Marked Gibbs point processes with unbounded interaction: an existence result

We construct marked Gibbs point processes in $\mathbb{R}^d$ under quite general assumptions. Firstly, we allow for interaction functionals that may be unbounded and whose range is not assumed to be uniformly bounded. Indeed, our typical interaction admits an a.s. finite but random range. Secondly, the random marks -- attached to the locations in $\mathbb{R}^d$ -- belong to a general normed space $\mathcal{S}$. They are not bounded, but their law should admit a super-exponential moment. The approach used here relies on the so-called entropy method and large-deviation tools in order to prove tightness of a family of finite-volume Gibbs point processes. An application to infinite-dimensional interacting diffusions is also presented

Locality properties for discrete and continuum Widom--Rowlinson models in random environments

We consider the Widom--Rowlinson model in which hard disks of two possible colors are constrained to a hard-core repulsion between particles of different colors, in quenched random environments. These random environments model spatially dependent preferences for the attachment of disks. We investigate the possibility to represent the joint process of environment and infinite-volume Widom--Rowlinson measure in terms of continuous (quasilocal) Papangelou intensities. We show that this is not always possible: In the case of the symmetric Widom-Rowlinson model on a non-percolating environment, we can explicitly construct a discontinuity coming from the environment. This is a new phenomenon for systems of continuous particles, but it can be understood as a continuous-space echo of a simpler non-locality phenomenon known to appear for the diluted Ising model (Griffiths singularity random field) on the lattice, as we explain in the course of the proof.Comment: 24 pages, 8 figure

Diffusion dynamics for an infinite system of two-type spheres and the associated depletion effect

We consider a random diffusion dynamics for an infinite system of hard spheres of two different sizes evolving in ℝd, its reversible probability measure, and its projection on the subset of the large spheres. The main feature is the occurrence of an attractive short-range dynamical interaction --- known in the physics literature as a depletion interaction -- between the large spheres, which is induced by the hidden presence of the small ones. By considering the asymptotic limit for such a system when the density of the particles is high, we also obtain a constructive dynamical approach to the famous discrete geometry problem of maximisation of the contact number of n identical spheres in ℝd. As support material, we propose numerical simulations in the form of movies

Ten simple rules for providing effective bioinformatics research support.

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Gibbs point processes on path space: Existence, cluster expansion and uniqueness

We study a class of infinite-dimensional diffusions under Gibbsian interactions, in the context of marked point configurations: The starting points belong to R^d, and the marks are the paths of Langevin diffusions. We use the entropy method to prove existence of an infinite-volume Gibbs point process and use cluster expansion tools to provide an explicit activity domain in which uniqueness holds

Gibbs point processes on path space: Existence, cluster expansion and uniqueness

We study a class of infinite-dimensional diffusions under Gibbsian interactions, in the context of marked point configurations: The starting points belong to R^d, and the marks are the paths of Langevin diffusions. We use the entropy method to prove existence of an infinite-volume Gibbs point process and use cluster expansion tools to provide an explicit activity domain in which uniqueness holds

Collective motion of living organisms: the Vicsek model

The purpose of this work is to study the Vicsek model for self-driven articles, in particular its time-continuous version. We will study its mean-field limit, as well as the large-scale behaviour of the model. In particular, we find that the equilibrium distributions change according to whether the density is above or below a given threshold. Below this value, the only equilibrium distribution is isotropic in velocity direction and is stable; moreover, the convergence to this equilibrium is exponentially fast. When the density is above the threshold, we have a second class of anisotropic equilibria, formed by Von-Mises-Fischer distributions of arbitrary orientation. In this case, the isotropic equilibria become unstable and there is exponentially fast convergence to the anisotropic ones

Ten simple rules for providing effective bioinformatics research support.

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support