In GenePattern 1.3, modules and pipelines have been enhanced to allow truly reproducible research. Developments supporting reproducible research include the following:
Module Versioning. Every version of a module is identified by a unique version number. This means that you can refer to a certain version of a module and know that, no matter how the code may change in the future, you will always get the same results using this version of the module.
Pipeline Versioning. As with modules, each version of a pipeline is identified by a unique version number. This means that if you have changed a pipeline and you want to retrieve a previous version of it, that version will be available.
Authorities. GenePattern allows you to have many different implementations of the same algorithm, such as Hierarchical Clustering from Broad or MeV. GenePattern 1.3 includes an "authority" for each module, allowing you to determine its origin and allowing you to select from different implementations of an algorithm with the same name.
Additional developments include:
MATLAB programming environment. You can call GenePattern modules from any MATLAB script and convert a pipeline to its equivalent MATLAB code.
Pipeline and module view mode. You can view a compact representation of a module or a pipeline without having to edit it.