2011 CBBE Calvin College, Day 2, Session 2
Visualization and Viewers

Wikipedia is actually a decent place to start in learning about scientific visualization, and the closely related field of data visualization, of which Edward Tufte is considered a real pioneer.

Examples

• The Inner Life of the Cell


• Science In Silico at Seed Magazine, which also produces excellent cribsheets that implement good data visualization principles. (But oops, what is this?)
  
  
  • Cribsheet #18 - Biofuels
  
  
  • Cribsheet #16 - Synthetic Biology
  
  
  • Cribsheet #12 - Genetics
  
  
  • Cribsheet #10 - Photosynthesis
  
  
  • Cribsheet #7 - Extinction
  
  
  • Cribsheet #3 - Avian Flu
  
  
  • Cribsheet #2 Climate Change
  
  
  • Cribsheet #1 Stem Cells


• DNA Replication


• Mitochondria at BioVisions

Collections

• MolecularMovies.org presents an organized directory of cell and molecular animations, as well as a collection of original tutorials for life science professionals learning 3D visualization. You can use this site to get to the collections of contributing institutions and artists


• Molecules in Motion includes a 3D animation library


• Dolan DNA Learning Center Resources page includes a 3D animation library


• DNATube is a scientific site providing video based studies, lecturers and seminars.


• Reciprocal Net is repository of small molecule structures that can be viewed, the Protein Data Bank is the repository of biomolecular structures, and includes the excellent Molecule of the Month archive.

Tools and Tutorials

• The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization.


• For data visualization it's hard to beat R, as evidenced by the R Graph Gallery.


• BioBlender is a software package built on the open-source 3D modeling software Blender.


• Molecular Maya is a free software toolkit that extends Maya's capabilities by allowing users to import, build, and animate molecular structures. Maya, however, is NOT FREE it costs $3500.


• Some microphysiology movies built using MCell and DReAMM: MCell is a General Monte Carlo Simulator of Microcellular Physiology. DReAMM is a visualization and analysis program designed to read MCell visualization output of virtually unlimited size, and then let you choose what to render and with what level of detail.


• Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and for nanometer-scale spatial resolution.


• NetLogo and other simulation tools can be thought of as visualization tools as well. For example:
  
  
  • Epinephrine signaling cascade
  
  
  • PKA Kinetics Simulation


• Molecular Dynamics Software for realistic biomolecule simulation typically needs to be paired with a viewer like VMD.
  
  
  • Here is the VMD online tutorial