Web services for chemoinformatics

Andrew Walkingshaw — Fri, 02 May 2008 17:40:52 -0700

Description

Chemoinformatics algorithms are moving onto the Web, alongside the datasets they operate on.

For example, the University of Indiana provides a wide range of both data-driven and computation-driven services. Scientists don't need to download large datasets to use these, they don't need to install software, and they're easier to integrate with the rest of the Web on workflows and mashups (especially if they use the RESTful architecture style).

As the rest of the Web includes databases like the US-government-backed PubChemPubChem:

PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.

there's quite a bit of power there, potentially; Web-accessible large databases and algorithms which work on them, all without having to install anything or even provide the computational resources, and all in public.

Future of chemistry

Source

http://www.chembiogrid.org/
http://en.wikipedia.org/wiki/Representational_State_Transfer
http://pubchem.ncbi.nlm.nih.gov/

Robotic laboratories are becoming commonplace, so computational data analysis has to as well

Andrew Walkingshaw — Fri, 02 May 2008 12:29:03 -0700

Description

It's not news that robots are better at routine experiments than postdocs are: Wikipedia points out, on the page on high-throughput screening, that

Automation is an important element in HTS's usefulness. Typically, an integrated robot system consisting of from one or more robots transports assay microplates from station to station for sample and reagent addition, mixing, incubation, and finally readout or detection. An HTS system can usually prepare, incubate, and analyze many plates simultaneously, further speeding the data-collection process. HTS robots currently exist which can test up to 100,000 compounds per day (Hann 2004). The term uHTS or ultra high throughput screening refers (circa 2008) to screening in excess of 100,000 compounds per day.

No scientist can review this many results by hand, but these methods are medically and technologically very important:

High-throughput screening methods have become essential for sifting through large chemical libraries in search of drug candidates, and several sensitive and reliable analytical techniques have been specifically adapted to high-throughput measurements of biocatalytic activity. High-throughput biocatalytic assay platforms thus enable rapid screening.

So to take advantage of the advances in experimental technique, we need advances in informatics to let us deal with this torrent of data.

Future of chemistry

Source

http://nihroadmap.nih.gov/
http://en.wikipedia.org/wiki/High-throughput_screening
http://dx.doi.org/10.1016/j.cbpa.2006.02.033