The PacBio Single Molecule Real Time (SMRT) analysis portal is an easy-to-use web-based platform for analyzing 3rd generation sequencing data generated from the PacBio SMRT platform. Currently, workflows for microbial whole genome assembly, resequencing analysis, transcriptome analysis and various data processing steps are available through the portal. For more information on the analysis portal itself, see http://www.pacb.com/devnet/ and the tutorial
Python is a high level programming language that aims to combine remarkable power with very clear syntax. Anaconda is a free cross-platform Python distribution from Continuum Analytics. It comes built in with various scientific Python packages such as NumPy, SciPy, Pandas, Matplotlib, Numba, etc.
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.
Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. Circos is flexible. Although originally designed for visualizing genomic data, it can create figures from data in any field.
Python is a high level programming language that aims to combine remarkable power with very clear syntax. The Enthought Python Distribution is a cross-platform environment for scientific computing in Python, and includes the Canopy IDE and package manager. MSI has installed an academic-licensed version that includes hundreds of modules, including tools that enable efficient parallel computations.
Origin is an easy-to-use data analysis and graphing software used by over 100,000 scientists and engineers worldwide.
Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. It includes tools for segmentation, rendering, registration of MRI, CT, US, nuclear medicine, and microscopy images.
Octave (a.k.a GNU Octave) is a open source computational software built to be compatible with Matlab. It is a interpreted language which provides commands that can be used to perform matrix manipulation, linear algebra, plotting, performing differentiation and integration, optimization, statistics and many more.
Avizo software is a powerful, multifaceted tool for visualizing, manipulating, and understanding scientific and industrial data.
VolView is an intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data on a standard PC. Users can easily generate informative images and navigate the data for further analysis. 3D tools include composite and MIP volume rendering, contouring, cropping, and oblique reformatting. Segmentation can be performed, and resulting structures can be analyzed using distance, angle, surface area and volume measurement tools. Polygonal surface models can be exported for rapid prototyping.
PyMOL is a Python-enhanced molecular graphics program. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. It also has a number of third party plugins available. Currently installed third party plugins at MSI are: Caver v2, Mole, and EMovie.