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Monitoring Bulletin – June 2020

This bulletin is prepared by the Datacc’ project team. It is a prototype in preparation for the future launch of a newsletter.

What’s new in your disciplines.

Chemistry preprints. In an article entitled “The Rise of Preprints in Chemistry”, published in Nature Chemistry, François-Xavier Coudert, research director at the Paris institute of chemistry recounts the growth of this practice despite the discipline joining the arXiv twin platform – known as ChemrXiv – as recently as 2017. In physics, preprint servers began way back in 1991. Computational, material and organic chemistry account for half of the preprints published in ChemrXiv. The author explains that this platform supports data linked to publications in machine-readable formats to facilitate reuse. This is more developed than traditional supporting material, usually communicated in PDFs and backed up by a journal article.

Geochemistry publications cost a fortune. In an article published on line on June 8, 2020, Olivier Pourret, earth-science researcher at the Institut Polytechnique UniLaSalle, outlines issues associated with publications in his field, where the total amount paid to publishers in article processing charges exceeds $7 million per year. Another article by the same author explains that these amounts “are not reinvested in the community”. “Reinvestment of the immense value of preprints in non-profit initiatives like EarthArXiv would provide enormous potential,” he explains.  

Lyon is candidate for hosting the next International Congress on Catalysis. The congress is scheduled for 2024 and Lyon’s application can be seen here. The project is led by Hélène Olivier-Bourbigou, head of the department of molecular catalysis department at the IFP in Lyon and David Ferrusseng, CNRS research director at Lyon’s research institute for catalysis and the environment.

Google takes an interest in biochemistry data. The company Mountain View has just partnered with X-chem Pharmaceuticals to facilitate the discovery of “hits” in a project called Chemome. The goal is to improve knowledge about molecules through machine learning rather than classic laboratory experimentation. 

The rising stars in chemistry and physics. In the May edition of our monitoring bulletin, we reported that China has a very high specialization index for chemistry of 1.6, compared with 0.8 for France. All ten establishments with the highest jump in the Nature Index ranking for chemistry (index specialized index in “high quality” articles) between 2015 and 2019, are Chinese. That is also the case for physics, with the exception of the University of Singapore. In 2019, the CNRS was third in the Nature Index for chemistry and physics.

The latest issue of Open Access Chemical News. The June 2020 edition is available free of charge.

Surveys and analysis

Laboratory Notebook Survey. Launched by a CNRS working group, the study investigates researchers’ practices for the conservation and traceability of their work. Survey closes: July 10.

Survey about researchers’ practices regarding digital tools. A study launched by the open science committee and organized by a research team from Université de Lyon (Mme Mariannig Le Béchec, ELICO, Urfist de Lyon) aims to reveal researchers’ practices for managing and presenting their data. The use of electronic lab notebooks is addressed. Survey closes: September 15.

44% of PhD students plan to create a start-up. This is the conclusion drawn by a study published at the end of May by Bpifrance. The highest number of survey respondents were biology PhD students, followed by chemistry PhD students.

Random data distribution.  According to a survey organized by researchers in the Montpellier area (118 respondents), 41.5% plan to distribute the data associated with their latest research project, as opposed to 36.4% who answered negatively. “Surprisingly, 22% have not yet decided if they will distribute their data,” the study concludes. 

Why do researchers publish their research results with open access? In an article published on June 22 in The Conversation, Chérifa Boukacem-Zeghmouri, IT and communications professor at Université de Lyon 1, explains the emergence of open science under the current conditions. She points out that researchers are faced with contradictory censorship. “Censorship is particularly prevalent in disciplines based on industrial partnerships (e.g. chemistry) that require confidentiality, both for research protocols, results and as a result, the data produced,” she explains.

Citations, Sci-Hub and data. A preprint published in ArXiv established a correlation between bibliometric performance publications and the use of Sci-Hub (sometimes described as “a black open-science model”). Referring to 12 journals from a variety of fields including economics and neurosciences, the authors conclude that references to articles downloaded from Sci-Hub were 1.72 times higher than others. “Apart from Sci-Hub, we also observed that, without exception, articles featuring high numbers of figures received the most references.

From the institutions’ point of view

The CERN’s roadmap. The CERN counsel has updated their roadmap after two years of discussion. Priorities include a study of the Higgs boson. It shows the evolution of the European strategy for particle physics. The document also details the consequences of CERN studies on a number of research areas: medical and biomedical technology, aerospace applications, cultural heritage, artificial intelligence, energy, massive data and robotics

Declaration about open science. Published on June 29 by the main research funding bodies (ANR, Inserm, Ademe, Anses, INCa, ANRS), the declaration recommends the adoption of a data-management plan for all projects they fund. 

Increase research budgets, but to what end? The bill for programming research over multiple years is on the agenda of the ministerial meeting of July 8. On June 5, academic societies, including the French chemistry and physics societies addressed an open letter to minister Frédérique Vidal. They say, “an increase in the ANR budget will have no effect on the three main problems in laboratories: lack of permanent staff, lack of recurring funding and lack of visibility in the medium and long term research strategy”.


Biostatistics tool. In this preprint cosigned by Boris Hejblum (Université de Bordeaux), the authors propose “a state of the art of reproducible research in the biostatistics field”. Several tools are cited, including Labkey and Copo project. Labkey is an open-source platform for the management and sharing of standardized metadata in immunological research. The COPO project (Collaborative Open Plant Omics) platform is an intermediary between plant biology research and data warehouses. Researchers import data once and it is then distributed towards potentially relevant warehouses.

> Chemists in the Covid-19 era

Materials chemists study homemade masks. Polypropylene (often used in shopping bags) is an effective filter of very small particles, according to Stanford researchers who have just published an article on the subject in NanoLetters.

Singing lessons on Zoom. RSC continues their series of portraits. The latest features John Woodland, currently undertaking post-doctorate studies at the University of Cape Town in South Africa. His research in pharmaceutical chemistry have been stopped, but he hasn’t abandoned his hobby – music – and conducts his choir of 30 singers on Zoom. 

Key events

Data management plans: constraint or opportunity? Members of research teams funded by the ANR or H2020 and required to submit a data-management plan are invited to meet on July 7 for an on-line workshop organized by GRICAD and the Grenoble Datacc’ team. 

Deciding which data to preserve. This is the theme for the next on-line meeting planned for July 9 by the Dialogu’IST network. One presentation will focus on electronic lab notebooks. Register here.

How to write an article with “excellent” data. In this webinar, “Writing an article with excellent supporting data” Mark A. Parsons, researcher at the Rensselaer Polytechnic Institute and head publisher of the CODATA Data Science Journal asks: Does data support the article or does the article support the data? The webinar on June 22 is followed by an additional presentation on July 7 at 1pm. Register here.

Conference on open data in chemistry. The RSC organizes a conference in London on November 12.

Les Rencontres Accélérateurs 2020 hosted by CERN. The annual Rencontres-Accélérateurs is scheduled by the French physics society from Tuesday, November 17 at 1pm to Wednesday, 18 November at midday on the CERN site. At this event, participants can visit the three CERN sites.

See here for all events concerning data and the issue of reproducibility. 


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