A scalable hardware and software control apparatus for experiments with hybrid quantum systems

Modern experiments with fundamental quantum systems - like ultracold atoms, trapped ions, single photons - are managed by a control system formed by a number of input/output electronic channels governed by a computer. In hybrid quantum systems, where two or more quantum systems are combined and made to interact, establishing an efficient control system is particularly challenging due to the higher complexity, especially when each single quantum system is characterized by a different timescale. Here we present a new control apparatus specifically designed to efficiently manage hybrid quantum systems. The apparatus is formed by a network of fast communicating Field Programmable Gate Arrays (FPGAs), the action of which is administrated by a software. Both hardware and software share the same tree-like structure, which ensures a full scalability of the control apparatus. In the hardware, a master board acts on a number of slave boards, each of which is equipped with an FPGA that locally drives analog and digital input/output channels and radiofrequency (RF) outputs up to 400 MHz. The software is designed to be a general platform for managing both commercial and home-made instruments in a user-friendly and intuitive Graphical User Interface (GUI). The architecture ensures that complex control protocols can be carried out, such as performing of concurrent commands loops by acting on different channels, the generation of multi-variable error functions and the implementation of self-optimization procedures. Although designed for managing experiments with hybrid quantum systems, in particular with atom-ion mixtures, this control apparatus can in principle be used in any experiment in atomic, molecular, and optical physics.Comment: 10 pages, 12 figure

Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis

BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. RESULTS. We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. CONCLUSION. Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.Dana-Farber Cancer Institute; National Human Genome Research Institute (P50HG004233); National Science Foundation Integrative Graduate Education and Research Traineeship grant (DGE-0654108

A framework for the simulation of structural software evolution

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2008 ACM.As functionality is added to an aging piece of software, its original design and structure will tend to erode. This can lead to high coupling, low cohesion and other undesirable effects associated with spaghetti architectures. The underlying forces that cause such degradation have been the subject of much research. However, progress in this field is slow, as its complexity makes it difficult to isolate the causal flows leading to these effects. This is further complicated by the difficulty of generating enough empirical data, in sufficient quantity, and attributing such data to specific points in the causal chain. This article describes a framework for simulating the structural evolution of software. A complete simulation model is built by incrementally adding modules to the framework, each of which contributes an individual evolutionary effect. These effects are then combined to form a multifaceted simulation that evolves a fictitious code base in a manner approximating real-world behavior. We describe the underlying principles and structures of our framework from a theoretical and user perspective; a validation of a simple set of evolutionary parameters is then provided and three empirical software studies generated from open-source software (OSS) are used to support claims and generated results. The research illustrates how simulation can be used to investigate a complex and under-researched area of the development cycle. It also shows the value of incorporating certain human traits into a simulation—factors that, in real-world system development, can significantly influence evolutionary structures

An augmented reality interface for visualising and interacting with virtual content

In this paper, a novel AR interface is proposed that provides generic solutions to the tasks involved in augmenting simultaneously different types of virtual information and processing of tracking data for natural interaction. Participants within the system can experience a real-time mixture of 3D objects, static video, images, textual information and 3D sound with the real environment. The userfriendly AR interface can achieve maximum interaction using simple but effective forms of collaboration based on the combinations of humancomputer interaction techniques. To prove the feasibility of the interface, the use of indoor AR techniques are employed to construct innovative applications and demonstrate examples from heritage to learning systems. Finally, an initial evaluation of the AR interface including some initial results is presented

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA

The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding

Luscus: molecular viewer and editor for MOLCAS

The novel program for graphical display and editing of molecular systems, luscus, is described. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling