Equipment, Software, & Tools
Film and animation software tha also allows 3D editing.
Vector graphics editor.
Graphics editing program that has a 3D plugin.
Python is an open-source, object-oriented programming language, particularly well-suited for scientific computing because of its extensive ecosystem of scientific libraries and environments. For more information, see the Python FAQ page and the Python Numeric and Scientific Wiki.
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.
NIH Library has one static license. Access requires a user account.
3D computer graphics software that is also used for designing games, film, and animation. Check out the following resources for Autodesk:
- Located: Bioinformatics Workstation 2
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.
The NIH Library has one static license. Access requires a user account.
Cytoscape is a free, open source visualization tool for modeling complex networks and integrating network points with attribute data. The program was designed for use in molecular and systems biology, genomics, and proteomics, but is also useful for creating visualizations of other types of network data. To learn more about Cytoscape, visit the Cytoscape homepage.
65" interactive digital display used to visualize and demonstration data.
Reservations are required. Reserve up to two hours daily for project work or demonstration. The interactive display is available on a first come, first served basis when not reserved.
Grant information and associated publications (if available) for projects funded by agencies across the US federal government.
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.
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.
Gephi is a free, open-source network exploration, analysis, and visualization tool. It can be used with a variety of different types of networks and complex systems, as well as to create dynamic and hierarchical graphs. To learn more about Gephi, visit the Gephi homepage.
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.
The HP Sprout is an All-in-One computer that turns your workspace in a digital-physical space.
Ask for assistance at the Information Desk or email the Technology Hub.
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(link is external) and enter the code 1881-6975-97565225 in the License Key field during the account registration process.
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.
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.
Inkscape is a free, open-source graphics program for creating and editing images in a variety of formats suitable for print and web use. Inkscape's features make it similar to Adobe Illustrator, Adobe Photoshop, and CorelDRAW. A variety of free plugins also provide additional functionality. To learn more about Inkscape, visit the Inkscape homepage.
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.
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.
Neo4J is a free, open-source graph database program. It can be used to model complex systems and networks to reveal patterns and connections. It also uses Cypher, a graph query language, to allow users to conduct complicated database queries. To learn more about Neo4J, visit the Neo4J homepage.
Use Netfabb Basic to make editing, repairing and analysing designs for 3D printing quick and easy. View, repair, and edit .STL files. Analyze and repair files to make models airtight. Make simple adjustments for proper fitting on build plate.
Grant information, associated publications, and associated patents (if available) for grants funded by NIH.
NVivo is a software program for analyzing qualitative data. NVivo allows you to collect, organize, and analyze content from interviews, focus group discussions, surveys, audio, social media, videos, and webpages. To learn more about NVivo, visit the NVivo homepage.
OpenRefine (formerly known as Google Refine) is a free, open source tool for working with messy data. With OpenRefine, users can process and clean their data, save to different formats, and upload to participating databases. To learn more, visit the OpenRefine homepage.
OpenSCAD is a software for creating solid 3D CAD models. It is free software and available for Linux/UNIX, Windows and Mac OS X. Unlike most free software for creating 3D models (such as Blender) it does not focus on the artistic aspects of 3D modelling but instead on the CAD aspects. Thus it might be the application you are looking for when you are planning to create 3D models of machine parts but pretty sure is not what you are looking for when you are more interested in creating computer-animated movies.
- Located: Bioinformatics Workstation 1
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.
- Located: Bioinformatics 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.
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.
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).
R is a programming language and environment for statistical computing and graphics. The R environment provides an integrated suite of software facilities for data manipulation, calculation and graphical display. R can import and export data in a variety of formats, both open source and proprietary, including plain text and comma-separated values (CSV), Excel spreadsheets (.XLS and .XLSX), files from a variety of statistical packages (including SAS, SPSS, and Stata), and more.
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.
CAD design software
Stata is an integrated statistical software package for data management, analysis, and visualization. Stata provides both a command syntax for users who are comfortable with scripting and a simple point-and-click interface for users who do not have experience with writing scripts. With either method, analyses are documented for easy reproducibility.
Reservations are required(link is external). Reserve up to two hours daily for project work or demonstration.
Tableau is a business analytics tool for creating a wide variety of interactive data visualizations. The software is available as a free version (Tableau Public) as well as a more robust full-scale version (Tableau Desktop).
Sci2 is a free, modular toolset designed by researchers at Indiana University for the study of science. It can be used for temporal, geospatial, topical, and network analysis, and visualizations of scholarly datasets.
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.