Typologie d'actualités: Team Theoretical and Computational Biophysics

Software is ubiquitous in science, yet overlooked

A recent article in the journal Nature Computational Science, co-authored by fourteen international authors, summarizes the many facets of software in scientific research.

At a time when the scientific world (and beyond) is talking about code, algorithms, and even artificial intelligence, talking about "software" seems to be just another semantic subtlety. Yet there are many facets of software, such as issues of licensing and file formats, that are not part of the definition of code or algorithms. The authors, humanities scholars and practitioners of scientific computing, draw attention to these facets of software that are neglected by researchers, research organizations and funding agencies alike: engineering, governance, licensing, circulation, infrastructure, embedded theory, and users.

Computational chemistry plays an important role in this analysis, because it was one of the first disciplines in which the tension between the industrial and academic approaches to quality assurance became evident. For some, software is reliable if it has been professionally developed according to the best practices of software engineering, while for others, it is the transparency and malleability of Open Source code that guarantees reliability.

See the article:
Hocquet, A., Wieber, F., Gramelsberger, G. et al. Software in science is ubiquitous yet overlooked. Nat Comput Sci (2024). https://doi-org.insb.bib.cnrs.fr/10.1038/s43588-024-00651-2

How the hydrothermal environment of Primeval Earth may have influenced the choice of sugar in DNA and RNA

CBM scientists give answers in a publication published in the Journal Nature Communications. Why is Furanose the only sugar found in the composition of DNA and RNA while this form of sugar is not the most stable, so not the most abundant, in temperature conditions and pressure we are currently experiencing? These are the hydrothermal sources, omnipresent on the surface of the primitive land, and their complex thermal influence, which could be at the origin of this selectivity. This study conducted by scientists from the Molecular Biophysics Center, which is the subject of an article in the Nature Communications journal, should make it possible to better understand why and how molecules come together to give life in a primitive geological context.

Reference

Avinash Vicholous Dass, Thomas Georgelin, Frances Westall, Frédéric Foucher, Paolo De Los Rios, Daniel Maria Busiello, Shiling Liand & Francesco Piazza
Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network
Nature Communications, 12 2749 (2021) https://www.nature.com/articles/s41467-021-22818-5

See the news on the site of the Institute of Chemistry

 




Does your ten-year-old code still run?

Computers have become indispensible tools in scientific research, and software is increasingly becoming a medium for expressing scientific models and methods. But contrary to journal articles, which are archived and remain accesssible for many decades, software is fragile and can become unusable within a few years.

CBM researcher Konrad Hinsen and computer scientists Nicolas Rougier from INRIA Bordeaux Sud-Ouest have launched a challenge to computational scientists: Can you still run code that you published at least ten years ago?

In response, the journal ReScience C, which they founded in 2015, received 28 submissions of detailed reproducibility reports, which have been summarized by a journalist for Nature.

ADOC Symposium – July 5, 2019 – CNRS Orléans

The association of doctoral students of the Center for Molecular Biophysics (ADOC) is organizing its 17th scientific symposium on Friday, July 5, 2019, whose theme is "Science Together".

This conference will take place in the amphitheater Charles Sadron CNRS.

Consult the event website

Poster

Programm

inscriptions

PhD students and post-docs are invited to present their work during a poster session. To be sent an abstract before June 25, 2019, preferentially in English (French tolerated), as well as the title and the names of the authors at the following address: cbmadoc@cnrs-orleans.fr