Equipment, Software, & Tools

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.

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.

The full MATLAB package includes:

Media Encoder is part of Adobe video editing suite and is responsible for encoding video files to the proper format to ensure they play on different devices.

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.

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.

Graphics editing program that has a 3D plugin.

Premiere Pro is a timeline-based video editing app developed by Adobe and published as part of the Adobe Creative Cloud. Premiere Pro is geared towards professional video editing, 

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.

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.

Base SAS includes a programming language that manages your data, includes procedures for data analysis, reporting, and managing SAS files, and a windowing environment for text editing and file management.

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.