• Seminar: One graph to rule them all

    May 12, 2014

    Francesco-VaccarinoTopdrim partner, Francesco Vacarino from ISI – PoliTO will give a seminar on May 14th at Bologna University Department of Mathematics. The topic of the seminar will be “One graph to rule them all“.

    Let P be a finite poset. We will show that for any P-persistent object X in the category of finite topological spaces there is a P- weighted graph, whose weighted clique complex has the same P-persistent homology as X. Joint work with A. Patania (ISI-PoliTO), M. Scolamiero (KTH) and G. Petri (ISI).

    More details can be found in the seminar website.


    March 18, 2014


    Topdrim partner Christian Reidys from the University of Southern Denmark will give a course on Topology and Combinatorics of RNA structures at the Excellence Course within the Ph.D. in Applied Mathematics at Politecnico di Torino. The course will run from the 5th of May to the 27th of May.

    This course first introduces basic topology, quotient spaces and polygonal regions. It then passes to the classification theorem of topological surfaces and introduces the notion of cell-complex. Next we introduce fatgraphs as cell complexes and unicellular maps. Thereafter we show how RNA structures fit into the picture. Then we discuss genus induction and its combinatorial corollaries. The course then analyses shape polynomials and application to RNA folding and the uniform generation of RNA structures of fixed topological genus.

    Toponets’14 call for abstracts

    March 18, 2014


    Topdrim partners Mario Rasetti and Giovanni Petri from the ISI Foundation, are organising Toponets’14. Toponets’14 is a Satellite Meeting at Netsci 2014 conference. The call for abstracts is now published and the event will take place at Berkeley, California at the Clark Kerr Campus of the University of California Monday, June 2nd, 2014.

    The aim of this workshop is to review and promote advances at the interface between network science and computational topology.

    The list of topics that we aim to cover at the satellite is the following:

    • Empirical characterisation and analysis of statistical properties of static and dynamical simplicial complexes obtained from social, technological and biological systems
    • Extension of network-theoretic concepts to simplicial complexes (connectivity patterns, centralities, community structure etc)
    • Generative and null models for observed complexes
    • Topological characterisation of dynamical processes defined on networks and simplicial complexes

    The first deadline is 14th of April 2014. More information can be obtained from the Toponets’14 website http://toponets14.weebly.com/

    Topology: The Secret Ingredient In The Latest Theory of Everything

    March 7, 2014

    Combine topology with symmetry and add a sprinkling of quantum mechanics. The result? A powerful new theory of everything

    Topology is the study of shape, in particular the properties that are preserved when a shape is squeezed, stretched and battered but not torn or ripped.

    In the past, topology was little more than an amusing diversion for mathematicians doodling about the difference between donuts and dumplings.

    But that is beginning to change. In recent years, physicists have begun to use topology to explain some of the most important puzzles at the frontiers of physics.

    from MIT Technology Review

    CS2Bio’14 : Call for Papers

    March 2, 2014

    5th International Workshop on Interactions between Computer Science and Biology

    Affiliated to DisCoTec’14
    June 6th, 2014
    Berlin, Germany

    Biological systems are complex systems whose modeling requires a dramatic change in paradigms that has seen reductionism challenged by holism and Systems Biology a stimulating field to let evolve the science of Complex Systems as a convergent branch (a sort of hyperedge) of Computer Science, Mathematics and Physics.

    The aim of this workshop is to gather researchers interested in the convergence of Computer Science, Biology and the Life Sciences. In particular, in this 5th edition, we solicit the contribution of original results, from any research areas, such as Mathematics, Physics, Complex Systems, and Computational Science that address both theoretical aspects of modelling and applied work on the comprehension of biological behaviour. Furthermore, to facilitate the integration of different research areas we encourage the presentation of main objectives and preliminary results of active projects on the CS2Bio topics conducted by interdisciplinary teams.


    Papers selected for presentation at CS2Bio should either present the modelling of a specific biological phenomenon using formal techniques, or a modelling, simulation, testing or verification approach in computer science that leads to a novel and promising application to a range of biological or medical systems. In the latter case, some emphasis on the scope and scalability of the approach will be required. The workshop intends to attract researchers interested in models, verification, tools, and programming primitives concerning the complex interactions encountered. In general, topics of interest include, but are not limited to:

    • Formal Biological Modelling
      • Formal methods for the representation of biological systems and their dynamics;
      • Theoretical links and comparisons between different formal models for the modelling of biological processes;
      • Quantitative (probabilistic, timed, stochastic, etc.) languages and calculi;
      • Spatial (geometrical, topological) languages and calculi;
      • Prediction of biological behaviour from incomplete information;
      • Model checking, abstract interpretation, type systems, etc.
    • Novel Computational Paradigms for Understanding Biological Complex Systems
      • Quantum information and life sciences;
      • Computational topology and biomathematics;
      • Information processing and biomedicine;
      • Statistical mechanics and biophysics;
      • Complex Networks and biomolecular dynamics
    • Tools and Simulations
      • Modelling, analysis and simulation tools for systems biology;
      • Emergence of properties in complex biological and medical systems;
      • Tools for parallel, distributed, and multi-resolution simulation methods;
      • Detailed biological case-studies.


    We solicit three kinds of contributions:

    • Regular papers: must report previously unpublished work and not be submitted concurrently to another conference with refereed proceedings (limited to 14 pages).
    • Tool presentations: describing new tools or platforms for the modelling of biological systems (limited to 14 pages).
    • Dissemination of project results: concern recent or ongoing work on topics relevant to CS2Bio and are intended to provide discussion and stimulate feedback during the workshop. The focus of a dissemination should be put on the main objectives and preliminary results of active projects on topics relevant to the workshop. There are no restrictions about previous or future publication of the contents of a dissemination, it could also be based on a recently published paper or on a work which has not yet been submitted (limited to 4 pages).

    Authors should submit their contributions via EasyChair in the form of a pdf file compiled using the ENTCS style for the workshop proceedings. If necessary, detailed proofs or other additional material can be added in an appendix (referees might review it at their discretion).


    The CS2Bio 2014 proceedings will be published in a volume of the Elsevier series “Electronic Notes on Theoretical Computer Science”. After the event, papers presented at the workshop will be invited to be further extended and submitted to a special issue of the journal “Theoretical Computer Science”. The special issue will have an open call and a separate review process up to the usual scientific standards of the journal.


    • Submission deadline: 24 March 2014
    • Notification to authors: 02 May 2014
    • Workshop: 06 June 2014
    • Tutorial day: 07 June 2014


    • Luca Cardelli, Microsoft Research Cambridge, UK
    • Erik de Vink, Technische Universiteit Eindhoven, the Netherlands
    • François Fages, INRIA Rocquencourt, France
    • Paola Giannini, Università del Piemonte Orientale, Italy
    • Radu Grosu, Stony Brook University, USA
    • Russ Harmer, CNRS & ENS Lyon, France
    • Jean Krivine, CNRS & Paris Diderot University, France
    • Pietro Lio, University of Cambridge, UK
    • Emanuela Merelli, University of Camerino, Italy (co-chair)
    • Ion Petre, Åbo Akademi University, Finland (co-chair)
    • Ovidiu Radulescu, University of Montpellier 2, France
    • David Safranek, Masaryk University, Czech Republic
    • Angelo Troina, Università di Torino, Italy
    • Verena Wolf, Saarland University, Germany


    • Erik de Vink
    • Paola Giannini
    • Jean Krivine
    • Angelo Troina

    New model able to predict earthquakes in the short term

    January 31, 2014

    srep03624-f1An international group of researchers, including Topdrim partner professor Peter Sloot from the University of Amsterdam (UvA) , has succeeded in predicting the location, time and magnitude of imminent earthquakes and their associated aftershocks. The results of the study were published in the online scientific journal Scientific Reports.

    Being able to predict earthquakes is essential in order to get people and goods to safety in time. Until now it has not been possible to make accurate short-term earthquake predictions. The team of researchers from Taiwan, Singapore and the Netherlands is about to change that: they have developed a mesoscopic model that can describe and measure the formation and disintegration of networks of granule clusters at the boundaries between tectonic plates. ‘Surprisingly enough, it is possible to use this mesoscopic theory to derive the existing phenomenological seismology laws, such as the well-known Gutenberg-Richter law’, says Peter Sloot, professor of Computational Science at the UvA.

    Very unbalanced

    ‘Earthquakes can be viewed as critical transitions in the state of the lithosphere. The tension created by shifting tectonic plates generates an unstable (very unbalanced), dynamic system’, Sloot explains. ’By integrating the time intervals between foreshocks and the non-linear energy signature in our mesoscopic model, we seem to be able to predict earthquakes of a magnitude of 6 or higher anything from several days to weeks in advance.’

    Kobe and Chi-Chi

    The team analysed a large number of historic earthquakes, including the infamous quake in Kobe, Japan (1995) which measured 7.2 on the Richter scale, and the Chi-Chi earthquake in Taiwan (1997), which had a magnitude of 7.3. In all cases it proved possible to predict the earthquakes several weeks to months in advance, including the number and severity of their aftershocks.

    Sloot: ’Strangely enough, the underlying theory bears a strong resemblance to that used to describe the formation and dissociation of terrorist and rebellious groups. In both theories, the dynamics are governed by the desire to establish as large a network as possible in order to guarantee success, while at the same time needing to be as small as possible in order to minimise the risk of detection.’

    Publication details

    Siew Ann Cheong, Teck Liang Tan, Chien-Chih Chen, Wu-Lung Chang, Zheng Liu, Lock Yue Chew, Peter M. A. Sloot, Neil F. Johnson: ‘Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes’, in: Scientific Reports (Nature Publishing Group, online 10 January 2014).

    See: http://www.nature.com/srep/2014/140110/srep03624/full/srep03624.html

    Peter Sloot receives grant to set up interdisciplinary institute in Singapore

    January 31, 2014


    Topdrim partner Prof. Peter Sloot from UvA has received a grant to set up an Institute of Complex Systems in Singapore.

    Together with Economist Prof. Brian W. Arthur and Anthropologist Prof. J. Stephen Lansing from the famous Santa Fe Institute in New Mexico (USA), Peter Sloot received a large grant to set up an inter- and cross-disciplinary complexity institute in the Nanyang University of Technology in Singapore.

    The aim of this institute is to research the common fundamental and universal principles in complex physical, computational, biological, and social systems that underlie many of the most profound problems facing science and society.

    Launch of Hypernetworks Website

    December 20, 2013


    The hypernetworks.eu website was launched during the month of December. This website aims to provide information and services for the research community interested in developing hypernetwork science.

    It will offer online support for the new book Hypernetworks in the Science of Complex Systems by Professor Jeffrey Johnson.

    Also, the website will be focal in coordinating the community interested in hypernetworks, Galois lattices and Q-analysis.

    In the future the website will also provide an open computational platform for users’ hypernetwork analysis of their own data.

    Jeffrey Johnson interviewed in BBC4 about Complexity

    December 19, 2013

    Complexity at BBC4 In Our Time

    Topdrim partner, Professor Jeffrey Johnson was one of the guests in the BBC’s show ‘In our time’ on the topic of complexity.

    Melvyn Bragg and his guests discuss complexity and how it can help us understand the world around us. When living beings come together and act in a group, they do so in complicated and unpredictable ways: societies often behave very differently from the individuals within them. Complexity was a phenomenon little understood a generation ago, but research into complex systems now has important applications in many different fields, from biology to political science. Today it is being used to explain how birds flock, to predict traffic flow in cities and to study the spread of diseases.

    Professor Jeffrey Johnson was accompanied by Professor Ian Stewart and Professor Eve Mitleton-Kelly. The MP3 is available for download.