Making the Case: Topological Maximum Cross Correlation

January 23, 2007

... For the Gasteiger partial charges, we took maximum values for positive and negative charges from the “fragmentlike” subset of the ZINC database, consisting of 49 134[sic] molecules, carrying out the calculation with Open Babel 2.0.0.

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... All structure handling, atom typing, and descriptor calculation was carried out using the open source Java library JOELib.

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Source code (in Java) to generate the TMACC descriptors is freely available from our Web site under the GNU General Public License at http://comp.chem.nottingham.ac.uk/download/tmacc/index.html.

James Melvile and Jonathan Hirst, J. Chem. Inf. Model.

Science happens when the experiments and conclusions of your fellow scientists can be freely questioned and independently verified. For example, readers of the cited paper may have questions about the assumptions in the TMACC method, or how to implement it. Questions may be raised about the suitability of the data set used and how others would perform. Readers may even have questions about how to extend TMACC to areas not considered by the authors.

By basing their work on open source software and open data, and by releasing their reference implementation as open source, Melvile and Hirst raise their work to the level of science. The questions that any reasonable scientist would have about the work described in the paper can be answered at any desired level of detail because all source code and all test data are freely available.

Why don't all authors adopt the same approach? Why doesn't a flagship journal such as J. Chem. Inf. Model. require it of all manuscript submissions? As far back as 1984, John Figueras was making this case. Thankfully, Melville and Hirst are taking the message seriously.