Bioinformatics Tools and Genomic Resources

image01The program uses an array of bioinformatics tools and genomics resources, which include publicly available, in-house developed and proprietary ones. A list of some of the bioinformatic tools and genomic resources is provided below. The list will be continously updated to add more tools and resources.  LSUHSC investigators are welcome to use these tools and resources independently or with support from BIG staff. However, all investigators using these tools and resources listed on this website must acknowledge and cite the original sources appropriately.

 

Bioinformatics Tools

Genepattern: The program provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a web interface with no programming experience required or with assistance from BIG staff. Genepattern is available for use through our Bioinformatics and Computational Genomics Lab or through the web at this site: http://www.broadinstitute.org/cancer/software/genepattern/

Pomelo II: This is web-based bioinformatics software for analysis of gene expression data. The software is all available through a web interface with no programming experience required or with assistance from BIG staff. Pomelo II is available for use through our Bioinformatics and Computational Genomics Lab or through the web at this site: http://pomelo2.iib.uam.es/

GENE-E: GENE-E is a matrix visualization and analysis platform designed to support visual data exploration. It includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, GENE-E also contains tools that are designed specifically for genomics data. GENE-E was created and is developed by Joshua Gould. When referencing your use of GENE-E, please cite this website. http://www.broadinstitute.org/cancer/softwareGENE-E/

GATK: The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data, developed by the Data Science and Data Engineering group at the Broad Institute. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. https://www.broadinstitute.org/gatk/

GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer. GenomeSpace does not perform any analyses itself; these are done within the member tools wherever they live – desktop, Web service, cloud, in-house server, etc. Rather, GenomeSpace provides tool selection and launch capabilities, and acts as a data highway automatically reformatting data as required when results move from the output of one tool to input for the next. http://www.genomespace.org/

Haploview: The program is designed to facilitate the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview

Genome Browser: It is useful software for navigating the genomes. The software can be accessed via the UCSC Genome Browser website: https://genome.ucsc.edu/.

Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations: https://www.broadinstitute.org/igv/.

Integrated Genome Browser (IGB) is a fast, free, and highly customizable genome browser you can use to view and explore big genomic datasets. IGB runs on your desktop and can load data from your local files and also from the internet. http://bioviz.org/igb/index.html

1000 Genomes Project:The 1000 Genomes Project is a public resource which ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. The International Genome Sample Resource (IGSR) was set up to do this. It is powered by the 1000 Genomes Browser, a genome navigation tool for browsing the genomes in the 1000 Genome Project: The project can be accessed via the following browser: http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/

 

 

Genomic Resources

The program uses an array of genomics resources. All scientists using the genomic resources listed on this website must acknowledge and cite the original sources appropriately. A list of some of the genomic resources is provided below.

Stanley S. Scott Cancer Center’s Genomics Core: This is a shared resource provide an array of genomic services through the SSSCC. Prospective users can contact Dr. Jovanny Zabaleta for details. The Core can be accessed via this website: http://www.louisianacancercenter.org/research/shared-resources/genomics/.

Louisiana Cancer Research Consortium’s Proteomics Core: This is a shared resource provide an array of genomic services through the LCRC. Prospective users can contact the Core Staff. The Core can be accessed via this website: http://www.louisianacancercenter.org/research/shared-resources/proteomics/.

LSUHSC-SOM-Departments and Centers of Excellence: The school of Medicine is home to many Departments and Centers that support genomic research. More information regarding the departments and centers can be found on this website: http://www.medschool.lsuhsc.edu/administration/department_listing.aspx.image12

The Ochsner Biobank Unit: This is a state-of-the-art Ochsner Biobank facility established in 2011 to create an extensive and robust biospecimen and clinical data repository that provides research investigators with a reliable ready source of a variety of biospecimen for cutting-edge translational and clinical research projects. The repository supports various omics studies.  Prospective users can contact Mr. Pukar Ratti, MSChE, MSHCM, CIM, CCRP, FACMPE. He is the Clinical and Biospecimen Research Manager at Ochsner Health System and is also a member of this program: https://research.ochsner.org/clinical-research/biobank/.

The Louisiana Cancer Registry at LSUHSC: Cancer registration in Louisiana began in 1947 at the Charity Hospital Tumor Registry in New Orleans. The Tumor registry is a vital resources for large-scale genomic studies on cancer. For detailed information please contact the Director of the LTR. The LTR can be accessed via the following website. http://sph.lsuhsc.edu/research-ltr.

Gene Expression Omnibus (GEO): is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. The database can be accessed through this website. http://www.ncbi.nlm.nih.gov/geo/

ArrayExpress: It is one of the repositories recommended by major scientific journals to archive functional genomics data to support reproducible research. Experiments are submitted directly to ArrayExpress or are imported from the NCBI Gene Expression Omnibus database. For high-throughput sequencing based experiments the raw data is brokered to the European Nucleotide Archive, while the experiment descriptions and processed data are archived in ArrayExpress. Tools are provided to help users query and download experiments and curated gene expression profiles. The database can be accessed through this website. https://www.ebi.ac.uk/arrayexpress/

Sequence Read Archive (SRA): The database makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD System®, Helicos Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®. http://www.ncbi.nlm.nih.gov/sra

dbGaP: The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans. http://www.ncbi.nlm.nih.gov/gap

The Cancer Genome Atlas: is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), two of the 27 Institutes and Centers of the National Institutes of Health, U.S. Department of Health and Human Services. For more details and how access the TCGA visit the following website: http://cancergenome.nih.gov/

IHEC: The International Human Epigenome Consortium (IHEC) is a global consortium with the primary goal of providing free access to high-resolution reference human epigenome maps for normal and disease cell types to the research community. The epigenome reference maps will be of great utility to LSUHSC researchers in basic and applied research. For detailed information and access, please visit the following website: http://ihec-epigenomes.org/

The NIH Roadmap Epigenomics Mapping Consortium: The project was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. This resource can be used by the LSHSC research community in support of their research. For details and access visit the following website: http://www.roadmapepigenomics.org/

ENCODE: The encode, Encyclopedia Of DNA Elements project was launched by the National Human Genome Research Institute (NHGRI) as a public research consortium in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project can be used as references for scientists conducting function genomics. The database can be accessed at this website https://www.genome.gov/encode/

The GWAS Catalog: This is a public genomics resource provided jointly by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EMBL-EBI). The catalogue contains genetic variants and genes associated with common human diseases and is an excellent resource for geneticists. The catalogue can be accessed through the following websites: http://www.ebi.ac.uk/gwas/docs/about or https://www.genome.gov/gwastudies/

The International HapMap Project: This is a multi-country effort to identify and catalog genetic similarities and differences in human beings. This is a great resource for LSUHSC researchers interested in understanding genomic variation. The resource can be accessed on the following website: https://hapmap.ncbi.nlm.nih.gov/

TARGET: (Therapeutically Applicable Research to Generate Effective Treatments) An excellent genomic resource supported by NIH and children’s oncology group. TARGET applies a comprehensive genomic approach to determine molecular changes that drive childhood cancers. The Bioinformatics and Genomics Program uses the resource for genomic studies on childhood cancers. The resource is accessible through the following websites: https://ocg.cancer.gov/programs/target