transverse

Software (mostly free software) used by all or many of the professions such as office tools, Internet browser
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 19/11/13
  • Minor correction: 19/11/13

ScientiFig : create publication-ready scientific figures

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: 2.6 - 02/10/2013
  • License(s): BSD -
    ScientiFig uses the Apache BATIK and XML-apis libraries as well as the BSD Rsession library.
  • Status: beta release
  • Support: maintained, no ongoing development
  • Designer(s): Benoit Aigouy
  • Contact designer(s): Benoit Aigouy
  • Laboratory, service:

 

General software features

Scientists often build figures for publications and talks. To create these figures, they usually rely on powerful tools that are designed for graphic designers to produce artistic figures and are therefore only poorly suited to build scientific figures.

We here present an ImageJ/FIJI plugin called ScientiFig that is devoted to the building of research figures. Our tool can assemble and maintain complex panels containing images with different aspect ratios and associate scalebars, text annotations and ROIs to these panels. Interestingly, our software will always preserve the position of these associated elements even when figure size changes. ScientiFig can export figures as png with a transparent background for a better integration in office documents and as vector graphics that can be finalized using a vector graphics editor. Last but not least, ScientiFig can format figures for various scientific reviews and for example offer to substitute fonts or to resize the figure to better match the journal guidelines (if a journal style does not exist, it can be created using the embedded editor).

For comparison, please find below two alternative tools:

Context in which the software is used

ScientiFig is a tool to buid and format images for scientific publications.

Publications related to the software

ScientiFig: a tool to build publication-ready scientific figures. Aigouy B, Mirouse V. Nat Methods. 2013 Oct 30;10(11):1048. doi: 10.1038/nmeth.2692.

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

TreeCloud : building tree cloud visualizations from texts

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 - 13/12/2009
  • License(s): GPL
  • Status: under development
  • Support: maintained, ongoing development
  • Designer(s): Philippe Gambette ; Jean VĂ©ronis
  • Contact designer(s):

    P. Gambette

  • Laboratory, service:

 

General software features

TreeCloud generates a tree cloud from a text, that is a word cloud whose words are arranged around a tree which reflects their semantic proximity inside the text.

Context in which the software is used

The main application of the tree clouds built by TreeCloud is to provide a quick overview of the content of a text. It is also possible to use them for a deeper analysis of the texts, included in a textometric approach (text analysis using software tools and statistical methods). Then, the tree cloud will help the user to fomalize some hypotheses, or test them. It can therefore lead to use other textometric tools to confirm these hypotheses, or to visualize the results of the output of those tools.

Publications related to the software

Philippe Gambette and Jean VĂ©ronis: Visualising a Text with a Tree Cloud, In Locarek-Junge H. and Weihs C., editors, Classification as a Tool of Research, Proc. of IFCS'09 (11th Conference of the International Federation of Classification Societies) Studies in Classification, Data Analysis, and Knowledge Organization 40, p. 561-570, 2010.

Delphine Amstutz and Philippe Gambette (in French): Utilisation de la visualisation en nuage arboré pour l'analyse littéraire, Statistical Analysis of Textual Data (Proc. of JADT'10), p. 227-238, 2010.

Philippe Gambette, Nuria Gala and Alexis Nasr(in French): Longueur de branches et arbres de mots, Corpus 11, p. 129-146, 2012.

William Martinez and Philippe Gambette (in French): L'affaire du Médiator au prisme de la textométrie, Texto !, to appear, 2013.

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: 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: 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: 05/04/10
  • Minor correction: 04/04/13

Paraloop : distributing parallel jobs

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 - 2008 September
  • License(s): CeCILL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Emmanuel COURCELLE
  • Contact designer(s): emmanuel.courcelle at toulouse.inra.fr
  • Laboratory, service: Service Bioinformatique

 

General software features

Paraloop distributes your jobs on several processors of a machine, independently of its architecture: it may be a single SMP computer with shared memory, as well as a cluster, or even a network of workstations.

Paraloop is best suited for the use cases when we have a high number of independant tasks to execute, as is often the case in the data treatment pipelines found in bioinformatics projects.

Paraloop is a tool for programmers, who are able to easily distribute their jobs, while using the same script whatever the machine they run on. It is a perl object program: data treatment is wrapped inside an object (called a "plugin"), the code responsible for the machine interaction is wrapped inside another object (called "scheduler"). It is thus relatively easy to adapt paraloop to a new architecture: it just means writing a new scheduler (in fact, just a few methods). The same is true for plugins: they are able to read and treat data, using some particular format.

A few plugins are delivered with paraloop: some of them are specific to the bioinformatics field (one of them is useful to execute BLAST in parallel, for instance), while others are completely generic (reading a text file, ...). However, writing plugins dedicated for other thematic fields would be a quite useful task.

When used in a queue context, with a limited cpu time per job, it is possible to configure paraloop so that the current job is interrupted before being killed by the system; the job is resubmitted to the queue just before the interruption, so that it will be resumed as soon as permitted by the system.

Besides, paraloop includes a command to print the progress report of each job.

Finally, a "load balancing mode" is available: it may be used to insure that all the jobs take approximately the same time to execute.

Context in which the software is used

We currently use paraloop for our bioinformatics computations, whether on SMP servers or computer clusters. Besides, paraloop is integrated to our bioinformatics projects (eugene, LeARN, Narcisse, ...)

Publications related to the software

Paraloop was described in a poster session a J-RES 2005 http://2005.jres.org/resume/poster/138.pdf and at JOBIM, in 2005 too http://pbil.univ-lyon1.fr/events/jobim2005/proceedings/P64Courcelle.pdf

Paraloop is currently hosted on the SourceSup forge: http://sourcesup.cru.fr/projects/paraloop

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 30/03/10
  • Minor correction: 30/03/10

PowerWatershed : 2D and 3D image segmentation

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): CeCILL
  • Status: beta release
  • Support: maintained, ongoing development
  • Designer(s): Camille Couprie, Laurent Najman and Hugues Talbot
  • Contact designer(s): najmanl at esiee.fr
  • Laboratory, service:

 

General software features

This software provides implementation of three algorithms for 2D and 3D image segmentation. The algorithms implemented are Prim, and Kruskal's algorithms for Maximum Spanning Forest computation, and the PowerWatershed algorithm (q=2) described in the article [Couprie, Grady, Najman and Talbot, ICCV'09].

Context in which the software is used

We use the PowerWatershed algorithm as a fast, useful algorithm in the optimisation step on problems related to image processing and visualization.

Publications related to the software

Camille Couprie, Leo Grady, Laurent Najman and Hugues Talbot , "Power Watersheds: A New Image Segmentation Framework Extending Graph Cuts, Random Walker and Optimal Spanning Forest", ICCV'09, 2009

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 08/04/09
  • Minor correction: 19/03/10

PLATINE : software platform used to support remote collaboration among users.

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: V3.0 - 24/01/2008
  • License(s): CeCILL-B
  • Status: beta release, internal use, under development
  • Support: maintained, ongoing development
  • Designer(s): VĂ©ronique Baudin , Michel Diaz, Philippe Owezarski, Thierry Villemur, Jean-Pierre Courtiat and a lot of students.
  • Contact designer(s): veronique.baudin@laas.fr
  • Laboratory, service:

 

General software features

The PLATINE environment is a software platform used to support remote collaboration among users. Two main kinds of interactions can be encountered within collaborative groups: asynchronous collaboration, that does not require the group members to be present at the same time and synchronous collaboration, where remote users work in co-presence; PLATINE is mainly devoted to synchronous collaboration.

The PLATINE environment is made up of the following components:

  • an off-line session preparation module: OSP
  • an asynchronous session state display with an “asynchronous” chat: ASSD
  • a synchronous session state display: SSD
  • a multi user visioconference: Jvisio
  • a multipoint chat: Jchat
  • an application sharing: AST
  • a shared whiteboard: SW
  • a session manager: SM

A session is composed of an asynchronous phase, and a synchronous phase.
Besides the administrator role which is associated with the single user in charge of the management of the session (creation/deletion, configuration of the session), four additional user roles have been defined, which are respectively: teacher, student, observer and expert. Thus, a user, when registering in a session, authenticates him/herself with a specific role. This role determines the rights that the user will have for using the collaboration and communication tools available in the session. The teacher and student roles are self-explanatory. The expert role is intended to implement some kind of help desk. It is detained by the users in charge of the problems and questions related to the use of the collaborative platform and/or to experiment specific applications. The observer role is intended to represent a degraded role of the student one. Typically, an observer will have a restricted access to the tools of the collaborative platform. This may be motivated by two main reasons:
- Political reasons related to the session management implying that some users are not allowed to use the full functionality of the platform
- Network QoS constraints implying that some distant users are not capable for technical reasons to use the full functionality of the platform.
Another important issue concerns the particular problem of who is in charge of controlling the floor in a active session. A typical solution to the floor control is the chaired-based control, where a human facilitator is in charge of explicitly granting and releasing floor.
In order to implement a chaired-based control, a chairman status has been defined, which may be assigned to one or a subgroup of roles. Persons who are associated with roles and are active users, are authorized to request the chairman status and to potentially gain it.

Context in which the software is used

PLATINE has been used for some experiments:

  • during the european project Lab@Future, with the following involved partners :
    ARTEC (Bremen - Germany), LAAS (Toulouse - France), ETHZ (Zurich - Switzland), TUV (Technical University of Vienna - Austria)
  • during a contract of collaboration (Co-supervision of thesis) between the University of Tokushima (Japan) and the LAAS for some sessions of e-learning (to learn english language) and for work sessions between some members of LAAS and a student at Tokushima University.

It is used today to illustrate various protocols in projects such as SatSIX , or UseNET for an automatic deployment of its components by using a OSGi technology.

Publications related to the software

A lot of documents and articles have been published :

  • A list of articles is available here
  • Some guides are available here
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