The Tripal Gateway project is intended to provide computational infrastructure for online data repositories housing genomic, genetic and breeding data.  An increasing number of online data repositories are using the open-source software package, Tripal (http://tripal.info/), to power their sites which typically offer data for one or more related species of plants or animals. Examples of online data repositories include several Tree databases including Tree Genes (https://treegenesdb.org/), The Hardwood Genomics Project (https://hardwoodgenomics.org/), the Citrus Genome Database (https://www.citrusgenomedb.org/) and the Genome Database for Rosaceae (https://www.rosaceae.org/).  These sites house data for trees of ecological and agricultural importance. Moreover, these and other sites provide tools to visualize, mine and analyze the data they house. 

DNA sequencing and other technologies are lowering the cost for data collection in biology, yet the costs for creating online websites to house the data remains a time consuming and expensive task.  Often groups that can collect the data do not have the resources to create a fully-searchable online data repository with computational tools that can support large datasets.  Tripal, therefore, is meant to ease the burden by providing a common infrastructure on which new sites can be built and the Tripal Gateway project is meant to provide improved support for large data.  By using a common infrastructure, Tripal-based sites can share software, ideas and tools which in turn decreases costs. 

The Tripal Gateway project, has expanded on the offering of tools for Tripal-based sites, allowing them to provide additional infrastructure to their end-user scientists.  First, this project now allows related sites, such as the tree sites listed previously, to exchange data amongst themselves without the need to duplicate the data housed in the other sites.  Tree researchers can more easily locate and find tree specific data (such as genes of interest) by visiting just one of the integrated tree sites where they can find data across them all.  This increases the ability for scientists to find data of importance without the need to visit multiple sites.  This same functionality is now available to any Tripal-based site wishing to exchange and share data with others and that installs the Tripal Gateway tools.

Second, scientists often desire to analyze data in these repositories in combination with their own data.  Yet, large data required for these analyses are difficult to process. Often these analyses require multiple data processing steps that occur in a specific order. These multi-step analyses, known as workflows, are best handled by software dedicated to automating execution.  The Galaxy Project (https://galaxyproject.org/) is one such tool and is popular with biology researchers and can use high performance computing data centers.  The Tripal Gateway project has integrated Galaxy with Tripal to allow for seamless execution of workflows using data from the website and data provided by the scientist.  The scientist can now provide parameters for execution of the workflow within a Tripal site and Tripal manages the workflow. This reduces the complexity for some scientists who need not worry about computational infrastructure nor workflow design.  Data and results are accessible within the same website.

The third benefit provided by this project are new resources to support movement of large data.  Often data analysis needed for workflows occurs on computers that are not in the same data center as the online Tripal database.  Moving large amounts of data across the internet for analysis can be challenging.  Internet2 is a national-level research network designed to support fast movement of data between research institutions.  The Tripal Gateway project provides software tools that support as-fast-as-possible movement of data using Internet2 (or standard commodity internet).  Thus, data needed for scientific workflows can be moved between Tripal sites and other data repositories using smarter internet pathways.

In summary, the Tripal Gateway project provides three major sets of tools meant to help Tripal-based sites better deal with increasing quantities of data.  Because all Tripal sites are built on a common framework, the Tripal Gateway tools can be installed by any Tripal-based sites, providing a “plug-and-play” like experience for site developers.   Such computational infrastructure will allow scientists who use these databases to more easily find, move and analyze large datasets.

Last Modified: 10/31/2018
Modified by: Stephen Ficklin