An Agent Oriented Software Engineering Approach for the Adult Stem-Cell Modeling, Simulation and Visualization

Resumo. Este artigo descreve os primeiros resultados obtidos na modelagem, simulacao e visualizacao do comportamento de celulas-tronco. Um modelo conceitual da celula foi gerado e, com base nesse modelo e nos processos do ciclo de vida, divisao e diferenciacao celular, modelou-se uma ferramenta de simulacao baseada em agentes. Em paralelo e considerando o mesmo modelo conceitual e processos, foi desenvolvido um simulador modelado em COOPN de modo a possibilitar a comparacao dos resultados obtidos atraves das duas abordagens. Acredita-se que a simulacao do comportamento das celulas-tronco seja um primeiro passo para facilitar a pesquisa do comportamento de celulas-tronco. Abstract. This paper presents the first results achieved towards an agent-based adult stem cell behavior modeling, simulation and visualization. We developed a cell conceptual model on which the model is based and we built the agent-based model and simulation considering the cell life-cycle and the basic processes related to the cell division and differentiation. Based in the same conceptual model, we also modeled and simulated the behavior through the COOPN technique to compare the results. We believe that stem cell simulation behavior is a first step towards the stem cell therapy costs minimization. With regard to the medicine point of view, if the model is sufficiently detailed and accurate, it serves as a reference, a guide for interpreting experimental results, and a powerful means of suggesting new hypotheses. Moreover, the simulation lets physicians test experimentally unfeasible scenarios and can potentially reduce experimental costs. It's our belief that the Agent-Oriented Software Engineering (AOSE) provides clean design in the modeling phase and efficient numerical routines in the simulation phase. Those techniques address the currents drawback of other existents approaches related to the model's semantic (it is more expressive), and to the model and software reuse (Jennings, 2000). Furthermore, the dynamic structures present in biological systems can

[1]  C. Potten,et al.  Tissue Stem cells: Biology and Applications , 2006 .

[2]  Rob Saunders,et al.  Agent-Based Modelling of Stem Cell Self-organisation in a Niche , 2004, Engineering Self-Organising Systems.

[3]  Jane Prophet,et al.  Transdisciplinary Research in CELL , 2006 .

[4]  Nicholas R. Jennings,et al.  On agent-based software engineering , 2000, Artif. Intell..

[5]  Paulo S. C. Alencar,et al.  Taming Agents and Objects in Software Engineering , 2002, SELMAS.

[6]  Jane Prophet,et al.  Mathematical Modeling of Stem Cells: A Complexity Primer for the Stem-Cell Biologist , 2006 .

[7]  Farhad Arbab,et al.  The IWIM Model for Coordination of Concurrent Activities , 1996, COORDINATION.

[8]  Carlos José Pereira de Lucena,et al.  From a Conceptual Framework for Agents and Objects to a Multi-Agent System Modeling Language , 2004, Autonomous Agents and Multi-Agent Systems.

[9]  D. Scadden,et al.  The stem-cell niche as an entity of action , 2006, Nature.

[10]  Agostino Poggi,et al.  Developing multi‐agent systems with a FIPA‐compliant agent framework , 2001 .

[11]  Mark d'Inverno,et al.  Understanding cell lineages as complex adaptive systems. , 2004, Blood cells, molecules & diseases.

[12]  Nelson Minar,et al.  The Swarm Simulation System: A Toolkit for Building Multi-Agent Simulations , 1996 .

[13]  Michael C. Mackey,et al.  Stochastic Differential Delay Equation, Moment Stability, and Application to Hematopoietic Stem Cell Regulation System , 2007, SIAM J. Appl. Math..

[14]  Michael J. North,et al.  AgentCell: a digital single-cell assay for bacterial chemotaxis , 2005, Bioinform..

[15]  N. Metropolis,et al.  The Monte Carlo method. , 1949 .

[16]  Nicolas Guelfi,et al.  Object-Oriented Nets with Algebraic Specifications: The CO-OPN/2 Formalism , 2001, Concurrent Object-Oriented Programming and Petri Nets.

[17]  Chris Hankin,et al.  Coordination Languages and Models: First International Conference, COORDINATION '96, Cesena, Italy, April 15-17, 1996. Proceedings. , 1996 .

[18]  Jane Prophet,et al.  Modelling , Simulation and Visualisation of Stem Cell Behaviour , 2004 .

[19]  Bruce Alberts,et al.  Essential Cell Biology , 1983 .

[20]  Nicholas R. Jennings On Agent-Based Software Engineering" Artificial Intelligence , 2000 .

[21]  Yuval Ginosar,et al.  The universal properties of stem cells as pinpointed by a simple discrete model , 2002, Journal of mathematical biology.