Laboratory information management system

A laboratory information management system (LIMS), sometimes referred to as a laboratory information system (LIS) or laboratory management system (LMS), is a software-based solution with features that support a modern laboratory's operations. Key features include—but are not limited to—workflow and data tracking support, flexible architecture, and data exchange interfaces, which fully "support its use in regulated environments". The features and uses of a LIMS have evolved over the years from simple sample tracking to an enterprise resource planning tool that manages multiple aspects of laboratory informatics. There is no useful definition of the term "LIMS" as it is used to encompass a number of different laboratory informatics components. The spread and depth of these components is highly dependent on the LIMS implementation itself. All LIMSs have a workflow component and some summary data management facilities but beyond that there are significant differences in functionality.

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

Whole Genome Sequencing is a process in the field of bioinformatics that transforms biological samples of DNA into an electronic dataset of genetic bases. The process consists of two sequential components. First, the laboratory process of sequencing transforms the biological DNA samples into a digital format by transcribing the sequence of bases that make up short snippets of DNA. Second, a genomic workflow uses software to transform this data into a representation that is useful for genomic analysis. Recent advancements in High-Throughput Sequencing technology enable the laboratory phase to produce data faster and at a lower cost than prior techniques were capable of. The applications and file formats used in workflows have not undergone commensurate technological advancement in order to accommodate this deluge of genomic data. This thesis introduces a redesign of genomic workflows, their component applications, and the underlying file formats in order to scale out workflows across a data center. The design builds upon on two design components. First, a unified file format supplants the myriad existing formats in order to accommodate scale-out multi-machine I/O. The file format imposes minimal feature requirements upon the storage system, thereby enabling its use in high- performance systems for processing and cost-effective cold storage systems for long-term storage. Second, a new cloud computing framework provides an API for composing workflows in an abstract logical description and delegating the execution of the logic to a common runtime. The framework's runtime executes the logical workflow description on scale-out hardware resources while abstracting the execution details. We combine the file format and framework to build a new set of workflows that scale out across data center resources. These scale-out workflows incorporate existing workflow applications (compartmentalized into libraries that the framework invokes) and new applications that leverage the features provided by the scale-out architecture. All workflows delegate work distribution and task concurrency to the framework's runtime and utilize a common set of subcomponents for auxiliary code (e.g., I/O with various storage systems, processing different file formats). These workflows are able to scale out across a data center to the point of saturating the throughput of one or more hardware resources.

EPFL2019

Peripersonal Space: An Index of Multisensory Body–Environment Interactions in Real, Virtual, and Mixed Realities

Javier Bello Ruiz, Fosco Bernasconi, Olaf Blanke, Elisa Canzoneri, Bruno Herbelin, Robin Mange, Jean-Paul Noel, Elisa Pellencin, Andrea Serino

Human–environment interactions normally occur in the physical milieu and thus by medium of the body and within the space immediately adjacent to and surrounding the body, the peripersonal space (PPS). However, human interactions increasingly occur with or within virtual environments, and hence novel approaches and metrics must be developed to index human–environment interactions in virtual reality (VR). Here, we present a multisensory task that measures the spatial extent of human PPS in real, virtual, and augmented realities. We validated it in a mixed reality (MR) ecosystem in which real environment and virtual objects are blended together in order to administer and control visual, auditory, and tactile stimuli in ecologically valid conditions. Within this mixed-reality environment, participants are asked to respond as fast as possible to tactile stimuli on their body, while task-irrelevant visual or audiovisual stimuli approach their body. Results demonstrate that, in analogy with observations derived from monkey electrophysiology and in real environmental surroundings, tactile detection is enhanced when visual or auditory stimuli are close to the body, and not when far from it. We then calculate the location where this multisensory facilitation occurs as a proxy of the boundary of PPS. We observe that mapping of PPS via audiovisual, as opposed to visual alone, looming stimuli results in sigmoidal fits—allowing for the bifurcation between near and far space—with greater goodness of fit. In sum, our approach is able to capture the boundaries of PPS on a spatial continuum, at the individual-subject level, and within a fully controlled and previously laboratory-validated setup, while maintaining the richness and ecological validity of real-life events. The task can therefore be applied to study the properties of PPS in humans and to index the features governing human–environment interactions in virtual or MR. We propose PPS as an ecologically valid and neurophysiologically established metric in the study of the impact of VR and related technologies on society and individuals.

2018

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

EPFL2019

Peripersonal Space: An Index of Multisensory Body–Environment Interactions in Real, Virtual, and Mixed Realities

Javier Bello Ruiz, Fosco Bernasconi, Olaf Blanke, Elisa Canzoneri, Bruno Herbelin, Robin Mange, Jean-Paul Noel, Elisa Pellencin, Andrea Serino

2018

Laboratory information management system

Identification of As-Cu-FA complexes in laboratory samples and characterization of association between arsenic and dissolved organic matter in China’s groundwater

Scaling Out Bioinformatics in the Data Center

Peripersonal Space: An Index of Multisensory Body–Environment Interactions in Real, Virtual, and Mixed Realities

Scaling Out Bioinformatics in the Data Center

Peripersonal Space: An Index of Multisensory Body–Environment Interactions in Real, Virtual, and Mixed Realities

Identification of As-Cu-FA complexes in laboratory samples and characterization of association between arsenic and dissolved organic matter in China’s groundwater