Monthly Archives: February 2015

Blogroll: Coding chemistry

Posted on by
Reply

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, See Arr Oh returns to pen the March 2015 column.

———-

Why the rise of the machines is a good thing for chemistry.

No matter your research interests, I’ll bet you depend more on computers — databases, scripts, templates, macros, electronic laboratory notebooks, sketching tools, machine learning — than ever before. Luckily, the chemblogosphere has you covered.

First of all, Mark Wolf, blogging at Magic Acid, wants to help you build a grad-school dream machine — capable of mapping 3D changes in battery electrodes — for less than US$1,000. Need to learn a programming language? Then take a look at Chemistry Apprentice, who has laid out a nice (and free!) path to learn JavaScript and Python using online resources.

Next, Martin Stoermer, of the aptly-named Chemistry and Computers blog, opines on indexing open-access chemistry data. He desires a model similar to that set by physics (with arXiv) or biomedical research (with PubMed). Meanwhile, Egon Willighagen at Chem-bla-ics, makes budding programmers aware of the Royal Society of Chemistry’s efforts to promote open science. They are providing access to their databases in exchange for Wikipedia contributions.

Finally, there was a lively debate at In the Pipeline over some seemingly odd structures from a molecular dynamics paper published in Nature Chemistry. Derek took issue with an extra methylene group and a potentially unstable hemiaminal before the lead author of the study quickly confirmed in the comments that they were simply drawing errors. The discussion continued, however, with academic heavyweights Henry Rzepa and Peter Murray-Rust chiming in, calling for reforms against what they consider to be outmoded publishing customs in the Internet age.

Written by See Arr Oh, who blogs at https://justlikecooking.blogspot.com.

———-

[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the March 2015 article]

Blindingly simple

Posted on by
Reply

Double-blind peer review is now an option for manuscripts submitted to Nature Chemistry – this post from a couple of weeks ago mentioned that it was coming and provided some links for further reading.

Authors who wish to choose this option should check the box ‘Yes I do want to participate in double-blind peer review’ during the submission procedure, and ensure their manuscript is prepared in a way that does not give away their identity. Below are some instructions on how to go about ensuring that your manuscript is ready for double-blind peer review. A PDF of these instructions can also be found here.

1. Do not include names or affiliations anywhere in the manuscript file or in any of the supplementary information files. This information should be included in the cover letter and it is important that you state very clearly in which order the authors should appear on the paper in the event of publication.

2. Ensure that there is no author information in the metadata of any of the submitted files. This information is usually added automatically from the identity information on your computer. In many commonly used programmes, such as Microsoft Word, author information is displayed (and can be edited) in the ‘File’ tab under ‘Properties’.

3. When referring to your own previously published work within the paper, use neutral terminology: that is, replace phrases like ‘we have previously reported that…’ with ‘it has previously been reported that…’ or similar.

4. Do not include unpublished work in the reference list. It is a requirement of submission, however, that you alert us to any related manuscripts from your group that are under consideration or in press at other journals, or are being written up for submission to other journals. Copies of these manuscripts should be clearly marked and included as separate files with your submission.

5. The Acknowledgments section and the Author information section (including the author contributions statement, to whom requests for correspondence and materials should be addressed, and any competing financial interests statement) should be included in the cover letter and not in the manuscript file. This information should be added back into the manuscript only after the peer-review process is complete and the paper is accepted for publication.

A PDF version of a one-page guide-to-authors summary for initial submissions to Nature Chemistry can also be found here.