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Molecular Profiling Facility, Bioinformatics (Penn)

Director: Tobias, John., PhD


The bioinformatics staff of the Penn Genomic Analysis Core is available to provide experimental design and analyical services to the basic and biomedical research community. Our services include support for Next-Gen Sequencing data as well as all platforms available in the core. We provide services as one-on-one meetings with customized approaches determined by the experimental design and goals of the investigator. We translate experimental goals into statistical, analytical and visual prioritization of genes and pathways.





  • Shared computers ( Computer )

    "Two computers are available in 528 Penn Tower (reserve blocks of time) on which users can do data analysis using a variety of tools"


  • Bioinformatics consultation service ( Support service )

    "Bioinformatics personnel provide consultation for experimental design and platform choice for maximization of statistical power. Plans are made for data analysis with the specification of customized solutions or scripts as necessary. Letters of support for grant applications and help with grant sections are also provided."

  • Bioinformatics data analysis service ( Data analysis service )

    "Whenever possible, data analysis is approached as a training opportunity. Biological value is maximzed by including the investigator throughout the design and analysis process. A fundamental understanding of the biology and experiment, which can only be supplied by the person who has done the work, is required for an appropriate analysis.

    Supported Platforms: Next-Gen Sequencing (RNA-seq, ChIP-seq), expression microarrays, Fludigm, Panomics, methylation microarrays, genotyping (SNP) assays, TaqMan assays and others - please inquire if your data source is not listed."

  • Bioinformatics education and training ( Training service )

    "We provide training primarily in one-on-one or small group (from a specific lab for example) settings as this has been determined empirically to be the most effective. We also provide workshops for specific bioinformatics packages or approaches to larger groups as needs are identified that can be addressed in this format. Talks have been and continue to be presented to departments (and faculty meetings) to inform investigators of the value of bioinformatics to their research and the services that we provide. Please contact John Tobias if you would like someone to talk to your department."

  • Bioinformatics/genomics resource identification ( Support service )

    "As bioinformatics/genomics needs arise in the research community at Penn or in individual laboratories, we will help identify and make available resources that will address these needs. We will also train persons to use these resources effectively."

  • Data storage ( Data storage service )

    Data storage is available:

    • external hard drives (1TB or 2TB)
    • data storage (PGFI SAN)

  • Desktop sequence analysis tools subscription ( Access service )

    "In response to many requests from the Penn community, the Facility has negotiated licenses and set up a centralized key server for a number of desktop sequence analysis packages. This enables us to provide these packages to Penn Scientists at a fraction of the cost for static licenses. An additonal advantage is that the packages can be run on multiple computers without the need for a hardware licensing device or key."

  • Genomic-scale sequencing analysis ( Data analysis service )

  • Grant preparation assistance for bioinformatics ( Support service )

    "Letters of support for grant applications and help with grant sections are also provided."

  • Sequence analysis application support ( Support service )

    "Support for running tools and analyses to analyze genomics data is provided. We do this primarily one-on-one but also offer workshops on different applications and analysis options as we identify specific needs."

  • Specialized analysis tools and support ( Access service )

    "The Facility has negotiated licenses for Partek Genomics Suite and Ingenuity Pathways Analysis. They are available to investigators in the Penn community which broadly defined includes Penn, the hospitial, CHOP, Wistar and Monell. We can presently provide Partek and Ingenuity Pathways Analysis for in-lab use on a subscription basis."

  • Transcript profiling application support ( Support service )

    "John Tobias provides application support for the analysis of microarray datasets on a variety of tools available in the Facility."

  • Transcript profiling consultation service ( Support service )

    "John Tobias provides a high level of consulting support for initial experimental design and determining the best analytical approaches given the data set. Letters of support for grant applications and help with grant sections are also provided."


  • DNASTAR LaserGene ( Software )

    "This is a full featured package and includes all the modules available for Lasergene."

  • Geneious Pro ( Software )

    "Geneious Pro™ is an integrated and extendable software platform for the organization and analysis of biological data that runs on all major operating systems."

  • GenePix ( Software )

  • Ingenuity IPA ( Software )

    "IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research.

    IPA helps you understand biology at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. Even if you don’t have experimental data, you can use IPA to intelligently search the Ingenuity®Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships to build biological models or get up to speed in a relevant area of research. IPA provides the right biological context to facilitate informed decision-making, advance research project design, and generate new testable hypotheses."

  • MacVector ( Software )

    "MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.

    Major Features:
    • graphical sequence editing
    • gateway and topo cloning
    • auto annotation
    • primer design
    • DNA analysis
    • protein analysis
    • database searching
    • multiple sequence alignment
    • sequence assembly"

  • Partek Genomics Suite ( Software )

    "Partek® Genomics Suite™ is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. The software is unique in supporting all microarray and next generation sequencing technologies including gene expression and digital gene expression (DGE), exon/alternative splicing and RNA-Seq, copy number and association, ChIP-chip, ChIP-seq, and microRNA in a single software package allowing for analysis of multiple applications in one complete solution."

  • Sequencher ( Software )

    "Next-generation or Traditional DNA data analysis features:

    • powerful reference sequence alignment
    • variance Table to discover SNPs quickly and easily
    • extensive data import and export capabilities
    • NCBI BLAST search
    • forensic mtDNA profiling"

  • Spotfire ( Software )

    Spotfire is an interactive data visualization tool with analytic and collaboration tools.

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Last updated: 2016-04-18T15:08:01.657-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016