Equipment, Software, & Tools
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.
The free Golden Helix GenomeBrowse® tool delivers visualizations of genomic data that give the ability to see what is occurring at each base pair in samples.
GeoDa is a user-friendly software program that has been developed to support the free and open-source spatial analysis research infrastructure.
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.
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.
GrabCAD Workbench offers a full set CAD collaboration tools to ensure that engineers and partners can find the right CAD file, avoid duplicate work, and get input from everyone involved.
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.
Vector graphics editor.
InDesign is a desktop publishing software application. It can be used to create works such as posters, flyers, brochures, magazines, newspapers, presentations, books and ebooks.
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.
JAWS is a computer screen reader program for Microsoft Windows that allows blind and visually impaired users to read the screen either with a text-to-speech output or by a refreshable Braille display.
JMP is the data analysis tool of choice for hundreds of thousands of scientists, engineers and other data explorers worldwide. Users leverage powerful statistical and analytic capabilities in JMP to discover the unexpected. With JMP you can perform data analysis, data acquisition and cleanup, data visualization, reliability analysis, text exploration, statistical modeling, and it integrates with SAS, MATLAB, and R.
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.
MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python.