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 |
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 |
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 |
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, Margaret Staton Assistant Professor Department of Entomology and Plant Pathology 370 PBB, 2505 EJ Chapman Drive Knoxville, TN 37996-4560 864-506-4515 Mobile ------------------------------------------------------------------------------ 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 |
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] > > > > ------------------------------------------------------------------------------ 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 |
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. MichaelOn 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. MichaelOn 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]------------------------------------------------------------------------------ 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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