Avogadro: Resources

Avogadro is a free and open source, advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc.

Avogadro has features for high quality rendering, interactive tools, commands and powerful plug-in architecture. The features also include easy import of chemical files from Open Babel, multiple computational packages, crystals and biomolecules.

It is easy to install and source code is available under GNU GPL.

Link to Avogadro Spoken Tutorials

ChemCollective Virtual Lab: Resources

The ChemCollective virtual lab is an online simulation of a chemistry lab.

It is designed to help students link chemical computations with authentic laboratory chemistry.
The lab allows students to select from hundreds of standard reagents (aqueous) and manipulate them in a manner resembling a real lab.

ChemCollective virtual labs are part of National Science Digital Library (NSDL) .

Link to ChemCollective Virtual Labs Spoken Tutorials

Jmol Application: Resouces

Jmol is an open-source Java viewer for chemical structures and biomolecules in 3D. It does not require 3D acceleration plugins. 3D models created by using Jmol may be used as a teaching tool or for research in chemistry and biochemistry. It is free and open source software, written in Java, it runs on Windows, Mac OS X, Linux and Unix systems. There is a standalone application and a development tool kit that can be integrated into other Java applications, such as Bioclipse and Taverna.

Link to Jmol Web Pages:

Link to Jmol Application Spoken Tutorials

Biopython: Resources

Biopython is a collection of Python tools for computational biology and bioinformatics. Biopython contains modules and classes to represent protein sequences, nucleic acid sequences and sequence annotations. Biopython tools can perform common operations such as transcription, translation, obtain complements, reverse complements, parsing, running BLAST etc. We can use Biopython modules to access online databases such as NCBI. Biopython modules can also be used for sequence alignment, phylogenetics, sequence motifs, protein structure etc.

Link to Biopython Spoken Tutorials

CellDesigner: Resources

CellDesigner is a process diagram editor for drawing gene-regulatory and biochemical networks. Intuitive user-interface helps to draw a diagram in rich graphical representation with our own design. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano.

CellDesigner is used for

  • User-friendly visualization
  • Modeling and simulation of genetic regulatory networks
  • Protein networks and metabolic networks.

Link to CellDesigner Spoken Tutorials

UCSF Chimera: Resources

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health (NIGMS P41-GM103311). UCSF Chimera is licensed for noncommercial use at no cost by the Regents of the University of California. You must agree to the terms and conditions of use as specified in the license agreement before you will be permitted to download Chimera.

Link to UCSF Chimera Spoken Tutorials

Freeplane : Resources

Freeplane is a mind mapping or concept mapping software. Concept mapping or Mind mapping was developed for learning purposes. In a concept map, the ideas or concept is presented visually in a connected fashion with fewer words. The visual representation helps to bring about better understanding and learning.

Learning resources such as notes, text, image, web page hyperlink, audio or video can be attached to nodes. Icons and formatting can make the nodes visually stand out in a map. Teachers can use it to teach and students can use it for structured learning. Freeplane is open source and is actively developed. The official website of Freeplane is at .

Link to Freeplane Spoken Tutorials

Grace : Resources

Xmgrace or Grace, is a software for plotting graphs, with a clickable GUI to set graph properties and one of the best liked plotting software in scientific community.It is a WYSIWYG(what you see is what you get) 2D plotting tool. The program is free to download, install and use.

QtGrace fork, provides a binary for Windows OS using Qt-SDK tool. Back-end plotting of many popular scientific and engineering software use Grace. Grace is interactive and generates 2D graphs, bar charts and executes data fitting routines. Multiple graphs can be plotted on the same canvas. .

Tutorials are available at this website for user convenience