All our software

All software packages

You find below all software developed by MaIAGE:

  • Agmial est une cha√ģne d'annotation de g√©nomes bact√©riens qui s'appuie sur un certain nombre d'outils d√©velopp√©s au laboratoire(SHOW, Prose,Pareo,...). Agmial est actuellement utilis√© pour l'annotation ou la r√©annotation de plus d'une dizaine de g√©nomes. Le logiciel est distribu√© sous licence GPL.

  • Alvis NLP/ML est une cha√ģne de traitement pour l'annotation s√©mantique de documents textuels, int√©grant des outils de traitement automatique des langues naturelles pour la segmentation en mots/phrases, la reconnaissance d'entit√©s nomm√©es, l'analyse de termes, le typage s√©mantique et l'extraction de relations. Ces outils exploitent des ressources externes, comme des terminologies ou des ontologies. AlvisNLP/ML propose plusieurs outils pour l'acquisition (semi)-automatique de ces ressources, fond√©es sur des techniques d'apprentissage automatique. La cha√ģne est facilement configurable et extensible par ajout de nouveaux composants. Ce travail a √©t√© partiellement financ√© par le projet europ√©en Alvis et le projet Quaero. Voir N√©dellec et al., Handbook on Ontology, 2009.

  • (Alvis Annotation Editor) est un √©diteur d'annotation en ligne. Il permet de visualiser et d'annoter les entit√©s et les relations d'un texte. Il inclut des fonctions de gestion de campagne d'annotation. Il permet d'annoter les entit√©s par les concepts d'une ontologie et de r√©viser l'ontologie en parall√®le. Il est int√©gr√© √† AlvisNLP. Ce travail a √©t√© partiellement financ√© par le projet Quaero. Voir LAW VI paper pour plus de d√©tails.

  • BioYaTeA is an extension of the YaTeA term extractor that deals with prepositional attachments and adjectival participle. It extracts terms from documents in French and in Eglish. Its distribution includes post-filtering of irrelevant terms. It is publicly available as CPAN module. Part of this work has been funded by the European project Alvis and the French project Quaero. See (Golik et al., CiCLING'2013) for more details.

  • BiPSim is a flexible and generic stochastic simulator of bacterial cellular processes, distributed under the GNU GPL licence. This work has been funded by the Lidex-IMSV.

  • Calculation of the Integrated flow of Particles between Polygons.
    CaliFloPP is a software that calculates flows of particles between pairs of polygons, when given a so-called individual dispersal function. The individual dispersal function describes the particle dispersion between pairs of points, and CaliFloPP deduces the total flow between pairs of polygons using an integration algorithm.

    URL : Web site

  • Matlab package for parametric identification, model comparison and optimal sequential sampling of experiments of complex microbiological dynamic systems by nonlinear filtering.

    URL : Web site

  • GGMselect is a R package dedicated to graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.

  • IDEAS is a Matlab¬ģ¬† toolbox for parameter identification of ordinary differential equation (ODE) models.¬† The parameter estimation is performed in the maximum-likelihood (ML) sense. IDEAS offers several options for the optimal criterion, depending on the¬†hypothesis on the covariance matrix of the measurement errors.
    The main feature of IDEAS is the assessment of the uncertainty of the estimates, based on the symbolic computation of sensitivity functions to evaluate the Fisher information matrix.

  • LINselect is a R package which allows to estimate the mean of a Gaussian vector, by choosing among a large collection of estimators. In particular it solves the problem of variable selection by choosing the best predictor among predictors emanating from different methods as lasso, elastic-net, adaptive lasso, pls, randomForest. Moreover, it can be applied for choosing the tuning parameter in a Gauss-lasso procedure.

  • The multisensi R package performs sensitivity analyses on multivariate model output. It calculates sensitivity indices on each output variable or on combinations of output variables arising from dimension reduction techniques.
     

  • nls2 is a set of R functions and programs to estimate the parameters of a non-linear regression model over a given set of observations.

    The regression function can be defined explicitly as a function of independent variables and of unknown parameters or it can be defined as the solution of a system of differential equations. Heteroscedasticity of errors can be taken into account by modelling the variance function.

    Several additional tools are included: plotting functions, functions to process series of estimations, calculate confidence intervals and confidence regions for parameters and functions of parameters, and process calibration study. The description of the models can be provided by using a symbolic syntax.

  • Parameter balancing is a computational method for obtaining consistent parameter sets for kinetic metabolic models. Experimentally measured values, when inserted into models directly, would be likely to yield incomplete and inconsistent parameter sets. Balanced parameter sets, computed from measured kinetic constants and other experimental data, respect constraints between biochemical quantities and assumptions about typical ranges, represented by prior values and bounds.¬† An online tool as well as Python and Matlab code are provided.

  • planor is a R package dedicated to the automatic generation of regular fractional factorial designs with one or several block systems.

  • Package R which computes sensitivity indexes by using a method based on a truncated Polynomial Chaos Expansion of the response and regression PLS, for computer models with correlated continuous inputs, whatever the input distribution. The truncated Polynomial Chaos Expansion is built from the multivariate Legendre orthogonal polynomials.
     The number of runs (rows) can be smaller than the number of monomials. It is possible to select only the most significant monomials.
     Of course, this package can also be used if the inputs are independent. Note that, when they are  independent and uniformly distributed, the package 'polychaosbasics' is more appropriate.

  • Package R which computes sensitivity indexes by using a method based on a truncated Polynomial Chaos Expansions of the response.
     The necessary condition of the method is: the inputs must be uniformly and independently sampled. Since the inputs are uniformly distributed, the truncated Polynomial Chaos Expansion is built from the multivariate Legendre orthogonal polynomials.

  • R'MES is a set of C++ programs dedicated to the identification of statistically unexpected motifs in biological sequences (DNA, protein).¬†R'MES is a free software package available under the GNU General Public License. It can be downloaded from¬†https://mulcyber.toulouse.inra.fr/projec ts/rmes/. Tutorial and user guide are available on the R'MES homepage.

  • R-package for Multidimensional Numerical Integration.

    R2Cuba is a R package which implements four general-purpose multidimensional integration algorithms: Vegas, Suave, Divonne and Cuhre. It is a wrapper around the Cuba-1.6 library by Thomas Hahn available from the URL http://www.feynarts.de/cuba/.

  • RCALI is a R package that makes interface between CaliFloPP and R.
    CaliFloPP is a software that calculates flows of particles between pairs of polygons, when given a so-called individual dispersal function. The individual dispersal function describes the particle dispersion between pairs of points, and CaliFloPP deduces the total flows between pairs of polygons.
    Moreover, RCALI allows to take into account the angle of the current point with the horizontal, and so, to analyze anisotropic dispersal function.

  • Systems Biologists combine data and models from various sources. Data often come in the form of spreadsheet or table files. SBtab is a set of syntax rules and conventions that simplify data processing and thereby facilitate data exchange. The conventions include, for example, defined column names and a syntax for semantic annotations. Models can be automatically interconverted between SBtab and SBML. SBtab is supported by software code for Python, Matlab, and R. A validation tool and a conversion to the SBML model format are available online.

  • Sensitivity indices with dependent correlated inputs, using a¬† method based on PLS regression.
    The sivipm R package computes total and individual sensitivity indices,   significant components, and confidence  intervals for the total sensitivity indices.  The total and individual sensitivity indices are calculated using a method based on the VIP of the PLS regression, proposed by J.P. Gauchi.
    The  significant components are calculated by the SIMCA software rule  and by the Lazraq &  Cléroux test.
    The confidence intervals for the total sensitivity indices are determined by the bootstrap method.