Research cluster

Here is reported a list of the collaboration and knowledge sharing activities in CIRCLE in addition to the CIRCLE Toolbox.

  • Blood (UCAM, CNIT, UNIPG): Knowledge sharing activities on MolCom systems in blood vessels. A survey of medical applications of Molecular Communications has been published in the Elsevier Nano Communication Networks journal (see the publications section). In addition, a further knowledge sharing activity is pursued by this cluster, based on staff exchange, focused on Molecular Communications techniques devoted to the early detection of circulating tumour cells (CTC) in blood vessels. UNIPG provided values of the key parameters (e.g. vessels and cells size, bloodstream velocity, receptor expressed on the surface of endothelial cells) by analysing the state of the art literature. UCAM provided models about the generation and the survival of CTCs. Finally, CNIT integrated models and simulations.
  • MolComML (UCAM, UPC, CNIT, WIT): Development of a mark-up language for Molecular Communications Systems (Molecular Communications Markup Language, MolComML). This markup language had a central role in the CIRCLE activities since it was defined to univocally specify simulation configuration (simulation parameters, topology, output format), also using different simulators. This would help to make in silico analysis comparable. A co-authored paper has been accepted and presented to the conference ACM Nanocom 2016. Given the strategic importance of MolComML for CIRCLE and in particular for the implementation of the CIRCLE MolCom Toolbox, an extensive description of this activity is reported here.
  • Neuronal (WIT, TUT, KU): Collaboration and knowledge sharing activity in the framework of neural dust motes to stimulate neuronal circuits molecular communications within the cortex. The context consists of investigating the development of neural dust motes that can be used to stimulate neuronal circuits molecular communications within the cortex.
    The aim here is to provide new, long-term solutions that will allow these devices to be embedded permanently within the cortex, and stimulate the neurons at single cell level.
    The mechanism of stimulation is through the process known as optogenetics, where light is used to stimulate the neurons that are genetically engineered. The key challenges of this activity is the development of such a small scale device that can interface and stimulate the neuron, and mechanism of powering the devices as well. The shared expertise of each of the organization is as follows: TUT – neural dust modelling, in particular light behaviour within the tissue; WIT – calcium signalling molecular communication within the neurons; Koc University – electro-chemical signalling between neurons. The collaboration includes a prestigious external organization, the University at Buffalo, State University of New York, coordinated by Prof. Josep Miquel Jornet, who has a sound expertise in the research on electromagnetic wireless nano sensor networks.
  • Bacteria (KU, WIT, and UCAM): Knowledge sharing activities relevant to testing molecular + electromagnetic communications between bacteria. KU, in collaboration with WIT and UCAM, is working on an initiative external to the CIRCLE project that consists of initiating a wet-lab experiment with the objective of realizing molecular + EM communication between bacterial populations located in different university campuses. The experiments are expected to evolve towards a multi-purpose testbed, which will be used to test synthetic biology based interfacing and transceiving capabilities of engineered bacteria. This will be a first major step towards realizing synthetic bacteria based bio-transceivers for molecular communication applications. Sharing of knowledge and best practices is in the scope of CIRCLE.
  • Nano_SDN (UPC, IMINDS): Software defined networking applied to nanonetworks. The algorithmic and routing knowledge of IMINDS together with the low layer expertise in nanonetworks gave rise to new ideas and concrete proposals to explore, in particular in the context of opportunistic routing with potential in vivo applications. The exchange aimed at performing research involving ideas from the fields of opportunistic & approximate routing to propose a routing algorithm that works in a range of applications that involve very large networks with devices that are limited in their computing and communication capabilities. These applications include applications of software defined networking to nanonetworks, involving metamaterials.

Given those research clusters, we have elaborated on them and extracted insights. For this purpose, we have used a weighted graph visualization approach:

In the graph, nodes are associated with research clusters, whereas edges represent the common institutions participating in two clusters. The size of nodes is proportional to the number of participating institutions, whereas the thickness of edges is proportional to the number of CIRCLE institutions participating to nodes connected by the considered edge. In order to make things clearer, we have reported these common institutions as labels of graph edges.
It is evident that, beyond a global participation in the CIRCLE MolCom Toolbox, which is a global project target, there are a number of interconnected, smaller research clusters. The participation of CIRCLE beneficiaries to those clusters is quite balanced.

 

CIRCLE Toolbox

As an example of intense collaboration of the CIRCLE beneficiaries, and the fruitful collaboration also through Staff Exchange, we illustrate the development of the CIRCLE MolCom Toolbox, which is a pivotal activity in CIRCLE. The beneficiaries that have mostly contributed to this toolbox are UPC, CNIT, UCAM, and WIT. Nevertheless, all the CIRCLE beneficiaries in CIRCLE have given a contribution for the design, implementation, experimentation, assessment, and dissemination of this toolbox. Most of partners have contributed by means of simulation platforms, and namely UPC (N3Sim), CNIT (BiNS2), TUT (NCSim), KU (NanoNS), and WIT (CalComSim). In addition, IMINDS contributed by providing knowledge about computationally efficient algorithms, with the target of lowering the computational requirement of MolCom Simulations. Finally, UNIPG contributed by providing realistic data by conducting a deep literature analysis, whereas UCAM contributed with a number of mathematical models in different simulators.

This activity tackles the need of harmonizing the various MolCom simulation tools in a single toolbox, able to provide users with a unified interface to interact with the simulator. This activity is strategic for the future of molecular communication research.

The CIRCLE MolCom toolbox has a modular software architecture, based on three main modules, as sketched below:

toolbox

These modules are the I/O module, the orchestration module and the execution module. The latter is a container including the functions and algorithms which are already available within the relevant packages. Note that the CIRCLE MolCom toolbox is not aimed at introducing a new simulator, or a different simulation strategy. On the contrary, it leverages the existing simulators, by taking advantage from all their peculiarities, and achieving ambitious results by their integration.