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With the amount of technical documentation available for GMOD the casual observer would be forgiven if they concluded that GMOD was a project about software. But it's not, GMOD has been created ''for biologists'' and in the real world it's used ''by biologists''. However, the creators of GMOD are mostly not practicing biologists and the look and the feel of most GMOD documentation reflects this. What we will attempt to do is discuss GMOD from the researchers' perspective. This does not simply mean describe what the software does. If you look, for example, at a typical GBrowse page like this [http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2 GBrowse view of human chromosome 7] you'll understand immediately what GBrowse is built to do, and a few more minutes of clicking and scrolling will reveal all sorts of useful ways to display and query the data. A modern biologist knows a great deal about bioinformatics functionality already. What we're more concerned with here are the practical details. Like ''given the data I have what database should I use? or do I even need a database?'' Or ''how hard is this going to be?'' | With the amount of technical documentation available for GMOD the casual observer would be forgiven if they concluded that GMOD was a project about software. But it's not, GMOD has been created ''for biologists'' and in the real world it's used ''by biologists''. However, the creators of GMOD are mostly not practicing biologists and the look and the feel of most GMOD documentation reflects this. What we will attempt to do is discuss GMOD from the researchers' perspective. This does not simply mean describe what the software does. If you look, for example, at a typical GBrowse page like this [http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2 GBrowse view of human chromosome 7] you'll understand immediately what GBrowse is built to do, and a few more minutes of clicking and scrolling will reveal all sorts of useful ways to display and query the data. A modern biologist knows a great deal about bioinformatics functionality already. What we're more concerned with here are the practical details. Like ''given the data I have what database should I use? or do I even need a database?'' Or ''how hard is this going to be?'' | ||
| − | In our experience we find that most biologists want to focus on the science. They may have little knowledge of programming languages or databases, and only passing interest in the IT minutiae. They have deep knowledge of their own data, needless to say, and are very familiar with how data like their own can be viewed and analyzed. What they want to know is how to create their own useful set of tools for their own data in as efficient a way as possible. And when this tool set is created they want to rest assured that their platform can be easily maintained in an environment where resources may be limited. | + | In our experience we find that most biologists want to focus on the science. They may have little knowledge of programming languages or databases, and only passing interest in the IT minutiae. They have deep knowledge of their own data, needless to say, and are very familiar with how data like their own can be viewed and analyzed. What they want to know is how to create their own useful set of tools for their own data in as efficient a way as possible. And when this tool set is created they want to rest assured that their platform can be easily maintained in an environment where resources may be limited. We will attempt to address these sorts of questions. |
By the way, the word ''we'' used here refers to the [[GMOD_Help_Desk|GMOD Help Desk]]. The Help Desk is a good resource for biologists who want to learn more about GMOD, for whatever reason. Feel free to email us at wg-emod@nescent.org. | By the way, the word ''we'' used here refers to the [[GMOD_Help_Desk|GMOD Help Desk]]. The Help Desk is a good resource for biologists who want to learn more about GMOD, for whatever reason. Feel free to email us at wg-emod@nescent.org. | ||
Revision as of 21:23, 6 March 2007
Contents
Introduction
With the amount of technical documentation available for GMOD the casual observer would be forgiven if they concluded that GMOD was a project about software. But it's not, GMOD has been created for biologists and in the real world it's used by biologists. However, the creators of GMOD are mostly not practicing biologists and the look and the feel of most GMOD documentation reflects this. What we will attempt to do is discuss GMOD from the researchers' perspective. This does not simply mean describe what the software does. If you look, for example, at a typical GBrowse page like this GBrowse view of human chromosome 7 you'll understand immediately what GBrowse is built to do, and a few more minutes of clicking and scrolling will reveal all sorts of useful ways to display and query the data. A modern biologist knows a great deal about bioinformatics functionality already. What we're more concerned with here are the practical details. Like given the data I have what database should I use? or do I even need a database? Or how hard is this going to be?
In our experience we find that most biologists want to focus on the science. They may have little knowledge of programming languages or databases, and only passing interest in the IT minutiae. They have deep knowledge of their own data, needless to say, and are very familiar with how data like their own can be viewed and analyzed. What they want to know is how to create their own useful set of tools for their own data in as efficient a way as possible. And when this tool set is created they want to rest assured that their platform can be easily maintained in an environment where resources may be limited. We will attempt to address these sorts of questions.
By the way, the word we used here refers to the GMOD Help Desk. The Help Desk is a good resource for biologists who want to learn more about GMOD, for whatever reason. Feel free to email us at wg-emod@nescent.org.
What is a GMOD?
At first it stood for a Generic Model Organism Database, this was back in the days when there were a handful of model organisms and it appeared that obtaining the genomic sequence of an organism was a prohibitively expensive proposition, taking months or years to accomplish. Now there are hundreds of such sequences, with thousands conceivable. However, few of the scientists studying organisms with sequence consider their organism a model, in this first sense of the word.
This is a problem for the acronym since any organism with any sequence associated with it is a good candidate as a subject for a GMOD database. So, for example, there are GMOD databases with just protein sequence in them like the S. cerevisiae Proteome Browser. There are GMOD databases with EST sequence only, such as the Cattle EST Gene Family Database. There are GMOD databases that are concerned primarily with gene expression, such as the Emiliania huxleyi Serial Analysis of Gene Expression database. We even find GMOD databases dedicated to RNA sequence like the Leishmania tarentolae RNA Editing database.
What is GBrowse?
What is Chado?
What is GMODWeb?
What is Bioperl?
What is Modware?
More Information
Resources
People
Hardware
Operating System
Software
Licenses
==Case Studies [Category:Needs Editing]]
