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start [2017/07/24 16:12]
gaignard
start [2017/10/09 11:16]
gaignard [Publications]
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-====== ​SyMeTRIC project ​====== +====== ​Objectives ​====== ​ 
-{{ :​poster-symetric.pdf | Poster (french)}}+
  
-SyMeTRIC is a regional federated project in Systems Medicine funded by the Pays de la Loire french region. Similarly to Systems Biology, Systems Medicine approaches aim at integrating several information sources to design and validate bio-models and biomarkers to anticipate and enhance patients following (diagnosis, treatment response prediction, prognosis).+SyMeTRIC is a regional federated project in **Systems Medicine** funded by the Pays de la Loire french region. Similarly to Systems Biology, Systems Medicine approaches aim at integrating several information sources to design and validate bio-models and biomarkers to anticipate and enhance patients following (diagnosis, treatment response prediction, prognosis).
  
 This novel and multi-disciplinary approach of medicine relies on computational and mathematical sciences to better exploit the massive production of heterogeneous biomedical data. This novel and multi-disciplinary approach of medicine relies on computational and mathematical sciences to better exploit the massive production of heterogeneous biomedical data.
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 The long term goal of SyMeTRIC is to build a common Systems Medicine computing infrastructure to accelerate the discovery and validation of biomarkers in the fields of oncology, transplantation,​ and chronic cardiovascular diseases. The long term goal of SyMeTRIC is to build a common Systems Medicine computing infrastructure to accelerate the discovery and validation of biomarkers in the fields of oncology, transplantation,​ and chronic cardiovascular diseases.
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 +{{ :​logos-all.png?​nolink&​800 |}}
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 +{{ :​poster-symetric.pdf | Poster (french)}}
  
 ====== Publications ======  ​ ====== Publications ======  ​
-  * [2017] M. Lefebvre, J. Bourdon, C. Guziolowski,​ A. Gaignard. **Regulatory and signaling network assembly through linked open data**, demo paper, Journées Ouvertes en BioInformatique ​et Mathématiques (JOBIM2017). [[https://​fr.slideshare.net/​MarieLefebvre11/​regulatory-and-signaling-network-assembly-through-linked-open-data-77947458|(Slides)]]+  * [2017] M. Lefebvre, J. Bourdon, C. Guziolowski,​ A. Gaignard. **Regulatory and signaling network assembly through linked open data**, demo paper, Journées Ouvertes en Biologie, Informatique ​et Mathématiques (JOBIM2017). [[https://​fr.slideshare.net/​MarieLefebvre11/​regulatory-and-signaling-network-assembly-through-linked-open-data-77947458|(Slides)]]
   * [2017] Y. Lelievre, A. Bihouée, E. Charpentier,​ A. Gaignard, S. Souchet and D. Vintache, **Developing and sharing reproducible bioinformatics pipelines: best practices**,​ poster, Journées Ouvertes en BioInformatique et Mathématiques (JOBIM2017). {{:​poster_jobim_2017.pdf|(Poster)}}   * [2017] Y. Lelievre, A. Bihouée, E. Charpentier,​ A. Gaignard, S. Souchet and D. Vintache, **Developing and sharing reproducible bioinformatics pipelines: best practices**,​ poster, Journées Ouvertes en BioInformatique et Mathématiques (JOBIM2017). {{:​poster_jobim_2017.pdf|(Poster)}}
-  * [2017] A. Gaignard, K. Belhajjame, H. Skaf-Molli. **SHARP: Harmonizing cross-workflow provenance**,​ research paper, Semantic Web solutions for large-scale biomedical data analytics (SeWebMeDA ‘17), full day workshop at ESWC2017, Portoroz, Slovenia. [[https://​fr.slideshare.net/​alban_gaignard/​sharp-harmonizing-crossworkflow-provenance|(Slides)]] +  * [2017] A. Gaignard, K. Belhajjame, H. Skaf-Molli. **SHARP: Harmonizing cross-workflow provenance**,​ research paper, Semantic Web solutions for large-scale biomedical data analytics (SeWebMeDA ‘17), full day workshop at ESWC2017, Portoroz, Slovenia. ​[[http://​ceur-ws.org/​Vol-1948/​paper5.pdf|(Paper)]][[https://​fr.slideshare.net/​alban_gaignard/​sharp-harmonizing-crossworkflow-provenance|(Slides)]] 
-  * [2017] A. Gaignard, K. Belhajjame, H. Skaf-Molli. **SHARP: Harmonizing Galaxy and Taverna workflow provenance**,​ demo paper, Sematic Web solutions for large-scale biomedical data analytics (SeWebMeDA ‘17), full day workshop at ESWC2017, Portoroz, Slovenia. [[https://​fr.slideshare.net/​alban_gaignard/​sharp-harmonizing-galaxy-and-taverna-worflow-provenance|(Slides)]]+  * [2017] A. Gaignard, K. Belhajjame, H. Skaf-Molli. **SHARP: Harmonizing Galaxy and Taverna workflow provenance**,​ demo paper, Sematic Web solutions for large-scale biomedical data analytics (SeWebMeDA ‘17), full day workshop at ESWC2017, Portoroz, Slovenia. ​[[http://​ceur-ws.org/​Vol-1948/​paper7.pdf|(Paper)]][[https://​fr.slideshare.net/​alban_gaignard/​sharp-harmonizing-galaxy-and-taverna-worflow-provenance|(Slides)]]
   * [2017] Sarah Cohen-Boulakia,​ Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal, Christophe Blanchet. **Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities**,​ Future Generation Computing Systems journal.[[http://​www.sciencedirect.com/​science/​article/​pii/​S0167739X17300316|(Paper)]]   * [2017] Sarah Cohen-Boulakia,​ Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal, Christophe Blanchet. **Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities**,​ Future Generation Computing Systems journal.[[http://​www.sciencedirect.com/​science/​article/​pii/​S0167739X17300316|(Paper)]]
   * [2016] Alban Gaignard, Hala Skaf-Molli, Audrey Bihouée. **From scientific workflow patterns to 5-star linked open data**, 8th USENIX Workshop on the Theory and Practice of Provenance (TaPP '16). [[https://​www.usenix.org/​system/​files/​conference/​tapp16/​tapp16-paper-gaignard.pdf|(Paper)]][[http://​fr.slideshare.net/​hala44/​poemtapp16|(Slides)]]   * [2016] Alban Gaignard, Hala Skaf-Molli, Audrey Bihouée. **From scientific workflow patterns to 5-star linked open data**, 8th USENIX Workshop on the Theory and Practice of Provenance (TaPP '16). [[https://​www.usenix.org/​system/​files/​conference/​tapp16/​tapp16-paper-gaignard.pdf|(Paper)]][[http://​fr.slideshare.net/​hala44/​poemtapp16|(Slides)]]
-====== ​Software ​======+====== ​Softwares ​======
   * **BRAvo: Biological netwoRk Assembly** -> https://​github.com/​symetric-group/​bionets-demo   * **BRAvo: Biological netwoRk Assembly** -> https://​github.com/​symetric-group/​bionets-demo
   * **SHARP provenance toolbox** -> https://​github.com/​albangaignard/​sharp-prov-toolbox   * **SHARP provenance toolbox** -> https://​github.com/​albangaignard/​sharp-prov-toolbox
   * **Galaxy-PROV:​ provenance capture for Galaxy workflows** -> https://​github.com/​albangaignard/​galaxy-PROV   * **Galaxy-PROV:​ provenance capture for Galaxy workflows** -> https://​github.com/​albangaignard/​galaxy-PROV
  
-{{ :​rpdl.png?​nolink&​300 |}} +====== Funding ====== 
 +SyMeTRIC was funded by the Région Pays de la Loire [[http://​www.connectalent.org|Connect Talent]] research call 
 +{{ :​rpdl.png?​nolink&​200 |}}
start.txt · Last modified: 2017/10/09 11:16 by gaignard