Released: Ready for Use

Mainlab Chado Loader (sequence, map, marker, QTL, genotype, phenotype, germplasm) Extension Module

ccheng's picture
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 (sequence, map, marker, QTL, genotype, phenotype, germplasm) Extension Module

ccheng's picture
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 (sequence, map, marker, QTL, genotype, phenotype, germplasm) Extension Module

ccheng's picture
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.

ND Genotypes Extension Module

laceysanderson's picture
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.

Tripal Daemon Extension Module

laceysanderson's picture
This module provides the ability to start a Daemon that executes Tripal Jobs. By default, jobs in Tripal's job queue are executed either manually using Drush or via the UNIX cron. However, at most cron can only execute once every minute. The Daemon allows jobs to execute once they are submitted. This is particularly useful if you are allowing non-Tripal Administrators to submit jobs such as is the case with the BLAST UI module.

Tripal BLAST UI Extension Module

ficklin's picture
This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+. It supports blastn, blastx, blastp and tblastx with separate forms depending upon the database/query type. It provides a simple interface allowing users to paste or upload a query sequence and then select from available databases. Additionally, a FASTA file can be uploaded for use as a database to BLAST against (this functionality can be disabled). Results are provided in a tabular listing with alignment information and are available for download in multiple formats (HTML, TSV, XML).

Tripal BLAST Analysis Extension Module

ficklin's picture
This module extends the Tripal Analysis Module that comes with Tripal, and provides loaders and viewers for BLAST results. It does not provide a service for performing BLAST analyses. This module imports BLAST results in XML format, and supports any number of database FASTA file formats. It natively supports NCBI and ExPASy formats, but allows for support of custom formats as well. Features that are loaded into Chado will automatically have BLAST results associated and results will be visible on the feature's page.

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