chem-bla-ics: December 2020

Journal of Chemical Information and Modeling introduces new editorial guidelines around Open Science

This week, the Journal of Chemical Information and Modeling introduced new editorial guidelines around data and source code sharing. They basically do not change much around their open science policies: they continue want to support closed science. Well, there has to be a journal for that too, perhaps. So, what changed?

The editorial is aimed at the needs of the reviewer. With that, it puts additional stress on that the review process as sole gatekeeper of the publication process. The two or three reviewers will now have new responsibility to assess the potentially temporarily access to the data and source code. As a reader, you have to trust that those reviewers actually reviewed the data and code sufficiently.

Dec

21 Tips on how to sound #openscience

One of the things around Open Science is how some think they can use the term. To me, when I was introduced to the term, back in 1999, it was from a USA-centric view that originated from and based on the ideas of open source software: You can find this back in literature. There is even earlier literature that uses the term in a more economic context tho.

Dec

Bacting: Code coverage, JaCoCo, codecov.io, and API coverage

I have been fan of code coverage. When combined with (unit) testing, it indicates which code of your software has been run and therefore tested. Some 15 years ago, when I worked on making the Chemistry Development Kit code base more stable, I worked on various things: modularization, documentation, (unit) testing. I explored the option in Java. I even extended PMD with CDK-specific unit tests.

Dec

new: "Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?"

I do not like questions as titles of articles: you either found an answer or not. In this case, the answer is likely a maybe. The paper milestones a discussion that started some years ago with the aim to create a standardized identifier for nanomaterials. Quite ambitious. I am happy to have been invited to contribute to this discussions and paper, but can hardly take much credit. The team dit an awesome job in capturing the complexities of representation of the chemistry of nanomaterials.

Dec

Open Standards mean independence, freedom

Open Standards, or Open Specifications as I personally prefer, remove another hurdle in locked-in science. They allow others to understand your language, the nuances of your message. They mean independence, freedom. One important international standard is the Open Document Format (ODF). It is supported by all major editors (yes, MS Word too). Indeed, scholars have been quite persistent and insisting on using closed source and semi-closed solutions like .docx files.