Toward Community Standards and Software for Whole-Cell Modeling.
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.



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.



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



We, therefore, propose several new WC modeling standards, software, and databases.



We anticipate that these new standards and software will enable more comprehensive models.
Dagmar
D
Waltemath
Jonathan R
JR
Karr
Frank T
FT
Bergmann
Vijayalakshmi
V
Chelliah
Michael
M
Hucka
Marcus
M
Krantz
Wolfram
W
Liebermeister
Pedro
P
Mendes
Chris J
CJ
Myers
Pinar
P
Pir
Begum
B
Alaybeyoglu
Naveen K
NK
Aranganathan
Kambiz
K
Baghalian
Arne T
AT
Bittig
Paulo E Pinto
PE
Burke
Matteo
M
Cantarelli
Yin Hoon
YH
Chew
Rafael S
RS
Costa
Joseph
J
Cursons
Tobias
T
Czauderna
Arthur P
AP
Goldberg
Harold F
HF
Gomez
Jens
J
Hahn
Tuure
T
Hameri
Daniel F Hernandez
DF
Gardiol
Denis
D
Kazakiewicz
Ilya
I
Kiselev
Vincent
V
Knight-Schrijver
Christian
C
Knupfer
Matthias
M
Konig
Daewon
D
Lee
Audald
A
Lloret-Villas
Nikita
N
Mandrik
J Kyle
JK
Medley
Bertrand
B
Moreau
Hojjat
H
Naderi-Meshkin
Sucheendra K
SK
Palaniappan
Daniel
D
Priego-Espinosa
Martin
M
Scharm
Mahesh
M
Sharma
Kieran
K
Smallbone
Natalie J
NJ
Stanford
Je-Hoon
JH
Song
Tom
T
Theile
Milenko
M
Tokic
Namrata
N
Tomar
Vasundra
V
Toure
Jannis
J
Uhlendorf
Thawfeek M
TM
Varusai
Leandro H
LH
Watanabe
Florian
F
Wendland
Markus
M
Wolfien
James T
JT
Yurkovich
Yan
Y
Zhu
Argyris
A
Zardilis
Anna
A
Zhukova
Falk
F
Schreiber
D019295:Computational Biology; D003198:Computer Simulation; D003584:Cytological Techniques; D005260:Female; D006801:Humans; D008297:Male; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000193:education / Q000458:organization & administration / Q000592:standards*