Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments.

Bitext alignment: building and evaluating a bilingual corpus and translation memory of academic course descriptions

Following the internationalization of contemporary higher education, academic institutions based in non-English speaking countries are increasingly urged to produce contents in English to address international prospective students and personnel, as well as to increase their attractiveness. The demand for English translations in the institutional academic domain is consequently increasing at a rate exceeding the capacity of the translation profession. Resources for assisting non-native authors and translators in the production of appropriate texts in L2 are therefore required in order to help academic institutions and professionals streamline their translation workload. Some of these resources include: (i) parallel corpora to train machine translation systems and multilingual authoring tools; and (ii) translation memories for computer-aided tools. The purpose of this study is to create and evaluate reference resources like the ones mentioned in (i) and (ii) through the automatic sentence alignment of a large set of Italian and English as a Lingua Franca (ELF) institutional academic texts given as equivalent but not necessarily parallel (i.e. translated). In this framework, a set of aligning algorithms and alignment tools is examined in order to identify the most profitable one(s) in terms of accuracy and time- and cost-effectiveness. In order to determine the text pairs to align, a sample is selected according to document length similarity (characters) and subsequently evaluated in terms of extent of noisiness/parallelism, alignment accuracy and content leverageability. The results of these analyses serve as the basis for the creation of an aligned bilingual corpus of academic course descriptions, which is eventually used to create a translation memory in TMX format.

An integrated system for building and running reproducible research

Our generation of computational scientists is living in an exciting time: not only do we get to pioneer important algorithms and computations, we also get to set standards on how computational research should be conducted and published. From Euclid’s reasoning and Galileo’s experiments, it took hundreds of years for the theoretical and experimental branches of science to develop standards for publication and peer review. Computational science, rightly regarded as the third branch, can walk the same road much faster. The success and credibility of science are anchored in the willingness of scientists to expose their ideas and results to independent testing and replication by other scientists. This requires the complete and open exchange of data, procedures and materials. The idea of a “replication by other scientists” in reference to computations is more commonly known as “reproducible research”. In this context the journal “EAI Endorsed Transactions on Performance & Modeling, Simulation, Experimentation and Complex Systems” had the exciting and original idea to make the scientist able to submit simultaneously the article and the computation materials (software, data, etc..) which has been used to produce the contents of the article. The goal of this procedure is to allow the scientific community to verify the content of the paper, reproducing it in the platform independently from the OS chosen, confirm or invalidate it and especially allow its reuse to reproduce new results. This procedure is therefore not helpful if there is no minimum methodological support. In fact, the raw data sets and the software are difficult to exploit without the logic that guided their use or their production. This led us to think that in addition to the data sets and the software, an additional element must be provided: the workflow that relies all of them.