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MOSAIC: MOdeling and StAtistical tools for ecotoxICology

20 Juillet 2017,

Publié par Bioécologie

MOSAIC is a web interface dedicated to the mathematical and statistical modelling of bioassay data. Bioassays are conducted in ecotoxicology to measure acute or chronic effects of potentially toxic substances on reproduction, growth and/or survival of living organisms.

MOSAIC is a turnkey decision-making tool for ecotoxicologists and regulators. Without wasting time on extensive mathematical and statistical technicalities, users are given advanced and innovative methods for a valuable quantitative environmental risk assessment.

MOSAIC is developed within the Biometry and Evolutionary Biology Laboratory (UMR CNRS 5558) of University Lyon 1.

MOSAIC: MOdeling and StAtistical tools for ecotoxICology

WAMWiki: the wild animal models wiki

5 Juillet 2017,

Publié par Bioécologie

WAMwiki is an on-line resource containing information and resources for anyone interested in learning more about and applying quantitative genetic methods - but especially for those interested in using quantitative genetics in natural populations.

Recent discussions at the Wild Animal Model BienniAl Meeting (WAMBAM 3) and work on a guide to the animal model for ecologists encouraged us to set up this wiki to allow the community of researchers working on wild populations to share their experience and tips for data analysis. We chose to develop a wiki as we would like the site to act as an easy and flexible way to share knowledge.

WAMWiki: the wild animal models wiki

Base de données DoneSol (base nationale des données sols).

14 Juin 2017,

Publié par Bioécologie

L'unité InfoSol (INRA, France) mets gracieusement à votre disposition des formations à l'utilisation de la base de données DoneSol (base nationale des données sols).

Vous avez 3 formations disponibles :

- une formation technique sur la saisie des données pédologiques dans DoneSol-web. Pour plus d'informations : http://www.gissol.fr/outils/formation/formation-donesol-663

- une formation technique sur l’interrogation des données en format DoneSol pour la réalisation d’une carte thématique. Au cours de cette formation "Expert", vous établirez la carte thématique du réservoir utilisable (RU) à partir d’une carte des sols au 1/250 000. Cet exemple vous donnera les clefs pour la réalisation de toutes cartes thématiques utilisant les données stockées dans DoneSol. La prochaine session aura lieu du 5 au 6 octobre 2017. Pour plus d'informations et/ou pour vous inscrire : http://www.gissol.fr/outils/formation-expert-de-la-base-de-donnees-donesol-a-la-carte-thematique-4027

- des vidéos en ligne sur la saisie des données dans DoneSol-web : http://www.gissol.fr/outils/formations-en-ligne-videos-sur-la-saisie-des-donnees-dans-donesol-web-3638

Base de données DoneSol (base nationale des données sols).

AnaEE-France (Analyses et Expérimentations sur les Ecosystèmes - France)

6 Mai 2017,

Publié par Bioécologie

AnaEE-France est une infrastructure nationale de recherche dédiée à l’étude des écosystèmes continentaux et de leur biodiversité.

Elle met à la disposition de la communauté scientifique internationale 22 services composés de plateformes expérimentales (en milieu contrôlé, semi-naturel ou naturel), de plateformes d’analyses et d’instrumentation partagée.

AnaEE France permet aussi un accès aux données et à des plateformes de modélisation.


Les activités humaines ont considérablement altéré les milieux naturels à travers le monde et soulèvent des questions sociétales vitales telles que la fourniture pérenne de ressources biologiques et de services écologiques. Dans ce contexte, un défi scientifique majeur consiste à comprendre et prédire la dynamique de la biodiversité et des écosystèmes. Pour cela, nous avons besoin d’une véritable biologie intégrée combinant les sciences du vivant et environnementales. L’infrastructure AnaEE France « Analyse et Expérimentation sur les Ecosystèmes - France » répond à cet enjeu. Elle est coordonnée par le CNRS, l’INRA et l’Université Joseph Fourier, et constitue la contribution française au projet européen AnaEE inscrit sur la feuille de route du Forum européen sur les infrastructures de recherche (ESFRI).

The eDNA platform

6 Avril 2017,

Publié par Bioécologie

This technical platform has been set up to allow ecologists to perform large-scale analysis of environmental DNA via a metabarcoding approach. DNA metabarcoding refers to high throughput DNA-based identification of multiple species from environmental DNA. The main applications consist in diet analysis from feces, in biodiversity assessment using soil or water samples, and in palaeo-environment reconstruction using lake sediments and permafrost samples.

The eDNA platform is composed of three pre-PCR extraction rooms dedicated to feces, soil, and ancient DNA, and to several post-PCR rooms dedicated to the purification and the titration of PCR products. The next generation sequencing on Illumina platforms (HiSeq or MiSeq) is outsourced.

The eDNA platform

Writing Manuscripts: The Alternative ‘Guide to Authors’

4 Mars 2017,

Publié par Bioécologie

Post provided by EMMA SAYER


“If the reviewer doesn’t get it, you haven’t explained it clearly enough!” This is one quote from my PhD supervisor that I haven’t forgotten. Getting research funded and published depends to a very large extent on our ability to get the point across. Although scientific texts appear to differ wildly from other forms of writing, a good research paper actually follows the same basic principles of effective communication as a newspaper article or advertising text.

There are some fairly simple guidelines on presenting and structuring written information to get the point across and highlight the key messages that are very useful for manuscripts, thesis chapters, proposals, basically any kind of academic writing. At Functional Ecology, we’ve collected tips and tricks from various sources to help authors effectively communicate their research and ideas. Here are our key points:

1) Know Your Audience

A research paper is about communicating your research in a way that makes sense to others. © Vinch

A research paper is about communicating your research in a way that makes sense to others. © Vinch

The central principle for any type of communication is: know your audience. A research paper isn’t just about presenting information – it’s about communicating your research to others. When you start preparing a manuscript, you need to think about who will read it. In the first instance, this is probably a busy editor or reviewer, so you should make sure that you get your key messages across without making your readers work too hard. Good science writing isn’t about using clever-sounding words and sentences, it’s about getting the point across in such a way that readers can understand the research and reach the right conclusion (i.e. the one you want them to reach).

There are some general principles of how to get a message across and to make it stick in people’s minds. These can be adapted to science writing and remembered with the acronym SUCCES:

  • Simple — keep it simple by finding the main message and sticking to it
  • Unexpected — use the unexpected to grab the reader’s attention (eg. a knowledge gap, unforeseen consequences, an unusual feedback…)
  • Concrete — make the central concept easily grasped and remembered
  • Credible —support your interpretation and discussion with evidence
  • Emotional —stimulate interest and highlight the relevance of the study to make people care about the research
  • Story — people enjoy and remember stories, so a good manuscript is a narrative about your research, with a logical train of thought

Although you’re constrained by scientific convention and the fixed format of most journals, you can still tell a simple, concrete and credible ‘story’ (non-fiction) about your research. You can use elements of the unexpected to show the novelty of the research and help the reader remember your paper by tapping into emotion (eg. curiosity, amazement).

2) A Different Take on Manuscript Structure

The title gets people reading the paper, so it should be brief and clear, summarising the main finding of the paper (think of a newspaper or magazine headline). It’s wise to avoid questions, convoluted sentences and too much detail. The title should be simple and concrete, and it can also incorporate something unexpected. The most important part of the title should come first because the second half may not appear in a list of search results. (See also Fox & Burns 2015)

Click here to read the rest

ZEN: Eco-evolutionary Software

13 Février 2017,

Publié par Bioécologie


Figure 1
Deployment of polymorphism in a population subjected to asymmetric competition
(ZEN simulation, model from Kisdi & Geritz 2001).
The distribution of phenotypes is shown along evolutionary time in ordinates.


Ecological models with an evolutionary component allow to study several biological phenomena: host-pathogens interactions, coevolution of plants and pollinisators, mimicry, development of the immune system, evolution of cooperation, evolution of life history traits, and more generally biodiversity and speciation.

What is simulated by ZEN ? The evolution of populations under the mutation-selection process 

ZEN uses an individual-based (in fact ‘phenotype-based’) approach with 3 components:

  • Stochastic equations in discrete time describing the dynamics of finite populations
  • Adaptive traits and their mutations (mutation rates and distributions)
  •  Ecological interactions between phenotypes

During the ZEN simulation, mutant phenotypes created by the triggering of mutations interact with resident phenotypes. They persist or go extinct, possibly leading to evolutionary branching and polymorphism (Figs. 1, 2).

How does ZEN work ?

Models are described in a text file using a reduced declaration language, and studied by means of a simple interface with convenient graphics. The ZEN kernel is a symbolic evaluator handling ‘polymorphic’ variables.

More information here

The Geant4-DNA project

1 Février 2017,

Publié par Bioécologie

The Geant4 general purpose particle-matter Monte Carlo simulation toolkit is being extended with processes for the modeling of early biological damage induced by ionising radiation at the DNA scale. Such developments are on-going in the framework of the Geant4-DNA project, originally initiated by the European Space Agency/ESTEC. They are fully included in Geant4.


Microbeam irradiation of a keratinocyte (HaCaT) with alpha particles (see the « microbeam » Geant4 advanced example) - courtesy of L. Garnier (CNRS) -