The modeling of cells and its compounds is an important subject of biological visualization and simulation. The CELLmicrocosmos project develops open source tools and workflows which support students and scientists of various life science-related disciplines in generating the model needed for their specific task in a user-friendly way.
The CELLmicrocosmos 2.2 MembraneEditor can be used to model membranes based on lipid and protein files in PDB format. It is possible to generate structural and compositional heterogeneous membrane patches as well as vesicles. The created structures can be used for visualization purposes, structural analysis or as a base for molecular simulations.
The attendees of this hands-on workshop will learn:
• How to acquire the information needed to generate their specific membrane
• Which data sources exist to solve their specific task(s)
• Which information is already provided by the MembraneEditor and applied to the semi-automatic membrane generation process
• How to use the MembraneEditor and its plug-in interface
• How to create renderings by exporting PDB files to Blender
• How to prepare and start a simple MD simulation in GROMACS by using the GMX-Plugin of the MembraneEditor
• How to make a structural analysis using the tool APL@Voro
All software packages utilized during this workshop are freely available and will be put to practical use. The documentation as well as the software is available at http://Cm2.CELLmicrocosmos.org.
Participants should bring their own laptop. No previous experience with modeling tools is required.
Please install Blender before the workshop starts. All participants who want to do experiments with the GMX-Plugin should install GROMACS on their Linux system.
Tags: CELLmicrocosmos, molecular modeling, tutorial, visualization, VIZBI, VIZBI 2014