LONI Pipeline Genomics and Informatics Workflow Solutions

Pipeline Genomics and Bioinformatics Workflows

This list represents the currently available informatics and genomics Pipeline modules are workflows (November 2010). This PDF Document also includes a guide to the use of these informatics protocols. See this 50-minute video stream demonstrating the Pipeline's functionality for managing bioinformatics and genomics analyses protocols.

Bioinformatics BLAST Workflow EMBOSS Bioinformatics Workflows mrFAST Bioinformatics Workflows GWASS Genomics Workflows PLINK GWAS Workflows Step I Analysis: Mapping and Assembly with Qualities (MAQ), SAMtools, Bowtie, CNVer Workflows Step II Analysis: Data Quality Control (QC) and Cleaning using Genome Analysis Toolkit (GATK) and SAMtools Workflows Microsatellite-based Ancestry and Parentage Analysis Workflows GENEPOP Migrate BATWING Fdist2 BayesAss+ Next Generation sequence (NGS) analysis modules for simulated data Additional (Pending) sequence analysis modules and workflows TrinityRNAseq

Additional features, extensions and recommendations for improvement of the Genomics and Informatics capabilities of the Pipeline are available here.

Documentations

• One-Page Pipeline Genomics-Informatics Guide (February 2011)
• Detailed Documentation on Pipeline Genomics Capabilities (March 2011)
• Graphical Pipeline Workflow Capability for Computational Genomics and Visual Informatics
• Some of these Pipeline Workflows are also available at MyExperiment.org

Acknowledgments

• These resources are designed, developed, tested and validated by a number of investigators at UCLA LONI (IvoDinov, AlenZamanyan, AlexGenco, Sam Hobel, LONI Pipeline Team (Petros Petrosyan, Zhizhong Liu, Paul Eggert), ArthurToga); UCI Human Genetics (Fabio Macciardi, Federica Torri, Harry Mangalam); USC/ZNI (Andrew Clark, Jim Knowles) and USC Epigenome Center (Ben Berman, Zack Ramjan); and BIRN (Joseph Ames, Carl Kesselman).
• This work was funded in part by the National Institutes of Health through Grants U54 RR021813, 9P41EB015922-15, 2-P41-RR-013642-15, R01 MH71940, U24-RR025736, U24-RR021992, U24-RR021760 and U24-RR026057.
• Members of the Laboratory of Neuro Imaging (LONI), the Biomedical Informatics Research Network (BIRN), the National Centers for Biomedical Computing (NCBC) and Clinical and Translational Science Award (CTSA) investigators, NIH Program officials, and many general users have contributed with beta-testing the Pipeline and for providing useful feedback about its state, functionality and usability.

Pipeline vs. Other Workflow Environments

• Comparison of the LONI Pipeline against other graphical workflow environments
• Pipeline vs. Taverna Workflow Comparison

Pipeline Genomics and Informatics Support Ticketing System

• Informatics.GoogleCode.com

Other Materials

• 1000 Genomes Dataset can be used for validation.
• BIRN Computational Genomics and Visual Informatics Workflow Capabilities
• The Genomics and Informatics Project code pages
  • GoogleCode Informatics Project Page
  • SourceForge Informatics Project Page
• Pending Genomics/Informatics Workflow Developments
• Pipeline Genomics/Informatics PPT/PDF Slides (April 2011)
• Pipeline Environment Multi-Client/Multi-Server Design Schematics