NIH Library Services Bioinformatics Analysis Tools and Databases

Analysis Tools and Databases

The NIH Library has secured licensing for a wide range of bioinformatics resources. The complete list and licensing information is below. 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 send your requests to Dr. Medha Bhagwat.

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 are dedicated to high high-throughput data analysis such as next generation sequence (NGS) data analysis or microarray data analysis.

Hardware Specifications

  • Workstation 1: Windows 7, 64-bit, 192 GB RAM, 8 cores, and 2 TB Storage
  • Workstation 2: Red Hat Linux 6, 64-bit, 512 GB RAM, 28 cores, and 24 TB Storage
  • Workstation 3: Windows 7, 64-bit, 64 GB RAM, 8 cores, and 2 TB Storage
​Loaded on each workstation is a link to the Bioinformatics Support Program portal, Cn3D, Cytoscape, and JMP. Other applications are unique to each workstation, see the descriptions below:

  • Workstation 1: BRB-ArrayTools, Cn3D, Cytoscape, JMP, Partek Genomics Suite, Partek Pathway
  • Workstation 2: CLC Biomedical Genomics Workbench, Cn3D, Cytoscape, JMP
  • Workstation 3: Cn3D, Cytoscape, DNASTAR - ArrayStar/QSEQ, Lasergene, SeqMan/NGen, GeneSpring, Genomatix Genome Analyzer, Golden Helix SNP and Variation Suite, JMP, Pathway Studio, Simmune, and VarSeq

Workstation Reservations

The workstations are located in the main Reading Room on the first floor of the Library (in Building 10). To reserve a workstation, please use our online reservation service, call the NIH Library at 301.496.1080, or visit the Information Desk.

Licensed Resources

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

ArrayStar QSeq (1 static license available on Workstation 3)
ArrayStar is software from DNASTAR for analyzing gene expression data. It also provides visualization tools and gene ontology integration. The library's license includes QSeq with ArrayStar for RNA-Seq, ChIP-Seq and miRNA analysis.

Access requires a user account.

CLC Biomedical Genomics Workbench (1 static license available on Workstation 2)
CLC Biomedical 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.

GeneSpring (2 floating licenses; 1 static license available on Workstation 3)

The uses of GeneSpring include visualization and analysis of expression data and genomic structural variation data. Statistical analysis and gene annotation updates are also provided. Examples of expression data are one and two color microarray data, quantitative real time PCR, and serial analysis of gene expression (SAGE) data. An example of genomic structural variation data is copy number data.

Access requires a user account. Sign up on the GeneSpring registration page. If you do not get a response within two business days, please contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Genomatix Genome Analyzer (1 static license available on Workstation 3)
Genomatix Genome Analyzer accepts aligned reads from next generation sequencing experiments: ChIP, RNA, DNA, methylation, and small RNA. It provides visualization and interpretation, including generating and evaluating networks and pathways; performing extended literature searches, and sequence analyses and extraction.

Access is via Workstation 3 which can be reserved online: http://nihlibrary.libcal.com/booking/bioinfo_workstations

Golden Helix SNP and Variation Suite (1 static license available on Workstation 3)
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.

Access is via Workstation 3 which can be reserved online: http://nihlibrary.libcal.com/booking/bioinfo_workstations

Human Gene Mutation Database Professional (Web Application) 
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.

Access requires a user account. Sign up on the BioBase Biological Databases page and enter the code 1881-6975-97565225 in the License Key field during the account registration process.

Ingenuity Pathways Analysis (IPA) (3 floating licenses)
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.

Access requires a user account which is linked to your NIH email address. Sign up on the IPA registration page. If you do not get a response within two business days, contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

IngenuityVariant Analysis (IVA)​ (Web Application) 
Human variant call format (VCF) files can be uploaded to IVA for identification as causal. Annotation of the variants using the Ingenuity Knowledge Base built on both human and computer curated literature and other databases facilitates the exploration of the functionality of the variants.

If you already have an IPA account, you can have IVA added to that account; otherwise, please register for a new account.  Both can be accomplished on the IVA registration page.  If you do not get a response within two business days, contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Lasergene (1 floating; 1 static license available on Workstation 3)
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.

Access requires a user account. Sign up on the LaserGene registration page. If you do not get a response within two business days, contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

MetaCore and Genomic Analysis Tools (3 floating licenses)
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.

Access requires a user account which is linked to your NIH email address. Sign up on the MetaCore registration page. If you do not get a response within two business days, please contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Partek Flow (Web Application)​.
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 to the NIH Library license for Partek Flow requires two accounts.  1) Obtain a Helix Systems Account by follwing these instructions.  2) Sign up on the Partek Flow registration page.  If you do not get a response within two business days, please contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Partek Genomics Suite (3 floating licenses; 1 static license available on Workstation 1)
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.

Access requires a user account. Sign up on the
 Partek registration page. If you do not get a response within two business days, please contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Access to Partek Pathway is included in the Workstation 1 license.

Pathway Studio (1 static license available on Workstation 3)
Ariadne's Pathway Studio is pathway analysis software for interpreting gene expression and other high throughput data; building, expanding and analyzing pathways; finding relationships among genes, proteins, cell processes and diseases; and drawing pathway diagrams. 

Protein Lounge (Web Application) ​
ProteinLounge is a collection of many interactive web-based databases and tools to help the life scientists access and analyze gene/protein data. The databases include Pathway Database, siRNA Database, Peptide-Antigen Database, Protein Interaction Database, Kinase-Phosphatase Database, Transcription Factors Database, Disease Genes Database, Biochemical Compound Database and Protein Database. The analysis tools include Pathways Builder Tool, Protein Hydroplotter, Peptide Finder, Easy siRNA, Clone Easy and Protein Vision.

Access is provided by an NIH Library license (NIH only access).

SeqMan NGen (1 floating; 1 static license available on Workstation 3)
SeqMan NGen is used for assembly of next generation sequencing data, including target resequencing, small genome assembly, and de novo transcriptome workflows. It currently has a limit of around 15 million reads, depending on read length. SeqMan NGen is available for 64-bit PC and Mac platforms.

Access requires a user account. Sign up on the SeqMan NGen registration page. If you do not get a response within two business days, please contact Dr. Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

VarSeq (1 static license available on Workstation 3)
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.

Access is via Workstation 3 which can be reserved online: http://nihlibrary.libcal.com/booking/bioinfo_workstations

NIH Library Resources

Search results from these sets are not comprehensive. Additional resources may be available from the NIH Library collections.

All Bioinformatics Research Tools in the NIH Library Collection

Bioinformatics Journals in the NIH Library Collection

Bioinformatics Databases in the NIH Library Collection

Bioinformatics Online Books in the NIH Library Collection

Bioinformatics Internet Resources Linked from the NIH Library Collection

External Resources

Automated Discovery and Categorization of Computational Molecular Biology Resources 

Computational Molecular Biology at NIH and Beyond - Manually curated through 2009

Portal Usage Data

NIH Library Bioinformatics Portal Usage (January 2011 - September 2011)

Bioinformatics Main​​​​​​​

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