An Algorithm for Initial Fluxes of Metabolic P Systems

Roberto Pagliarini, Giuditta Franco, Vincenzo Manca


A central issue in systems biology is the study of efficient methods inferring fluxes of biological reactions by starting from experimental data. Among the different techniques proposed in the last years, the theory of Metabolic P systems, which is based on the Log-Gain principle, proved to be helpful for deducing biologi- cal fluxes from temporal series of observed dynamics. According to this approach, the algebraic systems provided by the Log-Gain principle determine the reaction fluxes underlying a system dynamics when initial fluxes are known. Here we propose a heuristic algorithm for estimating the initial fluxes, that is tested in two case studies.


Biological modeling, P systems, MP systems, Metabolic flux esti- mation, Heuristic algorithms.

Full Text:



L. von Bertalanffy. General Systems Theory: Foundations, Developments, Applications. George Braziller Inc, New York, NY, 1967.

L. Bianco, F. Fontana, G. Franco, and V. Manca. P systems for biological dynamics. In [5], 81–126, 2006.

L. Bianco, F. Fontana, and V. Manca. P systems with reaction maps. International Journal of Foundations of Computer Science, 17(1):27–48, February 2006.

L. Bianco, D. Pescini, P. Siepmann, N. Krasnogor, F.J. Romero-Campero, and M. Gheorghe. To- wards a P Systems Pseudomonas Quorum Sensing Model. Lecture Notes in Computer Science, 4361:197–214, 2007.

G. Ciobanu, M. J. Pérez-Jiménez, and G. Păun (Eds.). Applications of Membrane Computing (Natural Computing Series). Springer-Verlag New York, Inc., Secaucus, NJ, USA, 2006.

F. Fontana and V. Manca. Discrete solution to differential equations by metabolic P systems. The- oretical Computer Science, 372:165–182, 2007.

J. S. Huxley. Problems of Relative Growth. 2nd Ed., Dover, New York, 1972.

D. S. Jones and B. D. Sleeman. Differential Equations and Mathematical Biology. Chapman & Hall/CRC, February 2003.

D. G. Luenberger. Optimization by Vector Space Methods, John Wiley & Sons, Inc., 1969.

V. Manca. Log-Gain Principles for Metabolic P Systems, In A. Condon et al. (Eds.), Algorithmic Bioprocesses, CHAPTER 28, Natural Computing Series, Springer-Verlag, Berlin Heidelberg, 2009.

V. Manca. The Metabolic Algorithm for P systems: Principles and Applications. Theoretical Computer Science, 404:142–157, 2008.

V. Manca. Fundamentals of metabolic P systems. In G. Păun, G. Rozenberg, and A. Salomaa, editors, Handbook of Membrane Computing, CHAPTER 16. Oxford University Press, 2009. To appear.

V. Manca. Metabolic P dynamics. In G. Păun, G. Rozenberg, and A. Salomaa, editors, Handbook of Membrane Computing, CHAPTER 17. Oxford University Press, 2009. To appear.

V. Manca and L. Bianco. Biological networks in metabolic P systems. BioSystems, 91(3):489–498, 2008.

V. Manca, L. Bianco, and F. Fontana. Evolution and oscillation in P systems: Applications to biological phenomena. Lecture Notes in Computer Science, 3365:63–84, 2005.

V. Manca, R. Pagliarini, and S. Zorzan. A photosynthetic process modelled by a metabolic P system. Natural Computing, 2009. DOI 10.1007/s11047-008-9104-x.

G. Nicolis and I. Prigogine. Exploring Complexity. An Introduction. Freeman ans Company, San Francisco, CA, 1989.

G. Păun. Membrane Computing: An Introduction. Springer, 2002.

G. Păun and G. Rozenberg. A guide to membrane computing. Theoretical Computer Science, 287(1):73–100, September 2002.

K. S. Scott. Chemical Chaos. Cambridge University Press, Cambridge, UK, 1991.

A. M. Zhabotinsky. Proc. Acc. Sci, USRR. 157:392, 1964.


Copyright (c) 2017 Roberto Pagliarini, Giuditta Franco, Vincenzo Manca

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

CC-BY-NC  License for Website User

Articles published in IJCCC user license are protected by copyright.

Users can access, download, copy, translate the IJCCC articles for non-commercial purposes provided that users, but cannot redistribute, display or adapt:

  • Cite the article using an appropriate bibliographic citation: author(s), article title, journal, volume, issue, page numbers, year of publication, DOI, and the link to the definitive published version on IJCCC website;
  • Maintain the integrity of the IJCCC article;
  • Retain the copyright notices and links to these terms and conditions so it is clear to other users what can and what cannot be done with the  article;
  • Ensure that, for any content in the IJCCC article that is identified as belonging to a third party, any re-use complies with the copyright policies of that third party;
  • Any translations must prominently display the statement: "This is an unofficial translation of an article that appeared in IJCCC. Agora University  has not endorsed this translation."

This is a non commercial license where the use of published articles for commercial purposes is forbiden. 

Commercial purposes include: 

  • Copying or downloading IJCCC articles, or linking to such postings, for further redistribution, sale or licensing, for a fee;
  • Copying, downloading or posting by a site or service that incorporates advertising with such content;
  • The inclusion or incorporation of article content in other works or services (other than normal quotations with an appropriate citation) that is then available for sale or licensing, for a fee;
  • Use of IJCCC articles or article content (other than normal quotations with appropriate citation) by for-profit organizations for promotional purposes, whether for a fee or otherwise;
  • Use for the purposes of monetary reward by means of sale, resale, license, loan, transfer or other form of commercial exploitation;

    The licensor cannot revoke these freedoms as long as you follow the license terms.

[End of CC-BY-NC  License for Website User]

INTERNATIONAL JOURNAL OF COMPUTERS COMMUNICATIONS & CONTROL (IJCCC), With Emphasis on the Integration of Three Technologies (C & C & C),  ISSN 1841-9836.

IJCCC was founded in 2006,  at Agora University, by  Ioan DZITAC (Editor-in-Chief),  Florin Gheorghe FILIP (Editor-in-Chief), and  Misu-Jan MANOLESCU (Managing Editor).

Ethics: This journal is a member of, and subscribes to the principles of, the Committee on Publication Ethics (COPE).

Ioan  DZITAC (Editor-in-Chief) at COPE European Seminar, Bruxelles, 2015:

IJCCC is covered/indexed/abstracted in Science Citation Index Expanded (since vol.1(S),  2006); JCR2018: IF=1.585..

IJCCC is indexed in Scopus from 2008 (CiteScore2018 = 1.56):

Nomination by Elsevier for Journal Excellence Award Romania 2015 (SNIP2014 = 1.029): Elsevier/ Scopus

IJCCC was nominated by Elsevier for Journal Excellence Award - "Scopus Awards Romania 2015" (SNIP2014 = 1.029).

IJCCC is in Top 3 of 157 Romanian journals indexed by Scopus (in all fields) and No.1 in Computer Science field by Elsevier/ Scopus.


 Impact Factor in JCR2018 (Clarivate Analytics/SCI Expanded/ISI Web of Science): IF=1.585 (Q3). Scopus: CiteScore2018=1.56 (Q2);

SCImago Journal & Country Rank

Editors-in-Chief: Ioan DZITAC & Florin Gheorghe FILIP.