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Basic Science Resources and Collections: Databases / Tools

A collection of basic science resources of interest to researchers and students.

Databases and Other Tools

REGISTER TO Ingenuity Pathway Analysis (IPA) an online software for the analysis of omics data. It is supported by a manually-curated knowledge base obtained from the peer-reviewed biomedical literature, public and private databases. With IPA you can identify relevant biomarkers, contextualize metabolomics, proteomics, toxicogenomics, and transcriptomics data, and perform network analysis among others. Login to IPA (once you are registered)

REGISTER TO ACCESS MetaCore (Thomson Reuters) MetaCore is an online software based on manually-curated knowledgebase of transcription factors, receptor/ligands, kinase, drugs from the biomedical literature. MetaCore can be used for the functional analysis of the NextGen sequence data, CNV, microarray, proteomics, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data. Login to MetaCore (once you are registered)

REGISTER TO ACCESS Partek Flow. This software is used for the analysis of next generation sequencing data including RNA, small RNA, and DNA sequencing. It has a user-friendly graphical interface that allows to build your own custom analysis pipelines for Alignment, Quantification, Quality control, Statistics, and Visualization. Login to Partek Flow (once registered)

REGISTER TO ACCESS Qlucore Omics Explorer facilitates a dynamic, visualization-guided analysis of OMICs data, applicable to various phases of a discovery cycle. With Qlucore you can: visualize, QC, apply statistics, create publication-ready graphics: 3D Principal Component Aanalysis, heatmaps and various 2D plots. GSEA and GO are available for biological exploration. Use valuable public data (TCGA, GEO) to test your ideas, or generate/narrow new hypotheses, with an easy download and integration into your data analysis.

BIOBASE Knowledge Library ( TRANSFAC ) The BIOBASE Knowledge Library™ (BKL), an expanded version of the Proteome Bioknowledge Database, is a collection of gene-regulation and protein oriented scientific databases created from the peer-reviewed scientific literature. The TRANSFAC®, and PROTEOME™ products are included in BIOBASE. If you do not have an accont, please REGISTER TO ACCESS tTRANSFAC AND PROTEOME leave the field for the Key empty.

The Human Gene Mutation Database (HGMD) contains comprehensive data on published human inherited disease mutations. The online interface enables quick look up of individual mutations and advanced search applications for identifying all published mutations known to be associated with a particular gene or disease, that disrupt a splice donor or acceptor site, result in a specific amino acid change and much more. Off-campus connection requires VPN  

BioCyc is a genome and metabolic pathway web portal covering more than 5500 organisms. It enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. In addition, it has online tools for browsing metabolic/regulatory networks, gene, metabolites within the networks, examine the connectivity of the network, and other functionalities. 

SciFinder Scholar is the interface to the following databases: Chemical Abstracts, CASReact, Registry, CHEMCATS, and Medline. The SciFinder Scholar interface allows users to search these databases using a chemical structure, chemical reaction, research topic, and author information. Registration is required to use this database.

Yale Research Accelerator

YCCI Research Accelerator logo The YCCI Research Accelerator is designed to facilitate scientific collaboration and resource sharing throughout Yale and beyond. Researchers can share and discuss data, reagents, human samples, laboratory protocols, validated antibodies, cell lines, research projects and more.  The Accelerator can be modified to work with researchers in professional organizations as well.   Check it out!

Biomedical Sciences Research Support

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Rolando Garcia-Milian
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