Macs in Chemistry

Insanely Great Science

Vortex does Biology


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.


BioBlocks:Programming protocols in biology made easier


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


Parallel CompuCell 3D


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.


Biology Applications for MacOSX


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.


Cytoscape 3.1.1