COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Process optimization for microstructure-dependent properties in thin film organic electronics

The processing conditions during solvent-based fabrication of thin film organic electronics significantly determine the ensuing microstructure. The microstructure, in turn, is one of the key determinants of device performance. In recent years, one of the foci in organic electronics has been to identify processing conditions for enhanced performance. This has traditionally involved either trial-and-error exploration, or a parametric sweep of a large space of processing conditions, both of which are time and resource intensive. This is especially the case when the process → structure and structure → property simulators are computationally expensive to evaluate. In this work, we integrate an adaptive-sampling based, gradient-free, Bayesian optimization routine with a phase-field morphology evolution framework that models solvent-based fabrication of thin film polymer blends (process → structure simulator) and a graph-based morphology characterization framework that evaluates the photovoltaic performance of a given morphology (structure → property simulator). The Bayesian optimization routine adaptively adjusts the processing parameters to rapidly identify optimal processing configurations, thus reducing the computational effort in process → structure → property explorations. This serves as a modular, parallel ‘wrapper’ framework that facilitates swapping-in other process simulators and device simulators for general process → structure → property optimization. We showcase this framework by identifying two processing parameters, the solvent evaporation rate and the substrate patterning wavelength, in a model system that results in a device with enhanced photovoltaic performance evaluated as the short-circuit current of the device. The methodology presented here provides a modular, scalable and extensible approach towards the rational design of tailored microstructures with enhanced functionalities

'BioNessie(G) - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

BioNessie - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology

Over the years, a variety of biochemical network modeling packages have been developed and used by researchers in biology. No single package currently answers all the needs of the biology community; nor is one likely to do so in the near future, because the range of tools needed is vast and new techniques are emerging too rapidly. It seems unavoidable that, for the foreseeable future, systems biology researchers are likely to continue using multiple packages to carry out their work. In this chapter, we describe the ERATO Systems Biology Workbench (SBW) and the Systems Biology Markup Language (SBML), two related efforts directed at the problems of software package interoperability. The goal of the SBW project is to create an integrated, easy-to-use software environment that enables sharing of models and resources between simulation and analysis tools for systems biology. SBW uses a modular, plug-in architecture that permits easy introduction of new components. SBML is a proposed standard XML-based language for representing models communicated between software packages; it is used as the format of models communicated between components in SBW

Why Ciao? An overview of the ciao system's design philosophy

Our intention in this note is not to provide a listing of the many features of the Ciao system: this can be found in part for example in the brochures announcing upcoming versions, in the Ciao website, or in more feature-oriented descriptions such as. Instead in this document we would like to describe the objectives and reasoning followed in our design as well as the fundamental characteristics that in our opinion make Ciao quite unique and hopefully really useful to you as a Ciao user

Placenames analysis in historical texts: tools, risks and side effects

International audienceThis article presents an approach combining linguistic analysis, geographic information retrieval and visualization in order to go from toponym extraction in historical texts to projection on customizable maps. The toolkit is released under an open source license, it features bootstrapping options, geocod-ing and disambiguation algorithms, as well as cartographic processing. The software setting is designed to be adaptable to various historical contexts, it can be extended by further automatically processed or user-curated gazetteers, used directly on texts or plugged-in on a larger processing pipeline. I provide an example of the issues raised by generic extraction and show the benefits of integrated knowledge-based approach, data cleaning and filtering

FM-track: a fiducial marker tracking software for studying cell mechanics in a three-dimensional environment

Tracking the deformation of fiducial markers in the vicinity of living cells embedded in compliant synthetic or biological gels is a powerful means to study cell mechanics and mechanobiology in three-dimensional environments. However, current approaches to track and quantify three-dimensional (3D) fiducial marker displacements remain ad-hoc, can be difficult to implement, and may not produce reliable results. Herein, we present a compact software package entitled “FM-Track,” written in the popular Python language, to facilitate feature-based particle tracking tailored for 3D cell micromechanical environment studies. FM-Track contains functions for pre-processing images, running fiducial marker tracking, and post-processing and visualization. FM-Track can thus aid the study of cellular mechanics and mechanobiology by providing an extensible software platform to more reliably extract complex local 3D cell contractile information in transparent compliant gel systems.https://www.sciencedirect.com/science/article/pii/S2352711019303474Published versio

Programming biological models in Python using PySB

Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis

LEGaTO: first steps towards energy-efficient toolset for heterogeneous computing

LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.Peer ReviewedPostprint (author's final draft