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Informatics & Data Analysis

Informatics & Data Analysis

Penn State College of Medicine offers a variety of resources to assist investigators in data analysis and management, including Bioinformatics and Research Informatics teams and the Clarity LabLink Laboratory Information Management System (LIMS).

Bioinformatics

Penn State College of Medicine provides a variety of bioinformatics and biostatistics services, including analysis, prediction and software support.

Learn more about Bioinformatics

(internal users only)

Services

  • DNA Next Generation Sequencing (NGS) analysis
  • Exome-Sequencing analysis
  • ChIP-Seq analysis (narrow peaks or wider domains)
  • RNA-Seq analysis
  • DNA Methylation Sequencing analysis
  • Ribo-Seq analysis
  • Differential expression (RNA-Seq and DNA methylation)
  • Variant discovery (DNA and RNA-Seq)
  • Junction-based analysis of splicing events
  • ENCODE correlations with NGS datasets
  • The Cancer Genome Atlas (TCGA) NGS datasets
  • Epigenetic signature discovery
  • Transcription Factor Motif discovery
  • Phosphorylation prediction
  • microRNA target prediction
  • Virus de novo Assembly
  • Microarray analysis
  • Biomarker panel design
  • Pathway analysis
  • Gene ontology analysis
  • Proteomics analysis
  • qPCR analysis
  • Machine learning
  • Custom scripts/software

Software Support

  • Ingenuity Pathways
  • MATLAB
  • Bioinformatics public software (bowtie, bwa, MACS, RSEG, tophat, cufflinks, samtools, picard, IGV, GATK, GSEA, DAVID, hmmer, etc.)
  • R, Python, Perl, Java and other programming languages

Contact Us

For details on Bioinformatics, email Yuka Imamura Kawasawa, PhD, at yimamura@pennstatehealth.psu.edu or call 717-531-0003, ext. 289250.

Research Informatics

Research Informatics is a division of Information Technology that has a unique mission at Penn State College of Medicine: to provide the research community with the resources (hardware, software, and people) necessary to meet their needs.

Research Informatics offers a number of services that include consulting, web application development, programming, system and software installation and administration, high-performance computing resources and training. The team is committed to providing innovative solutions that exceed customer expectations while delivering first-class customer care.

Service Highlights

Technical Support and Consulting Services

Research Informatics provides consultation services for hardware/software procurement, application development, programming, and data-management options, and also supports a growing portfolio of custom and off-the-shelf applications.

Programming and Application Development

  • Meeting with clients to analyze requirements for an application.
  • Designing, testing and developing software solutions.
  • Recommending upgrades and improvements for existing applications.
  • Assisting with implementation of externally developed applications (vendor and open-source).
  • Ensuring that applications function normally with maintenance and testing.
  • Working with end users for support and training.
  • Tuning software for maximum performance.
  • Troubleshooting malfunctioning programs.

High Performance Computing Resources

High Performance Computing and enterprise-level storage provide researchers at Penn State College of Medicine the ability to quickly and efficiently process large amounts of data while allowing results to be accessed for the life of the research project. The system also allows researchers to work on multiple projects simultaneously while maintaining fast data transfer rates. HPC systems are utilized by preeminent universities and government agencies that depend on complex data analysis and applications.

System and Software Administration

  • System and cluster hardware
  • Compilers, libraries and middleware
  • Broadly used applications

Application Highlights

  • REDCap (Research Electronic Data Capture) is a tool for secure survey data capture and management.
  • i2b2 (Informatics for Integrating Biology and the Bedside) is used for cohort identification through a database of de-identified patient information.
  • StudyFinder is a searchable database of clinical research trials.
  • Penn State Profiles is a profile and networking software that helps you find Penn State faculty.

Contact Us

For details on Research Informatics, email Jason Hughes, Research Informatics Officer, at jhughes7@pennstatehealth.psu.edu or call 717-531-3727.

Clarity LabLink LIMS

Several core facilities at Penn State College of Medicine use the Clarity LabLink Laboratory Information Management System.

Log in to Clarity LabLink LIMS

(registered users only)

Specifically, Clarity serves the Mass Spectrometry, Flow Cytometry, Microscopy Imaging and Genome Sciences core facilities.

Signing Up for Clarity LabLink LIMS

  • Click to request a Clarity LabLink account.
    • External users: Before you can request a LabLink account, you will need a Friends of Penn State ID, which you can apply for on the FPS website. When your account request has been approved by IT (usually takes 2 to 3 days), you will receive an email with your username and temporary password, which you can then use to log in.
    • Internal users: Use your Penn State Access Account ID (e.g., bas12) for your username.
  • The first time you log on, please change your password to something you can remember.

A detailed guide to registering for and using Clarity LabLink is available here.

Contact Us

For assistance with Clarity, email Janet Wood, Systems Analyst, at jwood7@pennstatehealth.psu.edu or call 717-531-0003, ext. 287455.

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