, so here you go.]]
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| | + | [[Image:Roadmap.png|thumb|600px|[[Media:Roadmap.png|Diagram full size]]]] |
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| − | * [[Common Documents]]
| + | '''Symbols used in this UML diagram''' |
| − | * [[Common Templates]] | + | * boxes |
| − | * [[Community Visualization]] | + | ** tabbed white boxes are packages -- logical groups of related components |
| − | * [[Comparative Genomics Visualization]] | + | ** boxes marked with ''<<interface>>'' are abstract interfaces required by GMOD-Web. All other labeled boxes are concrete components of the GMOD system. |
| − | * [[Database tools]] | + | * connectors |
| − | * [[Gene Expression Visualization]] | + | ** solid arrows indicate a relationship between components that currently exists. |
| − | * [[Genome Visualization & Editing]] | + | ** dashed arrows indicate a relationship between components that does NOT currently exist. |
| − | * [[GMODWeb]] | + | ** dashed arrows with a solid white head indicate an interface/realization relationship between a GMOD-Web required interface and a component that provides that interface. e.g. gbrowse implements the ''genomeVis'' interface. |
| − | * [[Literature Visualization]] | + | * coloration |
| − | * [[Molecular Pathway Visualization]] | + | ** white: components or interfaces that currently exist and integrated into the GMOD system. |
| − | * [[Ontology Visualization]] | + | ** green: components or interfaces that currently exist and are integrated into the GMOD system. |
| − | * [[Phenotype Visualization]] | + | ** pink: components or interfaces that currently exist, but the feasibility of integrating their functionality into the GMOD system is unknown. |
| − | * [[Sequence Alignment]] | + | ** red: components that do not currently exist, but may need to be implemented. |
| − | * [[Sequence Alignment Visualization]] | + | ** orange: a common set of templates to provide a consistent look and feel for all GMOD systems. The "common gene page" concept is in this group. |
| − | * [[Strain/Library Visualization]] | + | ** cyan: components that are specific to each MOD, and are not deployable as part of a GMOD system. |
| − | * [[Utilities]] | + | |
| − | * [[Workflow Management]] | + | |
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| − | | + | GMOD components fulfilling the requirements of an interface are linked to the interface, as well as to the Chado schema modules if they are known to interact with Chado. The requirements of an interface, as well as the components that implement a given interface are described in the documents linked at the end of this document. |
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| − | ! Attachment
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| − | ! Size
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| − | |- class="dark"
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| − | [http://www.gmod.org/files/roadmap.png roadmap.png]
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| − | | 45.53 KB
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| − | |- class="light"
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| − | [http://www.gmod.org/files/roadmap25.jpg roadmap25.jpg]
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| − | | 14.09 KB
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| − | |- class="dark"
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| − | [http://www.gmod.org/files/GMOD_components_roadmap.zuml GMOD_components_roadmap.zuml]
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| − | | 28.25 KB
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| − | |}
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| − | probably a good idea to turn this back on once the old content has all been ported over to the new site. i just added a new node on workflow/ergatis, and it would be difficult to know this had been added if not posted to the front b/c it is deep in the components book.
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| − | I think he said something to the effect that the front page looked too crowded. Most new posts will be noted on the front page: blog posts will go in their block, comments will go in their block. What will not go in is new 'book' pages, though it will still go into an RSS feed. We could make a block with the site's RSS feed, which would show recent posts on the side, without having to show content. If someone wanted to highlight a new book page, they can blog about it too. (That is very unlikely to happen in real life, though, I expect.)
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| − | RSS sounds like a reasonable compromise.
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| − | Moving things off the front page seems to have messed with the RSS feed, so that solution won't work. Here's what I did instead: I added a module called 'front_page' that lets you configure a custom front page, and then created a node that has just sticky nodes in it, and now requests from outside drupal for www.gmod.org will get redirected to that node. This is the 'clean' homepage. But any clicks on links from inside drupal to www.gmod.org will go to the default homepage with recent nodes. This is the 'working' homepage. I also reset blog entries and book nodes to display on the front page by default.
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| − | I thought I had it all figured out, but it doesn't seem to work yet. At the moment, all reqests for www.gmod.org, regardless of where they originate, go to what is supposed to be just the 'initial' homepage (node 86). I'll sort it out eventually.
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| − | I just had to write a little php.
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| − | zvvpkncyghnfiyqnarczuovgwqjgyq<br />[http://kaaop.sujbox.com link] [url=http://kxtus.xywiub.com]link[/url]
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| − | looks like we need to turn off anonymous comments.
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| − | Hey, where did the UML diagram go? I really liked having the mini-version on the frontpage, it's a good way to see what GMOD currently is and what is being or needs to be developed. If the diagram needs to be resized, recolored, cropped, etc let me know.
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| − | It was huge. I think you had it set at 600 pixels, so I put it after the break. It is a great picture, but if you shrink it more, it becomes completely non-informative but if you make it bigger it is much to big to have on a front page. I would say even at 600 pixels it was too distorted to be informative (I couldn't read any of the text).
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| − | guess it just seemed mini on my 1920x1280 24" widescreen. shall we make a smaller version?
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| − | Flat list - collapsedFlat list - expandedThreaded list - collapsedThreaded list - expanded Date - newest firstDate - oldest first 10 comments per page30 comments per page50 comments per page70 comments per page90 comments per page Select your preferred way to display the comments and click "Save settings" to activate your changes.
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GMOD is a collection of software applications (components) aimed at providing the functionality that is needed by all organism databases. The table below classifies GMOD components according to their functional categories.
