Toward community standards and software for whole-cell modeling
Identifieur interne : 001523 ( Main/Exploration ); précédent : 001522; suivant : 001524Toward community standards and software for whole-cell modeling
Auteurs : 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. G Mez ; Jens Hahn ; Tuure Hameri ; Daniel F. Hernandez Gardiol ; Denis Kazakiewicz ; Ilya Kiselev ; Vincent Knight-Schrijver ; Christian Knüpfer ; Matthias König ; 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 Touré ; Jannis Uhlendorf ; Thawfeek M. Varusai ; Leandro H. Watanabe ; Florian Wendland ; Markus Wolfien ; James T. Yurkovich ; Yan Zhu ; Argyris Zardilis ; Anna Zhukova ; Falk SchreiberSource :
- IEEE transactions on bio-medical engineering [ 0018-9294 ] ; 2016.
Abstract
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 SBML.
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.
Url:
DOI: 10.1109/TBME.2016.2560762
PubMed: 27305665
PubMed Central: 5451320
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Toward community standards and software for whole-cell modeling</title><author><name sortKey="Waltemath, Dagmar" sort="Waltemath, Dagmar" uniqKey="Waltemath D" first="Dagmar" last="Waltemath">Dagmar Waltemath</name></author><author><name sortKey="Karr, Jonathan R" sort="Karr, Jonathan R" uniqKey="Karr J" first="Jonathan R." last="Karr">Jonathan R. Karr</name></author><author><name sortKey="Bergmann, Frank T" sort="Bergmann, Frank T" uniqKey="Bergmann F" first="Frank T." last="Bergmann">Frank T. Bergmann</name></author><author><name sortKey="Chelliah, Vijayalakshmi" sort="Chelliah, Vijayalakshmi" uniqKey="Chelliah V" first="Vijayalakshmi" last="Chelliah">Vijayalakshmi Chelliah</name></author><author><name sortKey="Hucka, Michael" sort="Hucka, Michael" uniqKey="Hucka M" first="Michael" last="Hucka">Michael Hucka</name></author><author><name sortKey="Krantz, Marcus" sort="Krantz, Marcus" uniqKey="Krantz M" first="Marcus" last="Krantz">Marcus Krantz</name></author><author><name sortKey="Liebermeister, Wolfram" sort="Liebermeister, Wolfram" uniqKey="Liebermeister W" first="Wolfram" last="Liebermeister">Wolfram Liebermeister</name></author><author><name sortKey="Mendes, Pedro" sort="Mendes, Pedro" uniqKey="Mendes P" first="Pedro" last="Mendes">Pedro Mendes</name></author><author><name sortKey="Myers, Chris J" sort="Myers, Chris J" uniqKey="Myers C" first="Chris J." last="Myers">Chris J. Myers</name></author><author><name sortKey="Pir, Pinar" sort="Pir, Pinar" uniqKey="Pir P" first="Pinar" last="Pir">Pinar Pir</name></author><author><name sortKey="Alaybeyoglu, Begum" sort="Alaybeyoglu, Begum" uniqKey="Alaybeyoglu B" first="Begum" last="Alaybeyoglu">Begum Alaybeyoglu</name></author><author><name sortKey="Aranganathan, Naveen K" sort="Aranganathan, Naveen K" uniqKey="Aranganathan N" first="Naveen K" last="Aranganathan">Naveen K. Aranganathan</name></author><author><name sortKey="Baghalian, Kambiz" sort="Baghalian, Kambiz" uniqKey="Baghalian K" first="Kambiz" last="Baghalian">Kambiz Baghalian</name></author><author><name sortKey="Bittig, Arne T" sort="Bittig, Arne T" uniqKey="Bittig A" first="Arne T." last="Bittig">Arne T. Bittig</name></author><author><name sortKey="Pinto Burke, Paulo E" sort="Pinto Burke, Paulo E" uniqKey="Pinto Burke P" first="Paulo E." last="Pinto Burke">Paulo E. Pinto Burke</name></author><author><name sortKey="Cantarelli, Matteo" sort="Cantarelli, Matteo" uniqKey="Cantarelli M" first="Matteo" last="Cantarelli">Matteo Cantarelli</name></author><author><name sortKey="Chew, Yin Hoon" sort="Chew, Yin Hoon" uniqKey="Chew Y" first="Yin Hoon" last="Chew">Yin Hoon Chew</name></author><author><name sortKey="Costa, Rafael S" sort="Costa, Rafael S" uniqKey="Costa R" first="Rafael S." last="Costa">Rafael S. Costa</name></author><author><name sortKey="Cursons, Joseph" sort="Cursons, Joseph" uniqKey="Cursons J" first="Joseph" last="Cursons">Joseph Cursons</name></author><author><name sortKey="Czauderna, Tobias" sort="Czauderna, Tobias" uniqKey="Czauderna T" first="Tobias" last="Czauderna">Tobias Czauderna</name></author><author><name sortKey="Goldberg, Arthur P" sort="Goldberg, Arthur P" uniqKey="Goldberg A" first="Arthur P." last="Goldberg">Arthur P. Goldberg</name></author><author><name sortKey="G Mez, Harold F" sort="G Mez, Harold F" uniqKey="G Mez H" first="Harold F." last="G Mez">Harold F. G Mez</name></author><author><name sortKey="Hahn, Jens" sort="Hahn, Jens" uniqKey="Hahn J" first="Jens" last="Hahn">Jens Hahn</name></author><author><name sortKey="Hameri, Tuure" sort="Hameri, Tuure" uniqKey="Hameri T" first="Tuure" last="Hameri">Tuure Hameri</name></author><author><name sortKey="Hernandez Gardiol, Daniel F" sort="Hernandez Gardiol, Daniel F" uniqKey="Hernandez Gardiol D" first="Daniel F." last="Hernandez Gardiol">Daniel F. Hernandez Gardiol</name></author><author><name sortKey="Kazakiewicz, Denis" sort="Kazakiewicz, Denis" uniqKey="Kazakiewicz D" first="Denis" last="Kazakiewicz">Denis Kazakiewicz</name></author><author><name sortKey="Kiselev, Ilya" sort="Kiselev, Ilya" uniqKey="Kiselev I" first="Ilya" last="Kiselev">Ilya Kiselev</name></author><author><name sortKey="Knight Schrijver, Vincent" sort="Knight Schrijver, Vincent" uniqKey="Knight Schrijver V" first="Vincent" last="Knight-Schrijver">Vincent Knight-Schrijver</name></author><author><name sortKey="Knupfer, Christian" sort="Knupfer, Christian" uniqKey="Knupfer C" first="Christian" last="Knüpfer">Christian Knüpfer</name></author><author><name sortKey="Konig, Matthias" sort="Konig, Matthias" uniqKey="Konig M" first="Matthias" last="König">Matthias König</name></author><author><name sortKey="Lee, Daewon" sort="Lee, Daewon" uniqKey="Lee D" first="Daewon" last="Lee">Daewon Lee</name></author><author><name sortKey="Lloret Villas, Audald" sort="Lloret Villas, Audald" uniqKey="Lloret Villas A" first="Audald" last="Lloret-Villas">Audald Lloret-Villas</name></author><author><name sortKey="Mandrik, Nikita" sort="Mandrik, Nikita" uniqKey="Mandrik N" first="Nikita" last="Mandrik">Nikita Mandrik</name></author><author><name sortKey="Medley, J Kyle" sort="Medley, J Kyle" uniqKey="Medley J" first="J. Kyle" last="Medley">J. Kyle Medley</name></author><author><name sortKey="Moreau, Bertrand" sort="Moreau, Bertrand" uniqKey="Moreau B" first="Bertrand" last="Moreau">Bertrand Moreau</name></author><author><name sortKey="Naderi Meshkin, Hojjat" sort="Naderi Meshkin, Hojjat" uniqKey="Naderi Meshkin H" first="Hojjat" last="Naderi-Meshkin">Hojjat Naderi-Meshkin</name></author><author><name sortKey="Palaniappan, Sucheendra K" sort="Palaniappan, Sucheendra K" uniqKey="Palaniappan S" first="Sucheendra K." last="Palaniappan">Sucheendra K. Palaniappan</name></author><author><name sortKey="Priego Espinosa, Daniel" sort="Priego Espinosa, Daniel" uniqKey="Priego Espinosa D" first="Daniel" last="Priego-Espinosa">Daniel Priego-Espinosa</name></author><author><name sortKey="Scharm, Martin" sort="Scharm, Martin" uniqKey="Scharm M" first="Martin" last="Scharm">Martin Scharm</name></author><author><name sortKey="Sharma, Mahesh" sort="Sharma, Mahesh" uniqKey="Sharma M" first="Mahesh" last="Sharma">Mahesh Sharma</name></author><author><name sortKey="Smallbone, Kieran" sort="Smallbone, Kieran" uniqKey="Smallbone K" first="Kieran" last="Smallbone">Kieran Smallbone</name></author><author><name sortKey="Stanford, Natalie J" sort="Stanford, Natalie J" uniqKey="Stanford N" first="Natalie J." last="Stanford">Natalie J. Stanford</name></author><author><name sortKey="Song, Je Hoon" sort="Song, Je Hoon" uniqKey="Song J" first="Je-Hoon" last="Song">Je-Hoon Song</name></author><author><name sortKey="Theile, Tom" sort="Theile, Tom" uniqKey="Theile T" first="Tom" last="Theile">Tom Theile</name></author><author><name sortKey="Tokic, Milenko" sort="Tokic, Milenko" uniqKey="Tokic M" first="Milenko" last="Tokic">Milenko Tokic</name></author><author><name sortKey="Tomar, Namrata" sort="Tomar, Namrata" uniqKey="Tomar N" first="Namrata" last="Tomar">Namrata Tomar</name></author><author><name sortKey="Toure, Vasundra" sort="Toure, Vasundra" uniqKey="Toure V" first="Vasundra" last="Touré">Vasundra Touré</name></author><author><name sortKey="Uhlendorf, Jannis" sort="Uhlendorf, Jannis" uniqKey="Uhlendorf J" first="Jannis" last="Uhlendorf">Jannis Uhlendorf</name></author><author><name sortKey="Varusai, Thawfeek M" sort="Varusai, Thawfeek M" uniqKey="Varusai T" first="Thawfeek M" last="Varusai">Thawfeek M. Varusai</name></author><author><name sortKey="Watanabe, Leandro H" sort="Watanabe, Leandro H" uniqKey="Watanabe L" first="Leandro H." last="Watanabe">Leandro H. Watanabe</name></author><author><name sortKey="Wendland, Florian" sort="Wendland, Florian" uniqKey="Wendland F" first="Florian" last="Wendland">Florian Wendland</name></author><author><name sortKey="Wolfien, Markus" sort="Wolfien, Markus" uniqKey="Wolfien M" first="Markus" last="Wolfien">Markus Wolfien</name></author><author><name sortKey="Yurkovich, James T" sort="Yurkovich, James T" uniqKey="Yurkovich J" first="James T." last="Yurkovich">James T. Yurkovich</name></author><author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name></author><author><name sortKey="Zardilis, Argyris" sort="Zardilis, Argyris" uniqKey="Zardilis A" first="Argyris" last="Zardilis">Argyris Zardilis</name></author><author><name sortKey="Zhukova, Anna" sort="Zhukova, Anna" uniqKey="Zhukova A" first="Anna" last="Zhukova">Anna Zhukova</name></author><author><name sortKey="Schreiber, Falk" sort="Schreiber, Falk" uniqKey="Schreiber F" first="Falk" last="Schreiber">Falk Schreiber</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27305665</idno><idno type="pmc">5451320</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451320</idno><idno type="RBID">PMC:5451320</idno><idno type="doi">10.1109/TBME.2016.2560762</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">002D55</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002D55</idno><idno type="wicri:Area/Pmc/Curation">002C05</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">002C05</idno><idno type="wicri:Area/Pmc/Checkpoint">000518</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000518</idno><idno type="wicri:Area/Ncbi/Merge">003712</idno><idno type="wicri:Area/Ncbi/Curation">003712</idno><idno type="wicri:Area/Ncbi/Checkpoint">003712</idno><idno type="wicri:doubleKey">0018-9294:2016:Waltemath D:toward:community:standards</idno><idno type="wicri:Area/Main/Merge">001518</idno><idno type="wicri:Area/Main/Curation">001523</idno><idno type="wicri:Area/Main/Exploration">001523</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Toward community standards and software for whole-cell modeling</title><author><name sortKey="Waltemath, Dagmar" sort="Waltemath, Dagmar" uniqKey="Waltemath D" first="Dagmar" last="Waltemath">Dagmar Waltemath</name></author><author><name sortKey="Karr, Jonathan R" sort="Karr, Jonathan R" uniqKey="Karr J" first="Jonathan R." last="Karr">Jonathan R. Karr</name></author><author><name sortKey="Bergmann, Frank T" sort="Bergmann, Frank T" uniqKey="Bergmann F" first="Frank T." last="Bergmann">Frank T. Bergmann</name></author><author><name sortKey="Chelliah, Vijayalakshmi" sort="Chelliah, Vijayalakshmi" uniqKey="Chelliah V" first="Vijayalakshmi" last="Chelliah">Vijayalakshmi Chelliah</name></author><author><name sortKey="Hucka, Michael" sort="Hucka, Michael" uniqKey="Hucka M" first="Michael" last="Hucka">Michael Hucka</name></author><author><name sortKey="Krantz, Marcus" sort="Krantz, Marcus" uniqKey="Krantz M" first="Marcus" last="Krantz">Marcus Krantz</name></author><author><name sortKey="Liebermeister, Wolfram" sort="Liebermeister, Wolfram" uniqKey="Liebermeister W" first="Wolfram" last="Liebermeister">Wolfram Liebermeister</name></author><author><name sortKey="Mendes, Pedro" sort="Mendes, Pedro" uniqKey="Mendes P" first="Pedro" last="Mendes">Pedro Mendes</name></author><author><name sortKey="Myers, Chris J" sort="Myers, Chris J" uniqKey="Myers C" first="Chris J." last="Myers">Chris J. Myers</name></author><author><name sortKey="Pir, Pinar" sort="Pir, Pinar" uniqKey="Pir P" first="Pinar" last="Pir">Pinar Pir</name></author><author><name sortKey="Alaybeyoglu, Begum" sort="Alaybeyoglu, Begum" uniqKey="Alaybeyoglu B" first="Begum" last="Alaybeyoglu">Begum Alaybeyoglu</name></author><author><name sortKey="Aranganathan, Naveen K" sort="Aranganathan, Naveen K" uniqKey="Aranganathan N" first="Naveen K" last="Aranganathan">Naveen K. Aranganathan</name></author><author><name sortKey="Baghalian, Kambiz" sort="Baghalian, Kambiz" uniqKey="Baghalian K" first="Kambiz" last="Baghalian">Kambiz Baghalian</name></author><author><name sortKey="Bittig, Arne T" sort="Bittig, Arne T" uniqKey="Bittig A" first="Arne T." last="Bittig">Arne T. Bittig</name></author><author><name sortKey="Pinto Burke, Paulo E" sort="Pinto Burke, Paulo E" uniqKey="Pinto Burke P" first="Paulo E." last="Pinto Burke">Paulo E. Pinto Burke</name></author><author><name sortKey="Cantarelli, Matteo" sort="Cantarelli, Matteo" uniqKey="Cantarelli M" first="Matteo" last="Cantarelli">Matteo Cantarelli</name></author><author><name sortKey="Chew, Yin Hoon" sort="Chew, Yin Hoon" uniqKey="Chew Y" first="Yin Hoon" last="Chew">Yin Hoon Chew</name></author><author><name sortKey="Costa, Rafael S" sort="Costa, Rafael S" uniqKey="Costa R" first="Rafael S." last="Costa">Rafael S. Costa</name></author><author><name sortKey="Cursons, Joseph" sort="Cursons, Joseph" uniqKey="Cursons J" first="Joseph" last="Cursons">Joseph Cursons</name></author><author><name sortKey="Czauderna, Tobias" sort="Czauderna, Tobias" uniqKey="Czauderna T" first="Tobias" last="Czauderna">Tobias Czauderna</name></author><author><name sortKey="Goldberg, Arthur P" sort="Goldberg, Arthur P" uniqKey="Goldberg A" first="Arthur P." last="Goldberg">Arthur P. Goldberg</name></author><author><name sortKey="G Mez, Harold F" sort="G Mez, Harold F" uniqKey="G Mez H" first="Harold F." last="G Mez">Harold F. G Mez</name></author><author><name sortKey="Hahn, Jens" sort="Hahn, Jens" uniqKey="Hahn J" first="Jens" last="Hahn">Jens Hahn</name></author><author><name sortKey="Hameri, Tuure" sort="Hameri, Tuure" uniqKey="Hameri T" first="Tuure" last="Hameri">Tuure Hameri</name></author><author><name sortKey="Hernandez Gardiol, Daniel F" sort="Hernandez Gardiol, Daniel F" uniqKey="Hernandez Gardiol D" first="Daniel F." last="Hernandez Gardiol">Daniel F. Hernandez Gardiol</name></author><author><name sortKey="Kazakiewicz, Denis" sort="Kazakiewicz, Denis" uniqKey="Kazakiewicz D" first="Denis" last="Kazakiewicz">Denis Kazakiewicz</name></author><author><name sortKey="Kiselev, Ilya" sort="Kiselev, Ilya" uniqKey="Kiselev I" first="Ilya" last="Kiselev">Ilya Kiselev</name></author><author><name sortKey="Knight Schrijver, Vincent" sort="Knight Schrijver, Vincent" uniqKey="Knight Schrijver V" first="Vincent" last="Knight-Schrijver">Vincent Knight-Schrijver</name></author><author><name sortKey="Knupfer, Christian" sort="Knupfer, Christian" uniqKey="Knupfer C" first="Christian" last="Knüpfer">Christian Knüpfer</name></author><author><name sortKey="Konig, Matthias" sort="Konig, Matthias" uniqKey="Konig M" first="Matthias" last="König">Matthias König</name></author><author><name sortKey="Lee, Daewon" sort="Lee, Daewon" uniqKey="Lee D" first="Daewon" last="Lee">Daewon Lee</name></author><author><name sortKey="Lloret Villas, Audald" sort="Lloret Villas, Audald" uniqKey="Lloret Villas A" first="Audald" last="Lloret-Villas">Audald Lloret-Villas</name></author><author><name sortKey="Mandrik, Nikita" sort="Mandrik, Nikita" uniqKey="Mandrik N" first="Nikita" last="Mandrik">Nikita Mandrik</name></author><author><name sortKey="Medley, J Kyle" sort="Medley, J Kyle" uniqKey="Medley J" first="J. Kyle" last="Medley">J. Kyle Medley</name></author><author><name sortKey="Moreau, Bertrand" sort="Moreau, Bertrand" uniqKey="Moreau B" first="Bertrand" last="Moreau">Bertrand Moreau</name></author><author><name sortKey="Naderi Meshkin, Hojjat" sort="Naderi Meshkin, Hojjat" uniqKey="Naderi Meshkin H" first="Hojjat" last="Naderi-Meshkin">Hojjat Naderi-Meshkin</name></author><author><name sortKey="Palaniappan, Sucheendra K" sort="Palaniappan, Sucheendra K" uniqKey="Palaniappan S" first="Sucheendra K." last="Palaniappan">Sucheendra K. Palaniappan</name></author><author><name sortKey="Priego Espinosa, Daniel" sort="Priego Espinosa, Daniel" uniqKey="Priego Espinosa D" first="Daniel" last="Priego-Espinosa">Daniel Priego-Espinosa</name></author><author><name sortKey="Scharm, Martin" sort="Scharm, Martin" uniqKey="Scharm M" first="Martin" last="Scharm">Martin Scharm</name></author><author><name sortKey="Sharma, Mahesh" sort="Sharma, Mahesh" uniqKey="Sharma M" first="Mahesh" last="Sharma">Mahesh Sharma</name></author><author><name sortKey="Smallbone, Kieran" sort="Smallbone, Kieran" uniqKey="Smallbone K" first="Kieran" last="Smallbone">Kieran Smallbone</name></author><author><name sortKey="Stanford, Natalie J" sort="Stanford, Natalie J" uniqKey="Stanford N" first="Natalie J." last="Stanford">Natalie J. Stanford</name></author><author><name sortKey="Song, Je Hoon" sort="Song, Je Hoon" uniqKey="Song J" first="Je-Hoon" last="Song">Je-Hoon Song</name></author><author><name sortKey="Theile, Tom" sort="Theile, Tom" uniqKey="Theile T" first="Tom" last="Theile">Tom Theile</name></author><author><name sortKey="Tokic, Milenko" sort="Tokic, Milenko" uniqKey="Tokic M" first="Milenko" last="Tokic">Milenko Tokic</name></author><author><name sortKey="Tomar, Namrata" sort="Tomar, Namrata" uniqKey="Tomar N" first="Namrata" last="Tomar">Namrata Tomar</name></author><author><name sortKey="Toure, Vasundra" sort="Toure, Vasundra" uniqKey="Toure V" first="Vasundra" last="Touré">Vasundra Touré</name></author><author><name sortKey="Uhlendorf, Jannis" sort="Uhlendorf, Jannis" uniqKey="Uhlendorf J" first="Jannis" last="Uhlendorf">Jannis Uhlendorf</name></author><author><name sortKey="Varusai, Thawfeek M" sort="Varusai, Thawfeek M" uniqKey="Varusai T" first="Thawfeek M" last="Varusai">Thawfeek M. Varusai</name></author><author><name sortKey="Watanabe, Leandro H" sort="Watanabe, Leandro H" uniqKey="Watanabe L" first="Leandro H." last="Watanabe">Leandro H. Watanabe</name></author><author><name sortKey="Wendland, Florian" sort="Wendland, Florian" uniqKey="Wendland F" first="Florian" last="Wendland">Florian Wendland</name></author><author><name sortKey="Wolfien, Markus" sort="Wolfien, Markus" uniqKey="Wolfien M" first="Markus" last="Wolfien">Markus Wolfien</name></author><author><name sortKey="Yurkovich, James T" sort="Yurkovich, James T" uniqKey="Yurkovich J" first="James T." last="Yurkovich">James T. Yurkovich</name></author><author><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name></author><author><name sortKey="Zardilis, Argyris" sort="Zardilis, Argyris" uniqKey="Zardilis A" first="Argyris" last="Zardilis">Argyris Zardilis</name></author><author><name sortKey="Zhukova, Anna" sort="Zhukova, Anna" uniqKey="Zhukova A" first="Anna" last="Zhukova">Anna Zhukova</name></author><author><name sortKey="Schreiber, Falk" sort="Schreiber, Falk" uniqKey="Schreiber F" first="Falk" last="Schreiber">Falk Schreiber</name></author></analytic><series><title level="j">IEEE transactions on bio-medical engineering</title><idno type="ISSN">0018-9294</idno><idno type="eISSN">1558-2531</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="S1"><title>Objective</title><p id="P1">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.</p></sec><sec id="S2"><title>Methods</title><p id="P2">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 SBML.</p></sec><sec id="S3"><title>Results</title><p id="P3">Our analysis revealed several challenges to representing WC models using the current standards.</p></sec><sec id="S4"><title>Conclusion</title><p id="P4">We, therefore, propose several new WC modeling standards, software, and databases.</p></sec><sec id="S5"><title>Significance</title><p id="P5">We anticipate that these new standards and software will enable more comprehensive models.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Reed, Jl" uniqKey="Reed J">JL Reed</name></author><author><name sortKey="Patel, Tr" uniqKey="Patel T">TR 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Jc" uniqKey="Schaff J">JC Schaff</name></author><author><name sortKey="Lakshminarayana, A" uniqKey="Lakshminarayana A">A Lakshminarayana</name></author><author><name sortKey="Smith, Lp" uniqKey="Smith L">LP Smith</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Funahashi, A" uniqKey="Funahashi A">A Funahashi</name></author><author><name sortKey="Matsuoka, Y" uniqKey="Matsuoka Y">Y Matsuoka</name></author><author><name sortKey="Jouraku, A" uniqKey="Jouraku A">A Jouraku</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rohn, H" uniqKey="Rohn H">H Rohn</name></author><author><name sortKey="Junker, A" uniqKey="Junker A">A Junker</name></author><author><name sortKey="Hartmann, A" uniqKey="Hartmann A">A Hartmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Lp" uniqKey="Smith L">LP Smith</name></author><author><name sortKey="Bergmann, Ft" uniqKey="Bergmann F">FT Bergmann</name></author><author><name sortKey="Chandran, D" uniqKey="Chandran D">D Chandran</name></author><author><name sortKey="Sauro, Hm" uniqKey="Sauro H">HM Sauro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kolpakov, F" uniqKey="Kolpakov F">F Kolpakov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ebrahim, A" uniqKey="Ebrahim A">A Ebrahim</name></author><author><name sortKey="Lerman, Ja" uniqKey="Lerman J">JA Lerman</name></author><author><name sortKey="Palsson, Bo" uniqKey="Palsson B">BO Palsson</name></author><author><name sortKey="Hyduke, Dr" uniqKey="Hyduke D">DR Hyduke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hoops, S" uniqKey="Hoops S">S Hoops</name></author><author><name sortKey="Sahle, S" uniqKey="Sahle S">S Sahle</name></author><author><name sortKey="Lee, C" uniqKey="Lee C">C Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Madsen, C" uniqKey="Madsen C">C Madsen</name></author><author><name sortKey="Myers, Cj" uniqKey="Myers C">CJ Myers</name></author><author><name sortKey="Patterson, T" uniqKey="Patterson T">T Patterson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Somogyi, Et" uniqKey="Somogyi E">ET Somogyi</name></author><author><name sortKey="Bouteiller, J M" uniqKey="Bouteiller J">J-M Bouteiller</name></author><author><name sortKey="Glazier, Ja" uniqKey="Glazier J">JA Glazier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gillespie, Dt" uniqKey="Gillespie D">DT Gillespie</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hastings, J" uniqKey="Hastings J">J Hastings</name></author><author><name sortKey="Owen, G" uniqKey="Owen G">G Owen</name></author><author><name sortKey="Dekker, A" uniqKey="Dekker A">A Dekker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heller, Sr" uniqKey="Heller S">SR Heller</name></author><author><name sortKey="Mcnaught, A" uniqKey="Mcnaught A">A McNaught</name></author><author><name sortKey="Stein, S" uniqKey="Stein S">S Stein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Czauderna, T" uniqKey="Czauderna T">T Czauderna</name></author><author><name sortKey="Klukas, C" uniqKey="Klukas C">C Klukas</name></author><author><name sortKey="Schreiber, F" uniqKey="Schreiber F">F Schreiber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goldberg, Ap" uniqKey="Goldberg A">AP Goldberg</name></author><author><name sortKey="Chew, Yh" uniqKey="Chew Y">YH Chew</name></author><author><name sortKey="Karr, Jr" uniqKey="Karr J">JR Karr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, F" uniqKey="Zhang F">F Zhang</name></author><author><name sortKey="Meier Schellersheim, M" uniqKey="Meier Schellersheim M">M Meier-Schellersheim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nadkarni, Pm" uniqKey="Nadkarni P">PM Nadkarni</name></author><author><name sortKey="Ohno Machado, L" uniqKey="Ohno Machado L">L Ohno-Machado</name></author><author><name sortKey="Chapman, Ww" uniqKey="Chapman W">WW Chapman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Good, Bm" uniqKey="Good B">BM Good</name></author><author><name sortKey="Su, Ai" uniqKey="Su A">AI Su</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Villaverde, Af" uniqKey="Villaverde A">AF Villaverde</name></author><author><name sortKey="Egea, Ja" uniqKey="Egea J">JA Egea</name></author><author><name sortKey="Banga, Jr" uniqKey="Banga J">JR Banga</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kwiatkowska, M" uniqKey="Kwiatkowska M">M Kwiatkowska</name></author><author><name sortKey="Norman, G" uniqKey="Norman G">G Norman</name></author><author><name sortKey="Parker, D" uniqKey="Parker D">D Parker</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Alaybeyoglu, Begum" sort="Alaybeyoglu, Begum" uniqKey="Alaybeyoglu B" first="Begum" last="Alaybeyoglu">Begum Alaybeyoglu</name><name sortKey="Aranganathan, Naveen K" sort="Aranganathan, Naveen K" uniqKey="Aranganathan N" first="Naveen K" last="Aranganathan">Naveen K. Aranganathan</name><name sortKey="Baghalian, Kambiz" sort="Baghalian, Kambiz" uniqKey="Baghalian K" first="Kambiz" last="Baghalian">Kambiz Baghalian</name><name sortKey="Bergmann, Frank T" sort="Bergmann, Frank T" uniqKey="Bergmann F" first="Frank T." last="Bergmann">Frank T. Bergmann</name><name sortKey="Bittig, Arne T" sort="Bittig, Arne T" uniqKey="Bittig A" first="Arne T." last="Bittig">Arne T. Bittig</name><name sortKey="Cantarelli, Matteo" sort="Cantarelli, Matteo" uniqKey="Cantarelli M" first="Matteo" last="Cantarelli">Matteo Cantarelli</name><name sortKey="Chelliah, Vijayalakshmi" sort="Chelliah, Vijayalakshmi" uniqKey="Chelliah V" first="Vijayalakshmi" last="Chelliah">Vijayalakshmi Chelliah</name><name sortKey="Chew, Yin Hoon" sort="Chew, Yin Hoon" uniqKey="Chew Y" first="Yin Hoon" last="Chew">Yin Hoon Chew</name><name sortKey="Costa, Rafael S" sort="Costa, Rafael S" uniqKey="Costa R" first="Rafael S." last="Costa">Rafael S. Costa</name><name sortKey="Cursons, Joseph" sort="Cursons, Joseph" uniqKey="Cursons J" first="Joseph" last="Cursons">Joseph Cursons</name><name sortKey="Czauderna, Tobias" sort="Czauderna, Tobias" uniqKey="Czauderna T" first="Tobias" last="Czauderna">Tobias Czauderna</name><name sortKey="G Mez, Harold F" sort="G Mez, Harold F" uniqKey="G Mez H" first="Harold F." last="G Mez">Harold F. G Mez</name><name sortKey="Goldberg, Arthur P" sort="Goldberg, Arthur P" uniqKey="Goldberg A" first="Arthur P." last="Goldberg">Arthur P. Goldberg</name><name sortKey="Hahn, Jens" sort="Hahn, Jens" uniqKey="Hahn J" first="Jens" last="Hahn">Jens Hahn</name><name sortKey="Hameri, Tuure" sort="Hameri, Tuure" uniqKey="Hameri T" first="Tuure" last="Hameri">Tuure Hameri</name><name sortKey="Hernandez Gardiol, Daniel F" sort="Hernandez Gardiol, Daniel F" uniqKey="Hernandez Gardiol D" first="Daniel F." last="Hernandez Gardiol">Daniel F. Hernandez Gardiol</name><name sortKey="Hucka, Michael" sort="Hucka, Michael" uniqKey="Hucka M" first="Michael" last="Hucka">Michael Hucka</name><name sortKey="Karr, Jonathan R" sort="Karr, Jonathan R" uniqKey="Karr J" first="Jonathan R." last="Karr">Jonathan R. Karr</name><name sortKey="Kazakiewicz, Denis" sort="Kazakiewicz, Denis" uniqKey="Kazakiewicz D" first="Denis" last="Kazakiewicz">Denis Kazakiewicz</name><name sortKey="Kiselev, Ilya" sort="Kiselev, Ilya" uniqKey="Kiselev I" first="Ilya" last="Kiselev">Ilya Kiselev</name><name sortKey="Knight Schrijver, Vincent" sort="Knight Schrijver, Vincent" uniqKey="Knight Schrijver V" first="Vincent" last="Knight-Schrijver">Vincent Knight-Schrijver</name><name sortKey="Knupfer, Christian" sort="Knupfer, Christian" uniqKey="Knupfer C" first="Christian" last="Knüpfer">Christian Knüpfer</name><name sortKey="Konig, Matthias" sort="Konig, Matthias" uniqKey="Konig M" first="Matthias" last="König">Matthias König</name><name sortKey="Krantz, Marcus" sort="Krantz, Marcus" uniqKey="Krantz M" first="Marcus" last="Krantz">Marcus Krantz</name><name sortKey="Lee, Daewon" sort="Lee, Daewon" uniqKey="Lee D" first="Daewon" last="Lee">Daewon Lee</name><name sortKey="Liebermeister, Wolfram" sort="Liebermeister, Wolfram" uniqKey="Liebermeister W" first="Wolfram" last="Liebermeister">Wolfram Liebermeister</name><name sortKey="Lloret Villas, Audald" sort="Lloret Villas, Audald" uniqKey="Lloret Villas A" first="Audald" last="Lloret-Villas">Audald Lloret-Villas</name><name sortKey="Mandrik, Nikita" sort="Mandrik, Nikita" uniqKey="Mandrik N" first="Nikita" last="Mandrik">Nikita Mandrik</name><name sortKey="Medley, J Kyle" sort="Medley, J Kyle" uniqKey="Medley J" first="J. Kyle" last="Medley">J. Kyle Medley</name><name sortKey="Mendes, Pedro" sort="Mendes, Pedro" uniqKey="Mendes P" first="Pedro" last="Mendes">Pedro Mendes</name><name sortKey="Moreau, Bertrand" sort="Moreau, Bertrand" uniqKey="Moreau B" first="Bertrand" last="Moreau">Bertrand Moreau</name><name sortKey="Myers, Chris J" sort="Myers, Chris J" uniqKey="Myers C" first="Chris J." last="Myers">Chris J. Myers</name><name sortKey="Naderi Meshkin, Hojjat" sort="Naderi Meshkin, Hojjat" uniqKey="Naderi Meshkin H" first="Hojjat" last="Naderi-Meshkin">Hojjat Naderi-Meshkin</name><name sortKey="Palaniappan, Sucheendra K" sort="Palaniappan, Sucheendra K" uniqKey="Palaniappan S" first="Sucheendra K." last="Palaniappan">Sucheendra K. Palaniappan</name><name sortKey="Pinto Burke, Paulo E" sort="Pinto Burke, Paulo E" uniqKey="Pinto Burke P" first="Paulo E." last="Pinto Burke">Paulo E. Pinto Burke</name><name sortKey="Pir, Pinar" sort="Pir, Pinar" uniqKey="Pir P" first="Pinar" last="Pir">Pinar Pir</name><name sortKey="Priego Espinosa, Daniel" sort="Priego Espinosa, Daniel" uniqKey="Priego Espinosa D" first="Daniel" last="Priego-Espinosa">Daniel Priego-Espinosa</name><name sortKey="Scharm, Martin" sort="Scharm, Martin" uniqKey="Scharm M" first="Martin" last="Scharm">Martin Scharm</name><name sortKey="Schreiber, Falk" sort="Schreiber, Falk" uniqKey="Schreiber F" first="Falk" last="Schreiber">Falk Schreiber</name><name sortKey="Sharma, Mahesh" sort="Sharma, Mahesh" uniqKey="Sharma M" first="Mahesh" last="Sharma">Mahesh Sharma</name><name sortKey="Smallbone, Kieran" sort="Smallbone, Kieran" uniqKey="Smallbone K" first="Kieran" last="Smallbone">Kieran Smallbone</name><name sortKey="Song, Je Hoon" sort="Song, Je Hoon" uniqKey="Song J" first="Je-Hoon" last="Song">Je-Hoon Song</name><name sortKey="Stanford, Natalie J" sort="Stanford, Natalie J" uniqKey="Stanford N" first="Natalie J." last="Stanford">Natalie J. Stanford</name><name sortKey="Theile, Tom" sort="Theile, Tom" uniqKey="Theile T" first="Tom" last="Theile">Tom Theile</name><name sortKey="Tokic, Milenko" sort="Tokic, Milenko" uniqKey="Tokic M" first="Milenko" last="Tokic">Milenko Tokic</name><name sortKey="Tomar, Namrata" sort="Tomar, Namrata" uniqKey="Tomar N" first="Namrata" last="Tomar">Namrata Tomar</name><name sortKey="Toure, Vasundra" sort="Toure, Vasundra" uniqKey="Toure V" first="Vasundra" last="Touré">Vasundra Touré</name><name sortKey="Uhlendorf, Jannis" sort="Uhlendorf, Jannis" uniqKey="Uhlendorf J" first="Jannis" last="Uhlendorf">Jannis Uhlendorf</name><name sortKey="Varusai, Thawfeek M" sort="Varusai, Thawfeek M" uniqKey="Varusai T" first="Thawfeek M" last="Varusai">Thawfeek M. Varusai</name><name sortKey="Waltemath, Dagmar" sort="Waltemath, Dagmar" uniqKey="Waltemath D" first="Dagmar" last="Waltemath">Dagmar Waltemath</name><name sortKey="Watanabe, Leandro H" sort="Watanabe, Leandro H" uniqKey="Watanabe L" first="Leandro H." last="Watanabe">Leandro H. Watanabe</name><name sortKey="Wendland, Florian" sort="Wendland, Florian" uniqKey="Wendland F" first="Florian" last="Wendland">Florian Wendland</name><name sortKey="Wolfien, Markus" sort="Wolfien, Markus" uniqKey="Wolfien M" first="Markus" last="Wolfien">Markus Wolfien</name><name sortKey="Yurkovich, James T" sort="Yurkovich, James T" uniqKey="Yurkovich J" first="James T." last="Yurkovich">James T. Yurkovich</name><name sortKey="Zardilis, Argyris" sort="Zardilis, Argyris" uniqKey="Zardilis A" first="Argyris" last="Zardilis">Argyris Zardilis</name><name sortKey="Zhu, Yan" sort="Zhu, Yan" uniqKey="Zhu Y" first="Yan" last="Zhu">Yan Zhu</name><name sortKey="Zhukova, Anna" sort="Zhukova, Anna" uniqKey="Zhukova A" first="Anna" last="Zhukova">Anna Zhukova</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:5451320
|texte= Toward community standards and software for whole-cell modeling
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:27305665" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a AustralieFrV1
| This area was generated with Dilib version V0.6.33. |  |