Philippe Grosjean

Philippe Grosjean
Université de Mons · Numerical Ecology of Aquatic Systems

PhD in bioengineering

About

58
Publications
20,851
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2,122
Citations
Additional affiliations
December 2003 - present
Université de Mons
Position
  • Professor (Full)

Publications

Publications (58)
Article
Full-text available
The transportation of live coral nubbins is a major constraint of the coral trade. Corals must be transported within a timeframe of <20 hours using concentrated oxygen to avoid high post-transportation mortality. To understand the effects of transportation water quality on coral nubbin growth and post-transportation mortality, a series of transport...
Poster
Full-text available
Coral aquaculture has been developed worldwide, for live coral trade. Considering the large distance between the importers and exporters, shipping is one of the main constraints. Transporting live coral nubbins is one of the major constraints. Corals must be transported during <20h using concentrated oxygen to avoid high post-transportation mortali...
Preprint
Full-text available
Dynamics of the subsurface (2-3 m) mesozooplankton (i.e., > 200 µm) in the Bay of Calvi (Corsica, France) were explored, combining time series (2004-2016) of 14 zooplankton groups, wind gusts, water temperature, nitrate and chlorophyll-a. Zooplankton data was obtained through image analysis. While contrasted group-specific seasonal patterns were ob...
Article
Full-text available
Dynamics of the subsurface (2–3 m) mesozooplankton (i.e., > 200 μm) in the Bay of Calvi (Corsica, France) were explored, combining time series (2004–2016) of 14 zooplankton groups, wind gusts, water temperature, nitrate and chlorophyll-a. Zooplankton data was obtained through image analysis. While contrasted group-specific seasonal patterns were ob...
Article
This work focused on the reproductive cycle and cleaning process of follicles in Mytilus gallopro-vincialis and aimed to extend knowledge of the reproductive cycles of Mytilidae. Biometric and histological measurements were taken monthly over 12 months from mussels at a polluted site, the port of Oran in Algeria. Environmental parameters were monit...
Article
Full-text available
Nearly every popular programming language comes with one or more package managers. The software packages distributed by such package managers form large software ecosystems. These packaging ecosystems contain a large number of package releases that are updated regularly and that have many dependencies to other package releases. While packaging ecos...
Presentation
Full-text available
L'Algérie est un pays côtier qui n'échappe pas aux pressions anthropiques multiples dont la pollution environnementale liée au développement démesuré de son littoral. Les contaminants notamment issus des rejets urbains, agricoles et industriels impactent de manière croissante les écosystèmes aquatiques algériens. Ainsi, au niveau de la baie d'Oran,...
Poster
Full-text available
Algeria has a 1622 km long coastal strip where a large proportion of the population and the main economic and industrial activities of the country are concentrated. Its coastal fringe therefore suffers from various degradations. In particular, the Bay of Oran is housing industrial, commercial, fishing and recreational activities, where 80% of domes...
Poster
Full-text available
Marine magnoliophytes are major primary producers in coastal benthic habitats worldwide. They play a crucial role in the global carbon cycle (one of the more efficient blue carbon wells). Hence, it is necessary to characterise the eco-systemic services seagrass meadows provide. Posidonia oceanica (L.) Delile, the main Mediterranean seagrass species...
Article
Since a couple of decades, coral aquaculture has been developed in many countries to face an increasing live coral market and to support conservation of endangered natural coral reefs. To evaluate the potentiality of community-based coral aquaculture in Madagascar, we experienced suitable farming techniques using the species Acropora nasuta and Ser...
Conference Paper
When developing software packages in a software ecosystem, an important and well-known challenge is how to deal with dependencies to other packages. In presence of multiple package repositories, dependency management tends to become even more problematic. For the R ecosystem of statistical computing, dependency management is currently insufficient...
Research
Full-text available
Au sein du service de Génie logiciel du Prof. Tom Mens, qui fait partie du Département d’Informatique de la Faculté des Sciences, nous étudions l’évolution des systèmes logiciels. Les objectifs sont d’augmenter la qualité des logiciels, de permettre aux équipes de développeurs de travailler plus efficacement, et d’optimiser le potentiel d’évolution...
Data
Full-text available
Article
Full-text available
Software ecosystems-collections of software projects developed and used by the same community-are extremely complex. Comparing them with biological ecosystems can yield new strategies for improving their effectiveness and resilience.
Conference Paper
Full-text available
This paper explores the ecosystem of software packages for R, one of the most popular environments for statistical computing today. We empirically study how R packages are developed and distributed on different repositories: CRAN, BioConductor, R-Forge and GitHub. We also explore the role and size of each repository, the inter-repository dependenci...
Conference Paper
Full-text available
Code clone analysis is a very active subject of study, and research on inter-project code clones is starting to emerge. In the context of software package repositories specifically, developers are confronted with the choice between depending on code implemented in other packages, or cloning this code in their own package. This article presents an e...
Chapter
This chapter illustrates supervised classification of objects based on features measured on digital images, as it works in R using the zooimage and mlearning packages. It focuses mainly on plankton images, but it is also usable in different but similar contexts. Plankton is a diverse community of organisms that live in aquatic environments far away...
Article
Full-text available
The design and evaluation of replicated artificial mesocosms are presented in the context of a thirteen month experiment on the effects of ocean acidification on tropical coral reefs. They are defined here as (semi)-closed (i.e. with or without water change from the reef) mesocosms in the laboratory with a more realistic physico-chemical environmen...
Conference Paper
Full-text available
The R development community maintains thousands of packages through its Comprehensive R Archive Network CRAN. The growth and evolution of this archive makes it more and more difficult to maintain packages and their interdependencies, and the existing tools that aim to help developers in this process no longer suffice. We propose maintaine R, a web-...
Article
Full-text available
High sedimentation rates have been linked to reduced coral health within multiple systems; however, whether this is a direct result of compromised coral immunity has not been previously investigated. The potential effects of sedimentation on immunity of the hard coral Montipora patula were examined by comparing physiological responses of coral frag...
Conference Paper
Full-text available
form only given. As a bioengineer and marine ecologist, I probably have a different view on software complexity and evolution than specialists in this field. The literature as well as discussion with colleagues suggests that there may well be “hidden gems” in traditional ecology for software engineers. In this presentation, I will compare a couple...
Conference Paper
Full-text available
When writing software, developers are confronted with a trade-off between depending on existing components and reimplementing similar functionality in their own code. Errors may be inadvertently introduced because of dependencies to unreliable components, and it may take longer time to fix these errors. We study such issues in the context of the CR...
Conference Paper
Full-text available
Software ecosystems, collections of projects developed by the same community, are among the most complex artefacts constructed by humans. Collaborative development of open source software (OSS) has witnessed an exponential increase in two decades. Our hypothesis is that software ecosystems bear many similarities with natural ecosystems. While natur...
Chapter
Full-text available
Research on software evolution is very active, but evolutionary principles, models and theories that properly explain why and how software systems evolve over time are still lacking. Similarly, more empirical research is needed to understand how different software projects co-exist and co-evolve, and how contributors collaborate within their encomp...
Article
Full-text available
This article presents inlinedocs, an R package for generating documentation from comments. The concept of structured, interwoven code and documentation has existed for many years, but existing systems that implement this for the R programming language do not tightly integrate with R code, leading to several drawbacks. This article attempts to addre...
Article
Our current view about the relationship between metals and bacteria in marine sediments might be biased because most studies only use ex situ approaches to quantify metals. The aim of the present research was to compare ex situ and in situ methods of metal measurement (DET and DGT--diffusive equilibration or diffusive gradients in thin-films) and r...
Article
Full-text available
A new growth model is fitted on data from reared sea urchins, Paracentrotus lividus. Quantile regressions are used instead of least-square regressions, because they are insensitive to the dimension of the measurement and accommodate more than just symmetrical distributions. Quantile regressions allow comparison of fittings on various parts of the s...
Article
Full-text available
Seven combinations of aquatic plant extracts were tested to feed juveniles of H. scabra: Thalassia hemprichii, T. hemprichii with 3 % Spirulina, Sargassum latifolium, S. latifolium with 3 % Spirulina, Thalassodendron ciliatum, Syringodium isoetifolium and organic biofilm. A control test consisted in rearing epibenthic juveniles in tank without any...
Article
Two methods are generally used to measure the adhesive strength of invertebrate larvae: direct measurement with a force transducer connected to the organisms and indirect measurement with a water flow used to dislodge the organisms. Each of these methods, however, has its drawbacks. The present study aimed to design a simple and straightforward met...
Article
Full-text available
The objective of this study was to investigate whether successive recruitment failures in the anchovy fishery in the Bay of Biscay were due to changes in the zooplankton biomass or composition. Image analysis and automatic recognition were used to analyse zooplankton samples collected during diel egg production method spring surveys from 1998 to 20...
Article
Full-text available
When Victor Hensen deployed the first true plankton1 net in 1887, he and his colleagues were attempting to answer three fundamental questions: What planktonic organisms are present in the ocean? How many of each type are present? How does the plankton’s composition change over time? Although answering these questions has remained a central goal of...
Article
Full-text available
Kell, L. T., Mosqueira, I., Grosjean, P., Fromentin, J-M., Garcia, D., Hillary, R., Jardim, E., Mardle, S., Pastoors, M. A., Poos, J. J., Scott, F., and Scott, R. D. 2007. FLR: an open-source framework for the evaluation and development of management strategies. – ICES Journal of Marine Science, 64: 640–646. The FLR framework (Fisheries Library for...
Article
Full-text available
A turbulent channel flow apparatus was used to determine the adhesion strength of the three perimetamorphic stages of the asteroid Asterina gibbosa, i.e. the brachiolaria larvae, the metamorphic individuals and the juveniles. The mean critical wall shear stresses (wall shear stress required to dislodge 50% of the attached individuals) necessary to...
Article
Identifying and counting zooplankton are labour-intensive and time-consuming processes that are still performed manually. However, a new system, known as ZOOSCAN, has been designed for counting zooplankton net samples. We describe image-processing and the results of (semi)-automatic identification of taxa with various machine-learning methods. Each...
Article
G. 2004. Enumeration, measurement, and identification of net zooplankton samples using the ZOOSCAN digital imaging system. e ICES Journal of Marine Science, 61: 518e525. Identifying and counting zooplankton are labour-intensive and time-consuming processes that are still performed manually. However, a new system, known as ZOOSCAN, has been designed...
Article
Full-text available
SciViews aims to provide a unique, polymorph object-oriented interface (called "Plug") to dierent data analysis software like R, Octave, Scilab, MAT- LAB, S-PLUS, Ox, Mathematica,...It is thus possible to develop (Graphical) User Interfaces independently of the calculation kernel and adapt them easily to other systems. Moreover, the same GUI can po...
Article
Effect of delayed metamorphosis and food ration on late (competent) larvae and postlarvae of Paracentrotus lividus were investigated. Metamorphosis of competent larvae was either not delayed or delayed from 1 up to 4 days. Larvae were starved or submitted to two different food rations of the algal species Phaeodactylum tricornutum. Larvae during th...
Article
This study assessed the use of extruded feeds, in the form of pellets, for the growing of echinoid Paracentrotus lividus within a closed-culture system. Two feed types, one with soya-bean protein, the other with both soya-bean and fish protein were compared with dried Lessonia sp. and fresh Laminaria sp, as food sources. Pellets present a very high...
Article
Full-text available
The general allometric equations for the logarithmic helicospiral can fit many extraconical shapes, but the isometric conditions traditionally used limit study only to conical growth. We present evidence to show that in real gastropod shells, the logarithmic helicospiral equations fit the suture. Poor location of the coiling axis and/or an inapprop...
Article
A starvation and then feeding method was developed to produce about 100% marketable sea urchins, Paracentrotus lividus, in 3 1/2 months. This method is needed because the reproduction cycle is desynchronized in the conditions imposed during the somatic growth stage in land-based closed systems. The major advantages of starving the animals are reset...
Article
Full-text available
Today, most sea urchins fisheries worldwide must deal with overexploitation. Better management of exploited field populations and/or aquaculture is increasingly considered necessary to sustain sea urchin production in the future. In this context, we evaluate the potential of land-based, closed-cycle echiniculture. A long-term experiment with the ed...
Article
Full-text available
In the framework of echinoid cultivation, whose objective is to succeed in continuously producing large amounts of edible sea urchins (Paracentrotus lividus) under controlled conditions (aquaculture), gonadal growth is to be optimized. Among the various parameters influencing the production of roe, the quantity of food distributed was tested for op...
Article
Full-text available
The gonad and maturity index cycles of the echinoid Paracentrotus lividus and their relations with environmental abiotic parameters are assessed after 2 years of observation in southern Brittany, France. The gonadal cycle is briefly described and eight gonadal stages are characterized. The annual cycle, the time of spawning and the period of gonada...
Article
Multimodal size frequency distribution (i.e., a few individuals growing very fast and a few individuals growing very slowly) among an originally homogeneous cohort of juveniles Paracentrotus lividus is observed in reared conditions when they are 6–24 months old. The splitting of this cohort into homogeneous size-classed subgroups results in an incr...
Article
Full-text available
An intiative aimed at providing fisheries science with a comprehensive, open source and flex- ible toolbox based on R is presented here. The FLR project is organised around a core package (FLCore) that provides the basic S4 classes for many common fisheries data types and modelling tasks. The fundamental building block is a 5-dimensional array (an...
Article
Full-text available
Rpad (http://www.rpad.org) is an open-source program that provides interactive workbook- type web pages using R as the calculation engine. The R scripts that perform the calculations are embedded in the web page. All required code is embedded in a R package distributed on CRAN. The following topics are discussed: Server-side functionality. The serv...

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Projects (2)
Project
Project
This interdisciplinary research project aims to use techniques, mechanisms and ideas from ecology and natural ecosystems to better study, understand and support the evolution of software ecosystems.