====== Alban Gaignard  ======
==== PhD in Computer Science - CNRS Engineer ====
  * {{:public:gaignard:albangaignard-cv2014.pdf|CV (french)}}
  * [[http://fr.linkedin.com/in/albangaignard/|LinkedIn profile]]
  * [[http://hal.archives-ouvertes.fr/Public/afficheRequetePubli.php?auteur_exp=A.,%20Gaignard%20;%20Alban,%20Gaignard&CB_auteur=oui&CB_titre=oui&CB_article=oui&CB_Resume_court=oui&CB_typdoc=oui&langue=Anglais&tri_exp=annee_publi&tri_exp2=typdoc&tri_exp3=date_publi&ordre_aff=TA&Fen=Aff&css=../css/VisuRubriqueEncadre.css|HAL, open access publication list]] 
  * [[http://scholar.google.fr/citations?user=4ruSswgAAAAJ|Google scholar profile]] 

===== Contact =====


Laboratoire [[http://www.i3s.unice.fr/|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|http://www.i3s.unice.fr/~gaignard]] 


===== Background & positions =====

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 [[http://www.irisa.fr/visages|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 [[http://www.i3s.unice.fr|I3S laboratory]] (Sophia-Antipolis) from 2007. I have been involved in the   [[http://modalis.i3s.unice.fr|Modalis]] research group (**Grid/Cloud infrastructures for Life-Sciences & Model Driven Engineering**) for 6 years. I am now involved in the [[http://wimmics.inria.fr|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.
===== Research interests =====

== Knowledge Engineering ==

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


== Computational E-Sciences ==

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


===== Research projects =====
    * CNRS MASTODONS CrEDIBLE
    * ANR Ginseng
    * ANR VIP
    * ANR NeuroLOG 

===== PC member =====
    * CCGrid-Life'15
    * CCGrid-Health'14
    * HealthGrid'12
    * CrEDIBLE'14
    * CrEDIBLE'13
    * CrEDIBLE'12
===== PhD Thesis =====
Supervised by Johan Montagnat, obtained in march 2013. 

__Title__: // [[http://tel.archives-ouvertes.fr/tel-00827926|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. 

[[http://tel.archives-ouvertes.fr/docs/00/82/79/26/PDF/thesis-alban.gaignard.pdf|Manuscript]], [[http://tel.archives-ouvertes.fr/docs/00/82/79/26/ANNEX/phd-defense-alban.gaignard.pdf|Defense]], [[https://modalis.i3s.unice.fr/_media/members:gaignard:abstract-thesis-gaignard.pdf|Abstract]], [[https://modalis.i3s.unice.fr/_media/members:gaignard:resume-these-gaignard.pdf|Résumé]]. 
===== Publications =====


== Academic journals ==

    * [2014] __A. Gaignard__, J. Montagnat, B. Gibaud, G. Forestier, T. Glatard. **[[http://hal.archives-ouvertes.fr/docs/01/02/75/96/PDF/JWS-D-13-00125R4.pdf | 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. **[[http://www.hal.inserm.fr/docs/01/06/23/71/PDF/ontovip-for-hal.pdf | 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. **[[http://hal.archives-ouvertes.fr/index.php?halsid=u30g98d20u1npr3rkno6goci74&view_this_doc=inserm-00762497&version=1|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. **[[http://hal.archives-ouvertes.fr/index.php?halsid=njs56o622d3bvpgdae0ek1erb4&view_this_doc=hal-00733556&version=1|Composing Multiple Variability Artifacts to Assemble Coherent Workflows]]**, SQJo’2011 (Software Quality Journal, special issue in Quality Engineering for Software Product Lines).


== International conferences ==


    * [2012] O. Corby, __A. Gaignard__, C. Faron Zucker, J. Montagnat. **[[http://hal.archives-ouvertes.fr/hal-00746772|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. **[[http://hal.archives-ouvertes.fr/hal-00677829|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. **[[http://hal.archives-ouvertes.fr/hal-00683087|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. **[[http://hal.archives-ouvertes.fr/hal-00690921|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. **[[http://www.google.fr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CDQQFjAA&url=http%3A%2F%2Fneurolog.i3s.unice.fr%2F_media%2Fpublic_namespace%2Fhbm11-def.pdf&ei=SSk5U-DPKsaxhAfiyYG4BA&usg=AFQjCNFxWPvs_VncRW-kA4z8du2plzOYxw&sig2=FGhDvob_vAS69CkAnr-2Xw&bvm=bv.63808443,d.Yms|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. **[[http://hal.archives-ouvertes.fr/inserm-00512799|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. **[[http://hal.archives-ouvertes.fr/hal-00677795|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. **[[http://hal.archives-ouvertes.fr/hal-00461611|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. **[[http://hal.archives-ouvertes.fr/inria-00457129|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.**[[http://hal.archives-ouvertes.fr/inria-00477562|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. **[[http://hal.archives-ouvertes.fr/inserm-00152138|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. **[[http://hal.archives-ouvertes.fr/inserm-00141685|Federating Distributed and Heterogeneous Information Sources in Neuroimaging: The NeuroBase Project]]**  in Proceedings of the **HealthGrid'06**  conference, IOS Press, 120:3-13, Valencia.


== Workshops, national conferences & other communications ==

    * [2014] O. Seye, C. Faron Zucker, O. Corby, __A. Gaignard__. **[[http://hal.archives-ouvertes.fr/hal-01015281|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. **[[https://hal.archives-ouvertes.fr/hal-01048737|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. **[[http://hal.archives-ouvertes.fr/hal-00746765|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. **[[http://hal.archives-ouvertes.fr/hal-01018722|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. **[[http://hal.archives-ouvertes.fr/hal-00691827|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.


== Conference proceedings ==


    * [2012] S. Gesing, T. Glatard, J. Krüger, S. Delgado Olabarriaga, T. Solomonides, J. C. Silverstein, J. Montagnat, __A. Gaignard__, D. Krefting. **[[http://hal.archives-ouvertes.fr/hal-00842780|HealthGrid Applications and Technologies meet Science Gateways for Life Sciences]]**, proceedings of HealthGrid 2012, volume 175.
===== Softwares =====


    * **KGRAM-DQP**  : Extension to the Corese/KGRAM ([[http://wimmics.inria.fr/corese|http://wimmics.inria.fr/corese]] ) semantic web framework (SPARQL 1.1) dedicated to [[public:kgram_dqp_alban_gaignard|querying and reasoning on distributed knowledge graphs]]. Several query rewriting and dynamic optimizations for efficient distributed query processing. This software is under active development ([[https://modalis.i3s.unice.fr/_media/members/gaignard/kgram-dqp-demo.mp4|Video demonstration]])
    * **NeuSemStore**  : Semantic repositories dedicated to biomedical data management ([[http://nyx.unice.fr/projects/neusemstore|http://nyx.unice.fr/projects/neusemstore]] ). Plugins for the MOTEUR scientific workflow engine ([[http://modalis.i3s.unice.fr/moteur2|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|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)

===== Teaching =====


    * 2009-2014 : Image processing introduction {{:public:gaignard:imagesio-2014.pdf|course material}}, {{:public:gaignard:td-imagesio-2014-src.zip|skeleton source code}}, {{:public:gaignard:correction-td-image-2014.zip|filled source code}}. (//french//)
    * 2007 : Eclipse Modelling Framework : Polytech Engineering School, Sophia Antipolis (4h)
      * [[http://modalis.i3s.unice.fr/_media/gaignard:presentationcoursemf.pdf|Slides]] (//french//), [[http://modalis.i3s.unice.fr/_media/gaignard/supportcours.pdf|Printer friendly]] version (//french//)
      * [[http://modalis.i3s.unice.fr/_media/gaignard/trainingemf.pdf|Training]] (//french//)


===== Complementary formation =====

    * 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