Funannotate is a pipeline for genome annotation originally designed for use with fungi genomes, but it can also be applied for other eukaryotes.

PBSuite aka PBJelly

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. Each step in PBJelly’s workflow can be run on a cluster, thus parallelizing the gap filling process for rapid turn around, even for very large eukaryotic genomes.


Is no longer supported at MSI. 

SciTegic Pipeline Pilot

Pipeline Pilot, Accelrys' scientific informatics platform, was designed for scientists by scientists. It aggregates and provides immediate access to the volumes of disparate research data locked in silos, automates the scientific analysis of that data, and enables researchers to rapidly explore, visualize and report research results.


Cytoscape is an open source bioinformatics software platform for visualizing complex networks and integrating with gene expression profiles and other state data.


The Hadoop Map/Reduce framework harnesses a cluster of machines and executes user defined Map/Reduce jobs across the nodes in the cluster.  On itasca, a script exists to create an ephemeral Hadoop cluster on the set of nodes assigned by the scheduler.  The script setup_cluster will format a HDFS filesystem on the local scratch disks. 


OpenFOAM is an open source software package which is designed to scale well on large distributed memory systems. While originally written for CFD, with it's open source strategy and a large user base OpenFOAM has grown to be a general purpose finite element toolbox.


The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis.

The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.