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iPlant

Emailed Updates
February 28, 2013

Greetings Tree Biology Workgroup,

I am very pleased to announce that the CartograTree manuscript is now available online through the Molecular Ecology Resources Journal here: http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12067/abstract.

On another note, John Yu, our other lead developer that has contributed much in the user interface design, is leaving the team today. We wish him the best of luck in his future endeavors.

As always, we continue to welcome feedback and questions.

January 22, 2013

Greetings Tree Biology Workgroup,

Over the past month, we have been preparing for our production release of CartograTree 2.0 and our presentations at the Plant and Animal Genome conference. We posted a pre-release of CartograTree 2.0 the friday before PAG (1/11) so users could experiment with the new features we presented at the meeting. The updates in this current release stemmed from feature requests for input files to enable association studies with environmental and/or phenotypic data. In addition to our previous Common Amplicon tool, we now have: Common Genotype, Common Phenotype, and Get WorldClim Data tools available in the Selected Markers Pane drop down menu. These tools allow individuals to capture the phenotypes in common among a set of selected, genotyped tree samples. In addition, one can acquire several environmental measurements taken at specific locations associated with the samples. There are also several minor interface and backend changes which enhance the overall user experience and performance.

These are are all reflected in the documentation. The updated documentation is currently available from CartograTree or here: http://dendrome.ucdavis.edu/ftp/Documentation/CartogratreeDocumentation.pdf. As always, we continue to welcome feedback and questions.

December 4, 2012

Greetings Tree Biology Workgroup,

Over the past couple of months, we have been preparing for our production release of CartograTree 1.5.0. These updates stemmed from the reviewer critiques of our submitted manuscript to Molecular Ecology Resources we received about a month ago. Yesterday, we resubmitted the manuscript with updates to the editor for publication. Some of the updates we made follow:

1) a CSV download option for expanded data tables
2) a DiversiTree bulk uploader input file generator for the Selected Markers table
3) a button for DiversiTree results to generate a bulk uploader input file
4) new filtering options to display only sequenced, phenotyped, and/or genotyped tree samples
5) addition of phenotype information for TreeGenes tree samples, when available
6) keyword filtering for both tree sample phenotypes and TRY-DB traits
7) filtering options for the Common Amplicon tool results page

We have redesigned the updated interface for a more integrated workflow. We have made a lot more minor interface and backend changes which is reflected in the documentation. The updated documentation is currently available from CartograTree or here: http://dendrome.ucdavis.edu/ftp/Documentation/CartogratreeDocumentation.pdf.

We plan to continue development for even more features by PAG in January. As always, we continue to welcome feedback and questions.

August 31, 2012

Greetings Tree Biology Workgroup,

Over the past month, we have been preparing for our production release of CartograTree 1.0.0. In addition, we have been writing an article which we plan to submit for publication sometime in the next couple of the weeks. To go along with the production release, we are also releasing updated documentation and creating an instructional demo video. The updated documentation is currently available, and the videos should be released by September 14th.

Since the beta release, TreeGenes developer, John Yu, has been focused on enhancing the performance and adding features to the map interface. We have redesigned the interface for a more integrated workflow and updated the map icons. As of today, CartograTree is available for public use at the following URL: http://dendrome.ucdavis.edu/cartogratree. You can find documentation here, which is also linked from within DiversiTree and CartograTree.

We plan to continue development on this project for as long as funding is available. As always, we continue to welcome feedback.

July 31, 2012

Greetings Tree Biology Workgroup,

Over the past month, we have been preparing for our first beta release of CartograTree (0.5 beta). In addition, we applied for and were accepted for an extension to our Tree Biology project through the iPlant Collaborative which means we will continue development through Jan 31st, 2013.

We have had meetings with both Try-DB and WorldClim to improve data acquisition and display. As a result of these discussions, our Try-DB species count of information increased to 368 (from 8) forest tree species. TreeGenes developer, John Yu, has been focused on enhancing the performance and adding features to the map interface.

CartograTree is released to the public today at this permanent URL: http://dendrome.ucdavis.edu/cartogratree. In addition to this utility, we have updated DiversiTree to work with SSWAP to allow users to select lists of relevant sequences from within the DiversiTree interface. You can find documentation here, which is also linked from within DiversiTree.

We plan to provide a full production release by end of August 2012 with updated Documentation and a new video tutorial of how the three applications work together. As always, we continue to welcome feedback.

June 11, 2012

Greetings Tree Biology Workgroup,

Since last month, we have added 1 more web service, a service which will create multiFasta sequence format given a set of amplicons. This will allow scientist to generate, on the fly, multiFasta files which can be used in downstream services. An example of this would be to select an amplicon(s) and use the multiFasta service in order to run a MultipleSequenceAlignment program, such as ClustalW2 or MAFT, which is run on the High Performance Computing servers available through iPlant. You can find the list of available services here: http://dendrome.ucdavis.edu/iplant/

TreeGenes developer, John Yu, has been pushing more and more User Interface and feature changes to the Tree Map interface (http://dendrome.ucdavis.edu/_dev/jyu/main/iplant_map/index.php).

We have loaded the WorldClim data received through TryDB which is now visualized in the TreeMap interface. This is giving us many more abiotic data points. We will be contacting WorldClim in order to get the data directly from them at more regular intervals.

On June 11th (today), the development team had a virtual meeting with the iPlant committee to present our work thus far as well as our future development plans. We feel this meeting went very well and there was expressed interest in our project. The committee members will now discuss future plans and update the development team in regards to continuation. During this time, we will continue active development of the services/products and would appreciate any feedback or requests. We plan to provide a beta release by July 2012 and a full production release by August 2012.

As always, feel free to email me with comments or questions.

May 15, 2012

Greetings Tree Biology Workgroup,

Another month has passed, time for project updates. Since last month which had 5 standing services, now we have 9 web services pushed to production. The new additions include: an EST Service, Regional Sample Service, Primer Service, and Ameriflux Service. These all can be found in the listing on the projects' landing page (http://dendrome.ucdavis.edu/iplant/ ). TreeGenes developer, John Yu, has been pushing more and more User Interface and feature changes to the Tree Map interface (http://dendrome.ucdavis.edu/_dev/jyu/main/iplant_map/index.php ). Some of which include a polygon selection tool for Tree Sample and Ameriflux Site bulk selection, individual selection tool, pre-loaded map layers, and the ability to upload custom ArcGIS layers just to name a few.

On June 11th, the development team has a virtual meeting with the iPlant committee to present our work thus far as well as our future development plans. Knowing that this meeting is fast approaching, I am hoping to schedule a virtual meeting over Webex with as many of you as possible. I will be using this time to demonstrate the map interface and database communication via SSWAP. This will be a great opportunity for you to provide feedback on the value and accessibility of the developed tools, as well as suggestions for new features. I will be creating a Doodle poll to help coordinate a time when we can meet online.

As always, feel free to email me with comments or questions.

April 17, 2012

Greetings Tree Biology Workgroup,

We are long overdue to provide an update to the group regarding the iPlant Tree Biology Seed project. To review, the first goal of the project was to enable database communication by defining the genomic datatypes that exist in the TreeGenes database and translate common user queries into web services. Web services rely on defined standardized nomenclature to integrate data that would otherwise be impossible. Since our last update, I have completed five web services relating to sequence, polymorphism data, and geo-referenced individual trees currently housed in the TreeGenes database (http://dendrome.ucdavis.edu/treegenes/) and accessible through the DiversiTree interface (http://dendrome.ucdavis.edu/DiversiTree/). These services include: Contig Service, Contig Keyword Search Service, Amplicon Service, Alignment Service, and Tree Sample Service. These services can be launched through TreeGenes or through iPlant's SSWAP website (http://sswap.iplantcollaborative.org/).

You may recall that we selected two databases that serve as the pilot repositories for data integration with the genomic records, Ameriflux and Try-DB. Ameriflux holds ecological data for North and South America including metrics relating to soil temperature, wind direction, precipitation, and much more. We are now fully mirroring the data from AmeriFlux on our own servers and began importing the data into our PostGreSQL database. The map interface we are building within TreeGenes will display annual values of these data points as they are associated with geo-referenced trees. In addition, the raw hourly data as well as daily, weekly, and monthly aggregates will be linked so that users may download the data.

TRY-DB is an international repository for phenotypic traits, such as leaf width, height, photosynthetic measures, and much more. Many of their records are associated with individuals that have been geo-referenced and our goal is to allow users to obtain information recorded on an individual or region of interest. We have submitted a proposal to TRY-DB to gain access to this information for the ~1200 species that exist in the TreeGenes database.

In order to perform complex regional searches, our backend PostGreSQL database will need to be extended with the PostGIS spatial extension ( http://postgis.refractions.net/). This will allow TreeGenes to perform these complex distance within queries using GiST indexes which should improve performance. My goal is to complete the first Ameriflux web service by the end of April.

Concurrently during this development, TreeGenes developer John Yu, has began working on a mapping interface to visualize these data sets (http://dendrome.ucdavis.edu/_dev/jyu/main/iplant_map/index.php). This application is still under development and will eventually sit within the DiversiTree interface. Currently, the interface allows for html enabled tables to display data for a specific point on the map. The mapping system is built using Google API and a variety of mapping layers, including open layers and ArcGIS layers. The map will also allow users to bring in their own custom layers from ArcGIS online into the mapping system. With the use of SSWAP web services, we plan on allowing searches based on tree sample ID, species type, polymorphism, contig Id, etc. to generate the xml file in order to visualize the data on the mapping interface.

As always, feel free to email me with any comments or questions.

November 17, 2011

Greetings Tree Biology Workgroup,

It's been some time since I've emailed you guys, so I've decided to give you an update on the progress. I have been feverishly setting up the java backend for our project goal which is now complete. I have been working with the lead web service developer at iPlant to prototype some webservices with the data on the forest tree genomics database, TreeGenes. This will take some time, with current estimations being around 10 weeks. During the first week in December, Jill, Dave, and I, have a meeting with iPlant personnel to iron out the details of project. This will also give me the opportunity to get some face time with the SSWAP Web Services developer, Damian.

The current plan is to start with one database from each category (physiological/phenotype, genomics, and ecological). We want to start with widely used repositories that contain geo-referenced data (this has been the primary roadblock with identifying physiological databases to integrate with). We are planning to first incorporate those we have identified that have flat text files of information that can be easily queried (and do not rely on them implementing the same SSWAP technology). These include: AmeriFlux (ecological), TreeGenes (genomic), and TRY-DB (physiological/phenotype).

I have contacted the AmeriFlux database who has responded back with a promising email to access their data. TRY-DB is also interested in a long-term collaboration with data access and we are currently working out all of the details.

A list of other databases that we would like to work with after the technology has been fully developed include:

Databases (Type):
Fluxnet (Ecological)
NSF's LTER (Ecological)
NCEAS (Ecological) iPlant project initiated

We are still interested in growing this list, and the only current requirement is a stable underlying database structure, data availability, and geo-referenced coordinates (so we can connect the datasets at some level). As always, feel free to email me with any comments or questions.

Post Scriptum: We have submitted an abstract to PAG where we plan to have a poster for this project. Details can be found here: http://pag.confex.com/pag/xx/poster/papers/index.cgi?username=4353&password=141551 . We can make changes to the abstract until December 1st. Please let me know if you feel anything should be edited.





Icon 03 Updates

PineRefSeq project releases assembly (v2.0) of the Pinus taeda genome Walnut genome project releases assembly (v1.0) of the Juglans regia genome PineRefSeq project releases assembly (v1.0) of the Pseudotsuga menziesii genome PineRefSeq project releases assembly (v1.0) of the Pinus lambertiana genome CartograTree (v3.0), a map interface that works with DiversiTree to bring together genomics, ecological, and trait data is now live! PineRefSeq project releases assembly (v1.01) of the Pinus teada genome SMarTForests Project releases the third assembly of the Picea glauca genome

Icon 01 Events

AFoRGeN2017

Trentino, Italy
June 15-17, 2017
34th Southern Forest Tree Improvement Conference

Melbourne, Florida, USA
June 19-22, 2017