Integrating reconfigurable hardware-based grid for high performance computing.
Ontology highlight
ABSTRACT:
SUBMITTER: Dondo Gazzano J
PROVIDER: S-EPMC4385699 | biostudies-other | 2015
REPOSITORIES: biostudies-other
Similar Datasets
Project description:BACKGROUND:Biological Regulatory Networks (BRNs) are responsible for developmental and maintenance related functions in organisms. These functions are implemented by the dynamics of BRNs and are sensitive to regulations enforced by specific activators and inhibitors. The logical modeling formalism by René Thomas incorporates this sensitivity with a set of logical parameters modulated by available regulators, varying with time. With the increase in complexity of BRNs in terms of number of entities and their interactions, the task of parameters estimation becomes computationally expensive with existing sequential SMBioNET tool. We extend the existing sequential implementation of SMBioNET by using a data decomposition approach using a Java messaging library called MPJ Express. The approach divides the parameters space into different regions and each region is then explored in parallel on High Performance Computing (HPC) hardware. RESULTS:The performance of the parallel approach is evaluated on BRNs of different sizes, and experimental results on multicore and cluster computers showed almost linear speed-up. This parallel code can be executed on a wide range of concurrent hardware including laptops equipped with multicore processors, and specialized distributed memory computer systems. To demonstrate the application of parallel implementation, we selected a case study of Hexosamine Biosynthetic Pathway (HBP) in cancer progression to identify potential therapeutic targets against cancer. A set of logical parameters were computed for HBP model that directs the biological system to a state of recovery. Furthermore, the parameters also suggest a potential therapeutic intervention that restores homeostasis. Additionally, the performance of parallel application was also evaluated on a network (comprising of 23 entities) of Fibroblast Growth Factor Signalling in Drosophila melanogaster. CONCLUSIONS:Qualitative modeling framework is widely used for investigating dynamics of biological regulatory networks. However, computation of model parameters in qualitative modeling is computationally intensive. In this work, we presented results of our Java based parallel implementation that provides almost linear speed-up on both multicore and cluster platforms. The parallel implementation is available at https://psmbionet.github.io .
| S-EPMC6311083 | biostudies-other
Project description:Objective and designThe design and implementation of ImageMiner, a software platform for performing comparative analysis of expression patterns in imaged microscopy specimens such as tissue microarrays (TMAs), is described. ImageMiner is a federated system of services that provides a reliable set of analytical and data management capabilities for investigative research applications in pathology. It provides a library of image processing methods, including automated registration, segmentation, feature extraction, and classification, all of which have been tailored, in these studies, to support TMA analysis. The system is designed to leverage high-performance computing machines so that investigators can rapidly analyze large ensembles of imaged TMA specimens. To support deployment in collaborative, multi-institutional projects, ImageMiner features grid-enabled, service-based components so that multiple instances of ImageMiner can be accessed remotely and federated.ResultsThe experimental evaluation shows that: (1) ImageMiner is able to support reliable detection and feature extraction of tumor regions within imaged tissues; (2) images and analysis results managed in ImageMiner can be searched for and retrieved on the basis of image-based features, classification information, and any correlated clinical data, including any metadata that have been generated to describe the specified tissue and TMA; and (3) the system is able to reduce computation time of analyses by exploiting computing clusters, which facilitates analysis of larger sets of tissue samples.
| S-EPMC3128405 | biostudies-literature
Project description:Minimal hardware implementations able to cope with the processing of large amounts of data in reasonable times are highly desired in our information-driven society. In this work we review the application of stochastic computing to probabilistic-based pattern-recognition analysis of huge database sets. The proposed technique consists in the hardware implementation of a parallel architecture implementing a similarity search of data with respect to different pre-stored categories. We design pulse-based stochastic-logic blocks to obtain an efficient pattern recognition system. The proposed architecture speeds up the screening process of huge databases by a factor of 7 when compared to a conventional digital implementation using the same hardware area.
| S-EPMC4425430 | biostudies-literature
Project description:Highlights • Event-driven serverless architecture requiring low cost and maintenance effort.• Data processing, storage, visualization and sharing on fault-tolerant cloud services.• Backup grid monitoring and control given access to secure Internet connection.• Cloud-hosted operation logging simplies auditing and responsibility tracking.• Cyber security mechanism that complies with CIP requirements for the power grid. Operating a modern power grid reliably in case of SCADA/EMS failure or amid difficult times like COVID-19 pandemic is a challenging task for grid operators. In [11], a PMU-based emergency generation dispatch scheme has been proposed to help the system operators with the supply and demand balancing; however, its realization highly relies on the control center infrastructure for computing and communication. This work, rather than using the on-premises server and dispatch communication system, proposes and implements a cloud-centric serverless architecture to ensure the operation continuity regardless of local infrastructure’s availability and accessibility. Through its prototype implementation and evaluation at ISO New England, the solution has demonstrated two major advantages. Firstly, the cloud infrastructure is independent and fault-tolerant, providing grid monitoring and control capability even when EMS loses the corresponding functionality or when operators need to work remotely away from the control center. Secondly, the overall design is event-driven using serverless cloud services in response to the SCADA/EMS failure event. Thanks to “serverless”, the burden of the server provisioning and maintenance can be avoided from the user side. The cost of using public cloud services for this solution is extremely low since it is architected and implemented based on the event-driven Function-as-a-Service (FaaS) model. This work also develops a comprehensive cyber security mechanism to comply with critical infrastructure requirements for the power grid, which can serve as an exemplary framework for other grid operators to secure their cloud services.
| S-EPMC7377758 | biostudies-literature
Project description:Mechanical computing encodes information in deformed states of mechanical systems, such as multistable structures. However, achieving stable mechanical memory in most multistable systems remains challenging and often limited to binary information. Here, we report leveraging coupling kinematic bifurcation in rigid cube-based mechanisms with elasticity to create transformable, multistable mechanical computing metastructures with stable, high-density mechanical memory. Simply stretching the planar metastructure forms a multistable corrugated platform. It allows for independent mechanical or magnetic actuation of individual bistable element, serving as pop-up voxels for display or binary units for various tasks such as information writing, erasing, reading, encryption, and mechanologic computing. Releasing the pre-stretched strain stabilizes the prescribed information, resistant to external mechanical or magnetic perturbations, whereas re-stretching enables editable mechanical memory, akin to selective zones or disk formatting for information erasure and rewriting. Moreover, the platform can be reprogrammed and transformed into a multilayer configuration to achieve high-density memory.
| S-EPMC11204216 | biostudies-literature
Project description:Spiking Neural Networks (SNNs) have high potential to process information efficiently with binary spikes and time delay information. Recently, dedicated SNN hardware accelerators with on-chip synapse memory array are gaining interest in overcoming the limitations of running software-based SNN in conventional Von Neumann machines. In this paper, we proposed an efficient synapse memory structure to reduce the amount of hardware resource usage while maintaining performance and network size. In the proposed design, synapse memory size can be reduced by applying presynaptic weight scaling. In addition, axonal/neuronal offsets are applied to implement multiple layers on a single memory array. Finally, a transposable memory addressing scheme is presented for faster operation of spike-timing-dependent plasticity (STDP) learning. We implemented a SNN ASIC chip based on the proposed scheme with 65 nm CMOS technology. Chip measurement results showed that the proposed design provided up to 200X speedup over CPU while consuming 53 mW at 100 MHz with the energy efficiency of 15.2 pJ/SOP.
| S-EPMC6256061 | biostudies-literature
Project description:As deep neural network (DNN) models grow ever-larger, they can achieve higher accuracy and solve more complex problems. This trend has been enabled by an increase in available compute power; however, efforts to continue to scale electronic processors are impeded by the costs of communication, thermal management, power delivery and clocking. To improve scalability, we propose a digital optical neural network (DONN) with intralayer optical interconnects and reconfigurable input values. The path-length-independence of optical energy consumption enables information locality between a transmitter and a large number of arbitrarily arranged receivers, which allows greater flexibility in architecture design to circumvent scaling limitations. In a proof-of-concept experiment, we demonstrate optical multicast in the classification of 500 MNIST images with a 3-layer, fully-connected network. We also analyze the energy consumption of the DONN and find that digital optical data transfer is beneficial over electronics when the spacing of computational units is on the order of [Formula: see text]m.
| S-EPMC7862662 | biostudies-literature
Project description:In the last decade, bioinformatics has become an indispensable branch of modern science research, experiencing an explosion in financial support, developed applications and data collection. The growth of the datasets that are emerging from research laboratories, industry, the health sector, etc., are increasingly raising the levels of demand in computing power and storage. Processing biological data, in the large scales of these datasets, often requires the use of High Performance Computing (HPC) resources, especially when dealing with certain types of omics data, such as genomic and metagenomic data. Such computational resources not only require substantial investments, but they also involve high maintenance costs. More importantly, in order to keep good returns from the investments, specific training needs to be put in place to ensure that wasting is minimized. Furthermore, given that bioinformatics is a highly interdisciplinary field where several other domains intersect (such as biology, chemistry, physics and computer science), researchers from these areas also require bioinformatics-specific training in HPC, in order to fully take advantage of supercomputing centers. In this document, we describe our experience in training researchers from several different disciplines in HPC, as applied to bioinformatics under the framework of the leading European bioinformatics platform ELIXIR, and analyze both the content and outcomes of the course.
| S-EPMC6299036 | biostudies-literature
Project description:Due to the explosive increase of digital data creation, demand on advancement of computing capability is ever increasing. However, the legacy approaches that we have used for continuous improvement of three elements of computer (process, memory, and interconnect) have started facing their limits, and therefore are not as effective as they used to be and are also expected to reach the end in the near future. Evidently, it is a large challenge for computer hardware industry. However, at the same time it also provides great opportunities for the hardware design industry to develop novel technologies and to take leadership away from incumbents. This paper reviews the technical challenges that today's computing systems are facing and introduces potential directions for continuous advancement of computing capability, and discusses where computer hardware designers find good opportunities to contribute.
| S-EPMC8022507 | biostudies-literature
Project description:Technological advances in the past decade, hardware and software alike, have made access to high-performance computing (HPC) easier than ever. We review these advances from a statistical computing perspective. Cloud computing makes access to supercomputers affordable. Deep learning software libraries make programming statistical algorithms easy and enable users to write code once and run it anywhere-from a laptop to a workstation with multiple graphics processing units (GPUs) or a supercomputer in a cloud. Highlighting how these developments benefit statisticians, we review recent optimization algorithms that are useful for high-dimensional models and can harness the power of HPC. Code snippets are provided to demonstrate the ease of programming. We also provide an easy-to-use distributed matrix data structure suitable for HPC. Employing this data structure, we illustrate various statistical applications including large-scale positron emission tomography and ℓ1-regularized Cox regression. Our examples easily scale up to an 8-GPU workstation and a 720-CPU-core cluster in a cloud. As a case in point, we analyze the onset of type-2 diabetes from the UK Biobank with 200,000 subjects and about 500,000 single nucleotide polymorphisms using the HPC ℓ1-regularized Cox regression. Fitting this half-million-variate model takes less than 45 minutes and reconfirms known associations. To our knowledge, this is the first demonstration of the feasibility of penalized regression of survival outcomes at this scale.
| S-EPMC10168006 | biostudies-literature