Difference between revisions of "GMOD - Getting Started"

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(New page: This is a guide to getting started with chado Chado and GMOD. If you want to set up your own model organism database, this is a good place to start; however, if all you want is a par...)
 
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GMOD is a large project with many components and this page aims to give you some pointers on where you can start.
  
  
This is a guide to getting started with [[chado Chado]] and GMOD. If you want to set up your own model organism database, this is a good place to start; however, if all you want is a particular [[software_components software component]], like [[gbrowse GBrowse]], [[apollo Apollo]] or [[cmap CMap]], you would be better off to visit the pages for those applications.
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== Useful Pages ==
  
There are currently two ways to install the GMOD components to get a working model organism database, which I will refer to as the easy way and the hard way. The easy way assumes that you have a brand new computer with [http://download.fedora.redhat.com/pub/fedora/linux/core/2/ Fedora Core 2] installed so that you can take advantage of several 'short cut' packages that have been prebuilt for that operating system and are available from [http://www.biopackages.net/ Biopackages.net]. The hard way is for any other OS and requires just about everything to be built from source.
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* [[Overview]] is a broad introduction, that does not assume any prior knowledge of computing.  This is an excellent place to start.
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* [[GMOD Components]] is a complete list of the components in GMOD. This list can appear daunting, but it gives you a good idea of what sorts of things are available from GMOD.
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** If you already know the specific component you want to use (''e.g.'' [[GBrowse]], [[Apollo]], [[CMap]], ...) you can type the component name in the search box and go directly to the page for that component.
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* [[ParameciumDB]] describes how ParameciumDB implemented GMOD at their web site.
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* [[Chado_-_Getting_Started|Getting Started with Chado]] discusses GMOD's relational database schema. Chado is useful for organizing your data and is also integrated with several other GMOD components.
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* [[Computing Requirements]] discusses what sort of computing support you will need to install and run GMOD components.
  
A few particularly good pieces of documentation you might want to look at are:
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==Getting Advice==
  
* [[/schema-cvs/chado/doc/Chado_Schema_Documentation.doc Chado_Schema_Documentation.doc]], a MS Word document giving a detailed explaination of many Chado concepts (older).
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If you need advice or help you can write to one of a number of [[GMOD_Mailing_Lists|GMOD mailing lists]], these tend to focus on more technical aspects. Another good resource is the [[GMOD_Help_Desk|GMOD Help Desk]] - feel free to write them with questions on any type, they are tasked with providing support to newcomers and experts alike.
* [[/schema-cvs/chado/doc/chado-manual/ Chado Manual]], a set of html pages automatically generated from tex files, where some of those tex files were automatically generated from sql files (newer).
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* [[/schema-cvs/chado/doc/chado-scenarios.xml chado-scenarios.xml]], an XML file with Chado usage scenarios. This document has an xslt applied to it, so hopefully your browser will support that as well as mine.
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* [http://www.gmod.org/schema-cvs/chado/doc/ChadoCSHMay03Slides.pdf ChadoCSHMay03Slides.pdf], a presentation given by Stan Letovsky at the May, 2003 GMOD meeting to introduce the basic concepts in Chado.
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See [[Support]] for more information.
  
 
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[[Category:Help]]
* [[biopackages The easy way]]
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* [[the_hard_way The hard way]]
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Latest revision as of 20:32, 15 September 2009

GMOD is a large project with many components and this page aims to give you some pointers on where you can start.


Useful Pages

  • Overview is a broad introduction, that does not assume any prior knowledge of computing. This is an excellent place to start.
  • GMOD Components is a complete list of the components in GMOD. This list can appear daunting, but it gives you a good idea of what sorts of things are available from GMOD.
    • If you already know the specific component you want to use (e.g. GBrowse, Apollo, CMap, ...) you can type the component name in the search box and go directly to the page for that component.
  • ParameciumDB describes how ParameciumDB implemented GMOD at their web site.
  • Getting Started with Chado discusses GMOD's relational database schema. Chado is useful for organizing your data and is also integrated with several other GMOD components.
  • Computing Requirements discusses what sort of computing support you will need to install and run GMOD components.

Getting Advice

If you need advice or help you can write to one of a number of GMOD mailing lists, these tend to focus on more technical aspects. Another good resource is the GMOD Help Desk - feel free to write them with questions on any type, they are tasked with providing support to newcomers and experts alike.

See Support for more information.