developer

Software (mostly free software) useful for developers or activities related to the development of computer code
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 07/10/13
  • Minor correction: 07/10/13
  • Index card author: Luc Hogie (I3S)
  • Theme leader : Dirk Hoffmann (Centre de Physique des Particules de Marseille (CPPM-IN2P3))

jaseto : JAva SErialisation TOolkit

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 2013.08.30.14.13.40 - 2013.08.30
  • License(s): LGPL
  • Support: maintained, ongoing development
  • Designer(s): Luc Hogie
  • Contact designer(s): luc.hogie@cnrs.fr
  • Laboratory, service:

 

General software features

Jaseto is a Java library enabling the description of Java objects in XML, and conversely, the creation of Java object from their XML description. This process is commonly referred to as (de)serialization or (un)marshalling. It is usually employed to make the data persistent across executions, by storing the XML text on disk or into XML databases.

Other libraries such as XStream, Castor, and JAXB are other viable solutions. Compared to these, Jaseto offers a cleaner and shorter source code, better performance (its proves 10Ă— faster than Castor and XStream), a solution to some of their limitations: no need to know in advance the type of an object to be deserialized, no need to resort to annotations, no need to follow the JavaBean spec, etc.

Context in which the software is used

Jaseto is used in our lab in order to store and export graph and configuration data.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 11/09/13
  • Minor correction: 12/09/13

realtimez : Real-time diagrams generator for LaTeX in Python

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 0.0.1 - december 2011
  • License(s): BSD
  • Status: beta release, under development
  • Support: maintained, ongoing development
  • Designer(s): FrĂ©dĂ©ric Fauberteau
  • Contact designer(s): frederic@fauberteau.org
  • Laboratory, service:

 

General software features

LaTeX TikZ code generation for drawing diagrams according to temporal constraints of real-time jobs:

  • developped in python,
  • command line interface.
Context in which the software is used

Easy-to-use generation of real-time diagrams for scientific presentations.

Publications related to the software

Sûreté temporelle pour les systèmes temps réel multiprocesseurs, Frédéric Fauberteau, PhD thesis, University Paris-Est, december 2011.
http://pastel.archives-ouvertes.fr/tel-00668537

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 11/09/13
  • Minor correction: 12/09/13

rtmsim : Real-Time Multiprocessor Simulator in Java

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 0.0.2 - january 2013
  • License(s): BSD
  • Status: beta release, under development
  • Support: maintained, ongoing development
  • Designer(s): FrĂ©dĂ©ric Fauberteau
  • Contact designer(s): frederic@fauberteau.org
  • Laboratory, service:

 

General software features

Simulation of real-time multiprocessor scheduling:

  • real-time taskset generation,
  • schedulability test benchmark,
  • command line usage,
  • input/output files in XML.
Context in which the software is used

Benchmark of real-time multiprocessor scheduling algorithms.

Publications related to the software

Sûreté temporelle pour les systèmes temps réel multiprocesseurs, Frédéric Fauberteau, PhD thesis, University Paris-Est, december 2011.
http://pastel.archives-ouvertes.fr/tel-00668537

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 18/04/13
  • Minor correction: 18/04/13

PST-Cox : PSTricks library for drawing 2D-projections of regular complex polytopes

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.0 - fĂ©vrier 2008
  • License(s): LGPL
  • Status: stable release
  • Support: maintained, no ongoing development
  • Designer(s): Jean-Gabriel Luque
  • Contact designer(s): Jean-Gabriel.Luque@univ-mlv.fr
  • Laboratory, service:

 

General software features

PST-Cox is a library of LaTeX macros allowing to draw 2D-projections of regular complex polytopes. Regular complex polytopes are hyperplane arrangements satisfying certain constraints, and whose automorphism graphs are generated by pseudo-reflections (complex reflections). These objects generalize the classical Platonic solids.

Context in which the software is used

This software is used to illustrate research results (see references).

Publications related to the software
  • Briand, J.-G. Luque, J.-Y. Thibon, and F. Verstraete. The moduli space of three qutrit states. Journal of Mathematical Physics. Vol. 45. 2004. pp. 4855-4867.
  • J.-G. Luque. Invariants des hypermatrices. Habilitation Ă  diriger des recherches. I.G.M., UniversitĂ© de Marne-la-VallĂ©e. 2007.
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 18/07/12
  • Minor correction: 28/05/14

Morse : Generic simulator for robotics

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.2 - january 2014
  • License(s): BSD
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Main developers: Arnaud Degroote (LAAS-CNRS), Gilberto Echeverria (LAAS-CNRS), Michael Karg (TUM), SĂ©verin Lemaignan (LAAS-CNRS). See the full list.
  • Contact designer(s): morse-dev AT laas DOT fr
  • Laboratory, service: Technische Universität MĂĽnchen (TUM) full list

 

General software features

MORSE is a generic simulator for academic robotics. It focuses on realistic simulation of small to large environments, indoor or outdoor, with one to over a dozen of autonomous robots. It provides a set of standard sensors (cameras, laser scanner, GPS, odometry,...), actuators (speed controllers, high-level waypoints controllers, generic joint controllers) and robotic bases (ATRV, generic 4 wheel vehicle, PR2,...) used in robotics research laboratories. New components can easily be added.

Morse can use and test software components interacting through several middlewares used in robotics, including: Fiche Plume pocolibs, yarp and ROS.

One of the main design choice for MORSE is the ability to control the degree of realism of the simulation, form photo-realistic rendering for image processing to semantic levels, avoiding heavy processing to extract information.

Morse is based on the Fiche Plume Blender modelling and real-time 3D rendering environment and on the Bullet physics simulator engine.

Context in which the software is used

Academic research in robotics, development and debugging of software components, teaching,...

Publications related to the software
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 24/01/12
  • Minor correction: 24/01/12

D-LITe : framework to create and deploy distributed applications for Things

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 0.9 - juin 2011
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Equipe PASNet
  • Contact designer(s): sylvain.cherrier @ univ-paris-est.fr
  • Laboratory, service:

 

General software features

D-LITe is an universal and standardized platform to deploy the logic of a distributed application over a wireless sensor network (ie. Home Automation application). D-LITe uses 6LowPAN (IPv6 on sensors) and CoAP (REST compatible client-server protocol). The goal is to achieve quick deployments and complete reconfiguration of the behavior of the whole wireless sensor network. This is done without flashing each node.

The use of IPv6 and REST allows to abstract hardware and operating system's specificities.

Context in which the software is used

This program can be used for wireless sensor networks. The code works with Contiki and has been tested wich the COOJA simulator and on a real test bed (TelosB).

The access to each node and the logic deployment to be applied can be done with any CoAP client (coapy in Python, or copper as FireFox plugin). The complete description of SALT (the language for the description of the logic) is given on the web site of D-LITe.

Publications related to the software

D-LITe: Distributed Logic for Internet of Things sErvices.
Sylvain Cherrier, Yacine Ghamri-Doudane, Stephane Lohier, Gilles Roussel.
iThings 2011: The 2011 IEEE International Conference on Internet of Things. Dalian, China; October 19-22, 2011.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 15/12/11
  • Minor correction: 15/12/11

GMTE : the Graph Matching and Transformation Engine

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.0
  • License(s): CeCILL - freeware binary
  • Status: under development
  • Support: not maintained, ongoing development
  • Designer(s): Ismael Bouassida, Khalil Drira , Karim Guenoun
  • Contact designer(s): bouassida@redcad.org
  • Laboratory, service: ReDCAD (UniversitĂ© de Sfax)

 

General software features

GMTE, the graph matching and transformation engine is an efficient tool we have been implementing in C++ since a decade now. It is an efficient implementation of an extension of Messmer's algorithm. Our experiments show that the tool is capable of searching small and medium graph patterns in huge graphs in a short time. A computational complexity analysis of our algorithm has conducted and performant experimental results are obtained.We have also shown that, when only constant labels are considered, this complexity is similar to the complexity of UllmannÂ’s algorithm . Both pattern graph (called rule graph) and host graph have labelled nodes and edges. The rule graph labels may be totally or partially instatiated. Unification is conducted for non-instantiated labels. The tool can be used non-interactively as a C++ library providing a function that can be invoked from either a C++ or a Java main program. The tool can be used through as a C++ executable that reads rule graph and host graph description from input TXT or XML files.

Context in which the software is used

GMTE allows to execute rules to describe the dynamic evolution of architectures. It is also used to simulate the different instantiation component stages, behaviour change during implementation, migration, and other characteristics specific to the distributed systems software architecture. (Projet ITEA USENET) (self-healing web services : projet IST WS-DIAMOND).

Publications related to the software

I.BOUASSIDA , K.GUENNOUN , K.DRIRA , C.CHASSOT , M.JMAIEL
A rule-driven approach for architectural self adaptation in collaborative activities using graph grammars
International Journal of Autonomic Computing, Vol.1, N°3, pp.226-245, Mars 2010

I.BOUASSIDA , K.DRIRA , C.CHASSOT , M.JMAIEL
A model-based multi-level architectural reconfiguration applied to adaptability management in context-aware cooperative communication support systems
Working IEEE/IFIP Conference on Software Architecture & European Conference on Software Architecture, WICSA/ECSA 2009, Cambridge (Royaume- Unis), 14-17 Septembre 2009, pp.353-356

K.GUENNOUN , K.DRIRA , N.VAN WAMBEKE , C.CHASSOT , F.ARMANDO , E.EXPOSITO
A framework of models for QoS-oriented adaptive deployment of multi-layer communication services in group cooperative activities
Computer Communications, Vol.31, N°13, pp.3003-3017, Août 2008

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 18/11/11
  • Minor correction: 22/02/12

Ed'Nimbus : DNA sequence filtering

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.0 - july 2006
  • License(s): not yet chosen -
  • Status: stable release
  • Support: not maintained, no ongoing development
  • Designer(s): Pierre Peterlongo
  • Contact designer(s): Pierre.Peterlongo @ univ-mlv.fr
  • Laboratory, service:

 

General software features

The goal of this filter of DNA sequences is to filter sequences to extract some multiple repeats that full fill the specifications given by users. Ed'Nimbus can be used to find at least two repeats in a sequence, but also to find repeats in a set of sequences.

Context in which the software is used

Project HELIX of INRIA.

Publications related to the software
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 18/11/11
  • Minor correction: 18/11/11

Minbrkpts : performance testing of heuristics for the linearization of partial orders

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • System:
  • Current version: minbrkpts-1.0.0 - september 2006
  • License(s): not yet chosen - You can contact the author to get the binary file.
  • Status: internal use
  • Support: not maintained, no ongoing development
  • Designer(s): Pierre Guillon, Guillaume Blin
  • Contact designer(s): Pierre.Guillon @ univ-mlv.fr
  • Laboratory, service:

 

General software features

Linearization of partial orders.

Context in which the software is used

To get complexity results and to study the algorithmics of the problem of linearization of partial orders.
With this software we have validated research results of the following publications.

Publications related to the software
  • Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, and Nadia El-Mabrouk. Inferring gene orders from gene maps using the breakpoint distance. In, Guillaume Bourque, Nadia El-Mabrouk, editors, 4th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG'06). vol. 4205. LNBI. Montreal, Quebec. September 2006. pp. 99--112 Springer-Verlag.
  • Guillaume Blin, Eric Blais, Danny Hermelin, Pierre Guillon, Mathieu Blanchette, and Nadia El-Mabrouk. Gene maps linearization using genomic rearrangement distances. Journal of Computational Biology. Vol. 14. (4). 2007. pp. 394--407.
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 28/03/11
  • Minor correction: 21/05/19

Monolix : analysis of non linear mixed effects models

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 3.1 - 10/2009
  • License(s): CeCILL
  • Status: validated (according to PLUME), under development
  • Support: maintained, ongoing development
  • Designer(s): Marc Lavielle, Hector Mesa, Kaelig Chatel, BenoĂ®t Charles, Eric Blaudez
  • Contact designer(s): Marc.Lavielle@math.u-psud.fr
  • Laboratory, service:

 

General software features

MONOLIX is a free software dedicated to the analysis of non linear mixed effects models. The objective of this software is to perform: parameter estimation, model selection, goodness of fit plots and, data simulation.

Context in which the software is used
  • Research in statistic: University of Paris 5, 11 and 13
  • Research in pharmacology: INSERM - P7
  • Research in microbiology : INRA
Publications related to the software

SAEM algorithm

  • Delyon B., Lavielle M., and Moulines E. "Convergence of a stochastic approximation version of the EM algorithm" The Annals of Stat., vol 27, no. 1, pp 94-128, 1999.
  • Kuhn E., Lavielle M. "Coupling a stochastic approximation version of EM with a MCMC procedure" ESAIM P&S, vol.8, pp 115-131, 2004.
  • Kuhn E., Lavielle M. "Maximum likelihood estimation in nonlinear mixed effects models" Computational Statistics and Data Analysis, vol. 49, No. 4, pp 1020-1038, 2005.
  • Lavielle M., Meza C. "A Parameter Expansion version of the SAEM algorithm" Statistics and Computing, vol. 17, pp 121-130, 2007.
  • Donnet S., Samson A. "Estimation of parameters in incomplete data models defined by dynamical systems" Jour. of Stat. Planning and Inference, vol. 137, no. 9, pp 2815-2831, 2007.
  • Meza C., Jaffrezic F., Foulley J.L. "REML estimation of variance parameters in non linear mixed effects models using the SAEM algorithm" The Biometrical Journal 49, 1-13, 2007.
  • Donnet S., Samson A. "Parametric inference for mixed models defined by stochastic differential equations" ESAIM P&S, 12:196-218, (2008).

Applications

  • Makowski D., Lavielle M. "Using SAEM to estimate parameters of models of response to applied fertilizer" Journal of agricultural, Biological and Enviromental Statistics, vol. 11, n. 1, pp. 45-60, 2006.
  • Samson A., Lavielle M., MentrĂ© F. "Extension of the SAEM algorithm to left-censored data in non-linear mixed-effects model: application to HIV dynamics models" Computational Statistics and Data Analysis, vol. 51, pp. 1562--1574, 2006.
  • Jaffrezic F., Meza C., Lavielle M., Foulley J.L. "Genetics analysis of growth curves using the SAEM algorithm" Genetics Selection Evolution, vol. 38, pp. 583--600, 2006.
  • Lavielle M., MentrĂ© F. "Estimation of population pharmacokinetic parameters of saquinavir in HIV patients and covariate analysis with the SAEM algorithm" Journal of Pharmacokinetics and Pharmacodynamics, vol. 34, pp. 229--49, 2007.
  • Comets E, Verstuyft C, Lavielle M, Jaillon P, Becquemont L, MentrĂ© F. Modelling the influence of MDR1 polymorphism on digoxin pharmacokinetic parameters. European Journal of Clinical Pharmacology, 63, pp. 437-49, 2007.
  • Samson A., Lavielle M., MentrĂ© F. "The SAEM algorithm for group comparison tests in longitudinal data analysis based on nonlinear mixed-effects model" Statistics in Medicine, vol. 26, pp 4860-4875, 2007.
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