The NIH Library has secured licensing for a wide range of bioinformatics resources. The complete list is below. If you would like to recommend additional resources, please send your requests to Dr. Bhagwat.

Licensed Resources

ArrayStar QSeq

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 to ArrayStar QSeq is for NIH staff and requires a user account. The NIH Library has purchased 1 static license associated with a dedicated bioinformatics computer available to patrons in the NIH Library Reading Room.

CLC Genomics Workbench

CLC Genomics Workbench is software for analyzing and visualizing next generation sequencing data. Its funcitonality 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.

Access to CLC Genomics is for NIH staff and requires a user account. The NIH Library has purchased 1 static license associated with a dedicated bioinformatics computer available to patrons in the NIH Library Reading Room.

Eureka! from GeneGo

Eureka! provides a simple one-button one-window access to GeneGo's manually curated databases. Users can query the database with gene, protein, compound, drug names, diseases, and processes, pathological or toxic categories in a free text format. The results, ranked based on relevance, will present all categories of information and data from the database and links to external databases including third party vendors.

Access is provided at http://nihlibrary.nih.gov/ResearchTools/Pages/Eureka.aspx.

GeneIndexer by ComputableGenomix

GeneIndexer is a next-generation search engine developed specifically for genomic researchers. Using all gene and genomic-related papers collected by the National Library of Medicine, GeneIndexer offers a very fast method for confidently compressing a large gene list to a handful of research targets. Powered by patent-pending, next-generation, text-mining technology, GeneIndexer rapidly interrogates the scientific literature to extract both explicit and implicit gene associations. It then ranks these genes with respect to any user defined keyword query, identifies gene neighbors and gene hubs, and determines the overall functional cohesiveness of any group of genes.

Individual registration and login required. Please go to NIH GeneIndexer page and enter the following code in the license field: f6286-941c1-706a during the account registration process.

GeneSpring

GeneSpring – 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.

The NIH Library has two floating licenses for GeneSpring for NIH staff and 1 static license for a dedicated bioinformatics computer in the NIH Library Reading Room.

Genomatix

The NIH Library has purchased 1 floating license for Genomatix Software Suite for NIH staff. It allows researchers to perform a number of tasks such as:  conducting a scientific analysis of genomic data, gene regulation and expression; generating and evaluating networks and pathways; performing extended literature searches, sequence analyses and extraction; and visualizing comprehensive genome annotation.

Access requires a user account, which is linked to your NIH email address. Please go to the Genomatix registration page to sign up for an account. If you do not get a response within two business days, please contact Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

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. 

Access is provided at https://portal.biobase-international.com/cgi-bin/portal/login.cgi/. Individual registration and login required. Enter the code 1881-6975-97565225 in the license field during the account registration process.

Ingenuity Pathways Analysis (IPA)

Ingenuity is a web-based bioinformatics tool created by Ingenuity Systems that allows researchers to search, analyze, and graphically view molecular interactions, biological functions, and diseases. Access to Ingenuity is for NIH staff and requires a user account, which is linked to your NIH email address. The NIH Library has purchased 3 floating licenses for Ingenuity Pathways Analysis. Access is available for PC and Mac platforms. Please go to IPA registration page to sign up for an account. If you do not get a response within two business days, please contact Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

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.
Access to Lasergene is for NIH staff and requires a user account. The NIH Library has purchased 1 floating license for Lasergene and 1 static license associated with a dedicated bioinformatics computer available to patrons in the NIH Library Reading Room. Access is available for PC and Mac platforms. Please go to the LaserGene registration page to sign up for an account. If you do not get a response within two business days, please contact Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Metacore from GeneGo

The GeneGo flagship bioinformatics product in systems biology, MetaCore, provides tools to analyze data such as microarray gene expression, SNPs, metabolic profiles, high content screening (HCS) assays to identify the most relevant pathways, networks and cellular processes. It also allows searching information about genes, proteins, compounds, pathway maps and diseases. The MetaCore suite works on GeneGos manually curated database of mammalian biology and medicinal chemistry.

The NIH Library has purchased 3 floating licenses for MetaCore for NIH staff. Access requires a user account, which is linked to your NIH email address. Please go to the GeneGo registration page to sign up for an account. If you do not get a response within two business days, please contact Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

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.
Access to Partek is for NIH staff and requires a user account. The NIH Library has three floating licenses for Partek and 1 static license associated with a dedicated bioinformatics computer available to patrons in the NIH Library Reading Room. Access is available for PC, Mac, and Linux platforms. Please go to the Partek registration page to sign up for an account. If you do not get a response within two business days, please contact Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Pathway Studio from Ariadne

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.

The NIH Library has purchased 2 static licenses associated with dedicated bioinformatics computers available to patrons in the NIH Library Reading Room.

Protein Lounge

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 to the ProteinLounge Pathway Builder is provided by an NIH Library license (NIH only access).

SeqMan NGen

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.
Access to SeqMan NGen is for NIH staff and requires a user account. The NIH Library has purchased 1 floating license for Lasergene and 1 static license associated with a dedicated bioinformatics computer available to patrons in the NIH Library Reading Room. Access is available for 64-bit PC and Mac platforms. Please go to the SeqMan NGen registration page to sign up for an account. If you do not get a response within two business days, please contact Medha Bhagwat, Bioinformatics Support Program Coordinator at the NIH Library.

Additional Bioinformatics Resources

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 NIHL Collection

Bioinformatics Journals in the NIHL Collection

Bioinformatics Databases in the NIHL Collection

Bioinformatics Online Books in the NIHL Collection

Bioinformatics Internet Resources Linked from the NIHL Collection

Bioinformatics Main