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1

Evolution of computational models in BioModels Database and the Physiome Model Repository

Scharm, Martin, Gebhardt, Tom, Touré, Vasundra, Bagnacani, Andrea, Salehzadeh-Yazdi, Ali, Wolkenhauer, Olaf, Waltemath, Dagmar

Journal:

BMC Systems Biology

Année:

2018

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2018

2

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

Touré, Vasundra, Le Novère, Nicolas, Waltemath, Dagmar, Wolkenhauer, Olaf, Ouellette, Francis

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2018

3

Annotation-based feature extraction from sets of SBML models

Alm, Rebekka, Waltemath, Dagmar, Wolfien, Markus, Wolkenhauer, Olaf, Henkel, Ron

Journal:

Journal of Biomedical Semantics

Année:

2015

Langue:

english

Fichier:

PDF, 1.69 MB

english, 2015

4

Das Sombi-Framework zum Ermitteln geeigneter Suchfunktionen für biologische Modelldatenbasen

Dagmar Waltemath, Ron Henkel, Holger Meyer, Andreas Heuer

Journal:

Datenbank-Spektrum

Année:

2011

Langue:

german

Fichier:

PDF, 1.21 MB

german, 2011

5

Ranked retrieval of Computational Biology models

Ron Henkel, Lukas Endler, Andre Peters, Nicolas Le Novère, Dagmar Waltemath

Journal:

BMC Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2010

6

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, Jacky L Snoep, Nicolas Le Novère

Journal:

BMC Systems Biology

Année:

2011

Langue:

english

Fichier:

PDF, 927 KB

english, 2011

7

A call for virtual experiments: Accelerating the scientific process

Cooper, Jonathan, Vik, Jon Olav, Waltemath, Dagmar

Journal:

Progress in Biophysics and Molecular Biology

Année:

2015

Langue:

english

Fichier:

PDF, 875 KB

english, 2015

8

Minimum Information About a Simulation Experiment (MIASE)

Waltemath, Dagmar, Adams, Richard, Beard, Daniel A., Bergmann, Frank T., Bhalla, Upinder S., Britten, Randall, Chelliah, Vijayalakshmi, Cooling, Michael T., Cooper, Jonathan, Crampin, Edmund J., Garny

Journal:

PLoS Computational Biology

Année:

2011

Langue:

english

Fichier:

PDF, 96 KB

english, 2011

9

An algorithm to detect and communicate the differences in computational models describing biological systems

Scharm, Martin, Wolkenhauer, Olaf, Waltemath, Dagmar

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 626 KB

english, 2016

10

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Hua

Journal:

Standards in Genomic Sciences

Année:

2014

Langue:

english

Fichier:

PDF, 669 KB

english, 2014

11

Toward community standards and software for whole-cell modeling

Waltemath, Dagmar, Karr, Jonathan, Bergmann, Frank, Chelliah, Vijayalakshmi, Hucka, Michael, Krantz, Marcus, Liebermeister, Wolfram, Mendes, Pedro, Myers, Chris, Pir, Pinar, Alaybeyoglu, Begum, Aranga

Journal:

IEEE Transactions on Biomedical Engineering

Année:

2016

Langue:

english

Fichier:

PDF, 4.66 MB

english, 2016

12

How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine

Waltemath, Dagmar, Wolkenhauer, Olaf

Journal:

IEEE Transactions on Biomedical Engineering

Année:

2016

Langue:

english

Fichier:

PDF, 4.48 MB

english, 2016

13

Notions of similarity for systems biology models

Henkel, Ron, Hoehndorf, Robert, Kacprowski, Tim, Knüpfer, Christian, Liebermeister, Wolfram, Waltemath, Dagmar

Journal:

Briefings in Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 752 KB

english, 2016

14

SED-ML web tools: generate, modify and export standard-compliant simulation studies

Bergmann, Frank T., Nickerson, David, Waltemath, Dagmar, Scharm, Martin

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 235 KB

english, 2017

15

STON: exploring biological pathways using the SBGN standard and graph databases

Touré, Vasundra, Mazein, Alexander, Waltemath, Dagmar, Balaur, Irina, Saqi, Mansoor, Henkel, Ron, Pellet, Johann, Auffray, Charles

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2016

16

The JWS online simulation database

Peters, Martin, Eicher, Johann J., van Niekerk, David D., Waltemath, Dagmar, Snoep, Jacky L.

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 105 KB

english, 2017

17

COMODI: an ontology to characterise differences in versions of computational models in biology

Martin Scharm,Dagmar Waltemath,Pedro Mendes…

Journal:

Journal of Biomedical Semantics

Année:

2016

Langue:

english

Fichier:

PDF, 912 KB

english, 2016

18

Specifications of Standards in Systems and Synthetic Biology

Schreiber, Falk, Bader, Gary D., Golebiewski, Martin, Hucka, Michael, Kormeier, Benjamin, Le Novère, Nicolas, Myers, Chris, Nickerson, David, Sommer, Björn, Waltemath, Dagmar, Weise, Stephan

Journal:

Journal of Integrative Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 102 KB

english, 2015

19

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Schreiber, Falk, Bader, Gary D., Gleeson, Padraig, Golebiewski, Martin, Hucka, Michael, Novère, Nicolas Le, Myers, Chris, Nickerson, David, Sommer, Björn, Waltemath, Dagmar

Journal:

Journal of Integrative Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 829 KB

english, 2016

20

Notions of similarity for systems biology models

Henkel, Ron, Hoehndorf, Robert, Kacprowski, Tim, Knüpfer, Christian, Liebermeister, Wolfram, Waltemath, Dagmar

Journal:

Briefings in Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 35 KB

english, 2017

21

[IEEE 2017 Winter Simulation Conference (WSC) - Las Vegas, NV (2017.12.3-2017.12.6)] 2017 Winter Simulation Conference (WSC) - A brief history of COMBINE

Myers, Chris J., Bader, Gary, Gleeson, Padraig, Golebiewski, Martin, Hucka, Michael, Le Novere, Nicolas, Nickerson, David P., Schreiber, Falk, Waltemath, Dagmar

Année:

2017

Langue:

english

Fichier:

PDF, 456 KB

english, 2017

22

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Schreiber, Falk, Bader, Gary D., Gleeson, Padraig, Golebiewski, Martin, Hucka, Michael, Keating, Sarah M., Novère, Nicolas Le, Myers, Chris, Nickerson, David, Sommer, Björn, Waltemath, Dagmar

Journal:

Journal of Integrative Bioinformatics

Année:

2018

Langue:

english

Fichier:

PDF, 329 KB

english, 2018

23

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

Hucka, Michael, Nickerson, David P., Bader, Gary D., Bergmann, Frank T., Cooper, Jonathan, Demir, Emek, Garny, Alan, Golebiewski, Martin, Myers, Chris J., Schreiber, Falk, Waltemath, Dagmar, Le NovÃ¨r

Journal:

Frontiers in Bioengineering and Biotechnology

Année:

2015

Langue:

english

Fichier:

PDF, 453 KB

english, 2015

24

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Waltemath, Dagmar, Bergmann, Frank T., Chaouiya, Claudine, Czauderna, Tobias, Gleeson, Padraig, Goble, Carole, Golebiewski, Martin, Hucka, Michael, Juty, Nick, Krebs, Olga, Le Novère, Nicolas, Mi, Hua

Journal:

Standards in Genomic Sciences

Année:

2018

Langue:

english

Fichier:

PDF, 142 KB

english, 2018

25

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Bergmann, Frank T., Cooper, Jonathan, König, Matthias, Moraru, Ion, Nickerson, David, Le Novère, Nicolas, Olivier, Brett G., Sahle, Sven, Smith, Lucian, Waltemath, Dagmar

Journal:

Journal of Integrative Bioinformatics

Langue:

english

Fichier:

PDF, 2.29 MB

english

26

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Schreiber, Falk, Sommer, Björn, Bader, Gary D., Gleeson, Padraig, Golebiewski, Martin, Hucka, Michael, Keating, Sarah M., König, Matthias, Myers, Chris, Nickerson, David, Waltemath, Dagmar

Journal:

Journal of Integrative Bioinformatics

Année:

2019

Langue:

english

Fichier:

PDF, 442 KB

english, 2019

27

Managing Bio-Models: *Model Storage, Retrieval, Ranking and Versioning

Henkel, Ron, Waltemath, Dagmar, Wolkenhauer, Olaf

Journal:

Bioentrepreneur

Année:

2011

Langue:

english

Fichier:

PDF, 958 KB

english, 2011

28

Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY

Juty, Nick, Le Novère, Nicolas, Waltemath, Dagmar, Knuepfer, Christian

Journal:

Bioentrepreneur

Année:

2010

Langue:

english

Fichier:

PDF, 4.75 MB

english, 2010

29

SBML Level 3 Package Proposal: Annotation

Hucka, Michael, Laibe, Camille, Juty, Nick, Liebermeister, Wolfram, Keating, Sarah, Lloyd, Catherine, Knuepfer, Christian, Misirli, Goksel, Schulz, Marvin, Waltemath, Dagmar, Taschuk, Morgan, Swainsto

Journal:

Bioentrepreneur

Année:

2011

Langue:

english

Fichier:

PDF, 330 KB

english, 2011

30

Searching BioModels Database

Henkel, Ron, Waltemath, Dagmar, Peters, Andre, Endler, Lukas, le Novère, Nicolas

Journal:

Bioentrepreneur

Année:

2010

Langue:

english

Fichier:

PDF, 1.33 MB

english, 2010

31

Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1

Waltemath, Dagmar, Bergmann, Frank, Adams, Richard, Le Novere, Nicolas

Journal:

Bioentrepreneur

Année:

2011

Langue:

english

Fichier:

PDF, 5.17 MB

english, 2011

32

Kinetic Simulation Algorithm Ontology

Zhukova, Anna, Waltemath, Dagmar, Juty, Nick, Laibe, Camille, Le Novère, Nicolas

Journal:

Bioentrepreneur

Année:

2011

Langue:

english

Fichier:

PDF, 2.39 MB

english, 2011

33

SBML Level 3 Package Proposal: Annotation

Hucka, Michael, Laibe, Camille, Juty, Nick, Liebermeister, Wolfram, Keating, Sarah, Lloyd, Catherine, Knuepfer, Christian, Misirli, Goksel, Schulz, Marvin, Waltemath, Dagmar, Taschuk, Morgan, Swainsto

Journal:

Bioentrepreneur

Année:

2011

Fichier:

PDF, 330 KB

2011

34

Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY

Juty, Nick, Le Novère, Nicolas, Waltemath, Dagmar, Knuepfer, Christian

Journal:

Bioentrepreneur

Année:

2010

Fichier:

PDF, 4.75 MB

2010

35

Searching BioModels Database

Henkel, Ron, Waltemath, Dagmar, Peters, Andre, Endler, Lukas, le Novère, Nicolas

Journal:

Bioentrepreneur

Année:

2010

Fichier:

PDF, 1.33 MB

2010

36

Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1

Waltemath, Dagmar, Bergmann, Frank, Adams, Richard, Le Novere, Nicolas

Journal:

Bioentrepreneur

Année:

2011

Fichier:

PDF, 5.17 MB

2011

37

Kinetic Simulation Algorithm Ontology

Zhukova, Anna, Waltemath, Dagmar, Juty, Nick, Laibe, Camille, Le Novère, Nicolas

Journal:

Bioentrepreneur

Année:

2011

Fichier:

PDF, 2.39 MB

2011