267-426-7526 Jeff Pennington Trac University of Pennsylvania None CTSA No penningtonj@email.chop.edu No Mark Porter Project management and ticketing University of Pennsylvania Institute for Translational Medicine and Therapeutics CTSA 267-426-7203 Xiaowu Gai None University of Pennsylvania Institute for Translational Medicine and Therapeutics No Ingenuity Pathways Analysis gai@email.chop.edu No University of Pennsylvania Mark Porter Ingenuity Pathways Analysis (IPA) is an all-in-one software application that enables researchers to model, analyze, and understand the complex biological and chemical systems at the core of life science research. A customized and internally branded version of the SumTotal Access Enterprise Suite. The system hosts enterprise-wide and focused training for employees as well as seminars, and other online learning modules. None CTSA University of Pennsylvania Institute for Translational Medicine and Therapeutics Don Yanaitis 610-639-9591 LearningLink Mark Porter No No yanaitis@email.chop.edu University of Pennsylvania 267-426-7528 felmeistera@email.chop.edu University of Pennsylvania Institute for Translational Medicine and Therapeutics None Oncolog University of Pennsylvania Mark Porter No No Registry, Clinical Trial Management System, and Protocol Management for oncology-based studies Alex Felmeister CTSA University of Pennsylvania University of Pennsylvania Institute for Translational Medicine and Therapeutics CTSA TCL Inventory Management Tools No 215-573-3736 None angel@mail.med.upenn.edu Angel Pizarro A suite of tools for biological sample inventory management specifically tailored for the workflows of the ITMAT Translational Core Laboratory (TCL). No gai@email.chop.edu 267-426-7203 None No CTSA A collection of 5 separate sequencing analysis packages bundled into a single user license agreement and single installation module. Included are MacVector, Discovery Studio Gene, VectorNTI Advance, Sequencher, and Lasergene. Mark Porter Suite of basic sequence analysis packages No Xiaowu Gai University of Pennsylvania University of Pennsylvania Institute for Translational Medicine and Therapeutics CTSA No Freezerworks Lorri Schieri None University of Pennsylvania Institute for Translational Medicine and Therapeutics Installation of commercial application to support storage in Translational Core Lab 215-573-0900 schieril@upenn.edu University of Pennsylvania No CTSA University of Pennsylvania Institute for Translational Medicine and Therapeutics No No vekteris@email.chop.edu Mark Porter None Terese Vekteris Website content management University of Pennsylvania 267-426-0443 OpenCMS Code tracking and version control No CTSA Mark Porter University of Pennsylvania None Subversion University of Pennsylvania Institute for Translational Medicine and Therapeutics No 267-426-7526 Jeff Pennington penningtonj@email.chop.edu porterm1@email.chop.edu University of Pennsylvania Mark Porter No No Mark Porter Internally developed instance of a Confluence wiki for enterprise-wide academic research community. Allows department- and lab-based workspaces with full control by a PI over fluid content updates and permissions-based security. University of Pennsylvania Institute for Translational Medicine and Therapeutics http://share.chop.edu Limited 267-426-9348 Share CTSA Angel Pizarro No CTSA Mascot angel@mail.med.upenn.edu A proteomics search algorithm from Matrix Science, licensed to run on the ITMAT compute cluster on 4 compute nodes. University of Pennsylvania Institute for Translational Medicine and Therapeutics University of Pennsylvania 215-573-3736 None No No University of Pennsylvania 215-573-3736 No None CTSA angel@mail.med.upenn.edu University of Pennsylvania Institute for Translational Medicine and Therapeutics A proteomics search algorithm from Thermo Fisher, licensed to operate on the ITMAT compute cluster on 25 compute nodes. Angel Pizarro SEQUEST Cluster HS-ERA University of Pennsylvania CTSA Human Subjects Electronic Research Administration: Human Subjects TrackingThe Human Subjects Protocol Tracking module is a secure web-based application for the Office of Regulatory Affairs (ORA) that manages protocols currently active or under review by the Institutional Review Board (IRB), Institutional Animal Care and Use Committee (IACUC), and/or the Safety Committee. It provides authorized users the ability to create, generate, and distribute agendas, minutes, and associated communications to investigators and IRB Board members.This module is also available to prior users of the Penn Protocol Manager (PPM), including the Office of Environmental Health and Radiation Safety (OEHRS), University Laboratory Animal Resources (ULAR), the Office of Research Support Services (ORSS), and the Office of Research Integrity and Compliance (ORIC). Lorri Schieri No No 215-573-0900 None schieril@upenn.edu University of Pennsylvania Institute for Translational Medicine and Therapeutics Linux No University of Pennsylvania None Lorri Schieri University of Pennsylvania Institute for Translational Medicine and Therapeutics Beta CTSA No Other/Proprietary License PHP CTSA Registration Onlne system for researchers to request services from CTSA-related cores, programs and centers. Tracks results of research (publications, patents, etc). Will be used to capture annual report data in future years 215-573-0900 schieril@upenn.edu Jeff Connell University of Pennsylvania Institute for Translational Medicine and Therapeutics connellj@chop.edu University of Pennsylvania No CTSA No Mark Porter 267-426-0207 BaseCamp Project management and collaboration None A proteomics tool tailored for submitting proteomics database search analyses from mass spectrometry data stored within the ITMAT LIMS. The end point algorithms include SEQUEST, Mascot, The Transproteomic Pipeline and EBP. University of Pennsylvania angel@mail.med.upenn.edu None No CTSA No qInteract Angel Pizarro University of Pennsylvania Institute for Translational Medicine and Therapeutics 215-573-3736 Phenyx No University of Pennsylvania A proteomics search algorithm from GeneBio, licensed to run on the ITMAT compute cluster on 2 compute nodes. Angel Pizarro angel@mail.med.upenn.edu 215-573-3736 None University of Pennsylvania Institute for Translational Medicine and Therapeutics No CTSA Production/Stable Web-based system for researchers to apply for ITMAT pilot grants. Includes an admin component to review and approve applications. Linux University of Pennsylvania schieril@upenn.edu Other/Proprietary License None University of Pennsylvania Institute for Translational Medicine and Therapeutics Lorri Schieri PHP CTSA No ITMAT Pilot Grants 215-573-0900 No University of Pennsylvania Institute for Translational Medicine and Therapeutics None Progenesis SameSpots Angel Pizarro CTSA angel@mail.med.upenn.edu No 215-573-3736 No University of Pennsylvania An advanced image analysis package for 2D gel and DiGE experiments from Non-linear system. The package is installed on a community workstation and available to ITMAT researchers. No 215-573-0900 Online application for CTRC that will be developed as an add-on to HS-ERA; reduces investigator burden for applying for funding in the Clinical and Translational Research Center. myCTRC Lorri Schieri University of Pennsylvania Institute for Translational Medicine and Therapeutics None CTSA schieril@upenn.edu University of Pennsylvania No University of Pennsylvania Other/Proprietary License CTSA Redmine schieril@upenn.edu Lorri Schieri 215-573-0900 Linux open source project management software PHP University of Pennsylvania Institute for Translational Medicine and Therapeutics No Jonathan Crossette Epic Clarity None Clinical Data Warehouse University of Pennsylvania Institute for Translational Medicine and Therapeutics Mark Porter No CTSA University of Pennsylvania 267-426-2493 crossette@email.chop.edu angel@mail.med.upenn.edu No University of Pennsylvania CTSA University of Pennsylvania Institute for Translational Medicine and Therapeutics The ITMAT Bioinformatics Facility maintains the high-performance compute environment necessary for high-throughput proteomics research. This includes an enterprise level SAN (7TB), 28 node compute cluster, 5 dedicated application servers, and supporting network equipment. None High-Performance Computing environment 215-573-3736 No Angel Pizarro PHP None TCL OMS Web-based system for researchers to place lab orders to the Translational Core Lab. Researchers provide data on samples and choose the assays they want run. Includes an administrative component for managing orders and workflow. Includes a billing component for automatic billing of research grants, and generating invoices for external researchers. CTSA Production/Stable University of Pennsylvania Institute for Translational Medicine and Therapeutics Linux Other/Proprietary License University of Pennsylvania 215-573-0900 Lorri Schieri No schieril@upenn.edu No No None 215-573-3736 No Angel Pizarro CTSA angel@mail.med.upenn.edu A Web application for storing, organizing and describing data files resulting from high-throughput proteomics experiments. The ITMAT LIMS serves to archive and annotate such data, as well as act as the source for our data analysis pipelines. University of Pennsylvania University of Pennsylvania Institute for Translational Medicine and Therapeutics ITMAT LIMS Mark Porter 267-426-9348 No porterm1@email.chop.edu Mark Porter University of Pennsylvania ClickCommerce University of Pennsylvania Institute for Translational Medicine and Therapeutics No CTSA Multi-disciplinary eResearch Portal Software for support services such as grants management, IRB processing, and clinical trials administration. This is currently in development with a tiered rollout program over the next few years. No schieril@upenn.edu No Lorri Schieri Protomics Core OMS University of Pennsylvania Institute for Translational Medicine and Therapeutics No In development to replace legacy system for managing orders and billing for the Proteomics core facility 215-573-0900 None University of Pennsylvania CTSA University of Pennsylvania Institute for Translational Medicine and Therapeutics No Cardiac Knowledgebase Database derived from extraction of free text cardiology reports with web search interface. Finds individual patients with abnormalities listed in clinical reports. None 215-590-5241 white@genome.chop.edu Peter White CTSA No University of Pennsylvania Mark Porter Peter White 215-590-5241 Limited Fable white@genome.chop.edu University of Pennsylvania FABLE mines the biomedical literature for information about human genes and proteins. FABLE v3 allows a user to find articles mentioning a gene of interest (Article Finder), to generate a list of genes associated with one or more keywords (Gene Lister), or use a local mirror of the UCSC Genome Browser with a literature track (LitTrack) University of Pennsylvania Institute for Translational Medicine and Therapeutics CTSA Yes Mark Porter Yes http://fable.chop.edu/ Clinical Trials Search University of Pennsylvania CTSA University of Pennsylvania Institute for Translational Medicine and Therapeutics schieril@upenn.edu Linux Lorri Schieri 215-573-0900 Other/Proprietary License No Public search utility for finding clinical trials at PennMed and CHOP, using data from clinicaltrails.gov. Updates data nightly from XML documents. Uses XSL to transform clinical trial XML documents for online display. Production/Stable None No PHP Linux CTSA ITMAT Membership Management schieril@upenn.edu Other/Proprietary License Allows ITMAT members to update their research profile online. Publicly lists members and their profiles on the ITMAT website. Provides central management of membership data, 215-573-0900 University of Pennsylvania Lorri Schieri University of Pennsylvania Institute for Translational Medicine and Therapeutics Production/Stable PHP Production/Stable University of Pennsylvania Institute for Translational Medicine and Therapeutics Linux Other/Proprietary License Service Center Account Management Lorri Schieri 215-573-0900 Central account management system used by multiple service centers. Tracks the status of PennMed grant accounts. Business administrators use it to grant spending authority to users on grant accounts. Also used to report on account activity across PennMed service centers. PHP University of Pennsylvania CTSA schieril@upenn.edu white@genome.chop.edu Limited eGenome Yes http://egenome.chop.edu/ Mark Porter Peter White University of Pennsylvania Institute for Translational Medicine and Therapeutics eGenome is a comprehensive, position-based catalog of the human genome. eGenome catalogs a wide range of genomic landmarks, including transcripts, markers, polymorphisms, large-insert clones, and DNA sequences. The goals of eGenome are to eliminate boundaries between data sets and provide the most relevant data to users in a useful form CTSA Yes University of Pennsylvania 215-590-5241 Other/Proprietary License Linux University of Pennsylvania Institute for Translational Medicine and Therapeutics 215-573-0900 ITMAT Web site schieril@upenn.edu http://www.itmat.upenn.edu/ Lorri Schieri Web site with news, research support, education, training, membership, and funding information University of Pennsylvania CTSA PHP 215-746-5575 University of Pennsylvania A database containing all Penn and Penn-based CHOP faculty. The database can be used for searching, keyword matching, and displaying profiles on public and/or private directory views. No None No Mark Porter FEDS Database adamsben@mail.med.upenn.edu Mature CTSA University of Pennsylvania Institute for Translational Medicine and Therapeutics Ben Adams Yes 267-426-7023 Mark Porter No CHOPPY Limited University of Pennsylvania CTSA Copy Number Variation Analysis Pipeline gai@email.chop.edu Xiaowu Gai University of Pennsylvania Institute for Translational Medicine and Therapeutics