Tripal as Protein database

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Tripal as Protein database

Michael Dondrup-3
Hi,

we have a student who is developing a ‘special interest’ protein database drawing from various resources. Her task is to
build a database of annotated proteins of this class and enrich the annotation with
additional information, e.g. pairwise sequence similarity, and protein interaction data, cross references, etc.
I proposed that Tripal would be suitable for this. My questions:

- Protein data will mostly come from Uniprot and Genbank. Are there importers for supported formats used by
these databases, e.g. genbank or even csv?
- We should possibly start with Tripal 3 right away? Is there possibly a pre-configured vm for developers, so to avoid
any setup pain?

Thank you
Michael    



Michael Dondrup
Researcher
Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway


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Re: Tripal as Protein database

Stephen Ficklin-2
Hi Michael,

I agree that Tripal should be suitable :-)  When is your time frame for
beginning the project?  Tripal v3 is in beta and we are finding bugs
still so if you decide to go with Tv3 then you may encounter some of
these.  But the benefit is you won't have to upgrade from Tv2 to Tv3
later on.    We don't have a VM for Tripal v3 yet... what would be your
preference?  VMWare, Virtualbox or a container such as Docker?  There is
a Tv2 Docker image which you can find off of the Tripal website.

Do you have an exact format for the data?  If in CSV (or specifically
tab delimited) you could use the bulk loader?   I've been wanting to
have a training meeting before the end of March (next week).  But that
may get pushed to the second week of April. Perhaps a training session
with the bulk loader would be helpful? And as an example we could look
at your data files?

Stephen

On 3/21/2017 3:44 AM, Michael Dondrup wrote:

> Hi,
>
> we have a student who is developing a ‘special interest’ protein database drawing from various resources. Her task is to
> build a database of annotated proteins of this class and enrich the annotation with
> additional information, e.g. pairwise sequence similarity, and protein interaction data, cross references, etc.
> I proposed that Tripal would be suitable for this. My questions:
>
> - Protein data will mostly come from Uniprot and Genbank. Are there importers for supported formats used by
> these databases, e.g. genbank or even csv?
> - We should possibly start with Tripal 3 right away? Is there possibly a pre-configured vm for developers, so to avoid
> any setup pain?
>
> Thank you
> Michael
>
>
>
> Michael Dondrup
> Researcher
> Sea Lice Research Centre
> Department of Informatics
> University of Bergen
> Thormøhlensgate 55, N-5008 Bergen,
> Norway
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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Re: Tripal as Protein database

Michael Dondrup-3
Hi Stephen,

thank you for your confirmation. The time-frame for starting the implementation
is ’now’ ;) but to have a deployable version ready we have time until the end 2017.
So we could help with testing a bit. We will try to join the next user/developer meeting.

With respect to the type of VM, I think I like either Docker or Virtualbox best. In the
end, we might test and deploy on a local cloud instance running open stack.

I forgot about the bulk importer completely, but if it can import tab-delimited files
than it will most likely satisfy our needs.

Michael


> On Mar 21, 2017, at 5:44 PM, Stephen Ficklin <[hidden email]> wrote:
>
> Hi Michael,
>
> I agree that Tripal should be suitable :-)  When is your time frame for
> beginning the project?  Tripal v3 is in beta and we are finding bugs
> still so if you decide to go with Tv3 then you may encounter some of
> these.  But the benefit is you won't have to upgrade from Tv2 to Tv3
> later on.    We don't have a VM for Tripal v3 yet... what would be your
> preference?  VMWare, Virtualbox or a container such as Docker?  There is
> a Tv2 Docker image which you can find off of the Tripal website.
>
> Do you have an exact format for the data?  If in CSV (or specifically
> tab delimited) you could use the bulk loader?   I've been wanting to
> have a training meeting before the end of March (next week).  But that
> may get pushed to the second week of April. Perhaps a training session
> with the bulk loader would be helpful? And as an example we could look
> at your data files?
>
> Stephen
>
> On 3/21/2017 3:44 AM, Michael Dondrup wrote:
>> Hi,
>>
>> we have a student who is developing a ‘special interest’ protein database drawing from various resources. Her task is to
>> build a database of annotated proteins of this class and enrich the annotation with
>> additional information, e.g. pairwise sequence similarity, and protein interaction data, cross references, etc.
>> I proposed that Tripal would be suitable for this. My questions:
>>
>> - Protein data will mostly come from Uniprot and Genbank. Are there importers for supported formats used by
>> these databases, e.g. genbank or even csv?
>> - We should possibly start with Tripal 3 right away? Is there possibly a pre-configured vm for developers, so to avoid
>> any setup pain?
>>
>> Thank you
>> Michael
>>
>>
>>
>> Michael Dondrup
>> Researcher
>> Sea Lice Research Centre
>> Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

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Re: Tripal as Protein database

Meg Staton-2
Hi, Michael,
Here is link to Ming's Docker image on tripal repo:

The README has some instructions to get it started. Let us know how it goes!

Meg


On Wed, Mar 22, 2017 at 4:41 AM, Michael Dondrup <[hidden email]> wrote:
Hi Stephen,

thank you for your confirmation. The time-frame for starting the implementation
is ’now’ ;) but to have a deployable version ready we have time until the end 2017.
So we could help with testing a bit. We will try to join the next user/developer meeting.

With respect to the type of VM, I think I like either Docker or Virtualbox best. In the
end, we might test and deploy on a local cloud instance running open stack.

I forgot about the bulk importer completely, but if it can import tab-delimited files
than it will most likely satisfy our needs.

Michael


> On Mar 21, 2017, at 5:44 PM, Stephen Ficklin <[hidden email]> wrote:
>
> Hi Michael,
>
> I agree that Tripal should be suitable :-)  When is your time frame for
> beginning the project?  Tripal v3 is in beta and we are finding bugs
> still so if you decide to go with Tv3 then you may encounter some of
> these.  But the benefit is you won't have to upgrade from Tv2 to Tv3
> later on.    We don't have a VM for Tripal v3 yet... what would be your
> preference?  VMWare, Virtualbox or a container such as Docker?  There is
> a Tv2 Docker image which you can find off of the Tripal website.
>
> Do you have an exact format for the data?  If in CSV (or specifically
> tab delimited) you could use the bulk loader?   I've been wanting to
> have a training meeting before the end of March (next week).  But that
> may get pushed to the second week of April. Perhaps a training session
> with the bulk loader would be helpful? And as an example we could look
> at your data files?
>
> Stephen
>
> On 3/21/2017 3:44 AM, Michael Dondrup wrote:
>> Hi,
>>
>> we have a student who is developing a ‘special interest’ protein database drawing from various resources. Her task is to
>> build a database of annotated proteins of this class and enrich the annotation with
>> additional information, e.g. pairwise sequence similarity, and protein interaction data, cross references, etc.
>> I proposed that Tripal would be suitable for this. My questions:
>>
>> - Protein data will mostly come from Uniprot and Genbank. Are there importers for supported formats used by
>> these databases, e.g. genbank or even csv?
>> - We should possibly start with Tripal 3 right away? Is there possibly a pre-configured vm for developers, so to avoid
>> any setup pain?
>>
>> Thank you
>> Michael
>>
>>
>>
>> Michael Dondrup
>> Researcher
>> Sea Lice Research Centre
>> Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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--
Margaret Staton
Assistant Professor
Department of Entomology and Plant Pathology
370 PBB, 2505 EJ Chapman Drive
Knoxville, TN 37996-4560

864-506-4515 Mobile





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Re: Tripal as Protein database

Michael Dondrup-3
Hi Meg,

Thank you very much!
The image is working out of the box for me.

Michael


> On Apr 7, 2017, at 5:58 PM, Meg Staton <[hidden email]> wrote:
>
> Hi, Michael,
> Here is link to Ming's Docker image on tripal repo:
> https://github.com/tripal/docker-tripal-centos
>
> The README has some instructions to get it started. Let us know how it goes!
>
> Meg
>
>
> On Wed, Mar 22, 2017 at 4:41 AM, Michael Dondrup <[hidden email]> wrote:
> Hi Stephen,
>
> thank you for your confirmation. The time-frame for starting the implementation
> is ’now’ ;) but to have a deployable version ready we have time until the end 2017.
> So we could help with testing a bit. We will try to join the next user/developer meeting.
>
> With respect to the type of VM, I think I like either Docker or Virtualbox best. In the
> end, we might test and deploy on a local cloud instance running open stack.
>
> I forgot about the bulk importer completely, but if it can import tab-delimited files
> than it will most likely satisfy our needs.
>
> Michael
>
>
> > On Mar 21, 2017, at 5:44 PM, Stephen Ficklin <[hidden email]> wrote:
> >
> > Hi Michael,
> >
> > I agree that Tripal should be suitable :-)  When is your time frame for
> > beginning the project?  Tripal v3 is in beta and we are finding bugs
> > still so if you decide to go with Tv3 then you may encounter some of
> > these.  But the benefit is you won't have to upgrade from Tv2 to Tv3
> > later on.    We don't have a VM for Tripal v3 yet... what would be your
> > preference?  VMWare, Virtualbox or a container such as Docker?  There is
> > a Tv2 Docker image which you can find off of the Tripal website.
> >
> > Do you have an exact format for the data?  If in CSV (or specifically
> > tab delimited) you could use the bulk loader?   I've been wanting to
> > have a training meeting before the end of March (next week).  But that
> > may get pushed to the second week of April. Perhaps a training session
> > with the bulk loader would be helpful? And as an example we could look
> > at your data files?
> >
> > Stephen
> >
> > On 3/21/2017 3:44 AM, Michael Dondrup wrote:
> >> Hi,
> >>
> >> we have a student who is developing a ‘special interest’ protein database drawing from various resources. Her task is to
> >> build a database of annotated proteins of this class and enrich the annotation with
> >> additional information, e.g. pairwise sequence similarity, and protein interaction data, cross references, etc.
> >> I proposed that Tripal would be suitable for this. My questions:
> >>
> >> - Protein data will mostly come from Uniprot and Genbank. Are there importers for supported formats used by
> >> these databases, e.g. genbank or even csv?
> >> - We should possibly start with Tripal 3 right away? Is there possibly a pre-configured vm for developers, so to avoid
> >> any setup pain?
> >>
> >> Thank you
> >> Michael
> >>
> >>
> >>
> >> Michael Dondrup
> >> Researcher
> >> Sea Lice Research Centre
> >> Department of Informatics
> >> University of Bergen
> >> Thormøhlensgate 55, N-5008 Bergen,
> >> Norway
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> Check out the vibrant tech community on one of the world's most
> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >> _______________________________________________
> >> Gmod-tripal mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
> >
> >
> > ------------------------------------------------------------------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > _______________________________________________
> > Gmod-tripal mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
>
>
> --
> Margaret Staton
> Assistant Professor
> Department of Entomology and Plant Pathology
> 370 PBB, 2505 EJ Chapman Drive
> Knoxville, TN 37996-4560
>
> 864-506-4515 Mobile
> [hidden email]
>
>
>
>


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Re: Tripal as Protein database

Eric Rasche-3
Hi Michael,

I saw that you already filed one issue, but if you have any questions about our docker image, please feel to email or just file more issues. Either Anthony or I can surely help. That tripal image is currently working with our dockerized GMOD stack if you wish to add any of those resources to your planned deployment.

Meg: I had not known about the other docker image! That's exciting to see.

Cheers,
Eric

On 04/07/2017 05:12 PM, Michael Dondrup wrote:
Hi Meg,

Thank you very much! 
The image is working out of the box for me.

Michael


On Apr 7, 2017, at 5:58 PM, Meg Staton [hidden email] wrote:

Hi, Michael,
Here is link to Ming's Docker image on tripal repo:
https://github.com/tripal/docker-tripal-centos

The README has some instructions to get it started. Let us know how it goes!

Meg


On Wed, Mar 22, 2017 at 4:41 AM, Michael Dondrup [hidden email] wrote:
Hi Stephen,

thank you for your confirmation. The time-frame for starting the implementation
is ’now’ ;) but to have a deployable version ready we have time until the end 2017.
So we could help with testing a bit. We will try to join the next user/developer meeting.

With respect to the type of VM, I think I like either Docker or Virtualbox best. In the
end, we might test and deploy on a local cloud instance running open stack.

I forgot about the bulk importer completely, but if it can import tab-delimited files
than it will most likely satisfy our needs.

Michael


On Mar 21, 2017, at 5:44 PM, Stephen Ficklin [hidden email] wrote:

Hi Michael,

I agree that Tripal should be suitable :-)  When is your time frame for
beginning the project?  Tripal v3 is in beta and we are finding bugs
still so if you decide to go with Tv3 then you may encounter some of
these.  But the benefit is you won't have to upgrade from Tv2 to Tv3
later on.    We don't have a VM for Tripal v3 yet... what would be your
preference?  VMWare, Virtualbox or a container such as Docker?  There is
a Tv2 Docker image which you can find off of the Tripal website.

Do you have an exact format for the data?  If in CSV (or specifically
tab delimited) you could use the bulk loader?   I've been wanting to
have a training meeting before the end of March (next week).  But that
may get pushed to the second week of April. Perhaps a training session
with the bulk loader would be helpful? And as an example we could look
at your data files?

Stephen

On 3/21/2017 3:44 AM, Michael Dondrup wrote:
Hi,

we have a student who is developing a ‘special interest’ protein database drawing from various resources. Her task is to
build a database of annotated proteins of this class and enrich the annotation with
additional information, e.g. pairwise sequence similarity, and protein interaction data, cross references, etc.
I proposed that Tripal would be suitable for this. My questions:

- Protein data will mostly come from Uniprot and Genbank. Are there importers for supported formats used by
these databases, e.g. genbank or even csv?
- We should possibly start with Tripal 3 right away? Is there possibly a pre-configured vm for developers, so to avoid
any setup pain?

Thank you
Michael



Michael Dondrup
Researcher
Sea Lice Research Centre
Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway


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-- 
Margaret Staton
Assistant Professor
Department of Entomology and Plant Pathology
370 PBB, 2505 EJ Chapman Drive
Knoxville, TN 37996-4560

864-506-4515 Mobile
[hidden email] 





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