This module enables functional testing on Tripal extension modules through Drupal Simpletest module (Drupal core). Examples of .test file can be found here: * https://github.com/tripal/tripal_dt/blob/master/tripal_dt.test * http://cgit.drupalcode.org/tripal_cvb/tree/tripal_cvb.test?h=7.x-1.x * http://cgit.drupalcode.org/brapi/tree/brapi.test
Released: Ready for Use
This module can be used to display and browse a hierarchical tree representation of any controlled vocabulary (CV) stored into Chado (cvterm table). The vocabulary to browse must have relationships stored into the cvterm_relationship table where the children term is the subject (subject_id) and the parent term is the object (object_id).
MCL (Mainlab Chado Loader) is a module that enables users to upload their biological data to chado database schema. Users are required to transfer their biological data into various types of data template files. MCL, then, uploads these data template files into a chado schema. MCL requires each type of data template to have a corresponding class file. MCL predefines the class files for major data template types such as marker, QTL, germplasm, map, project. The flexibility of Chado schema often allows, however, the same type of biological data to be stored in various ways..
Mainlab Chado Search is a module that enables advanced search function for biological data stored in a Tripal/Chado database. By default, a set of search interfaces are provided, such as 'Gene Search' for searching genes and/or transcripts, 'Marker Search' for searching genetic markers, and 'Sequence Search' for searching any sequences stored in the Chado feature table.
Mainlab Tripal Data Display contains a set of Drupal/PHP templates that organize and extend the default display of the biological data hosted on a Tripal-enabled site (i.e. http://tripal.info). Supported data type includes orgainsm, marker, QTL, germplasm (stock), map (featuremap), project, heritable phenotypic marker (MTL), environment (ND geolocation), haplotype block, polymorphism, eimage, generic gene (genes created by parsing Genbank files using the Mainlab 'tripal_genbank_parser' module), feature, and pub. Each of the templates can be turned on/off as desired.
Provides a content type for downloadable files. Individual downloads can optionally be exposed as JBrowse tracks through Tripal JBrowse API.
This module exposes Chado as a JBrowse-compatible REST API.
Implementation of the popular search engine Elasticsearch for the chado database tables.
Tripal Analysis Expression modules allows users to upload a differential expression analysis, including expression values for a feature across many biomaterials (such as RNASeq libraries or microarrays). The expression levels are visualized as a heatmap or bar chart on each feature page.
This module provides a more specialized interface to genotypic information stored in the Chado Natural Diversity module tables including adding summaries of this information to feature pages and providing a powerful marker by germplasm matrix. The module adds specialized panes to marker and variant features to better display/summarize genotypic data.