Reply to "Do genome-scale models need exact solvers or clearer standards?"
In their Correspondence entitled, “Do genome‐scale models need exact solvers or clearer standards?”, Ebrahim et al (2015) suggest an unnecessary dichotomy. They discuss the findings of our paper, “An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network...
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| Natura: | Articolo |
| Lingua: | en_US |
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EMBO Press
2016
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| Accesso online: | http://hdl.handle.net/1721.1/104072 https://orcid.org/0000-0001-8567-2049 https://orcid.org/0000-0002-2724-7228 |
| _version_ | 1826193625861586944 |
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| author | Chindelevitch, Leonid Regev, Aviv Berger Leighton, Bonnie Trigg, Jason |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Chindelevitch, Leonid Regev, Aviv Berger Leighton, Bonnie Trigg, Jason |
| author_sort | Chindelevitch, Leonid |
| collection | MIT |
| description | In their Correspondence entitled, “Do genome‐scale models need exact solvers or clearer standards?”, Ebrahim et al (2015) suggest an unnecessary dichotomy. They discuss the findings of our paper, “An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models” (Chindelevitch et al, 2014), and suggest that our work highlights the need for better model encoding standards. Moreover, the authors dispute our claims that multiple previously published metabolic network models are unable to produce growth when analyzed with an exact arithmetic approach. They attribute discrepancies between their findings and ours solely to a misinterpretation of the formatting conventions used to encode these models. The authors conclude that genome‐scale metabolic network models need better standards, rather than the improvements in accuracy obtained with exact arithmetic. We argue here that improved standards and exact arithmetic are complementary advances that both benefit this field. Thus, the answer to the question posed by Ebrahim et al (2015) is “both.” |
| first_indexed | 2024-09-23T09:42:07Z |
| format | Article |
| id | mit-1721.1/104072 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T09:42:07Z |
| publishDate | 2016 |
| publisher | EMBO Press |
| record_format | dspace |
| spelling | mit-1721.1/1040722022-09-26T13:14:25Z Reply to "Do genome-scale models need exact solvers or clearer standards?" Chindelevitch, Leonid Regev, Aviv Berger Leighton, Bonnie Trigg, Jason Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Department of Mathematics Chindelevitch, Leonid Trigg, Jason A. Regev, Aviv Berger Leighton, Bonnie In their Correspondence entitled, “Do genome‐scale models need exact solvers or clearer standards?”, Ebrahim et al (2015) suggest an unnecessary dichotomy. They discuss the findings of our paper, “An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models” (Chindelevitch et al, 2014), and suggest that our work highlights the need for better model encoding standards. Moreover, the authors dispute our claims that multiple previously published metabolic network models are unable to produce growth when analyzed with an exact arithmetic approach. They attribute discrepancies between their findings and ours solely to a misinterpretation of the formatting conventions used to encode these models. The authors conclude that genome‐scale metabolic network models need better standards, rather than the improvements in accuracy obtained with exact arithmetic. We argue here that improved standards and exact arithmetic are complementary advances that both benefit this field. Thus, the answer to the question posed by Ebrahim et al (2015) is “both.” National Institute of General Medical Sciences (U.S.) (Grant GM108348) 2016-08-30T19:01:46Z 2016-08-30T19:01:46Z 2015-10 Article http://purl.org/eprint/type/JournalArticle 1744-4292 http://hdl.handle.net/1721.1/104072 Chindelevitch, L., J. Trigg, A. Regev, and B. Berger. “Reply to ‘Do Genome-Scale Models Need Exact Solvers or Clearer Standards?’” Molecular Systems Biology 11, no. 10 (October 14, 2015): 830–830. https://orcid.org/0000-0001-8567-2049 https://orcid.org/0000-0002-2724-7228 en_US http://dx.doi.org/10.15252/msb.20156548 Molecular Systems Biology Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ application/pdf EMBO Press European Molecular Biology Organization (EMBO) |
| spellingShingle | Chindelevitch, Leonid Regev, Aviv Berger Leighton, Bonnie Trigg, Jason Reply to "Do genome-scale models need exact solvers or clearer standards?" |
| title | Reply to "Do genome-scale models need exact solvers or clearer standards?" |
| title_full | Reply to "Do genome-scale models need exact solvers or clearer standards?" |
| title_fullStr | Reply to "Do genome-scale models need exact solvers or clearer standards?" |
| title_full_unstemmed | Reply to "Do genome-scale models need exact solvers or clearer standards?" |
| title_short | Reply to "Do genome-scale models need exact solvers or clearer standards?" |
| title_sort | reply to do genome scale models need exact solvers or clearer standards |
| url | http://hdl.handle.net/1721.1/104072 https://orcid.org/0000-0001-8567-2049 https://orcid.org/0000-0002-2724-7228 |
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