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Analysis Tools & Databases

The NIH Library has secured licensing for a wide range of bioinformatics resources. The licenses are either floating (access is provided from any NIH computer) and/or static (access is provided from one of the NIH Library Bioinformatics workstations). If you would like to recommend additional resources, please submit a request.

NIH Library Bioinformatics Workstations

The Bioinformatics Support Program provides three workstations to NIH staff that offer access to licensed and open source bioinformatics software programs. These workstations, located in the main reading room, are dedicated to high-throughput data analysis such as next generation sequence (NGS) data analysis or microarray data analysis. To use a workstation, reserve online, call the NIH Library at 301-496-1080, or visit the Information Desk.

Workstation Hardware
1 Windows 10, 64-bit, 768 GB RAM, 8 cores, and 12 TB Storage
2 Red Hat Linux 6, 64-bit, 512 GB RAM, 28 cores, and 24 TB Storage
3 Windows 10, 64-bit, 768 GB RAM, x64-based processor, and 12 TB Storage

Licensed Resources

NOTE: Access to these resources are for NIH staff only.

Tool Description Access
Biomedical Genomics Workbench

CLC Genomics Workbench is software for analyzing and visualizing next generation sequencing data. Its functionality includes de novo assembly of Sanger, 454, Illumina Genome Analyzer and SOLiD data and also de novo assembly from a combination of these platforms. Additionally, it provides contig reports, read mapping, SNP, and DIP detection.

NIH Library has one static license (use in the library).

Reserve workstation online.

Cytoscape

Cytoscape is a free, open source visualization tool for modeling complex networks and integrating network points with attribute data.  Cytoscape can create visualizations of a variety of different types of networks, including molecular and genetic, social networks, and semantic Web.  Adding free plugins to Cytoscape also provides functionality including literature mining, network inference, topological clustering, and network comparison. 

A variety of apps extend Cytoscape's basic functionality by adding support for automatic data import, pathway analysis, and more.  For a list of free apps, visit the Cytoscape App Store. Cytoscape can read delimited text files, Excel files (.XLS and .XLSX), and network/pathway files in many common standard formats.  Several free apps also allow users to automatically download and import data from online sources like KEGG, WikiPathways, BioPAX L3.  To download network import apps, visit the Cytoscape App Store.

Reserve workspace online.

Golden Helix SNP and Variation Suite

This tool includes SNP Analysis, CNV Analysis, DNA-Seq Analysis, and RNA-Seq Analysis. Additional features are variant maps, Manhattan plots and a Python scripting interface.

Reserve workstation online.

Golden Helix VarSeq

VarSeq software streamlines the process of annotating and filtering variants obtained from next generation sequencing pipelines to find variants of interest. VarSeq simplifies the user interface and provides a scalable architecture featuring repeatable workflows, note taking and reporting, and filter parameter prototyping.

Reserve workstation online.

Human Gene Mutation Database Professional

The professional version of the Human Gene Mutation Database (HGMD) provides up-to-date information on human inherited gene mutations. It allows researchers to assess the novelty of identified gene mutations. The mutations in the database are manually curated from the scientific literature. They are mapped to the genome and can be searched by motif, type of nucleotide or amino acid substitution, and location within a splice site or regulatory region.

NIH Library patrons can Register for an account. Please make sure to use the Join Institution License tab.

Enter the code NIH-Library-Bioinformatics in the License Key field during the account registration process.

Ingenuity Pathways Analysis (IPA)

IPA is a web-based bioinformatics application that allows researchers to upload data analysis results from high-throughput experiments such as microarray and next generation sequencing for functional analyze, integration, and further understanding. This includes both microarray and RNA-Seq gene expression, miRNA, SNP, metabolomics, and proteomics data. In general, lists of genes or chemicals can be analyzed using IPA. It also has a search capability for information on genes, proteins, chemicals, and drugs and allows interactive building of networks to represent biological systems.

Register for an account using you NIH email address.

Lasergene

Lasergene provides users a full range of tools for manipulation of sequence data. Lasergene is applicable to both nucleic acid and protein sequences. Example functions operating on sequences are editing, annotating, virtual cloning, primer design, and SNP discovery. Lasergene is available for PC and Mac platforms.

NIH Library has one static license (use in the library) or register to access the floating license (use from the NIH network).

Reserve workstation online.

MetaCore and Genomic Analysis Tools

MetaCore is a web-based bioinformatics suite that allows researchers to upload data analysis results from experiments such as microarray, next generation sequencing, metabolic, SAGE, siRNA, microRNA, and screening. It provides functional analysis to identify the most relevant pathways, networks, and cellular processes in the data. Additionally, gene, protein, compound, pathwaymap, and disease searches are available. The license for the Genomic Analysis Tool is included for studying genetic variance and is particularly useful for studying a set of variants resulting from next generation sequencing experiments.

Register for an account using your NIH email address.

Partek Flow

Partek Flow is for the analysis of next generation sequencing data: RNA, small RNA, and DNA sequencing. Functionality provided is quality control, alignment, quantification, statistics, and visualization.

Access requires two accounts: (1) obtain a Helix Systems account on the Partek Flow website and (2) register for an account through the NIH Library.

Reserve workstation online.

Partek Genomics Suite

Partek Genomics Suite is used to analyze high throughput data, for example, from microarray experiments and next generation sequencing experiments. It can be used to analyze any data set with lists of values associated with identifiers and experiment factors. It has a number of clustering and statistical algorithms to aid in the visualization and discovery of patterns in large data sets. Partek is available for PC, Mac and Linux platforms.

NIH Library has one static license (use in the library) or register to access the floating license (use from the NIH network).

Reserve workstation online.

Partek Pathway

Partek® Pathway™ integrates with Partek Genomics Suite to allow you to interactively browse the KEGG database, then apply advanced statistical models for accurate results.

Reserve workstation online.

Qiagen Clinical Insight Interpret Translational (QCI-IT)

QCI Interpret Translational is a variant analysis and interpretation tool for basic and translational research involving the analysis of human genetics data and is not intended to be used for diagnostic purposes. QCI Interpret Translational evaluates genomic variants in the context of published/unpublished biomedical evidence, professional association guidelines, publicly available databases, annotations, drug label data, and clinical trials.

QCI Interpret Translational (QCI-IT) is a web-based software application and the users can log into their account using the URL given below:
https://variants.ingenuity.com/qci/ (please use the institutional email address as the username).