Re: newbie help

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Re: newbie help

girlwithglasses
Hello Susanne,

Thanks for your email and apologies that it is not clearer how to set up a Chado database. Have you had a look at the Chado tutorial, http://gmod.org/wiki/Chado_Tutorial? The second part may be of interest as it's about the more practical side, adding data to the db, etc. I've cc'd the Chado mailing list on this email so that other Chado users can give their input.

You might also like to consider using Tripal, http://tripal.info, a web-based interface to a Chado database that provides a very nice, customizable website for display and managing your data. You can also integrate tools like GBrowse (sequence visualizer) directly into Tripal for a smooth, integrated experience. Have a look at some of the sites using Tripal (links on the front page of the Tripal website), particularly the Banana Genome Hub; they've been able to set up a comprehensive resource with built-in tools very quickly. Tripal has a bulk loader that allows you to insert data into Chado as tab-separated values and similar simple formats.

We are also running the GMOD Summer School in July (http://gmod.org/wiki/2013_GMOD_Summer_School), which provides training on setting up and configuring GMOD tools, including a Chado DB.

I hope someone on the Chado list can respond directly to your Chado question, but please feel free to email the help desk again if you have any more questions.

Best wishes,
Amelia
GMOD Help Desk and Community Support



On Wed, Apr 24, 2013 at 7:37 AM, Howard, Susanne F <[hidden email]> wrote:
Hi,
I am a non-programmer, non-bioinformatics and worst of all non-LINUX (ubuntu) person but I have been put into a situation to work with a complete genome sequencing project which in the end is also going to be made available to the public. The organism is grape, vitis, and the end goal is something modelled after the genoscope vits site. That will happen in a few years from now.
Planning ahead like this though led us to the attempt of using the Chado database system right now at the start. All I need to do right now is to put 2 sets of reads into a db, then later the scaffolds, chromosomes etc. and way much later annotation and other actual gene related features.

I believe it will be the main sequence module I need to use, but I am ignorant enough to not even know how to start/run a database .
I can use MS Access dbs, create my own dbs, edit the underlying tables etc, and i do know what relational dbs imply. I can generally follow the theoretical descriptions found in the various Chado tutorials, about relationships, keys, ID's and so on, what I am missing is perhaps a practical example of how to enter simple data based on an actual example?
Usually I can find examples on the web, googling things like how to import fasta  and fastq data into Chado, but I drew a complete blank this time. I tried just about any tutorial I could find, but they are either speaking a foreign language to me, or just explain the structure/schema. I have not found anything related to actually populating a database, or how to modify a table (since I am not sure that something like reads are an option with the existing schema.
Any help you can give will be GREATLY appreciated!!
Susanne Howard
Research Specialist, Missouri State University, Mountain Grove Campus
[hidden email]
<a href="tel:417-496-0707" value="+14174960707">417-496-0707



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GMOD Community Support
http://gmod.org || @gmodproject


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Re: newbie help

girlwithglasses
Did anyone respond to Susanne's query about getting FASTA / FASTQ into a
Chado DB? See below:



Susanne F wrote

>> I am a non-programmer, non-bioinformatics and worst of all non-LINUX
>> (ubuntu) person but I have been put into a situation to work with a
>> complete genome sequencing project which in the end is also going to be
>> made available to the public. The organism is grape, vitis, and the end
>> goal is something modelled after the genoscope vits site. That will
>> happen
>> in a few years from now.
>> Planning ahead like this though led us to the attempt of using the Chado
>> database system right now at the start. All I need to do right now is to
>> put 2 sets of reads into a db, then later the scaffolds, chromosomes etc.
>> and way much later annotation and other actual gene related features.
>>
>> I believe it will be the main sequence module I need to use, but I am
>> ignorant enough to not even know how to start/run a database .
>> I can use MS Access dbs, create my own dbs, edit the underlying tables
>> etc, and i do know what relational dbs imply. I can generally follow the
>> theoretical descriptions found in the various Chado tutorials, about
>> relationships, keys, ID's and so on, what I am missing is perhaps a
>> practical example of how to enter simple data based on an actual example?
>> Usually I can find examples on the web, googling things like how to
>> import
>> fasta  and fastq data into Chado, but I drew a complete blank this time.
>> I
>> tried just about any tutorial I could find, but they are either speaking
>> a
>> foreign language to me, or just explain the structure/schema. I have not
>> found anything related to actually populating a database, or how to
>> modify
>> a table (since I am not sure that something like reads are an option with
>> the existing schema.
>> Any help you can give will be GREATLY appreciated!!
>> Susanne Howard
>> Research Specialist, Missouri State University, Mountain Grove Campus

--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject




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Re: newbie help

Scott Cain
In reply to this post by girlwithglasses
Hi Susanne,

I would suggest against using Chado for storing reads; I just don't think you'd get much value from doing that.  Chado isn't really a database for storing "raw materials" like reads; rather it is a data warehouse for storing results in a safe and consistent way.  That's why you didn't find any tutorials for importing fastq into Chado--I don't think anybody does it.  People do import fasta, but generally only for larger features like scaffolds or chromosomes or other assemblies, like from a transcriptome.  And when that sort of fasta is imported, its usually in the context of a feature that is being created from GFF3, where the feature is fully defined in GFF3 and the fasta is provided as "supplemental" information, like this:

scaffold1    .    scaffold    1    123456    .    .    .    ID=scaffold1;Name=scaffold1
##FASTA
>scaffold1
atgcatgc....

Scott



On Wed, Apr 24, 2013 at 11:04 AM, Amelia Ireland <[hidden email]> wrote:
Hello Susanne,

Thanks for your email and apologies that it is not clearer how to set up a Chado database. Have you had a look at the Chado tutorial, http://gmod.org/wiki/Chado_Tutorial? The second part may be of interest as it's about the more practical side, adding data to the db, etc. I've cc'd the Chado mailing list on this email so that other Chado users can give their input.

You might also like to consider using Tripal, http://tripal.info, a web-based interface to a Chado database that provides a very nice, customizable website for display and managing your data. You can also integrate tools like GBrowse (sequence visualizer) directly into Tripal for a smooth, integrated experience. Have a look at some of the sites using Tripal (links on the front page of the Tripal website), particularly the Banana Genome Hub; they've been able to set up a comprehensive resource with built-in tools very quickly. Tripal has a bulk loader that allows you to insert data into Chado as tab-separated values and similar simple formats.

We are also running the GMOD Summer School in July (http://gmod.org/wiki/2013_GMOD_Summer_School), which provides training on setting up and configuring GMOD tools, including a Chado DB.

I hope someone on the Chado list can respond directly to your Chado question, but please feel free to email the help desk again if you have any more questions.

Best wishes,
Amelia
GMOD Help Desk and Community Support



On Wed, Apr 24, 2013 at 7:37 AM, Howard, Susanne F <[hidden email]> wrote:
Hi,
I am a non-programmer, non-bioinformatics and worst of all non-LINUX (ubuntu) person but I have been put into a situation to work with a complete genome sequencing project which in the end is also going to be made available to the public. The organism is grape, vitis, and the end goal is something modelled after the genoscope vits site. That will happen in a few years from now.
Planning ahead like this though led us to the attempt of using the Chado database system right now at the start. All I need to do right now is to put 2 sets of reads into a db, then later the scaffolds, chromosomes etc. and way much later annotation and other actual gene related features.

I believe it will be the main sequence module I need to use, but I am ignorant enough to not even know how to start/run a database .
I can use MS Access dbs, create my own dbs, edit the underlying tables etc, and i do know what relational dbs imply. I can generally follow the theoretical descriptions found in the various Chado tutorials, about relationships, keys, ID's and so on, what I am missing is perhaps a practical example of how to enter simple data based on an actual example?
Usually I can find examples on the web, googling things like how to import fasta  and fastq data into Chado, but I drew a complete blank this time. I tried just about any tutorial I could find, but they are either speaking a foreign language to me, or just explain the structure/schema. I have not found anything related to actually populating a database, or how to modify a table (since I am not sure that something like reads are an option with the existing schema.
Any help you can give will be GREATLY appreciated!!
Susanne Howard
Research Specialist, Missouri State University, Mountain Grove Campus
[hidden email]
<a href="tel:417-496-0707" value="+14174960707" target="_blank">417-496-0707



--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject


------------------------------------------------------------------------------
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browser, app, & servers with just a few lines of code. Try New Relic
and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
_______________________________________________
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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