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 | |
| Publication status | Published - 1 Oct 2016 |
Keywords
- Computational biology
- Education
- Simulation
- Standards
- Systems biology
- Whole-cell (WC) modeling
Cite this
}
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
UR - http://www.scopus.com/inward/record.url?scp=84993897548&partnerID=8YFLogxK
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 -