Continuing MITs philosophy to support open educationally resources (MIT OpenCourseWare launched in 2002) there are some software tools and classroom materials for biology, physics and civil/environmental engineering. As part of the STAR programme staff at MIT are seeking “to bridge the divide between scientific research and the classroom”. As part of this project the MIT STAR team have been working with their faculty staff and other educational institutions to design software to explore core scientific concepts.
STAR educational tools are FREELY available. To complement our educational software, the STAR website contains curriculum components/modules which can facilitate the use of STAR educational tools in a variety of educational settings. Students, teachers, and professors should feel welcome to download software and curriculum modules for their own use.
Here is a list of the current tools on offer:
StarBiochem is a 3D protein viewer that allows students to learn key concepts in structural biology in an interactive manner. This software allows for the visualization and manipulation of many of the Protein Data Bank (http://www.rcsb.org/) molecules in a 3D environment.
StarGenetics provides a set of tools for analyzing genetic traits. This software simulates mating experiments between organisms that are genetically different across a range of traits and allows students to analyze the nature of the traits in question.
StarORF facilitates the identification of the protein(s) encoded within a DNA sequence. Using StarORF, the DNA sequence is first transcribed into RNA and then translated into all the potential ORFs (Open Reading Frame) encoded within each of the six translation frames (3 in the forward direction and 3 in the reverse direction). This allows students to indentify the translation frame that results in the longest protein coding sequence.
StarBiogene is a set of visual and analytic software tools for the analysis of genomic gene expression data generated through microarray analysis. This software allows students to compare the expression of multiple genes across a range of biological samples (cell lines, tumors, etc). For example, students can use StarBiogene to compare different patient tumor samples and identify characteristics that are common to one set of tumors based on global patterns of gene expression.
StarHydro is an application for distributed hydrological analysis. It allows the user to delineate watersheds and explore various watershed statistics.
StarHPC provides an on-demand computing cluster configured for parallel programming in both OpenMP and OpenMPI technologies. StarHPC uses Amazon’s EC2 web service to completely virtualize the entire parallel programming experience allowing anyone to quickly get started learning MPI and OpenMP programming.
StarMolsim is a collection of molecular dynamics and atomistic materials modeling research software available via the web. It enables the user to run molecular dynamics simulations on a distributed compute cluster and retrieve the results, all from a web browser.