Just saw an interesting article "CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments" DOI.

Integrative computational modeling is currently the method of choice for studying the detailed mesoscale molecular structure of cellular environments. However, current methods are highly compute intensive and require extensive and diverse domain knowledge. We have developed an interactive mesoscale illustration method, cellPAINT, that allows non-expert users to create mesoscale models that integrate a variety of biological data. CellPAINT uses the approach of popular digital painting software, providing users with a palette of “brushes” to paint molecules and infrastructure into a mesoscale scene, and coloring tools and visual filters to customize the rendering. CellPAINT also incorporates a variety of mesoscale properties, such as an interactive temperature slider that controls diffusive motion and interaction of proteins within membranes. The current release allows creation of scenes with an HIV virion, blood plasma, and a simplified T-cell.

The software can be downloaded from Sourceforge

 

I was at the Dotmatics UGM recently and they gave an insight into some of the future directions. One of the areas under consideration is the use of Vortex support for Biological data analysis.

Vortex is a very high performance data analysis and plotting tool, capable of handling many millions of rows of data. It also has chemical intelligence built in, allowing structure-based searching, physicochemical properties calculation, clustering and match pair analysis.

The support for biology is a new addition and I've written a brief review here.

Added to the growing list of software reviews.

 

The increased use of robotics and automation in experiments is rapidly developing field but coding the experiments can be a tedious and require expert programming knowledge. A recent publication “BioBlocks: Programming protocols in biology made easier” DOI describes a simple drag and drop web interface.

Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments.

The Software, Tutorials and Code available on the webpage http://www.lia.upm.es/index.php/software/Bioblocks.

 

I've been asked if I could give a mention of Parallel CompuCell 3D, a multi-scale, multi- cell simulation environment.

There is a listing of publications describing the use of Parallel CompuCell 3D here.

 

I’ve been asked if I could include some biology/bioinformatics tools in the alphabetical listing, and I’m happy to add any that are sent to me, this week I’ve added.

CellDesigner

Cytoscape 3.1.1

GenomeBrowse

VarSeq