A wide variety of research software is licensed by Penn State University and is available to assist investigators with data collection and analysis. The following table presents the most widely utilized software applications – all of which are free to authorized users. Keep in mind that it is illegal to distribute or copy software in a manner other than as prescribed in the license agreement. The majority of licenses held by Penn State University are academic licenses that restrict use to non-commercial research purposes. Some license agreements stipulate the number of concurrent users. Keep in mind that if software will be used for publication purposes, proper acknowledgement should be included in submitted manuscripts. For a complete listing of commercial software packages available for purchase, visit the Penn State Software Store.

Software Application
Description
User Access
IT Requirements
Technical Support
Agilent GeneSpring GeneSpring is a Java application that runs on a variety of operating systems. It is a package of statistical analysis and visualization tools that support analysis of transcriptomics, genomics, proteomics and metabolomics data. The following modules are available for GeneSpring:
GeneSpring GX for data from microarray technologies.
Pathway Architect to perform pathway and network analysis across data types and organisms.
Version(s) Supported: 12.6 and newer
License: Academic license held by Penn State University and hosted at the University Park campus.
License allows an unlimited number of concurrent users. Application is installed in user’s computing environment (not browser-based). Application is available for Windows 32-bit and 64-bit Mac (Universal)3 Linux 32-bit and 64-bit. The application requires internal network connectivity to run (due to license server). Installation support: Users should contact the IT Helpdesk (717) 531-6281 to submit an installation request.
Web: http://genespring-support.com/support
Email: informatics_support@agilent.com
Phone: (800)-227-9770 (Option 3, Option 5, Option 2)
Ingenuity Pathway Analysis (IPA) IPA is a web-based software application that supports ontological, pathway, and network analysis. The software can analyze data derived from gene expression, microRNA and SNP microarrays,  metabolomics, proteomics, and RNA-Seq experiments.
Version(s)Supported: Current release
License: Academic license is held by Penn State University. Software is server-supported and hosted at the University Park campus.
License allows one (1) concurrent user The University’s version of IPA requires internal network connectivity to run (due to license server). Account Support: To obtain a login on the University license, users should contact the IT Help Desk (717) 531-6281.  Please provide full name, PSU e-mail address, Department and PI information.
Web: ingenuity.force.com/ipa/
Email: support@ingenuity.com
Phone: (650) 381-5111
i2b2 i2b2 (Informatics for Integrating Biology & the Bedside) is an informatics framework created through NIH funding to leverage existing data for research cohort discovery. i2b2 was designed to support cohort identification, retrospective data analysis, and hypothesis generation. The web client is designed with a user-friendly, drag-and-drop interface to enable users to perform data queries without extensive training or technical expertise. The i2b2 application receives financial support from the NIH through the Penn State Clinical and Translational Science Institute (CTSI). i2b2 is hosted at the Penn State Hershey campus.
License: i2b2 is an open-source application
License allows an unlimited number of concurrent users Users can access this application internally at the Penn State Hershey campus or internally at the University Park campus. External access is only available via remote access to the Hershey network (i.e. Citrix). Account Support: To create an account, users must have a Penn State Access Account ID (e.g. bas12). Users should contact the IT Help Desk (717) 531-6281 for information on how to submit an account request.
Training: Training is required to access the i2b2 application. Information on available training can be accessed on the CTSI website here
Product Support: Users should contact the IT Helpdesk (717) 531-6281 to request help with the application.
Mathematica Mathematica is a fully integrated software environment for technical and scientific computing. Mathematica combines numerical and symbolic computation, visualization, and programming in a single, flexible interactive software system.
Version(s)Supported: Version 10
License: Academic license is held by Penn State University.
License allows 100 concurrent users Three access options are available:
(1) Installed application in user’s computing environment. Available for: Windows, Mac, Linux. Requires internal network connectivity to run (due to license server)
(2) To make use of the version that the University has licensed for use in the high-performance computing environment, you must get access to Hammer (hammer.rcc.psu.edu) by applying via e-mail to rcc@rcc.its.psu.edu.
(3) Available via webapps.psu.edu portal
Installation Support: Users should contact the IT Help Desk (717) 531-6281 to submit an installation request. Departments can also purchase a separate Mathematica license to support unlimited use within their department. For a nominal fee, students can purchase a student license to install the software on a personal machine. Mathematica software is available from the Penn State Software Store.
Web: http://www.wolfram.com/support/
Phone: (800) WOLFRAM
LabLink LabLink has two components: Geneus serves the Genomic Sciences and DNA Sequencing Cores with sample submission and data retrieval. Proteus serves the Mass Spec, Flow Cytometry, and Microscopy Imaging Cores with sample submission and data retrieval.
Version(s) Supported: 7.19.16
License: Academic license is held by Penn State University. Software is server-supported and hosted at the Penn State Hershey campus.
License allows an unlimited number of concurrent users User must be on internal network in order to access application. Account Support: Proteus LabLink and Geneus LabLink are separate LIMS systems. An account on one system does NOT allow you access to the other system. To create an account, internal users must have a Penn State Access Account ID (e.g., bas12) and external users must establish a Friends of Penn State Account ID. To access Proteus or Geneus, visit the Section of Research Resources website at http://www.pennstatehershey.org/web/core/lablink.
Web: http://www.genologics.com/support
Email: support@genologics.com
Phone: (866) 457-5467
LabManager LabManager is a web-based application and database for investigators to search for existing equipment in labs by category, brand, and model. Investigators can also blindly query lab managers about specific equipment via integrated email capability.
Version(s) Supported: 1.0.3
License: Internally-developed application that is hosted at the Penn State Hershey campus.
The application supports an unlimited number of concurrent users  User must be on internal network in order to access application. Account Support: To create an account, users must have a Penn State Access Account ID (e.g. bas12). Users should contact the IT Helpdesk (717) 531-6281 for information on how to submit an account request.
Product Support: Users should contact the IT Help Desk (717) 531-6281 to request help with the application.
Penn State Profiles Developed by Harvard University, Profiles is Research Networking Software (RNS) that provides professional profiles of faculty at Penn State. The tool, which is used by hundreds of academic institutions across the country, automatically populates an investigator’s profile with his/her publication history from PubMed. Investigators can customize their profiles to highlight professional accomplishments, research interests, and expertise. Profiles can be a powerful tool for identifying potential research collaborators. Profiles receives financial support from the NIH through the Penn State Clinical and Translational Science Institute (CTSI).
Version(s) Supported: 1.0.4
License: No license agreement is required for Penn State University to use this software.
The application supports an unlimited number of concurrent users   User can access application internally or externally. Account Support: Anyone on the Internet has the ability to search and browse the Penn State Profiles system. However, only members with Penn State Access Accounts are able to login and perform additional tasks, such as editing their profile. A few staff members have “proxy” access, which permits them to edit other peoples’ profiles. Users should contact the Help Desk (717) 531-6281 for information on how to submit an account request through Research Informatics.
Product Support: If you discover that information displayed on your profile is incorrect, you can request changes be made to your profile by sending an email to: profiles@hmc.psu.edu. For a list of FAQs and contacts, visit the Infonet at https://profiles.psu.edu/profiles/about/default.aspx.
REDCap REDCap (Research Electronic Data Capture) is a secure web application designed to support data capture for research studies. It provides user-friendly web-based case report forms and surveys, real-time data entry validation (e.g. for data types and range checks), audit trails and a de-identified data export mechanism to common statistical packages (SPSS, SAS, Stata, R/S-Plus). REDCap receives financial support from the NIH through the Penn State Clinical and Translational Science Institute (CTSI).
Version(s) Supported: 5.9.18
License: Academic license held by Penn State University
License allows an unlimited number of concurrent users Users can access this application internally or externally. It is available from either desktop or mobile environments. Account Support: To create an account, users must have a Penn State Access Account ID (e.g. bas12). Users should contact the IT Help Desk (717) 531-6281 for information on how to submit an account request.
Training: Training is required to access REDCap. Information on available training can be accessed on the CTSI website at http://ctsi.psu.edu/ctsi-programs/clinical-services-core/redcap-home/accesstraining/.
Product Support: Users should contact the IT Helpdesk (717) 531-6281 to request help with the application.
Secure File Transfer Secure File Transfer (SFT) is an application which allows internal and external researchers to share sensitive or confidential information through a subscribed collaboration space. The tool also provides for email notification to external researchers when files are uploaded to the shared space. The SFT available enterprise-wide at the Penn State College of Medicine is Acellion’s Kite Drive.
Version(s) Supported: 9.11.90
Users can access this application internally or externally. It is available from either desktop or mobile environments. Account Support: Log into the SFT web interface at http://filedrop.pennstatehershey.net using your hmc.psu.edu email address and ePass account password. To create an ePass account, users should contact the IT Help Desk (717) 531-6281.
ScholarSphere ScholarSphere is a secure online repository that helps users share and preserve research and scholarly work. ScholarSphere is an optimal service for making federally funded research openly accessible to the public and meeting the requirements of federal funding agencies. The tool does not support Personal Health Information (PHI).
Version(s) Supported: 2.0
This web-based resource supports an unlimited number of concurrent users Users can access this application internally or externally. It is available from either desktop or mobile environments. Account Support: A Penn State Access ID is required to use ScholarSphere. If you need to report a problem using ScholarSphere, or would like to request service assistance, consultation, or share feedback, you can submit an issue via a contact form, available here. The form will go to ScholarSphere User Services, and a librarian will get back to you within 2 business days. Or you can contact the ScholarSphere phone line: (814) 865-2486. Your call will be answered, or voicemail returned, by staff in Publishing and Curation Services in the University Libraries.