collective

Software generally installed on a server for collective use
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 19/09/13
  • Minor correction: 19/09/13
  • Index card author: Eric Hivon (IAP)
  • Theme leader : Dirk Hoffmann (Centre de Physique des Particules de Marseille (CPPM-IN2P3))

HEALPix : data analysis, simulation and visualisation on the sphere

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: 3.11 - April 2013
  • License(s): GPL - GPLv2
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Eric Hivon; Martin Reinecke; Krzysztof M. Gorski; Anthony J. Banday; Benjamin D. Wandelt; Emmanuel Joliet; William O'Mullane; Cyrille Rosset; Andrea Zonca
  • Contact designer(s): hivon at iap.fr
  • Laboratory, service: MPA (Garching, Allemagne), Caltech (Pasadena, CA,Etats-Unis), TAC (Copenhague, Danemark), ESAC (Madrid, Espagne), JPL (Pasadena, CA, Etats-Unis), ESO (Garching, Allemagne)

 

General software features

The HEALPix software implements the HEALPix (Hierarchical Equal Area iso-Latitude Pixelation) pixelation of the sphere. Initially developed for the simulation and analysis of ESA Planck satellite observations (dedicated to the study of the Cosmic Microwave Background (CMB) anisotropies, whose first results were delivered in March 2013), this software and its pixelation algorithm have become standard tools in the simulation and analysis of data on the sphere, including the NASA WMAP satellite, also dedicated to CMB observation, and the Pierre Auger ground based observatory for high energy cosmic rays, and are used for other astrophysical and geological studies.

Main features of the pixelation

At a given resolution, all HEALPix pixels have the same surface area, even if their shape varies slightly. Thanks to the hierarchical feature of the pixelation, upgrading its resolution to the next level simply amounts to divide each pixel into four sub-pixel of the same area. This allows quick and efficient upgrading and downgrading operations of existing maps.

Since the pixels are regularly spaced on iso-latitude rings, Spherical Harmonics can be computed very efficiently. The synthesis or analysis up to multipole Lmax  of a spherical data set containing Npix pixels is reduced from    Npix Lmax2   to   Npix½ Lmax2  compared to non iso-latitude pixelation.

Features of the software package

The represents data on the sphere, and enables analysis or simulation of these maps in (scalar or spin-weighted) Spherical Harmonics, as well as various kinds of statistical analyses and processing. Portable FITS files are used for input and output. The list of available functions includes:

  • generation of random maps (gaussian or not) from an arbitrary angular power spectrum,
  • computation of the angular power spectrum (or angular correlation function) of a map,
  • convolution of a spherical map with an arbitrary circular window,
  • tessellation of the sphere and pixel processing supported down to a pixel size of 0.4 milliarcseconds (equivalent to 3.5 1018 pixels on the sphere),
  • median filtering of a map,
  • search of local extrema in a map,
  • query of pixels located in user defined disks, triangles, polygons, ...
  • processing of binary masks to identify 'holes' in order to fill them, or to apodize masks,
  • visualization of HEALPix sky maps either on the whole sky (using Mollweide or orthographic projections) or on a patch (gnomic or cartesian projections),
  • output in Google Map/Google Sky and DomeMaster format.

The most expensive operations, such a Spherical Harmonics Transform have been carefully optimised and benefit from a shared memory parallelisation based on OpenMP.

Contents of the software package

The software is available in C, C++, Fortran90, IDL/GDL, Java and python. The following modules are provided in each of these languages:

  • a library of tools (subroutines, functions, procedures, modules, classes, ...depending on languages) covering most of the functionnalities described above, as well as supporting ancillary tools (eg, parameter file parsing),
  • a set of stand-alone facilities based on the library above and each implementing one of HEALPix major features (map generation or analysis, filtering, resolution udgrade or downgrade, visualization). These applications are generally run via an interactive dialog or an ASCII parameter file. Their source code can be used as a starting point for user specific developments,
  • an extensive PDF and/or HTML documentation describing in details the API, inner working and limitations of each tool and application.

Finally, some tools (interactive script and Makefile) are provided to manage and facilitate the compilation and installation of one or several of the libraries and facilities, for most combinations of hardwares, operating systems, compilers, ...

Third Party Developements

One can distinguish two kinds of third party developements (defined as not (yet) being part of the official HEALPix package described above):

  • new functionalities, for instance many tools based on Minkowski functionals, wavelets (iSAP, MRS, S2LET, SphereLab), or structure identification (DisPerSE) developed by various research teams can be applied to data stored in HEALPix format,
  • translations, re-implementations or wrapping of (some of) existing functionalities, for instance in Matlab/Octave (Mealpix) and Yorick (YHeal) are available. (See (almost) exhaustive list.)

Context in which the software is used

Software used for the analysis of Planck satellite data.
Data format supported by Aladin visualisation software to represent diffuse astronomical data on the sky.

Publications related to the software

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 02/08/12
  • Minor correction: 02/08/12

Stratuslab : complete IaaS cloud distribution

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: v2.0 - 25 June 2012
  • License(s): Other - Apache-2, AGPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): StratusLab Collaboration (CNRS, UCM, GRNET, SixSq, TID, et TCD)
  • Contact designer(s): support@stratuslab.eu
  • Laboratory, service: Universidad Complutense de Madrid (Madrid, Spain), GRNET (Athens, Greece), SixSq (Geneva, Switzerland), TelefĂłnica I+D (Madrid, Spain), Trinity College Dublin (Dublin, Irland)

 

General software features

logo stratuslab
The distribution contains all of the necessary for deploying an Infrastructure-as-a-Service (IaaS) cloud: network, storage, and virtual machine management. Moreover, it provides innovative features like the Marketplace that facilitates sharing of virtual appliances, service management that allows deployment and autoscaling of multi-machine services, and support for multi-cloud scenarios. The distribution supports multiple operating systems (CentOS 6.2, Fedora16, and OpenSuSE 12.1) and is ideal for both public and private cloud deployments. The StratusLab client, written in Python, provides a simple command line interface to access to StratusLab cloud infrastructures from GNU/Linux, Mac OS X, and Windows machines.

Source code for the distribution can be found on GitHub.

Context in which the software is used

StratusLab is used at LAL to provide one of the StratusLab reference cloud infrastructures, a public cloud open to anyone for non-commercial use. The other StratusLab reference cloud is operated by GRNET in Greece. LAL also operates a second, private cloud infrastructure for deployment of laboratory services; existing services are gradually being migrated to this cloud infrastructure.

CNRS/IBCP operates a StratusLab cloud to support bioinformatics research and services. This public cloud infrastructure is available to users of the ReNaBi network. A portal, customized for bioinformatics users, facilitates use of the IBCP cloud and simplifies access to relevant virtual appliances and databases.

There are also commercial deployments of the StratusLab cloud distribution that support software engineering processes (such as deployment of ESA's SCOS-2000 platform) and scientific use (like the Atos Helix Nebula cloud infrastructure).

Publications related to the software

All of the related publications of the project are available from :

The chapter of the book "European Research Activities in Cloud Computing" contains a general description of the StratusLab project and its cloud distribution.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 20/03/12
  • Minor correction: 20/03/12

HINTS : network on demand diagnostic tool

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.

 

General software features

HINTS is a tool that provides quick network troubleshooting between two "probes", which are usually installed in remote geographical locations.
Although HINTS was primarily designed to diagnose potential network problems between two nodes of a grid, it is completely usable in a classical context, between two standard sites not involved in a grid infrastructure.

Historically, HINTS was born as part of the european project Enabling Grids for E-sciencE - EGEE, and continues today its evolution within the European Grid Infrastructure - EGI. HINTS is developed and maintained by CNRS, partner of France Grilles, the French National Grid Initiative and GARR, partner of the Italian Grid Initiative.

HINTS allows a user, from a centralized web interface, to initiate basic network tests between two specific agents (probes) previously deployed within local networks one want to qualify the link.

The qualification of the network between two probes is done through the following traditional system tools:

  • Ping
  • Traceroute,
  • Nmap,
  • DNS Resolution,
  • Iperf.

The main benefits of HINTS are:

  • A user may (subject to accreditation) test the quality of the network between its site and another site without involving an administrator of that other site,
  • All tests are symmetric (made in both directions between the selected probes),
  • Direct access to the probes (and thus access to the various diagnostic tools) is not possible, everything is done only via a centralized interface,
  • Fine and flexible user management (certification, delegation of rights),
  • The probes are based on those proposed by the well known PerfSONAR project.
Context in which the software is used

HINTS becomes useful when a user wants to diagnose the network between two sites without involving a network administrator and above all without disturbing the network administrator at the remote site.

If HINTS highlights some dysfunction between these two sites, network administrators will then not be disturbed for nothing.

If HINTS finds no problem, then the problems faced by users are likely not due to the network and is the reason to be searched elsewhere (application layers).

Today, HINTS is available in Scientific Linux 6.x RPM format.

Publications related to the software

  • Presentation at the EGI Technical forum, Lyon, September 2011
  • Poster for the EGI Community Forum, Munich, March 2012
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: 02/01/12
  • Minor correction: 02/01/12

Datum : web application for sharing data from databases

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:
  • License(s): GPL - v2
  • Status: internal use, under development
  • Support: maintained, ongoing development
  • Designer(s): Olivier Maury
  • Contact designer(s): Olivier.Maury (chez) grignon.inra.fr
  • Laboratory, service:

 

General software features

Datum is a web application, so a server-based software for use with a web browse. It aims sharin data from databases and information related to these databases:

  • sharing data and files, with access rights (management of users and permissions)
    • browsing tables and data from the database
    • data reports with charts (defined with SQL queries)
    • dynamic charts
  • display of the database schema
  • integration of datasets (CSV files)
  • project information : news, little CMS feature
  • user history, internationalisation, help, database management, statistics, ...

Some databases use specific module to :

  • change the interface layout
  • create template files for the integration
  • add specific integrations and data extractions

One software instance can manage several databases.
A daemon can run asynchronous tasks, as data extraction, without blocking the page display.

Datum is based on the PHP framework, Yii.

Context in which the software is used

Developed for one project, the application was made generic to interface the database of the research unit.

So, this common code base is used by several projects in the "Biosphere-Atmosphere" research team at INRA "Environnement et Grandes Cultures" and for the information system of SOERE PRO (Systems of observation and long-term experimentation for environmental research on organic wast products).

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 13/09/11
  • Minor correction: 28/09/11

SIGDEF : system for the management and distribution of software licenses

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: 1.0 - 02/05/2011
  • License(s): GPL, CeCILL - En Ă©tude.
  • Status: internal use, under development
  • Support: maintained, no ongoing development
  • Designer(s): IRD - DSI - Service Informatique Scientifique : StĂ©phane DEBARD (conception), Geoffrey PASCAL (conception et dĂ©veloppement)
  • Contact designer(s): stephane.debard@ird.fr
  • Laboratory, service:

 

General software features

SIGDEF is a generic designed application to deliver and manage licences. This tool is intended for IT support services. Two interfaces (one for users and another for administrators) allow to send orders to activate software licenses and to manage them easily.

1 - User Interface:

  • Identification (with a directory, a .htaccess file) or no identification.
  • Choice of the software and its version (management of both individual or grouped orders), choice of the installation of the application(s) following validation instructions.
  • Downloading documents related to usage and access rights (agreements, contracts, letters ...).
  • Summary and acceptance of the users' charter.

2 - Administrator Interface:

  • Control and validation of submitted orders (control of the user information and the user choices).
  • Email license sending after validation, validation may be done ​​by one or several services.
  • Synthesis and search of current orders, committed or sent.

Future work:
- Export raw results of the synthesis of commands.
- Specific requests and crossing data to make assessments on the controls.

The documentation is complete: installation, utilization and assessment, including the design documentation (database, workflow).

Context in which the software is used

Software editors allow software vendors to group the purchasing of licenses for several software packages in order to reduce costs. Companies delegate license management to the IT support services. These licenses are often distributed with the help of ID or activation files provided to the manager without the support of monitoring or management tools.

SIGDEF provide tools for the license management and deployment on a large scale.

SIGDEF is currently used in production (for more than one year) to manage licenses in Geographic Information Systems.
Two independent teams of the same ISD use this application to validate and distribute the licenses to their users (200 users).

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 25/10/10
  • Minor correction: 28/10/10

EDNA : framework for plugin-based applications for online data analysis

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 (Application MXv1 june 2009) - revision SVN 1930
  • License(s): GPL -

    EDNA kernel and many plugins are LGPLv3+

    EDNA applications (like MXv1) and some plugins are GPLv3+

  • Status: stable release, internal use, under development
  • Support: maintained, ongoing development
  • Designer(s):

    Executive Committee Chair: Andrew Leslie (MRC-LMB)

    Project Manager: Olof Svensson (ESRF)

    Project Coordinator: Alun Ashton (Diamond)

    Currently around 10 developers but 40 people have been involved in the project.

  • Contact designer(s): edna-support@esrf.fr
  • Laboratory, service: DLS, MRC-LMB, CCP4, Bessy (HZB), Max Lab. NSLS, SLS-PSI, Univ Sydney, Univ York, Global Phasing

 

General software features

Platform
The EDNA kernel runs on all platforms which can provide a Python interpreter. The MXv1 application runs on all Unix/Linux platforms that have bash, Python (version 2.5 and later) and which can run the programs MOSFLM, LABELIT, RADDOSE and BEST. The EDNA framework and MXv1 application are installed and regularly used at the Diamond Light Source (Didcot), EMBL Hamburg, ESRF Grenoble and NSLS Brookhaven National Laboratory (New York).

EDNA-based applications are designed and developed with the aim of being easily configurable, extensible and smoothly maintainable. This has been made possible thanks to the technical facilities that the EDNA framework provides, including configuration facilities, a library of re-usable components, datamodel-driven code generation machinery and a testing framework.

Modularity
The components are organized in a logical class hierarchy that makes it straightforward to develop new functional plugins by deriving them from the appropriate parent. Two families of plugins have been designed: the first branch contains the execution plugins (EDPluginExec classes) that are responsible for the execution of a particular action (e.g. execution of third-party software); the second branch contains the control plugins (EDPluginControl classes) that are responsible for the data flow (propagation of the data), the workflow (sequential or parallel execution of appropriate execution plugins) and the error-tracking mechanism (propagation of the errors).

Datamodel
The EDNA kernel provides a data model tool kit that allows the construction of elaborate data models needed by advanced applications. In addition, it allows the design of unitary data models that can be unit-tested, so that a plugin can be launched and tested independently of any application context. This tool kit consists of generic low-level class definitions including general types (XSDataString, XSDataFloat etc.) and X-ray experiment classes which can be re-used when designing specific components data models. It is available in several standard data formats including XMI (XML metadata interchange) and XSD (XML schema definition) in order to facilitate importing into UML (unified modeling language) data modeling tools and/or XSD files. The framework also provides (external) code generation machinery generateDS that allows automatic code generation from UML diagrams to Python code via XSD format.

Testing framework
A testing framework has been developed and integrated with the kernel in order to test the applications and the components easily and efficiently. To ensure the reliability and robustness of the components, the testing framework provides all the necessary utilities to check a class (EDTestCase) and a plugin (EDTestCasePlugin) either in a unitary manner (EDTestCasePluginUnit) or by testing its execution in an application context (EDTestCasePluginExecute). These families of tests can be automatically launched via test suites. An automatic analysis of the test results is performed by comparing the obtained result with the expected one (assert mechanism), so that a successful test proves that a result conforms to the expectation. This allows a high degree of confidence when implementing new components or re-implementing features of existing components.

Configuration facilities
Each plugin is configured (path of the controlled executable, batch queuing system configuration, ...) by the mean of XML files. The configuration is selected according to the EDNA_SITE environment variable.

Context in which the software is used

EDNA is used to create online data analysis applications on synchrotron beam-lines (but not only), among them:

  • Mxv1 application for fast characterization of protein crystals; in regular use at the ESRF, the DLS and the NSLS.
  • MXv2 application is in preparation to take advantage of kappa goniostats.
  • Dimple application has been written by CCP4 for doing molecular replacement and ligand location in proteins.
  • Diffraction computed tomography application with azimuthal integration and online sinogram generation with dynamic region of interest for Nano-Analysis Beamlines.
  • Saxs pre-processing (azimuthal integration and averaging) and downstream processing for BioSaxs Beamline.
  • A Tutorial for Raw digital camera development that explains how to take advantage of the parallel capabilities of EDNA.
Publications related to the software

EDNA: a framework for plugin-based applications applied to X-ray experiment online data analysis
M.-F. Incardona, G. P. Bourenkov, K. Levik, R. A. Pieritz, A. N. Popov and O. Svensson
J. Synchrotron Rad. (2009). 16, 872-879 [ doi:10.1107/S0909049509036681 ]

Abstract: EDNA is a framework for developing plugin-based applications especially for online data analysis in the X-ray experiments field. This article describes the features provided by the EDNA framework to ease the development of extensible scientific applications. This framework includes a plugins class hierarchy, configuration and application facilities, a mechanism to generate data classes and a testing framework. These utilities allow rapid development and integration in which robustness and quality play a fundamental role. A first prototype, designed for macromolecular crystallography experiments and tested at several synchrotrons, is presented.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 22/10/10
  • Minor correction: 22/10/10

Indico : event organization

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: v0.96.2 (v0.97 en release candidate) - 27 June 2008
  • License(s): GPL
  • Status: validated (according to PLUME), stable release
  • Support: maintained, ongoing development
  • Designer(s): DĂ©partement IT du CERN
  • Contact designer(s): project-indico-administrators@cern.ch
  • Laboratory, service:

 

General software features

Indico allows management of meetings, workshops and conferences. The agenda system is the most common and the easiest to master function but Indico goes beyond this simple functionality. It allows any kind of multimedia file (presentations, images, documents...) to be attached, and to create surveys on line (for example satisfaction surveys). The management of conferences is complete, from registration to production of the proceedings, including multi-track submissions and badges.

Indico has been successfully used to manage meetings with more than a thousand attendees.

To master the utilization of all the available functionalities needs a learning period.

Indico can be hosted at the laboratory level, but is at its best in large communities.

Context in which the software is used

In France, Indico is mainly used at IN2P3, both with a national scope and at the lab level at LPSC and LAL.
Indico world wide: http://indico-software.org/wiki/IndicoWorldWide

Publications related to the software

Indico's new face goes live, by José Benito Gonzalez and José Pedro Ferreira, IT-UDS, on behalf of the Indico team, CERN Computer Newsletter, September 2009

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 16/08/10
  • Minor correction: 01/06/11

CiGri : lightweight computing grid

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: 1.3 - Aout 2009
  • License(s): GPL - v2
  • Status: validated (according to PLUME), stable release, under development
  • Support: maintained, ongoing development
  • Designer(s): Bruno Bzeznik, Nicolas Capit, Olivier Richard, Elton Nicoletti Mathias, Yiannis Georgiou, and various contributors (internships, google summer of code)
  • Contact designer(s): Bruno.Bzeznik@imag.fr
  • Laboratory, service: CIMENT (University of Grenoble Computing center)

 

General software features

The CiGri software allows to set up a grid center to exploit a pre-existing set of super-computers. It is specialised on the management of "bag-of-tasks" jobs. It gathers the unused computing resources from an intranet infrastructure and makes it available for large set of tasks.

More information (in French) at fiche logiciel Fiche Plume.

Context in which the software is used

CiGri software is used at the computing center at Joseph Fourier University of Grenoble (CIMENT) since 2002.

Publications related to the software
  • Yiannis Georgiou, Olivier Richard, et Nicolas Capit.
    Evaluations of the lightweight grid cigri upon the grid5000 platform. In E-SCIENCE '07: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing, pages 279-286, Washington, DC, USA, 2007. IEEE Computer Society.
  • Yiannis Georgiou, Nicolas Capit, Bruno Bzeznik, et Olivier Richard.
    Simple, fault tolerant, lightweight grid computing approach for bag-of-tasks applications. 3rd EGEE User Forum, 2008.
    http://indico.cern.ch/contributionDisplay.py?contr....
  • Yvan Calas, Nicolas Capit, et Estelle Gabarron.
    Cigri : Expériences autour de l’exploitation d’une grille légère. JRES, 2005.
    http://2005.jres.org/paper/90.pdf.
  • F. Dupros, F. Boulahya, J. Vairon, P. Lombard, N. Capit, et J-F. MĂ©haut.
    Iggi, a computing framework for large scale parametric simulations: Application to uncertainty analysis with toughreact. TOUGH Symposium, 2006.
    http://esd.lbl.gov/TOUGHsymposium/pdf/Dupros_IGGI.pdf.
  • J. Aoun, V. Breton, L. Desbat, B. Bzeznik, M. Leabadand, et J. Dimastromatteo.
    Validation of the Small Animal Biospace Gamma Imager Model Using GATE Monte Carlo Simulations on the Grid. In J. Montagnat S. D. Olabarriaga, D. Lingrand, editor, Proceedings of MICCAI-Grid Workshop Medical imaging on grids: achievements and perspectives, MICCAI-Grid Workshop, New York États-Unis d'Amérique, 2008.
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 10/05/10
  • Minor correction: 10/05/10

Narcisse : compared genomes browser

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: 2.0 - 18 DĂ©cembre 2009
  • License(s): CeCILL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s):

    Thomas Faraut, JĂ©rĂ´me Gouzy, Emmanuel Courcelle
    All co-authors

  • Contact designer(s): http://listes.inra.fr/wws/info/narcisse
  • Laboratory, service:

 

General software features

Narcisse is a tool dedicated to the comparison of completely sequenced genomes. Narcisse is essentially a comparative genome browser enabling the exploration of genome conservation at different levels of resolution (from the nucleotide level to the whole chromosome).

The Narcisse software is made of two main components :

  1. A genome comparison pipeline. From completely sequenced genomes (sequence and annotation) local sequence similarities are identified (local alignments are obtained with a program developed by the team and distributed with Narcisse). These local similarities are subsequently used to reconstruct conserved segments at different resolution levels.
  2. A genome browser displaying the syntenies at the different resolution levels described above. The browser is able to display local conservations in the genes neighbourghood as well a conservation of chromosomal segments. Several representations are available: dotplots; comparative maps, circular representation of conserved syntenies using the circos software. In addition personal data or personal sequences can be uploaded and represented or compared against available genomes.

A Narcisse installation is maintained at the developers place, giving access to the comparisons of animals, plants, fungi and bacteria genomes obtained from public data. Narcisse data may be accessed through Biomoby webservices.

Narcisse may be downloaded and locally installed for specific needs. An API, based upon the ensembl API, is available to access genomic data, and a dedicated API may be used to access comparison data.

Context in which the software is used

Exploration of completely sequenced genomes, manual annotation transfer using a comparative genomics approach.

Publications related to the software

Courcelle E, Beausse Y, Letort S, Stahl O, Fremez R, Ngom-Bru C, Gouzy J, Faraut T (2008). Narcisse: a mirror view of conserved syntenies. Nucleic Acids Res 36(Database issue):D485-90.

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