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Basic Science Resources and Collections: Databases / Tools

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

Bioinformatics tools licensed by the Medical Library

REGISTER TO Ingenuity Pathway Analysis (IPA) A manually-curated knowledge base obtained from the peer-reviewed biomedical literature, public and private databases. With IPA you can do functional analysis of omics data, 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) Also based on manually-curated data/information of transcription factors, receptor/ligands, kinase, drugs from the biomedical literature. MetaCore can be used for the functional analysis of the NextGen sequence data. Login to MetaCore (once you are registered)

REGISTER TO ACCESS Partek Flow. Analysis of next generation sequencing data including RNA, small RNA, and DNA sequencing, epigenomics,, etc. 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 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, hierarchical clustering, heatmaps. GSEA and GO are available for functional analysis. Easy download of GEO datasets and analysis.

BIOBASE Knowledge Library ( TRANSFAC )  A collection of gene-regulation and protein oriented scientific databases created from the peer-reviewed scientific literature. you can do ranscription factor analysis, functional analysis, etc. 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.

REGISTER TO ACCESS Ingenuity Variant Analysis. You can identify variants and verify them. Find disease-causing variants faster by using 16+ years of expert manual curation of the scientific literature. By indexing all known disease-causing biological processes, it can deliver new insights and increased likelihood of homing in on the causal variant you’re seeking. 

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. 

Contact us

Please contact Rolando Milian for consultation on bioinformatics-related research questions and/or on how to use the bioinformatics tools licensed by the Medical Library. Consultation is provided via email, phone, in-person, and in in the form of group presentations.