HPCI: A Perl module for writing cluster-portable bioinformatics pipelines

BackgroundMost biocomputing pipelines are run on clusters of computers. Each type of cluster has its own API (application programming interface). That API defines how a program that is to run on the cluster must request the submission, content and monitoring of jobs to be run on the cluster. Sometimes, it is desirable to run the same pipeline on different types of cluster. This can happen in situations including when:different labs are collaborating, but they do not use the same type of clustera pipeline is released to other labs as open source or commercial softwarea lab has access to multiple types of cluster, and wants to choose between them for scaling, cost or other purposesa lab is migrating their infrastructure from one cluster type to anotherduring testing or travelling, it is often desired to run on a single computerHowever, since each type of cluster has its own API, code that runs jobs on one type of cluster needs to be re-written if it is desired to run that application on a different type of cluster. To resolve this problem, we created a software module to generalize the submission of pipelines across computing environments, including local compute, clouds and clusters.ResultsHPCI (High Performance Computing Interface) is a Perl module that provides the interface to a standardized generic cluster.When the HPCI module is used, it accepts a parameter to specify the cluster type. The HPCI module uses this to load a driver HPCD∷<cluster>. This is used to translate the abstract HPCI interface to the specific software interface.Simply by changing the cluster parameter, the same pipeline can be run on a different type of cluster with no other changes.ConclusionThe HPCI module assists in writing Perl programs that can be run in different lab environments, with different site configuration requirements and different types of hardware clusters. Rather than having to re-write portions of the program, it is only necessary to change a configuration file.Using HPCI, an application can manage collections of jobs to be runs, specify ordering dependencies, detect success or failure of jobs run and allow automatic retry of failed jobs (allowing for the possibility of a changed configuration such as when the original attempt specified an inadequate memory allotment).

Bio::DB::NextProt: A Perl Module for neXtProt Database Information Retrieval

The neXtProt database is a comprehensive knowledge platform recently adopted by the Chromosome-centric Human Proteome Project as the main reference database. The primary goal of the project is to identify and catalog every human protein encoded in the human genome. For such, computational approaches have an important role as data analysis and dedicated software are indispensable. Here we describe Bio::DB::NextProt, a Perl module that provides an object-oriented access to the neXtProt REST Web services, enabling the programatically retrieval of structured information. The Bio::DB::NextProt module presents a new way to interact and download information from the neXtProt database. Every parameter available through REST API is covered by the module allowing a fast, dynamic and ready-to-use alternative for those who need to access neXtProt data. Bio::DB::NextProt is an easy-to-use module that provides automatically retrieval of data, ready to be integrated into third-party software or to be used by other programmers on the fly. The module is freely available from from CPAN (metacpan.org/release/Bio-DB-NextProt) and GitHub (github.com/Leprevost/Bio-DB-NextProt) and is released under the perl\_5 license.

Bio::DB::NextProt: A Perl Module for neXtProt Database Information Retrieval

The neXtProt database is a comprehensive knowledge platform recently adopted by the Chromosome-centric Human Proteome Project as the main reference database. The primary goal of the project is to identify and catalog every human protein encoded in the human genome. For such, computational approaches have an important role as data analysis and dedicated software are indispensable. Here we describe Bio::DB::NextProt, a Perl module that provides an object-oriented access to the neXtProt REST Web services, enabling the programatically retrieval of structured information. The Bio::DB::NextProt module presents a new way to interact and download information from the neXtProt database. Every parameter available through REST API is covered by the module allowing a fast, dynamic and ready-to-use alternative for those who need to access neXtProt data. Bio::DB::NextProt is an easy-to-use module that provides automatically retrieval of data, ready to be integrated into third-party software or to be used by other programmers on the fly. The module is freely available from from CPAN (metacpan.org/release/Bio-DB-NextProt) and GitHub (github.com/Leprevost/Bio-DB-NextProt) and is released under the perl\_5 license.