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iViS (In Vivo - In Silico) - Grand Challenge Website

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Biological Modeling Software

VisBio - A biological tool for Visualization and Analysis

Description

Screenshots

Yasara


Yet Another Scientific Artificial Reality Application
YASARA is a molecular-graphics, -modeling and -simulation package for Linux and Windows, that finally makes it really easy to answer your questions. With an intuitive user interface and support for affordable shutter glasses, autostereoscopic displays and data gloves, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs (see benchmarks). You can push and pull molecules around and work with dynamic models instead of static pictures. Because our primary goal is to advance science, all methods introduced by YASARA are described in peer-reviewed journals . You can obtain the initial stage 'YASARA View' for free, while higher stages (YASARA Model,YASARA Dynamics ) require a license fee that allows us to guarantee new developments, updates and support also in the future, independent of temporary grants. As a YASARA user, you are not limited to the role of a consumer. If you decide to share your developments with the community (macros, movies, Python plugins or just feedback), you receive credits that in turn give you free access to all stages of YASARA.

Web: Yasara
Local download link: download

   

Chimera


An extensible Molecular Modeling System
UCSF Chimera is a highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus; however, it has been completely redesigned to maximize extensibility and leverage advances in hardware. UCSF Chimera can be downloaded free of charge for academic, government, non-profit, and personal use. It includes full user documentation and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix. UCSF Chimera development is funded by the NIH National Center for Research Resources (grant P41-RR01081).

Web: Chimera
Local download link: download

   

Cn3D


3D Structures from NCBI's Entrez retrival service.
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.

Web: Cn3D 4.1
Local download link: download

   

E-Cell


Model and reconstruct biological phenomena in silico, and developing necessary theoritical supports, technologies and software platforms to allow precise whole cell simulation.
Web: E-Cell Project
Local download link: download
 
   

Cell-O-Sim


Simulation of Cell Growth - Video
Web: Cell-O-Sim
Local download link: download
 
©2004 Ioannis Elpidis / Ronan Sleep