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/

Spontaneous Publication of Raw Research Data

Jean-Claude Bradley — Thu, 01 May 2008 15:46:18 -0700

Description

Despite the lack of extrinsic motivating factors, such as formal publication recognition or financial gain, some researchers have been attempting to post the raw data of their experiments using any means available, and often involving considerable work and care. (1)

Virtually every researcher has been doing this in a different way, reflecting not only differences between fields but also how the information is represented within each individual's mental framework. (2)

This is a clear signal that information wants to be free, or at least that is how it is behaving.

Going forward I would expect an increase in data sharing, irrespective of any change in the scientific research reward structure. I do not expect a single standard representational system to emerge quickly. It seems more likely that the data will be posted first, then later duplicated and converted to adhere to the conventions of various databases as they arise.

Redundant data has survival value.

As a recent example, Frank Gibson writes (3):

Several months ago - about 3, I made a public commitment to make the data I have generated during my Phd open and available online. Well I have not ignored this and in the interim I have been investigating various ways I can do this. Not only do I want to make it available but I want to structure it in a standard form, namely the gelML format. In addition, I was involved in developing it the specification and therefore, I have somewhat an obligation to use it. As it is an XML transfer format I needed to be make changes and revision it, like developing code, so in that sense recording the data on a wiki or blog would not be appropriate. For this reason I have chosen to create a google code project for gel electrophoresis data and do everything in subversion. You can browse the subversion repository or check it out anonymously. The geML file that will eventually (as its still very much a work in progress) contain the data is here. As I am doing this, I though I might as well publish my lab book while I was at it. This will be done using LateX and the pdf that gets generated can be found here.

Future of chemistry

Source

1) http://www.michaelbarton.me.uk/2008/04/relection-on-ons/
2) http://blog.openwetware.org/scienceintheopen/2008/04/29/protocols-for-open-science/
3) http://peanutbutter.wordpress.com/2008/04/30/open-ed-gel-electrophoresis-data/

open notebook science

Web services for chemoinformatics

Description

Source

Spontaneous Publication of Raw Research Data

Description

Source