---
_id: '5587'
abstract:
- lang: eng
  text: "Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC
    NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E.
    coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix
    enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose
    limited minimal medium, \r\nobtained from the soichiometric matrix by standard
    linear algebra  (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John
    ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in
    a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter
    of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli
    catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with
    the Lovasz method.\r\n\r\nlovasz.cpp  \r\nThis c++ code file receives in input
    the polytope of the feasible steady states of a metabolic network, \r\n(matrix
    and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding
    the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults
    to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we
    refer to  PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp  \r\nThis c++
    code file receives in input the polytope of the feasible steady states of a metabolic
    network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point
    inside and  \r\nit gives in output a max entropy sampling at fixed average growth
    rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov
    chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli
    network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015)."
article_processing_charge: No
author:
- first_name: Daniele
  full_name: De Martino, Daniele
  id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
  last_name: De Martino
  orcid: 0000-0002-5214-4706
- first_name: Gasper
  full_name: Tkacik, Gasper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
citation:
  ama: De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC
    NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:<a href="https://doi.org/10.15479/AT:ISTA:62">10.15479/AT:ISTA:62</a>
  apa: De Martino, D., &#38; Tkačik, G. (2018). Supporting materials “STATISTICAL
    MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science
    and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:62">https://doi.org/10.15479/AT:ISTA:62</a>
  chicago: De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL
    MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science
    and Technology Austria, 2018. <a href="https://doi.org/10.15479/AT:ISTA:62">https://doi.org/10.15479/AT:ISTA:62</a>.
  ieee: D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS
    FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology
    Austria, 2018.
  ista: De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS
    FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology
    Austria, <a href="https://doi.org/10.15479/AT:ISTA:62">10.15479/AT:ISTA:62</a>.
  mla: De Martino, Daniele, and Gašper Tkačik. <i>Supporting Materials “STATISTICAL
    MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.”</i> Institute of Science
    and Technology Austria, 2018, doi:<a href="https://doi.org/10.15479/AT:ISTA:62">10.15479/AT:ISTA:62</a>.
  short: D. De Martino, G. Tkačik, (2018).
datarep_id: '111'
date_created: 2018-12-12T12:31:41Z
date_published: 2018-09-21T00:00:00Z
date_updated: 2024-02-21T13:45:39Z
day: '21'
ddc:
- '530'
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:62
ec_funded: 1
file:
- access_level: open_access
  checksum: 97992e3e8cf8544ec985a48971708726
  content_type: application/zip
  creator: system
  date_created: 2018-12-12T13:05:13Z
  date_updated: 2020-07-14T12:47:08Z
  file_id: '5641'
  file_name: IST-2018-111-v1+1_CODES.zip
  file_size: 14376
  relation: main_file
file_date_updated: 2020-07-14T12:47:08Z
has_accepted_license: '1'
keyword:
- metabolic networks
- e.coli core
- maximum entropy
- monte carlo markov chain sampling
- ellipsoidal rounding
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: 254E9036-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28844-B27
  name: Biophysics of information processing in gene regulation
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '161'
    relation: research_paper
    status: public
status: public
title: Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE
  GROWTH"
tmp:
  image: /images/cc_0.png
  legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
  name: Creative Commons Public Domain Dedication (CC0 1.0)
  short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...