Curator Dashboard

Core assists faculty, staff, and students with conducting research projects using electronic health record data.Facilitates access to clinical data and performs data analysis using artificial intelligence, ontologies, natural language processing, machine learning, and visual analytics. Provides innovative research services by applying data science to clinical data in order to learn actionable healthcare knowledge and develop impactful solutions for improving patient care. Services include facilitating access to Penn Medicine clinical data resources, performing data analysis using diverse computational methods, and providing tools for exploratory data analysis/visualize with priority access to the IBI Idea Factory for immersive display of data and research results. �

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.

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• SciCrunch
• 13 years ago - by Anonymous

Resource for investigators requiring viral vectors for preclinical studies and other basic research applications such as gene therapies for acquired and inherited diseases.Provides production of high quality vectors and distribution of improved vector technologies services.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

VideoScribbler is a program that makes it possible to trace directly onto live video. It was developed to provide a way to outline and count cells in a video image. The program displays the live video image in a 640x480 window. Userrs can click and drag the mouse to outline cells, while releasing the mouse button will complete the outline and increment the "Object Count" display at the bottom of the window.

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• SciCrunch
• 17 years ago - by Anonymous

Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided.

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• RRID
• 4 years ago - by Anonymous

Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies

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• SciCrunch
• 17 years ago - by Anonymous

Facilitates scientific research of nervous system function to enhance development and testing of novel therapeutic strategies for treatment of nervous system disorders. Provides resource capacity typically unavailable or impractical in individual laboratory. Major areas of specialization include surgical approaches to model production and assessment, behavior testing of sensorimotor functions, in vivo electrophysiological recording (EEG, EMG, ERP). Procedures are intended for mice and rats. Procedures can be developed based on client interests.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

General database of genetic variations maintained by the NCBI. Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

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• SciCrunch
• 17 years ago - by Anonymous

Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.

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• RRID
• 4 years ago - submitted by Caty Chung

Database of data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Users can search the Flu database, build queries, retrieve sequences, and apply analysis tools. This includes selecting influenza sequences by virus, subtype, host, and other criteria, finding complete genome sets, aligning sequence and others in the database (up to 1000 sequences), viewing clustering and phylogenetic trees, BLAST searching a flu sequence against the database, and more.

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• SciCrunch
• 17 years ago - by Anonymous

Provides set of services that encompass experimental design, data generation and data interpretation. Expert genomics and bioinformatics teams are available to consult and collaborate at every step of process and work closely together to develop optimized experimental strategies to ensure that appropriate technology and data analysis tools are used to address each unique scientific question.

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• SciCrunch
• 4 years ago - submitted by Cassie Sather

Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.

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• SciCrunch
• 17 years ago - by Anonymous

Supplies mononuclear cells, stem cells or other enriched cell populations. Provides stem cells and other tissue samples from normal donor or patient populations such as disease specific repositories or specific research studies requiring sample processing. Samples are provided fresh or cryopreserved according to availability, unprocessed or with further lab processing.Common processing techniques include PBMC isolation,Serum and plasma isolation,Separation of marker specific populations,Flow cytometric characterization of samples,Interferon gamma EliSpot.Additional services may be available upon request

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

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• SciCrunch
• 16 years ago - by Anonymous

Facility manufactures lentiviral and retroviral vectors in support of early phase clinical trials.Services include large scale GMP lentiviral and retroviral vector and small to mid scale GMP like manufactured products. Supports certification and stability studies.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.

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• SciCrunch
• 15 years ago - by Anonymous

Software R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

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• RRID
• 4 years ago - by Anonymous

Database of human histone variants, sites of their post-translational modifications and various histone modifying enzymes. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. HIstome is a combined effort of researchers from two institutions, Advanced Center for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai and Center of Excellence in Epigenetics (CoEE), Indian Institute of Science Education and Research (IISER), Pune.

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• SciCrunch
• 15 years ago - by Anonymous

Provides support for design, execution, and analysis of experiments involving Next Generation Sequencing through access and use of Illumina HiSeq 1500. Sequencer performs wide range of analysis including target preparation for RNAseq, Exome Seq, ChIP seq, Methyl Seq, whole genome sequencing, and small RNA sequencing.Core is involved in all aspects of Nanopore sequencing.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

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• SciCrunch
• 14 years ago - by Anonymous