Alban Gaignard

• CV (french)
• LinkedIn profile
• HAL, open access publication list
• Google scholar profile

Laboratoire I3S, UNSA-CNRS 2000, route des lucioles Les Algorithmes - bât. Euclide B BP.121, 06903 Sophia Antipolis - Cedex France

• Email : alban.gaignard /at/ cnrs.fr
• Web : http://www.i3s.unice.fr/~gaignard

I was born in France in 1980, and I obtained in 2004 a postgraduate engineering degree in computer science and telecommunications. Then, I've been working in a spanish R&D company, NewBiotechnic S.A., during a 6 month internship period in bioinformatics and grid technologies. I came back to France, with a 2 years engineer position at INRIA, Rennes in the Visages team. I was working in medical image processing and medical (meta-)data management.

I'm now working as a permanent CNRS engineer in the I3S laboratory (Sophia-Antipolis) from 2007. I have been involved in the Modalis research group (Grid/Cloud infrastructures for Life-Sciences & Model Driven Engineering) for 6 years. I am now involved in the Wimmics CNRS/INRIA joint research group (Web-Instrumented Man-Machine Interactions, Communities, and Semantics).

I defended my PhD thesis in Computer Science in 2013, at University of Nice-Sophia Antipolis. This thesis addressed the distributed knowledge production and sharing in the context of collaborative e-Science platforms.

• Semantic Web, Linked Data
• Data sharing and integration (mediation systems, distributed query processing)
• Life-science ontologies and inference rules
• Provenance

• Large-scale infrastructures (grids, clouds)
• Scientific workflows
• Medical imaging

• CNRS MASTODONS CrEDIBLE
• ANR Ginseng
• ANR VIP
• ANR NeuroLOG

• CCGrid-Life'15
• CCGrid-Health'14
• HealthGrid'12
• CrEDIBLE'14
• CrEDIBLE'13
• CrEDIBLE'12

Supervised by Johan Montagnat, obtained in march 2013.

Title: Distributed knowledge sharing and production through collaborative e-Science platforms

Keywords: Scientific workflows, Semantic web services, Provenance, Semantic web, Web of Linked Data, Federated knowledge bases, Distributed data integration, e-Science, e-Health.

Jury: Oscar Corcho, Ollivier Haemmerlé, Olivier Corby, Bernard Gibaud, Catherine Faron Zucker, Johan Montagnat, Andrea Tettamanzi.

Manuscript, Defense, Abstract, Résumé.

• [2014] A. Gaignard, J. Montagnat, B. Gibaud, G. Forestier, T. Glatard.  Domain-specific summarisation of Life-Science e-experiments from provenance traces, Web Semantics: Science, Services and Agents on the World Wide Web.
• [2014] B. Gibaud, G. Forestier,H. Benoit-Cattin, F. Cervenansky, P. Clarysse, D. Friboulet, A. Gaignard, P. Hugonnard, C. Lartizien, H. Liebgott, J. Montagnat, J. Tabary, T. Glatard. OntoVIP: an ontology for the annotation of object models used for medical image simulation, Journal of Biomedical Informatics.
• [2013] T. Glatard, C. Lartizien, B. Gibaud, R. Ferreira da Silva, G. Forestier, F. Cervenansky, M. Alessandrini, H. Benoit-Cattin, O. Bernard, S. Camarasu-Pop, N. Cerezo, P. Clarysse, A. Gaignard, P. Hugonnard, H. Liebgott, S. Marache, A. Marion, J. Montagnat, J. Tabary and D. Friboulet. A Virtual Imaging Platform for multi-modality medical image simulation, IEEE Transactions on Medical Imaging (TMI), 32 (1), pages 110-118, January 2013.
• [2011] M. Acher, P. Collet, A. Gaignard, P. Lahire, J. Montagnat, R. B. France. Composing Multiple Variability Artifacts to Assemble Coherent Workflows, SQJo’2011 (Software Quality Journal, special issue in Quality Engineering for Software Product Lines).

• [2012] O. Corby, A. Gaignard, C. Faron Zucker, J. Montagnat. KGRAM versatile data graphs querying and inference engine, WI'2012 (International Conference on Web Intelligence), Macao.
• [2011] A. Gaignard, J. Montagnat, B. Wali, B. Gibaud. Characterizing semantic service parameters with Role concepts to infer domain-specific knowledge at runtime, KEOD’2011 (International Conference on Knowledge Engineering and Ontology Development), Paris.
• [2011] B. Gibaud, G. Kassel, M. Dojat, B. Batrancourt, F. Michel, A. Gaignard, J. Montagnat. NeuroLOG: sharing neuroimaging data using an ontology-based federated approach, AMIA'2011 (American Medical Informatics Association), Washington.
• [2011] B. Gibaud, F. Ahmad, C. Barillot, F. Michel, B. Wali, B. Batrancourt, M. Dojat, P. Girard, A. Gaignard, D. Lingrand, J. Montagnat, J. Rojas Balderrama, G. Malandain, X. Pennec, D. Godard, G. Kassel, M. Pélégrini-Issac. A federated system for sharing and reuse of images and image processing tools in neuroimaging in Proceedings of the Computer Assisted Radiology and Surgery (CARS'11), Berlin.
• [2011] M. Dojat, M. Pélégrini-Issac, F. Ahmad, C. Barillot, B. Batrancourt, A. Gaignard, B. Gibaud, P. Girard, D. Godard, G. Kassel, D. Lingrand, G. Malandain, F. Michel, J. Montagnat, X. Pennec, J. Rojas Balderrama, B. Wali. NeuroLOG: A framework for the sharing and reuse of distributed tools and data in neuroimaging in Proceedings of the Organization for Human Brain Mapping (HBM'11), Québec city.
• [2010] F. Michel, A. Gaignard, F. Ahmad, C. Barillot, B. Batrancourt, M. Dojat, B. Gibaud, P. Girard, D. Godard, G. Kassel, D. Lingrand, G. Malandain, J. Montagnat, M. Pélégrini-Issac, X. Pennec, J. Rojas Balderramma, B. Wali. Grid-wide neuroimaging data federation in the context of the NeuroLOG project in Proceedings of the HealthGrid'10 conference, Paris.
• [2009] A. Gaignard, J. Montagnat. A distributed security policy for neuroradiological data sharing in Proceedings of the HealthGrid'09 conference, pages 257–262, IOS Press, Berlin, Germany, jun 2009
• [2008] J. Montagnat, A. Gaignard, D. Lingrand, J. R. Balderrama, P. Collet, P. Lahire. NeuroLOG: a community-driven middleware design in Proceedings of the HealthGrid'08 conference, pages 49–58, IOS Press, Chicago.
• [2008] B. Morin, G. Vanwormhoudt, P. Lahire, A. Gaignard, O. Barais, J.-M. Jézéquel. Managing Variability Complexity in Aspect Oriented Modelling (long paper) in Proceedings of the Models 2008 (MoDELS 08), ACM/IEEE, Springer LNCS, Toulouse.
• [2007] P. Lahire, B. Morin, G. Vanwormhoudt, A. Gaignard, O. Barais, and J.-M. Jézéquel.Introducing Variability into Aspect-Oriented Modeling Approaches. In Procedings of ACM/IEEE 10th International Conference on Model Driven Engineering Languages and Systems (MoDELS 07), Nashville.
• [2006] B. Gibaud, C. Barillot, H. Benali, M. Dojat, A. Gaignard, S. Kinkingnéhun, J.P. Matsumoto, M. Pélégrini-Issac, E. Simon, L. Temal. Sharing data and image processing tools in neuroimaging. In Computer Assisted Radiology and Surgery (CARS 06), Osaka.
• [2006] C. Barillot, H. Benali, M. Dojat, A. Gaignard, B. Gibaud, S. Kinkingnehun, J. P. Matsumoto, M. Pelegrini-Issac, E. Simon, L. Temal. Federating Distributed and Heterogeneous Information Sources in Neuroimaging: The NeuroBase Project in Proceedings of the HealthGrid'06 conference, IOS Press, 120:3-13, Valencia.

• [2014] O. Seye, C. Faron Zucker, O. Corby, A. Gaignard. Publication, partage et réutilisation de règles sur le Web de Données, national conference IC'14 (Ingénierie des Connaissances), Clermont-Ferrand.
• [2014] S. Cipière, G. Ereteo, A. Gaignard, N. Boujelben, S. Gaspard, V. Breton, F. Cervenansky, D. Hill, T. Glatard, D. Manset, J. Montagnat, J. Revillard, L. Maigne. Global Initiative for Sentinel e-Health Network on Grid (GINSENG), Medical data integration and semantic developments for epidemiology, workshop CCGrid-Health'14, Chicago.
• [2012] A. Gaignard, J. Montagnat, C. Faron Zucker, O. Corby. Semantic Federation of Distributed Neurodata, MICCAI-DCITAI workshop, Data- and Compute-Intensive Clinical and Translational Imaging Applications, Nice.
• [2012] A. Gaignard, J. Montagnat, C. Faron Zucker, O. Corby. Fédération multi-sources en neurosciences : intégration de données relationnelles et sémantiques. National workshop “Knowledge engineering for semantic interoperability in e-Health”, IC'12 (Ingénierie des Connaissances), Paris.
• [2012] H. Benoit-Cattin, P. Clarysse, D. Friboulet, A. Gaignard, B. Gibaud, T. Glatard, H. Liebgott, D. Manset, J. Tabary. A multi-modality Virtual Imaging Platform for the evaluation of image analysis algorithms ECR’2012 conference, EIBIR IMAGINE Workshop, Vienna.
• [2011] F. Michel, B. Batrancourt, M. Dojat, A. Gaignard, B. Gibaud, J. Montagnat, M. Pélégrini-Issac, X. Pennec, J. Rojas-Balderrama. NeuroLOG : a fede- rated system to share distributed and heterogeneous neuroimaging resources. ECR’2011 conference, EIBIR IMAGINE Workshop, Vienna.
• [2011] J. Montagnat, F. Michel, A. Gaignard, J. Rojas Balderrama, B. Wali, D. Godard, B. Gibaud, D. Lingrand. NeuroLOG platform: federating multi-centric neuroscience resources (presentation and demonstrations). EGI User Forum, Vilnius.
• [2011] M. Dojat, M. Pélégrini-Issac, B. Batrancourt, A. Gaignard, B. Gibaud, D. Godard, G. Kassel, F. Michel, J. Montagnat, X. Pennec. NeuroLOG: A federated software architecture for the sharing and reuse of distributed data and processing tools in neuroimaging in Proceedings of the Recherche en Imagerie et Technologies pour la Santé (RITS'11), Rennes.
• [2010] A. Gaignard, J. Montagnat. Intégration des connaissances en neurosciences dans un environnement multi-centrique “Ingénierie des Connaissances (IC) 2010” conference, “Medical Semantic Web” workshop, Nîmes.
• [2010] F. Michel, A. Gaignard, F. Ahmad, C. Barillot, B. Batrancourt, M. Dojat, B. Gibaud, P. Girard, D. Godard, G. Kassel, D. Lingrand, G. Malandain, J. Montagnat, M. Pélégrini-Issac, X. Pennec, J. Rojas Balderrama, B. Wali. NeuroLOG multi-centric neuroimaging data federation layer, VPH'2010 (Virtual Physiological Human), Brussels.
• [2010] A. Gaignard, J. Rojas Balderrama, F. Michel, D. Godard, D. Lingrand, J. Montagnat. Building collaborative multi-centric federations of neurological resources with Grid technologies. 5th EGEE User Forum, Uppsala.

• [2012] S. Gesing, T. Glatard, J. Krüger, S. Delgado Olabarriaga, T. Solomonides, J. C. Silverstein, J. Montagnat, A. Gaignard, D. Krefting. HealthGrid Applications and Technologies meet Science Gateways for Life Sciences, proceedings of HealthGrid 2012, volume 175.

• KGRAM-DQP : Extension to the Corese/KGRAM (http://wimmics.inria.fr/corese ) semantic web framework (SPARQL 1.1) dedicated to querying and reasoning on distributed knowledge graphs. Several query rewriting and dynamic optimizations for efficient distributed query processing. This software is under active development (Video demonstration)
• NeuSemStore : Semantic repositories dedicated to biomedical data management (http://nyx.unice.fr/projects/neusemstore ). Plugins for the MOTEUR scientific workflow engine (http://modalis.i3s.unice.fr/moteur2 ) including a semantic registry of composable services, and a provenance tracker allowing for inferring domain-scpecific e-science experiment summaries. This software is under active development.
• NeuroLOG middleware : Web service based middleware to setup secured multi-centric studies for neurosciences, including a semantic based federation layer to address neuroimaging data distribution and heterogeneity (2010). (http://neurolog.polytech.unice.fr )
• SmartAdapters : experimental eclipse framework for composing concerns (programs and models), and introducing variability in aspect oriented modeling approaches (AOM), Rainbow team. (2007)
• PLogICI “Plateforme Logicielle pour l'Imagerie Cérébrale et Interventionnelle” - “Software framework for brain imaging and image guided neurosurgery”, VisAGeS team. (2006)
• Distributed platform for comparing genomic sequences (ESTs) with grid technologies (InnerGrid Nitya Gridsystems, Blast), Newbiotechnic S.A.. (2004)

• 2009-2014 : Image processing introduction course material, skeleton source code, filled source code. (french)
• 2007 : Eclipse Modelling Framework : Polytech Engineering School, Sophia Antipolis (4h)
  • Slides (french), Printer friendly version (french)
  • Training (french)

• 2014 : Parallel and distributed data analytics http://www-hpc.cea.fr/SummerSchools2014-CS.htm
• 2009 : International Summer School of Grid Computing, ISSGC'09, Sophia-Antipolis, France
• 2009 : Biomed Grid School'09, Varena, Italy
• 2009 : TechSiCom, Scientific and Professional Communication in English, Gary Burkhart, Nice.
• 2008 : ICAR'08 Intergiciels et Construction d'Applications Réparties, research course in Nice, France
• 2005 : Research course in Bioinformatics, INRIA-IRISA, Rennes, France