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1

Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Cohen-Boulakia, Sarah, Belhajjame, Khalid, Collin, Olivier, Chopard, Jérôme, Froidevaux, Christine, Gaignard, Alban, Hinsen, Konrad, Larmande, Pierre, Bras, Yvan Le, Lemoine, Frédéric, Mareuil, Fabien

Journal:

Future Generation Computer Systems

Année:

2017

Langue:

english

Fichier:

PDF, 988 KB

english, 2017

2

Similarity search for scientific workflows

Starlinger, Johannes, Brancotte, Bryan, Cohen-Boulakia, Sarah, Leser, Ulf

Journal:

Proceedings of the VLDB Endowment

Année:

2014

Langue:

english

Fichier:

PDF, 787 KB

english, 2014

3

Addressing the provenance challenge using ZOOM

Sarah Cohen-Boulakia, Olivier Biton, Shirley Cohen, Susan Davidson

Journal:

Concurrency and Computation: Practice and Experience

Année:

2008

Langue:

english

Fichier:

PDF, 277 KB

english, 2008

4

Special Issue: The First Provenance Challenge

Luc Moreau, Bertram Ludäscher, Ilkay Altintas, Roger S. Barga, Shawn Bowers, Steven Callahan, George Chin JR., Ben Clifford, Shirley Cohen, Sarah Cohen-Boulakia, Susan Davidson, Ewa Deelman, Luciano D

Journal:

Concurrency and Computation: Practice and Experience

Année:

2008

Langue:

english

Fichier:

PDF, 714 KB

english, 2008

5

Proteome informatics II: Bioinformatics for comparative proteomics

Frédérique Lisacek, Sarah Cohen-Boulakia, Ron D. Appel

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 441 KB

english, 2006

6

Proteome informatics II: Bioinformatics for comparative proteomics

Frédérique Lisacek, Sarah Cohen-Boulakia, Ron D. Appel

Journal:

Année:

2006

Fichier:

PDF, 114 KB

2006

7

Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008

Amos Bairoch, Sarah Cohen-Boulakia, Christine Froidevaux

Journal:

BMC Bioinformatics

Année:

2008

Langue:

english

Fichier:

PDF, 140 KB

english, 2008

8

[Lecture Notes in Computer Science] Data Integration in the Life Sciences Volume 5109 || Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System

Bairoch, Amos, Cohen-Boulakia, Sarah, Froidevaux, Christine

Année:

2008

Langue:

english

Fichier:

PDF, 631 KB

english, 2008

9

Distilling structure in Taverna scientific workflows: a refactoring approach

Cohen-Boulakia, Sarah, Chen, Jiuqiang, Missier, Paolo, Goble, Carole, Williams, Alan R, Froidevaux, Christine

Journal:

BMC Bioinformatics

Année:

2014

Langue:

english

Fichier:

PDF, 2.39 MB

english, 2014

10

[IEEE 2012 IEEE 8th International Conference on E-Science (e-Science) - Chicago, IL, USA (2012.10.8-2012.10.12)] 2012 IEEE 8th International Conference on E-Science - Scientific workflow rewriting while preserving provenance

Cohen-Boulakia, Sarah, Froidevaux, Christine, Chen, Jiuqiang

Année:

2012

Langue:

english

Fichier:

PDF, 852 KB

english, 2012

11

[IEEE 2009 IEEE 25th International Conference on Data Engineering (ICDE) - Shanghai, China (2009.03.29-2009.04.2)] 2009 IEEE 25th International Conference on Data Engineering - Differencing Provenance in Scientific Workflows

Bao, Zhuowei, Cohen-Boulakia, Sarah, Davidson, Susan B., Eyal, Anat, Khanna, Sanjeev

Année:

2009

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2009

12

[IEEE 2008 IEEE 24th International Conference on Data Engineering (ICDE 2008) - Cancun, Mexico (2008.04.7-2008.04.12)] 2008 IEEE 24th International Conference on Data Engineering - Querying and Managing Provenance through User Views in Scientific Workflows

Biton, Olivier, Cohen-Boulakia, Sarah, Davidson, Susan B., Hara, Carmem S.

Année:

2008

Langue:

english

Fichier:

PDF, 5.47 MB

english, 2008

13

[IEEE 2011 IEEE International Conference on Data Engineering (ICDE 2011) - Hannover, Germany (2011.04.11-2011.04.16)] 2011 IEEE 27th International Conference on Data Engineering - Next generation data integration for Life Sciences

Cohen-Boulakia, Sarah, Leser, Ulf

Année:

2011

Langue:

english

Fichier:

PDF, 100 KB

english, 2011

14

PATH-BASED SYSTEMS TO GUIDE SCIENTISTS IN THE MAZE OF BIOLOGICAL DATA SOURCES

COHEN-BOULAKIA, SARAH, DAVIDSON, SUSAN, FROIDEVAUX, CHRISTINE, LACROIX, ZOÉ, VIDAL, MARIA-ESTHER

Journal:

Journal of Bioinformatics and Computational Biology

Année:

2006

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2006

15

[Lecture Notes in Computer Science] Data Integration in the Life Sciences Volume 4544 || CONANN: An Online Biomedical Concept Annotator

Cohen-Boulakia, Sarah, Tannen, Val

Année:

2007

Langue:

english

Fichier:

PDF, 261 KB

english, 2007

16

[Lecture Notes in Computer Science] Data Integration in the Life Sciences Volume 4544 || Automatically Constructing a Directory of Molecular Biology Databases

Cohen-Boulakia, Sarah, Tannen, Val

Année:

2007

Langue:

english

Fichier:

PDF, 732 KB

english, 2007

17

Search, adapt, and reuse

Cohen-Boulakia, Sarah, Leser, Ulf

Journal:

ACM SIGMOD Record

Année:

2011

Langue:

english

Fichier:

PDF, 543 KB

english, 2011

18

PDiffView

Bao, Zhuowei, Cohen-Boulakia, Sarah, Davidson, Susan B., Girard, Pierrick

Journal:

Proceedings of the VLDB Endowment

Année:

2009

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2009

19

Rank aggregation with ties

Brancotte, Bryan, Yang, Bo, Blin, Guillaume, Cohen-Boulakia, Sarah, Denise, Alain, Hamel, Sylvie

Journal:

Proceedings of the VLDB Endowment

Année:

2015

Langue:

english

Fichier:

PDF, 498 KB

english, 2015

20

[ACM Press the 27th International Conference - La Jolla, California (2015.06.29-2015.07.01)] Proceedings of the 27th International Conference on Scientific and Statistical Database Management - SSDBM '15 - OpenAlea

Pradal, Christophe, Fournier, Christian, Valduriez, Patrick, Cohen-Boulakia, Sarah

Année:

2015

Langue:

english

Fichier:

PDF, 549 KB

english, 2015

21

Effective and efficient similarity search in scientific workflow repositories

Starlinger, Johannes, Cohen-Boulakia, Sarah, Khanna, Sanjeev, Davidson, Susan B., Leser, Ulf

Journal:

Future Generation Computer Systems

Année:

2015

Langue:

english

Fichier:

PDF, 2.04 MB

english, 2015

22

[IEEE 2014 IEEE 10th International Conference on e-Science (e-Science) - Sao Paulo, Brazil (2014.10.20-2014.10.24)] 2014 IEEE 10th International Conference on e-Science - Layer Decomposition: An Effective Structure-Based Approach for Scientific Workflow Similarity

Starlinger, Johannes, Cohen-Boulakia, Sarah, Khanna, Sanjeev, Davidson, Susan B., Leser, Ulf

Année:

2014

Langue:

english

Fichier:

PDF, 707 KB

english, 2014

23

InfraPhenoGrid: A scientific workflow infrastructure for plant phenomics on the Grid

Pradal, Christophe, Artzet, Simon, Chopard, Jérôme, Dupuis, Dimitri, Fournier, Christian, Mielewczik, Michael, Nègre, Vincent, Neveu, Pascal, Parigot, Didier, Valduriez, Patrick, Cohen-Boulakia, Sarah

Journal:

Future Generation Computer Systems

Année:

2016

Langue:

english

Fichier:

PDF, 3.46 MB

english, 2016

24

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Maui, Hawaii (3 – 7 January 2006)] Biocomputing 2006 - SELECTING BIOLOGICAL DATA SOURCES AND TOOLS WITH XPR, A PATH LANGUAGE FOR RDF

COHEN-BOULAKIA, SARAH, FROIDEVAUX, CHRISTINE, PIETRIGA, EMMANUEL

Langue:

english

Fichier:

PDF, 809 KB

english

25

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Naldi, Aurélien, Hernandez, Céline, Levy, Nicolas, Stoll, Gautier, Monteiro, Pedro T., Chaouiya, Claudine, Helikar, Tomáš, Zinovyev, Andrei, Calzone, Laurence, Cohen-Boulakia, Sarah, Thieffry, Denis,

Journal:

Frontiers in Physiology

Année:

2018

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2018

26

[IEEE 2018 IEEE 14th International Conference on e-Science (e-Science) - Amsterdam (2018.10.29-2018.11.1)] 2018 IEEE 14th International Conference on e-Science (e-Science) - Designing Scientific SPARQL Queries Using Autocompletion by Snippets

Rafes, Karima, Abiteboul, Serge, Cohen-Boulakia, Sarah, Rance, Bastien

Année:

2018

Langue:

english

Fichier:

PDF, 10 KB

english, 2018

27

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Lemoine, Frédéric, Correia, Damien, Lefort, Vincent, Doppelt-Azeroual, Olivia, Mareuil, Fabien, Cohen-Boulakia, Sarah, Gascuel, Olivier

Journal:

Nucleic Acids Research

Année:

2019

Langue:

english

Fichier:

PDF, 3.34 MB

english, 2019

28

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

Lemoine, Frédéric, Correia, Damien, Lefort, Vincent, Doppelt-Azeroual, Olivia, Mareuil, Fabien, Cohen-Boulakia, Sarah, Gascuel, Olivier

Journal:

Nucleic Acids Research

Année:

2019

Fichier:

PDF, 3.34 MB

2019

29

VersionClimber: Version Upgrades Without Tears

Pradal, Christophe, Cohen-Boulakia, Sarah, Valduriez, Patrick, Shasha, Dennis, Hinsen, Konrad, Turk, Matthew

Journal:

Computing in Science & Engineering

Année:

2019

Langue:

english

Fichier:

PDF, 153 KB

english, 2019

30

FAIR Computational Workflows

Goble, Carole, Cohen-Boulakia, Sarah, Soiland-Reyes, Stian, Garijo, Daniel, Gil, Yolanda, Crusoe, Michael R., Peters, Kristian, Schober, Daniel

Journal:

Data Intelligence

Année:

2019

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2019

31

[IEEE 2019 15th International Conference on eScience (eScience) - San Diego, CA, USA (2019.9.24-2019.9.27)] 2019 15th International Conference on eScience (eScience) - Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data

Andrieu, Pierre, Brancotte, Bryan, Bulteau, Laurent, Cohen-Boulakia, Sarah, Denise, Alain, Pierrot, Adeline, Vialette, Stephane

Année:

2019

Fichier:

PDF, 475 KB

2019