Java

Java (computer language)
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: 24/04/13
  • Minor correction: 24/04/13

X!TandemPipeline : edit, filter, merge and group your peptide/protein identifications from MS/MS mass spectra

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: 3.3.0 - 7 juillet 2012
  • License(s): GPL - v3
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Benoit Valot, Olivier Langella
  • Contact designer(s): olivier.langella@moulon.inra.fr
  • Laboratory, service:

 

General software features

X!TandemPipeline is a free software (GPL v3) that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.

Main features :

Context in which the software is used

X!TandemPipeline is designed for a day use by biologists. It performs MS identifications, filters and groups huge data very quickly.

Publications related to the software

Ludovic Bonhomme, Benoit Valot, Francois Tardieu, Michel Zivy. “Phosphoproteome Dynamics Upon Changes in Plant Water Status Reveal Early Events Associated with Rapid Growth Adjustment in Maize Leaves.” Molecular & Cellular Proteomics: MCP (July 10, 2012). http://www.ncbi.nlm.nih.gov/pubmed/22787273.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 03/01/12
  • Minor correction: 03/01/12

XtremWeb-HEP : middleware for distributed data processing

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: 7.6.4 - 12/12/2011
  • License(s): GPL
  • Status: validated (according to PLUME)
  • Support: maintained, ongoing development
  • Designer(s): Oleg LODYGENSKY
  • Contact designer(s): xtremweb (at) lal.in2p3.fr
  • Laboratory, service:

 

General software features
  • ’XtremWeb-HEP’ is a middleware for Distributed Data Processing (grids) :
    –  It permits Administrators to :
        - manage various Users and Applications, by providing adequate access rights to them,
        - catalog various Data and Computing Resources :
           Â· PC farms managed by an IT department,
           Â· PC grids contributed by volunteer citizens,
    –  It permits Users to submit Jobs referencing these Applications,
    –  From Job descriptions, it dynamically deploys and executes these Applications on available Computing Resources, then it provides the results to authorized Users,
    –  It protects the Computing Resources running Mac OS X by starting the Application inside MAC OS X Sandbox,
    –  For the access to data, it permits the usage of HTTP, HTTPS, and any URI scheme whose driver is provided by the User.

Secured three tiers Architecture.  Scheduler and data repository managed by a software administrator on a server;  Client installed on the machine of each User (for ex. scientist);  Worker installed on the resource of each contributor.

  • Soon will come in production the version of XtremWeb-HEP additionally managing the submission of complete virtual machines for execution inside VirtualBox.

  • Interoperability with other grid middleware stacks :
    –  XtremWeb-HEP accepts X509 certificates and proxies for user management, in particular those of the DEGISCO international project.
    –  XtremWeb-HEP integrates a bridge permitting suitable XtremWeb-HEP jobs to be accepted by the gLite middleware in order to be executed by the EGI European infrastructure.
    –  On the other way, thanks to the 3G Bridge of the EDGI European project, the resources gathered by XtremWeb-HEP are available for the many users of the EGI infrastructure (gLite, ARC and Unicore middleware stacks).

  • Domain, Infrastructures, Documentation and Maintenance :
    –  In spite of its name, XtremWeb-HEP is used way beyond High Energy Physics :  Biology,  ADN Research,  Mathematics,  Physics of Solids,  Signal Processing.
    –  XtremWeb-HEP is powering at least 2 production grids (For each grid, look at the 'Statistics' page) :
        - http://www.xtremweb-hep.org/lal/xw_lal/
        - http://xw.lri.fr:4330/XWHEP
    –  XtremWeb-HEP has a complete up to date set of user manuals, presented at http://www.xtremweb-hep.org/spip.php?rubrique16
    –  XtremWeb-HEP is maintained by the software team presented at http://www.xtremweb-hep.org/spip.php?rubrique35 and is strongly supported by Institut des Grilles et du Cloud, INRIA, ENS Lyon, GRID5000

Context in which the software is used
  • Distributed Data Processing
  • Distributed Computing
  • Resource Sharing
  • Computing Grid (PC Grid)
  • Job Submission
Publications related to the software
  • Hybrid Distributed Computing Infrastructure Experiments in Grid5000 : Supporting QoS in Desktop Grids with Cloud Resources   http://users.lal.in2p3.fr/lodygens/gc/g5k.pdf
    G. Fedak, S. Delamare, O. Lodygensky.   Grid 5000 School, Reims, France - April 18-21, 2011

  • Extending the EGEE grid with XtremWeb-HEP Desktop Grid   http://users.lal.in2p3.fr/lodygens/gc/PCGrid2010.pdf
    H. He, G. Fedak, P. Kacsuk, Z. Farkas, Z. Balaton, O. Lodygensky, E. Urbah, G. Caillat, F. Aurajo, A. Emmen.   4th Workshop on Desktop Grids and Volunteer Computing Systems, Melbourne, Australia - May 17-20, 2010

  • EDGeS : Bridging EGEE to BOINC and XtremWeb   http://users.lal.in2p3.fr/lodygens/gc/EDGeS-Bridgi...
    E. Urbah, P. Kacsuk, Z. Farkas, G. Fedak, G. Kecskemeti, O. Lodygensky, A. Marosi, Z. Balaton, G. Caillat, G. Gombas, A. Kornafeld, J. Kovacs, H. He, and R. Lovas.   JoGC Journal of Grid Computing, Volume 7, Number 3, 2009.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 16/11/11
  • Minor correction: 16/11/11

NemoFish : three-dimensional fluorescence in situ hybridization (3D-FISH)

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: 1.5 - 2009/12/07
  • License(s): Other - Creatice Commons V2 (freeware, not open source)
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Eddie Iannuccelli, Thomas Boudier
  • Contact designer(s): eddie.iannuccelli@toulouse.inra.fr
  • Laboratory, service:

 

General software features

Three-dimensional fluorescence in situ hybridization (3D-FISH) is used to study the organization and the positioning of chromosomes or specific sequences such as genes or RNA in cell nuclei. Many different programs (commercial or free) allow image analysis for 3D-FISH experiments. One of the more efficient open-source programs for automatically processing 3D-FISH microscopy images is Smart 3D-FISH, an ImageJ plug-in designed to automatically analyze distances between genes. One of the drawbacks of Smart 3D-FISH is that it has a rather basic user interface and produces its results in various text and image files thus making the data post-processing step time consuming. We developed a new Smart 3D-FISH graphical user interface, NEMO, which provides all information in the same place so that results can be checked and validated efficiently. NEMO gives users the ability to drive their experiments analysis in either automatic, semi-automatic or manual detection mode. We also tuned Smart 3D-FISH to better analyze chromosome territories.

Context in which the software is used

Three-dimensional fluorescence in situ hybridization (3D-FISH)

Publications related to the software

NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments
E. Iannuccelli; F. Mompart; J. Gellin; Y. Lahbib-Mansais; M. Yerle; T. Boudier
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq013

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 17/02/11
  • Minor correction: 17/02/11

Sprintabout : visitor pattern concept 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: Octobre 2007
  • License(s): LGPL
  • Status: stable release
  • Support: maintained, no ongoing development
  • Designer(s): RĂ©mi Forax, Etienne Duris, Gilles Roussel.
  • Contact designer(s): forax @ univ-mlv.fr
  • Laboratory, service:

 

General software features

Java Library to implement the visitor pattern concept, it adds multi-dispatch (with a single parameter) to Java without changing the compiler or the Java Virtual Machine.

Context in which the software is used

Research on Java and object-oriented programming languages.

Publications related to the software

Rémi Forax, Etienne Duris, and Gilles Roussel. Reflection-based implementation of Java extensions: the double-dispatch use-case. Proceedings of the 2005 ACM Symposium on Applied Computing (SAC'05). New York, NY, USA. 2005. pp. 1409–1413.ACM Press.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 17/02/11
  • Minor correction: 17/02/11

JMMF : Java multi-method framework

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: v0.8.10 - avril 2002
  • License(s): GPL
  • Status: stable release
  • Support: maintained, no ongoing development
  • Designer(s): RĂ©mi Forax, Etienne Duris, et Gilles Roussel.
  • Contact designer(s): forax @ univ-mlv.fr
  • Laboratory, service:

 

General software features

JMMF is a Java framework that provides multi-methods without extending the base Java language nor modifying its semantics but intensively using the reflection mechanism of the language.

Context in which the software is used

Research on Java and object-oriented programming languages.

Publications related to the software

Rémi Forax, Etienne Duris, and Gilles Roussel. Java Multi-Method Framework. International Conference on Technology of Object-Oriented Languages and Systems (TOOLS'00). Sydney, Australia. November 2000. pp. 45–56.IEEE Computer Society.

Rémi Forax. Les multi-méthodes en Java. Thèse de doctorat. I.G.M., Université de Marne-la-Vallée. 2001.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 01/08/13
  • Minor correction: 01/08/13

CASSIS : analysis and treatment of astrophysical data

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: 3.4 - August 1, 2013
  • License(s): not yet chosen
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Jean-Michel Glorian, Mickael Boiziot, Samuel Adam, Romaric Benech, Cedric Chappert, Ludovic Deveaux, Damien Faral, Thomas Floquet, Sebastien Fort, Alexandre Girard, Nicolas Guegan, Alain Klotz, Rose Neriere, Guillaume Pelouas, Brice Quillerie, Ngoc thach Ta, Laure Tamisier, Samuel Thiriot.
  • Contact designer(s): Jean-Michel@irap.omp.eu
  • Laboratory, service:

 

General software features
  • Display of astrophysical spectra
  • Identification of lines of transitions of molecules
  • Creation of LTE and Radex theoretical spectra
  • Use of atomic and molecular databases JPL, CDMS, NIST

  • Coded in Java, use sqlite Card Plume

Context in which the software is used
Publications related to the software
  • Pagani, Vastel, Hugo et al., 2009, A&A 494, 623, "Chemical modeling of L183 (L134N): an estimate of the ortho/para H2 ratio"
  • Hezareh, Houde, McCoey et al., 2008, ApJ 684, 1221, "Simultaneous Determination of the Cosmic Ray Ionization Rate and Fractional Ionization in DR 21(OH)"
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 21/04/10
  • Minor correction: 21/04/10

GraMoFoNe : a Plugin for Cytoscape

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: 0.1 - 30/03/2010
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Florian Sikora
  • Contact designer(s): sikora @ univ-mlv.fr
  • Laboratory, service:

 

General software features

GraMoFoNe (Graph Motif For Networks) is developed as a plugin for Cytoscape Fiche Plume. Cytoscape is an open-source software platform for network visualization and analysis, which supports the development of external plugin tools to extend its functionalities.

Our plugin seeks for connected occurrences of a motif (set or multiset of proteins), given by the user, into a Protein-Protein Interaction network previously loaded into the Cytoscape workspace (many file formats are supported). Similarity is measured among sequence-similarity via a Blastp analysis: proteins in the motif got different colors, proteins of the network are colored with the colors of motif proteins which are homologous.

Note that a network node can have 0, 1 or more colors. GraMoFoNe allows deletions (proteins in the motif but not in the resulting connected subnetwork), and insertions (proteins in the results but not in the motif)
of colored or uncolored network nodes.

Context in which the software is used

It is an implementation of a known algorithmic problem in a widely used platform.

Publications related to the software

Guillaume Blin, Florian Sikora, and Stéphane Vialette. GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks. In, Hisham Al-Mubaid, editors, 2nd International Conference on Bioinformatics and Computational Biology (BICoB'10). Honolulu, USA. 24-26 March 2010. pp. 38?43.International Society for Computers and their Applications (ISCA). Note: hal-00425661

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 31/03/10
  • Minor correction: 16/09/10

ChemAzTech : chemical product library & management software

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: 0.6a - 07-30-2010
  • License(s): GPL
  • Status: beta release, under development
  • Support: maintained, ongoing development
  • Designer(s): RĂ©my Dernat (CNRS, IBMM). Contributions are wellcome.
  • Contact designer(s): remy(_dot_)dernat(_at_)univ-montp1(_dot_)fr
  • Laboratory, service:

 

General software features

Chemical product library & management software

This software includes lots of features. Main objective is to involve a maximum of people around a single interface, avalaible from a browser. It's a freely OpenSource and powerfull tool based on existing OpenSource chemical softwares.
You can download and see documentation and sources on sourceforge : http://chemaztech.sourceforge.net

Main features :

  •  Manage chemical products (with structures, place of storage, references, experiment number...).
  •  Draw, Ă©dit structures with JChemPaint.
  •  See your molecules 3D with JMol, in 2D with JChemPaint (java) or with the python librairy OASA (SVG pictures)
  •   Search by sub-structures with MyChem.
  •  Automated threatment for mol properties, with Smiles codes, Inchi with MyChem.
  •   Import molecules from a single MOL file, or CDX (ChemDraw)** or all a database from a SDF file (eg : from ISIS/Base) **
  •   Extract CSV, export as PDF or XLS(X)...
  •  Manage storage and accounting.
  •  Manage users and groups and a visibility level for products

** These softwares are not OpenSource but are very usefull in chemistry.

Other softwares used by ChemAzTech are OpenSource, under GPL or LGPL for JMol and
JChemPaint (JChemPaint is associated to Chemistry Development Kit (CDK)).
Thus, I can use them as building blocks for ChemAzTech, without forgetting OpenBabel, which is an important component of MyChem and which I use to convert files CDX and the MOL into MOL2 for 3D visualization .

On plume : OpenBabel

Context in which the software is used

First of all, this software needs a LAMP (Linux Apache MySQL PHP) server with OpenBabel and MyChem. Then you will have to install java and python (+ OASA library). It's a powerfull software for the management of chemical products, but as you can see, you need a lot a lot of features on your server to install it.

It's a beta software. Use it at your own risks.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 12/03/10
  • Minor correction: 12/03/10

String process : implementation of algorithms for automatic processing of natural language

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 - 2001
  • License(s): not yet chosen
  • Status: stable release
  • Support: maintained, no ongoing development
  • Designer(s): Maxime Crochemore, Christophe Hancart, Thierry Lecroq
  • Contact designer(s): Thierry.Lecroq @ univ-rouen.fr
  • Laboratory, service:

 

General software features

Set of C and Java code to implement algorithms on strings :

  • Pattern matching automata
  • String searching with a sliding window
  • Suffix arrays
  • Structures for indexes
  • Indexes
  • Alignments
  • Approximate patterns
  • Local periods

These algorithms are presented in [Crochemore, Hancart, Lecroq, 2001].

Context in which the software is used

This set of programs was provided to explain the algorithms of the book [Crochemore, Hancart, Lecroq, 2001].
This is the first French book dedicated to string process algorithms.

Publications related to the software
  • Algorithmique du texte, M. Crochemore, C. Hancart et T. Lecroq, Vuibert, 2001
  • Algorithms on Strings, M. Crochemore, C. Hancart et T. Lecroq, Cambridge University Press, 2007
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