Journal of Cheminformatics - Latest Comments

Sharing workflows and integrated training/validation?

Egon Willighagen — 2011-09-07T17:21:57Z

When reading the paper I was wondering if the visual aspects of workflow system can be used to visualize how model validation is performed. The current Figure 3 shows clearly that the model parameter optimization is done, and Figure 5 clearly shows that this is done prior to external validation. I assume the workflows of Figure 3 and 5 can be combined without the parameter optimization affecting the external validation. But I was wondering if it could be visualized in the same integrated workflow, how the test set extraction is done (for which you use a stratified random sampling) and perhaps the method that is used for the cross-validation? I can understand that the diversity of modeling methods may make this hard.

Another thing I was wondering is how easy it is to share AZOrange workflows with others? Can workflows be shared, for example, on MyExperiment.org? Has such been explored yet?

A minor question is about the GPL license. This is bound to be the GNU GPL license, but which version (v2 or v3)? The GitHub repository lists only the GNU LGPL v3 license, and did not answer that question either.

That leaves me you thank you for this interesting work. After Taverna and KNIME (and others) AZOrange may indeed have a high impact as python is a popular language among scientists.

Missing parts

Brad Sherborne — 2010-02-03T08:28:44Z

Hi

I'm finding it difficult to assess an alternative method on the benchmark data.
Is the part that describes how one might segregate the provided data sets into training and test sets missing from the Data section of the article which appears to start mid paragraph (Starts "other case, they are known ot elicit ..")?

Thanks in advance

Brad

References for the CDK, Blue Obelisk, and Bioclipse.

Egon Willighagen — 2010-02-03T08:28:18Z

It is also gratifying to see the
advent of open source movement in cheminformatics on the Internet, as advocated for
example by the Blue Obelisk Group (40) and witnessed by collaborative projects like
Chemistry Development Kit CDK (41), Jmol (42), Bioclipse (43) and several others.

I like to point to reader to the following papers regarding references 40, 41, en 43.

Blue Obelisk (ref 40 in the paper)
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R. Guha, M. T. Howard, G. R. Hutchison, P. Murray-Rust, H. Rzepa, C. Steinbeck, J. Wegner, E. L. Willighagen, 'The Blue Obelisk-interoperability in chemical informatics.', Journal of Chemical Information and Modeling, Vol. 46, No. 3. (2006), pp. 991-998. (doi:10.1021/ci050400b)

Chemistry Development Kit (ref 41)
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C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann, E. Willighagen, 'The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.', J Chem Inf Comput Sci, Vol. 43, No. 2. (2003), pp. 493-500. (doi:10.1021/ci025584y)

Bioclipse (ref 43)
------------------
Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Masak, Gilleain Torrance, Johannes Wagener, Egon Willighagen, Christoph Steinbeck, Jarl Wikberg, 'Bioclipse 2: A scriptable integration platform for the life sciences Export', BMC Bioinformatics, Vol. 10, No. 1. (2009), 397. (doi:10.1186/1471-2105-10-397)