Curator Dashboard

A data analysis pipeline for the Methyl-MAPS method.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data.

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• SciCrunch
• 12 years ago - by Anonymous

A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA.

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• SciCrunch
• 12 years ago - by Anonymous

An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10.

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• SciCrunch
• 12 years ago - by Anonymous

Commercial antibody vendor that provides products that utilize in-vitro cloning technology to create rabbit clonal and monospecific clonal antibodies. This company produces antibodies which correspond strictly to the conserved linear epitope of the antigen molecule.

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• SciCrunch
• 12 years ago - by Anonymous

An anatomy ontology covering the vertebrate skeletal system that integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.

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• SciCrunch
• 12 years ago - by Anonymous

Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture.

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• SciCrunch
• 12 years ago - by Anonymous

An ontology for standardized, systematic description of effects, consequences and mechanisms of variations.

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• SciCrunch
• 12 years ago - by Anonymous

Ontology for representing events, time, and their relationships.

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• SciCrunch
• 12 years ago - by Anonymous

An ontology for DICOM as used in the SeDI project.

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• SciCrunch
• 12 years ago - by Anonymous

Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries

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• SciCrunch
• 12 years ago - by Anonymous

A collection of both commercial and noncommercial software products which includes: Mascot Distiller, Mascot Parser, and Mascot Server. Mascot Distiller is commercial and provides a single interface to process raw data into de-isotoped peak lists. This tool can also be used for the easy distribution of search and quantitative results to colleagues. The non-commercial Mascot Parser software provides an API (Application Programmer Interface) that makes it easier to access search results written in C++, Java, Python and Perl. Mascot Server is non-commercial, and is a collection of peptide mass fingerprints as well as a MS/MS database. A selection of popular sequence databases are available online and include SwissProt, NCBInr, and the EST divisions of EMBL. This server is best used for evaluating and searching for smaller data sets.

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• SciCrunch
• 12 years ago - by Anonymous

A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.

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• SciCrunch
• 12 years ago - by Anonymous

A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.

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• SciCrunch
• 12 years ago - by Anonymous

An informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System.

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• SciCrunch
• 12 years ago - by Anonymous

Software which converts DICOM images to NIfTI format.

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• SciCrunch
• 12 years ago - by Anonymous

A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA and Brainwaver User interfaces.

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• SciCrunch
• 12 years ago - by Anonymous

Core facility that provides the following services: Clinical data management, Project operations and compliance support, Custom database application development, Research technology support, Proposal development service. The Clinical Research Computing Unit (CRCU) is a designated core research facility within Penn Medicine, specializing in clinical research informatics (CRI) collaboration and research IT services with a growing number of clinical and translational research investigators at Penn. The CRCU currently supports 58 funded projects, valued at more than $336 M (total costs, all years) to Penn. Although situated within the Center for Clinical Epidemiology and Biostatistics (CCEB), the CRCU supports an increasing volume of its research portfolio led by PIs external to the CCEB. This year the total value of these research programs was $ 243 M, so that the proportion attributable to PIs external to CCEB exceeded 70% ($243 M / $336 M = 72%). Established originally on April 1, 1997, within the Biostatistics Unit of the Center for Clinical Epidemiology and Biostatistics (CCEB) at the University of Pennsylvania School of Medicine, the primary foci were to develop a research computing base for the new program in Biostatistics, as well as to create the capacity and resources to compete successfully for data coordinating centers (DCCs) of federally funded, large-scale, multi center clinical trials, and epidemiological studies. These technology resources also permitted CCEB faculty and staff to provide essential collaborative CRI support for Penn investigators throughout the wide array of basic science and clinical departments, centers, and institutes, thus enhancing their likelihood of funding success. On July 1, 2002, the CRCU restructured its operations and expanded its focus in response to the overall research project growth within the CCEB and the University. The CRCU, as an organizational unit, moved from within the Biostatistics Unit of the CCEB to a CCEB-wide organizational service center for both the Biostatistics and Clinical Epidemiology units. With this restructuring, the CRCU now has two faculty co-directors; one representing each of the CCEB units. The faculty directors ensure that the overall strategy and goals of the service center are aligned with the overall goals of the CCEB, as well as Penn Medicine. In 2005, the leadership model was expanded with the appointment of four (4) Directors of Operations, each of whom report directly to the faculty directors and manage a specialty sub-unit of staff to more effectively coordinate the evolving complexities of the more than 58 sponsored project teams. The original two (2) Senior Directors now focus their leadership efforts on technology infrastructure, new methodologies, special projects and fostering strategic collaborations with other Penn departments, commercial vendors, and other institutions. The University of Pennsylvania aspires to excellence in all domains. The CRCU embraces these ideals, as it partners with faculty and staff to conduct biomedical, behavioral, clinical and translational biomedical research at the highest levels of excellence. Advances in healthcare and improvements in quality of life through research depend on thoughtful science and uncompromising integrity in the collection and handling of information. The CRCU excels in the support of biomedical and clinical research by providing expertise in all facets of research information management, and by understanding the regulatory and cultural environments in which research is conducted. The CRCU fosters collaborative relationships with investigators in the CCEB, other Centers and Institutes throughout the School of Medicine, and across the University, to take an active partnership role in meeting their research goals. The CRCU is committed to continuous improvement in the expertise offered and the services provided, through an emphasis on education and training for staff and through the use of leading technologies and creative solutions.

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• SciCrunch
• 12 years ago - by Anonymous

Core facility that provides the following services: Maintenance of transgenic or mutant zebrafish lines, Zebrafish research training, Zebrafish embryo supply service. The CDB Zebrafish Core facility provides services and training to Penn faculty interested in using the zebrafish model system as part of their research program.

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• SciCrunch
• 12 years ago - by Anonymous

A basic fastq compressor, designed primarily for high performance.

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• SciCrunch
• 12 years ago - by Anonymous