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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Open Badges Research

Characterization of the emergent properties of a synthetic quasi-cellular system

Lorenzo Lazzerini-Ospri1, Pasquale Stano2, PierLuigi Luisi2 and Roberto Marangoni13*

Author Affiliations

1 Dipartimento di Informatica, Università di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy

2 Dipartimento di Biologia, Università di Roma III, Via G. Marconi 446, 00146 Roma, Italy

3 Istituto di Biofisica del CNR, Via G. Moruzzi 1, 56124 Pisa, Italy

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BMC Bioinformatics 2012, 13(Suppl 4):S9  doi:10.1186/1471-2105-13-S4-S9

Published: 28 March 2012

Additional files

Additional file 1:

Formal specification of the PURE system in the QDC input language: This file contains, in ASCII format, an example of the complete input file for a PURE system containing liposomes. Accordingly with QDC syntax, the file is divided into blocks: the first contains the declaration of the chemical species present in the system; the second block contains the vesicle volume; the third block contains the chemical reactions that can take place (each is described as: "k, R1 + R2 > P1 + P2", where k is the deterministic kinetic coefficient, R1 and R2 are the reagents; P1 and P2 are the products); the fourth (and last) block contains the initial number of molecules for each chemical species.

Format: TXT Size: 4KB Download file

Open Data

Additional file 2:

This file contains the list of each chemical species declared in the file puresys.txt along with the description of which real chemical species it is referred to.

Format: TXT Size: 2KB Download file

Open Data