Toward community standards and software for whole-cell modeling

Dagmar Waltemath; Jonathan R. Karr; Frank T. Bergmann; Vijayalakshmi Chelliah; Michael Hucka; Marcus Krantz; Wolfram Liebermeister; Pedro Mendes; Chris J. Myers; Pinar Pir; Begum Alaybeyoglu; Naveen K. Aranganathan; Kambiz Baghalian; Arne T. Bittig; Paulo E. Pinto Burke; Matteo Cantarelli; Yin Hoon Chew; Rafael S. Costa; Joseph Cursons; Tobias Czauderna; Arthur P. Goldberg; Harold F. Gomez; Jens Hahn; Tuure Hameri; Daniel F. Hernandez Gardiol; Denis Kazakiewicz; Ilya Kiselev; Vincent Knight-Schrijver; Christian Knupfer; Matthias Konig; Daewon Lee; Audald Lloret-Villas; Nikita Mandrik; J. Kyle Medley; Bertrand Moreau; Hojjat Naderi-Meshkin; Sucheendra K. Palaniappan; Daniel Priego-Espinosa; Martin Scharm; Mahesh Sharma; Kieran Smallbone; Natalie J. Stanford; Je-Hoon Song; Tom Theile; Milenko Tokic; Namrata Tomar; Vasundra Toure; Jannis Uhlendorf; Thawfeek M. Varusai; Leandro H. Watanabe; Florian Wendland; Markus Wolfien; James T. Yurkovich; Yan Zhu; Argyris Zardilis; Anna Zhukova; Falk Schreiber

doi:10.1109/TBME.2016.2560762

Toward community standards and software for whole-cell modeling

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias CzaudernaArthur P. Goldberg, Harold F. Gomez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knupfer, Matthias Konig, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Toure, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

Drug Discovery Biology

Research output: Contribution to journal › Article › Research › peer-review

28 Citations (Scopus)

Abstract

Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.

Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.

Results: Our analysis revealed several challenges to representing WC models using the current standards.

Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance: We anticipate that these new standards and software will enable more comprehensive models.

Original language	English
Article number	7489010
Pages (from-to)	2007-2014
Number of pages	8
Journal	IEEE Transactions on Biomedical Engineering
Volume	63
Issue number	10
DOIs	https://doi.org/10.1109/TBME.2016.2560762
Publication status	Published - 1 Oct 2016

Keywords

Computational biology
Education
Simulation
Standards
Systems biology
Whole-cell (WC) modeling

Access to Document

10.1109/TBME.2016.2560762

Link to publication in Scopus

Cite this

Waltemath, D., Karr, J. R., Bergmann, F. T., Chelliah, V., Hucka, M., Krantz, M., Liebermeister, W., Mendes, P., Myers, C. J., Pir, P., Alaybeyoglu, B., Aranganathan, N. K., Baghalian, K., Bittig, A. T., Burke, P. E. P., Cantarelli, M., Chew, Y. H., Costa, R. S., Cursons, J., ... Schreiber, F. (2016). Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering, 63(10), 2007-2014. [7489010]. https://doi.org/10.1109/TBME.2016.2560762

Waltemath, Dagmar ; Karr, Jonathan R. ; Bergmann, Frank T. ; Chelliah, Vijayalakshmi ; Hucka, Michael ; Krantz, Marcus ; Liebermeister, Wolfram ; Mendes, Pedro ; Myers, Chris J. ; Pir, Pinar ; Alaybeyoglu, Begum ; Aranganathan, Naveen K. ; Baghalian, Kambiz ; Bittig, Arne T. ; Burke, Paulo E. Pinto ; Cantarelli, Matteo ; Chew, Yin Hoon ; Costa, Rafael S. ; Cursons, Joseph ; Czauderna, Tobias ; Goldberg, Arthur P. ; Gomez, Harold F. ; Hahn, Jens ; Hameri, Tuure ; Gardiol, Daniel F. Hernandez ; Kazakiewicz, Denis ; Kiselev, Ilya ; Knight-Schrijver, Vincent ; Knupfer, Christian ; Konig, Matthias ; Lee, Daewon ; Lloret-Villas, Audald ; Mandrik, Nikita ; Medley, J. Kyle ; Moreau, Bertrand ; Naderi-Meshkin, Hojjat ; Palaniappan, Sucheendra K. ; Priego-Espinosa, Daniel ; Scharm, Martin ; Sharma, Mahesh ; Smallbone, Kieran ; Stanford, Natalie J. ; Song, Je-Hoon ; Theile, Tom ; Tokic, Milenko ; Tomar, Namrata ; Toure, Vasundra ; Uhlendorf, Jannis ; Varusai, Thawfeek M. ; Watanabe, Leandro H. ; Wendland, Florian ; Wolfien, Markus ; Yurkovich, James T. ; Zhu, Yan ; Zardilis, Argyris ; Zhukova, Anna ; Schreiber, Falk. / Toward community standards and software for whole-cell modeling. In: IEEE Transactions on Biomedical Engineering. 2016 ; Vol. 63, No. 10. pp. 2007-2014.

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title = "Toward community standards and software for whole-cell modeling",

abstract = "Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.Results: Our analysis revealed several challenges to representing WC models using the current standards.Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance: We anticipate that these new standards and software will enable more comprehensive models.",

keywords = "Computational biology, Education, Simulation, Standards, Systems biology, Whole-cell (WC) modeling",

author = "Dagmar Waltemath and Karr, {Jonathan R.} and Bergmann, {Frank T.} and Vijayalakshmi Chelliah and Michael Hucka and Marcus Krantz and Wolfram Liebermeister and Pedro Mendes and Myers, {Chris J.} and Pinar Pir and Begum Alaybeyoglu and Aranganathan, {Naveen K.} and Kambiz Baghalian and Bittig, {Arne T.} and Burke, {Paulo E. Pinto} and Matteo Cantarelli and Chew, {Yin Hoon} and Costa, {Rafael S.} and Joseph Cursons and Tobias Czauderna and Goldberg, {Arthur P.} and Gomez, {Harold F.} and Jens Hahn and Tuure Hameri and Gardiol, {Daniel F. Hernandez} and Denis Kazakiewicz and Ilya Kiselev and Vincent Knight-Schrijver and Christian Knupfer and Matthias Konig and Daewon Lee and Audald Lloret-Villas and Nikita Mandrik and Medley, {J. Kyle} and Bertrand Moreau and Hojjat Naderi-Meshkin and Palaniappan, {Sucheendra K.} and Daniel Priego-Espinosa and Martin Scharm and Mahesh Sharma and Kieran Smallbone and Stanford, {Natalie J.} and Je-Hoon Song and Tom Theile and Milenko Tokic and Namrata Tomar and Vasundra Toure and Jannis Uhlendorf and Varusai, {Thawfeek M.} and Watanabe, {Leandro H.} and Florian Wendland and Markus Wolfien and Yurkovich, {James T.} and Yan Zhu and Argyris Zardilis and Anna Zhukova and Falk Schreiber",

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Waltemath, D, Karr, JR, Bergmann, FT, Chelliah, V, Hucka, M, Krantz, M, Liebermeister, W, Mendes, P, Myers, CJ, Pir, P, Alaybeyoglu, B, Aranganathan, NK, Baghalian, K, Bittig, AT, Burke, PEP, Cantarelli, M, Chew, YH, Costa, RS, Cursons, J, Czauderna, T, Goldberg, AP, Gomez, HF, Hahn, J, Hameri, T, Gardiol, DFH, Kazakiewicz, D, Kiselev, I, Knight-Schrijver, V, Knupfer, C, Konig, M, Lee, D, Lloret-Villas, A, Mandrik, N, Medley, JK, Moreau, B, Naderi-Meshkin, H, Palaniappan, SK, Priego-Espinosa, D, Scharm, M, Sharma, M, Smallbone, K, Stanford, NJ, Song, J-H, Theile, T, Tokic, M, Tomar, N, Toure, V, Uhlendorf, J, Varusai, TM, Watanabe, LH, Wendland, F, Wolfien, M, Yurkovich, JT, Zhu, Y, Zardilis, A, Zhukova, A & Schreiber, F 2016, 'Toward community standards and software for whole-cell modeling', IEEE Transactions on Biomedical Engineering, vol. 63, no. 10, 7489010, pp. 2007-2014. https://doi.org/10.1109/TBME.2016.2560762

Toward community standards and software for whole-cell modeling. / Waltemath, Dagmar; Karr, Jonathan R.; Bergmann, Frank T.; Chelliah, Vijayalakshmi; Hucka, Michael; Krantz, Marcus; Liebermeister, Wolfram; Mendes, Pedro; Myers, Chris J.; Pir, Pinar; Alaybeyoglu, Begum; Aranganathan, Naveen K.; Baghalian, Kambiz; Bittig, Arne T.; Burke, Paulo E. Pinto; Cantarelli, Matteo; Chew, Yin Hoon; Costa, Rafael S.; Cursons, Joseph; Czauderna, Tobias; Goldberg, Arthur P.; Gomez, Harold F.; Hahn, Jens; Hameri, Tuure; Gardiol, Daniel F. Hernandez; Kazakiewicz, Denis; Kiselev, Ilya; Knight-Schrijver, Vincent; Knupfer, Christian; Konig, Matthias; Lee, Daewon; Lloret-Villas, Audald; Mandrik, Nikita; Medley, J. Kyle; Moreau, Bertrand; Naderi-Meshkin, Hojjat; Palaniappan, Sucheendra K.; Priego-Espinosa, Daniel; Scharm, Martin; Sharma, Mahesh; Smallbone, Kieran; Stanford, Natalie J.; Song, Je-Hoon; Theile, Tom; Tokic, Milenko; Tomar, Namrata; Toure, Vasundra; Uhlendorf, Jannis; Varusai, Thawfeek M.; Watanabe, Leandro H.; Wendland, Florian; Wolfien, Markus; Yurkovich, James T.; Zhu, Yan; Zardilis, Argyris; Zhukova, Anna; Schreiber, Falk.

In: IEEE Transactions on Biomedical Engineering, Vol. 63, No. 10, 7489010, 01.10.2016, p. 2007-2014.

Research output: Contribution to journal › Article › Research › peer-review

TY - JOUR

T1 - Toward community standards and software for whole-cell modeling

AU - Waltemath, Dagmar

AU - Karr, Jonathan R.

AU - Bergmann, Frank T.

AU - Chelliah, Vijayalakshmi

AU - Hucka, Michael

AU - Krantz, Marcus

AU - Liebermeister, Wolfram

AU - Mendes, Pedro

AU - Myers, Chris J.

AU - Pir, Pinar

AU - Alaybeyoglu, Begum

AU - Aranganathan, Naveen K.

AU - Baghalian, Kambiz

AU - Bittig, Arne T.

AU - Burke, Paulo E. Pinto

AU - Cantarelli, Matteo

AU - Chew, Yin Hoon

AU - Costa, Rafael S.

AU - Cursons, Joseph

AU - Czauderna, Tobias

AU - Goldberg, Arthur P.

AU - Gomez, Harold F.

AU - Hahn, Jens

AU - Hameri, Tuure

AU - Gardiol, Daniel F. Hernandez

AU - Kazakiewicz, Denis

AU - Kiselev, Ilya

AU - Knight-Schrijver, Vincent

AU - Knupfer, Christian

AU - Konig, Matthias

AU - Lee, Daewon

AU - Lloret-Villas, Audald

AU - Mandrik, Nikita

AU - Medley, J. Kyle

AU - Moreau, Bertrand

AU - Naderi-Meshkin, Hojjat

AU - Palaniappan, Sucheendra K.

AU - Priego-Espinosa, Daniel

AU - Scharm, Martin

AU - Sharma, Mahesh

AU - Smallbone, Kieran

AU - Stanford, Natalie J.

AU - Song, Je-Hoon

AU - Theile, Tom

AU - Tokic, Milenko

AU - Tomar, Namrata

AU - Toure, Vasundra

AU - Uhlendorf, Jannis

AU - Varusai, Thawfeek M.

AU - Watanabe, Leandro H.

AU - Wendland, Florian

AU - Wolfien, Markus

AU - Yurkovich, James T.

AU - Zhu, Yan

AU - Zardilis, Argyris

AU - Zhukova, Anna

AU - Schreiber, Falk

PY - 2016/10/1

Y1 - 2016/10/1

N2 - Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.Results: Our analysis revealed several challenges to representing WC models using the current standards.Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance: We anticipate that these new standards and software will enable more comprehensive models.

AB - Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.Results: Our analysis revealed several challenges to representing WC models using the current standards.Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance: We anticipate that these new standards and software will enable more comprehensive models.

KW - Computational biology

KW - Education

KW - Simulation

KW - Standards

KW - Systems biology

KW - Whole-cell (WC) modeling

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U2 - 10.1109/TBME.2016.2560762

DO - 10.1109/TBME.2016.2560762

M3 - Article

AN - SCOPUS:84993897548

VL - 63

SP - 2007

EP - 2014

JO - IEEE Transactions on Biomedical Engineering

JF - IEEE Transactions on Biomedical Engineering

SN - 0018-9294

IS - 10

M1 - 7489010

ER -