ATGC BioInformatics Platform
IBiSA-Certified in 2010, the ATGC Platform is financed through Projets d’Investissement d’Avenir (French Government Research and Education long-term investment programs), such as: IFB (Institut Français de Bioinformatique), France Génomique, and Labex NUMEV. The platform is backed by LIRMM’s the MAB (Méthodes et Algorithmes pour la Bioinformatique) Team, and also benefits from research performed by the IBC (Institut de Biologie Computationelle).
Its three-pronged goal is: 1) to popularize bioinformatics tools designed by the Montpellier research community; 2) to foster collaborative projects between computer scientists and biologists; and 3) to support these researchers by providing them with bioinformatics services directly related to their work.
The Plaform’s software tools are available online and free of charge. They can be downloaded/executed on LIRMM clusters. They enjoy significant international traction: PhyML software (developed within the MAB teal and categorized a « Current Classic » since October 2007 by Science Watch) has been cited more than 15,000 times (in Web of Science).
The platform hosts software developed in the laboratory in the field of artificial intelligence, in particular, in the field of knowledge representation and reasoning, in the field of multi-agent systems and for the analysis and processing of visual data. These developments range from proof of concept to production.
Keywords: Knowledge representation, multi-agent systems.
Software under CeCILL Free Software License Agreement :
- GRAAL is a Java toolbox dedicated to the storage and interrogation of knowledge bases in the framework of existential rules with the Datalog +/- language.
- MaDKit is a multi-agent development platform written in Java. MaDKit is designed to build distributed applications and simulations using multi-agent functionalities.
Unlicensed software :
- DisChoco (COCONUT) is a Java library platform for distributed constraint reasoning (DCR), 2012
- AOC poset builder is a classification tool written in Java, and is also available online. It is used to build AOC posets (or Galois Sub-hierarchies), which are sub-structures of the Galois concept lattice.
- FCP-Miner (COCONUT) enables fault location based on constrained set pattern extraction, 2016
- LocGenAOC (MAREL) local generation of AOC-poset, 2018
- IBEX is a C ++ library for processing constraints on real numbers.
- COGUI (GRAPHIK) is a software developed in Java. It allows to build knowledge bases based on graphs, 2019
- Constraint Acquisition Platform (COCONUT) learns a constraint network from a set of examples and a library of constraints, 2019
- MorphoNet (ICAR) MorphoNet is an interactive anatomical browser for 3D, 3D+t segmented datasets. It provides a comprehensive palette of interaction tools to explore the structure, dynamics and variability of biological shapes, from fossils to developing embryos.
Software under GNU General Public License:
- LinBox (ECO) is a high performance library for exact linear algebra, LGPL, 2012;
- Mathemagix (ECO) is free software for algebra and analysis, GNU General Public License, 2012;
- SageMath (ECO) is free and open source software for mathematical computation, GPL, 2012;
- CADO-NFS, An Implementation of the Number Field Sieve Algorithm (ECO) is an implementation of the Number Field Sieve Algorithm (NFS) for integer factorization and discrete logarithm computation in finite fields, GNU Lesser General Public License
v2.1 or later, 2017;
- IBEX (COCONUT) is a C++ library for handling constraints on real numbers, GNU Lesser General Public License, 2019
- FFLAS-FFPACK (ECO) is a set of linear algebra routines on finite fields, LGPL, 2019
Software under CeCILL Free Software License Agreement:
- CGPE (DALI) is a code generator for polynomial evaluation, CeCILL v2, 2013;
- Givaro (ECO) is a C++ library for arithmetic and algebraic calculation, CeCILL-B, 2017;
- OMSMO Software – Oriented Matroids for Shape Modeling (ALGCO) for the use of oriented matroids for interdisciplinary applications, CeCILL Free Software License Agreement v2.1, 2019.
- PerPI (DALI) is an instruction parallelization performance measurement and analysis tool, 2014;
- Reproducible Software (DALI) is an efficient and accurate linear algebra software, 2015;
- Image Processing (ICAR) is an open source software package for online image processing, 2017;
- SOFA (ICAR) is a framework for research, prototyping and development of physics-based simulations, 2019;
- Medical Image Segmentation Tool (ICAR) is a tool for medical image segmentation, 2019.
The platform provides technical support for the development of software to analyse large databases and extract new knowledge, to analyse natural language or to manage scientific data.
Keywords: Ontologies, Data analysis, Data management
Software under Creative Common License:
- FEEL: a French Expanded Emotion Lexicon (ADVANSE) is a French lexicon containing over 14,000 distinct words expressing emotions and feelings, Creative Commons Attribution Non Commercial 4.0, 2016;
- AgroPortal (FADO) is a portal of agronomic ontologies that allows users to upload, browse and download ontologies, as well as annotate texts from these ontologies or create mappings between ontologies, Creative Commons, 2016;
- SIFR BioPortal (FADO) is a biological ontology portal that allows users to upload, browse and download ontologies, as well as annotate text from these ontologies or create mappings between ontologies, Creative Commons, 2016;
- SumGra: Mining Frequent Subgraphs in Multigraphs (ADVANSE), is a new approach to subgraph mining that can be applied to multigraphs, Creative Commons Attribution Non Commercial 3.0, 2017;
- The MultiStream Implementation: A Multiresolution Streamgraph Approach to Explore Hierarchical Time Series (ADVANSE) is a new approach to convey the hierarchical structure of multiple time series, Creative Commons Attribution Non Commercial Share Alike 4.0, 2019;
- JGetMove: Mining Multiple Movement Patterns (ADVANSE) is a Java version of the GetMove algorithm, Creative Commons Attribution 3.0, 2019,
- AttentiveEmocontext System at SemEval-2019 Task 3 for Emotional Classification in short Conversation (ADVANSE) for emotional classification, Creative Commons Attribution Non Commercial 3.0, 2019;
- Temporal Mood Variation: at the CLEF eRisk-2018 (ADVANSE) models temporal mood variation detected from user messages, Creative Commons Attribution Non Commercial 3.0, 2019;
- LogMagnet (ZENITH) is a software for analysing streaming data, and in particular log data, Creative Commons Attribution 2.0, 2019
Software under GNU General Public License:
- Shared-data Overlay Network (SON) (ZENITH) is an open source development platform for P2P networks using web services, GNU Library General Public License v2 or later, 2014;
- WebSmatch (ZENITH) is an integration environment for heterogeneous web data sources. It is used by Data Publica in its open data processing chain, and by our partners IBC (CIRAD and IRD), GNU Lesser General Public License v2.1 only, 2014, LinearOne (TEXTE), GNU Lesser General Public License v3.0 only, 2016;
- Triton Server (ZENITH) is a server for managing graphical data and applications for mobile social networks, GNU Lesser General Public License v2.1 or later, 2017;
- SAVIME (Simulation And Visualization IN-Memory) (ZENITH) is a DBMS-like system that stores data in the form of typed multidimensional tables. It is designed to facilitate querying and visualisation of computer simulation data, GNU General Public License v3.0 only, 2017;
- SciFloware (ZENITH) is designed to be a middleware for running workflows on different systems and software, GNU Library General Public License v2 or later, 2017;
- Grail (TEXT) includes a set of theorem provers for modern logic-like grammars, GNU Lesser General Public License v3.0 or later, 2018;
- Grail Light (TEXT) includes a set of theorem provers for modern logic-like grammars. It includes a broad-spectrum parser specialized on the French language, as well as general theorem provers for designing natural language grammars, GNU Lesser General Public License v3.0 or later, 2019.
Software under CeCILL Free Software License Agreement:
- OpenAlea is a scientific workflow management system for modeling, simulation and analysis in the field of plant architecture,CeCILL-C Free Software License Agreement, 2019.
Software under other licenses:
- FP-Hadoop (ZENITH) is an enhancement to the Hadoop framework, Apache License 2.0, 2016;
- Imitates (ZENITH) is a tool for indexing very large time series, Apache License 2.0, 2019;
- CloudMdsQL (ZENITH) is a so-called polystore system, with a functional SQL language capable of querying several heterogeneous data stores (relational DBMS, NoSQL, HDFS, etc.) , MIT License, 2016;
- DfAnalyzer (ZENITH) provides file and data element flow analysis based on a data flow abstraction, MIT License, 2018;
- Museval (ZENITH) is a python package for evaluating source separation results using the MUSDB18 dataset (MUSDB18 is a set of 150 complete music tracks (duration ~10h)), MIT License, 2018;
Snoop (ZENITH) is a general purpose C++ library dedicated to data management and efficient similarity search, proprietary license, 2019.
- Pl@ntNet (ZENITH) is a participatory science project available as an application that helps you identify plants from your photos;
- The PlantGame (ZENITH) is a participatory game with the aim of producing large amounts of taxonomic data to improve our knowledge of biodiversity. The interest of the game is twofold: to initiate, train or perfect the practice of botany while having fun (with a principle of increasing competence) and to participate in a large-scale participatory science project on biodiversity;
- PlantRT, (ZENITH) is a distributed content sharing platform, allowing keyword search for plant observation and recommendation based on GPS position, 2014;
- Yam++ (FADO) is an ontology alignment tool, 2019;
- LEGATO (FADO) is an automatic and open source system for linking heterogeneous and diverse RDF knowledge graphs. Legato reduces the user’s configuration efforts by implementing efficient data filtering and instance representation methods. In particular, the system is able to resolve ambiguities between distinct but very similar instances in their description, 2019;
- Claims Explorer (FADO) is a search engine that allows browsing the ClaimsKG knowledge graph which gathers information on a large amount of claims and their meta-data extracted from reference fact-checking sites, 2019;
- Coda (FADO) is a prototype web application used to easily and quickly validate identity links (such as owl:sameAs) manually. The tool can be used by ontology developers or dataset curators to manually select automatically generated links, 2019;
- Jeux de Mots (TEXTE) is an online software tool aiming at building a large lexical-semantic network of French. This tool is composed of several games (GWAP – games with a purpose) and contributing environments, 2019
- Hadoop_g5k (ZENITH) is a repository containing scripts to facilitate the deployment and experimental evaluation of hadoop-based projects in Grid5000, 2019;
- SmartFlore (ZENITH) is an application for plant identification, 2019;
- Chiaroscuro (ZENITH) is a new privacy preserving solution for aggregating massively distributed personal time series, 2019.
OpenAlea is a scientific workflow management system for modelling, simulation and analysis in the field of plant architecture, CeCILL-C Free Software License Agreement, 2019
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