Saturday, 29 March 2014

Biology resources in UBUNTU

Biology resources in EDUBUNTU
Prepared by
M.Sc., M.Ed., JRF & NET
Lecturer in Physical Science, Arafa Institute for Teacher Education
Attur, Thrissur.

A large number of applications for Science (Biology) Education including PhET, BioPerl, ClustalW, Emboss, Muscle etc are included in Edubuntu. More over a number of biological resources for secondary school students are added to EDUBUNTU as a part of  IT@ school project. These includes Biological teaching resources for secondary level, 3D pictures, animations etc of Human body, (Lungs, Heart, blood cells etc) various plants and animals.
1)     PhET: PhET is a suite of research-based interactive computer simulations for teaching and learning physics, chemistry, biology, maths, and other sciences. PhET simulations can be run online or downloaded for free from the PhET website. The simulations are animated, interactive, and game-like environments where students learn through exploration. They emphasize the connections between real-life phenomena and the underlying science, and help make the visual and conceptual models of expert scientists accessible to students. PhET simulations are primarily developed for and tested with university and high school students, but have been found to be educational and fun for students of all ages.

More over a number of resources useful for biologists is also available in UBUNTU.

 BioPerl  - a collection of Perl modules that are useful for programmers in bioinformatics/biology.
 Clustalw - This program performs an alignment of multiple nucleotide or amino acid sequences.
 Emboss - a suite of bioinformatics tools.
 Muscle - A program for multiple alignment of protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation.
 Phylip  - A Package of programs for inferring phylogenies.
 Tree View X  - Tree View X is an open source program to display phylogenetic trees on Linux, and Windows platforms.
 Tree-puzzle  - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
 DIALIGN2 - a command line tool to perform multiple alignment of protein or DNA sequences.
  UGENE  - an integrated bioinformatics suite with handy visual interface. Integrates tool for  multiple sequence alignment, protein secondary structure prediction and others.