EPFL Magazine N° 29

ÉDITO

Après ses portes, l’EPFL ouvre sa science!


OPEN SCIENCE

Promoting open science

open_sommaire

A fund to support open science


Microscope-building workshops


Sharing data. All data


50 ANS DE L’EPFL

«Dès que je me sens trop à l’aise, j’ai envie d’apprendre autre chose»


ACTUALITÉS SCIENTIFIQUES

Une main artificielle combine contrôles humain et robotique

actu_sommaire

Une voie pour les métastases cérébrales du cancer du sein


Un dispositif de haute précision pour l’ophtalmologie


INTERVIEW

Eric Mazur, une onde de choc dans l’enseignement

interview_sommaire

VU ET ENTENDU SUR LE CAMPUS

Faute de mieux


EN IMAGES

L’EPFL célèbre ses 1028 nouveaux diplômés


CAMPUS

Nouvelles nominations de professeurs


La face cachée des portes ouvertes


La mobilité vers l’EPFL est de plus en plus douce


A l’EPFL, les légumes poussent dans les cafétérias


Partager sa science autour d’une bière


EN IMAGES

Enorme succès pour les portes ouvertes 2019

campus_sommaire_image

A roulette with curves and surfaces


Arsenic et vieilles dentelles


How strategic alliances benefit education


Emplois


Un masque antipollution de haute qualité pour sauvegarder la santé de millions de citadins


Le bateau léger de l’EPFL remporte l’HydroContest 2019


Deux étudiants de l’EPFL champions universitaires de triathlon


LECTURE

La sélection des libraires


CULTURE

Les défis de la construction au Bangladesh face au changement climatique

culture_sommaire

Un restoroute comme lieu de résistance?


Danses-performances au Datasquare d’ArtLab


Les événements à venir


ÉVÉNEMENTS

Les points forts des 50 ans de l’EPFL


OPEN SCIENCE

Sharing data. All data

Data and metadata generated by transmission electron microscopes exist in a format that makes them difficult to share openly. Cécile Hébert, the director of EPFL's Electron Spectrometry and Microscopy Laboratory (LSME), wants to change that.

A PhD student at EPFL’s LSME lab who came into possession of a fragment of a meteorite managed to extract the secrets of this priceless nugget using a transmission electron microscope. These bulky and relatively expensive instruments allow researchers to determine the chemical composition of natural and artificial materials down to the atomic level. The microscopes produce terabytes of data and metadata – which are just as precious as the extra-terrestrial sample analyzed by the PhD student. However, because of the format adopted by the instrument’s manufacturer, the data are next to impossible to share with the rest of the scientific community. It’s even a struggle for another LSME researcher to use them.

“These instruments are made and sold by companies that also provide maintenance services,” says Cécile Hébert. “Developments in electronics have increased the stability, resolution and accuracy of these instruments, and they are now entirely controlled by computer, including their data acquisition. This means that the suppliers develop the software, deciding which data acquisition and storage formats are used and which metadata are produced. As a result, if we turn them into open-access data, they become almost unusable.” Even when a lab owns the instrument and the software, some of the data will be recorded in the scientists’ lab books, making it hard to search for information.

“The raw data generated by the instrument must be accessible to users,” Hébert continues. “We want to develop formats and ways of distributing and documenting this data so that they are genuinely open access.” The plan is to focus initially on EPFL, so that other labs here that use microscopes can make their data openly accessible. Outside labs could eventually adopt the same approach. “If we can show the community that it’s possible, we’ll have more leverage with the manufacturers,” concludes Hébert.

Cécile Hébert, in her LSME Laboratory.

Open standard, open tools

The lab plans to hire a post-doctoral researcher to convert the data and document them with metadata. The post-doc will need to identify which metadata are important, find ways of obtaining any of those data that are missing, and document and develop tools that can do that work semi-automatically. This will result in an open standard and a system for obtaining the right metadata, along with open-access tools for reading, converting and processing data from transmission electron microscopes.

The work, which is expected to take around two years, will be funded by the Open Science Fund and the LSME’s own budget. As Hébert explains, “although this isn’t a core area of research for my lab, I started the project because I just don’t find the current situation workable.”