High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment

Bioinformatics applications are naturally distributed, due to distribution of involved data sets, experimental data and biological databases. They require high computing power, owing to the large size of data sets and the complexity of basic computations, may access heterogeneous data, where heterogeneity is in data format, access policy, distribution, etc., and require a secure infrastructure, because they could access private data owned by different organizations. The Problem Solving Environment (PSE) is an approach and a technology that can fulfil such bioinformatics requirements. The PSE can be used for the definition and composition of complex applications, hiding programming and configuration details to the user that can concentrate only on the specific problem. Moreover, Grids can be used for building geographically distributed collaborative problem solving environments and Grid aware PSEs can search and use dispersed high performance computing, networking, and data resources. In this work, the PSE solution has been chosen as the integration platform of bioinformatics tools and data sources. In particular an experiment of multiple sequence alignment on large scale, supported by the LIBIPSE, is presented

Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators

In a 2016 survey of 704 National Science Foundation (NSF) Biological Sciences Directorate principal investigators (BIO PIs), nearly 90% indicated they are currently or will soon be analyzing large data sets. BIO PIs considered a range of computational needs important to their work, including high performance computing (HPC), bioinformatics support, multistep workflows, updated analysis software, and the ability to store, share, and publish data. Previous studies in the United States and Canada emphasized infrastructure needs. However, BIO PIs said the most pressing unmet needs are training in data integration, data management, and scaling analyses for HPC-acknowledging that data science skills will be required to build a deeper understanding of life. This portends a growing data knowledge gap in biology and challenges institutions and funding agencies to redouble their support for computational training in biology

Simplifying gene expression microarray comparative analysis.

Gene Expression Comparative Analysis allows bioinformatics researchers to discover the conserved or specific functional regulation of genes. This is achieved through comparisons between quantitative gene expression measurements obtained in different species on different platforms to address a particular biological system. Comparisons are made more difficult due to the need to map orthologous genes between species, pre-processing of data (normalization) and post-analysis (statistical and correlation analysis). In this paper we introduce a web-based software package called EXP-PAC which provides on line interfaces for database construction and query of data, and makes use of a high performance computing platform of computer clusters to run gene sequence mapping and normalization methods in parallel. Thus, EXP-PAC facilitates the integration of gene expression data for comparative analysis and the online sharing, retrieval and visualization of complex multi-specific and multi-platform gene expression results.<br /

CCP4 Cloud for structure determination and project management in macromolecular crystallography

Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.The following funding is acknowledged: Biotechnology and Biological Sciences Research Council (grant No. BB/L007037/1; grant No. BB/S007040/1; grant No. BB/S007083/1; grant No. BB/S005099/1; grant No. BB/S007105/1; award No. BBF020384/1); Medical Research Council (grant No.MC_UP_A025_1012; grant No. MC_U105184325); Ro¨ntgenA˚ ngstro¨m Cluster (grant No. 349-2013-597); Nederlandse Wetenschappelijke Organisatie (grant No. TKI 16219)

A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.Comment: preprint, draft, 2 tables, 47 references, 7 files, Codes that can solve three dimensional linear elastostatic problems using constant boundary elements (of triangular shape) while ignoring body forces are provided as supplementary files; codes are distributed under the MIT License in three versions: i) MATLAB version ii) Fortran 90 version (sequential code) iii) Fortran 90 version (parallel code

Neuro-memristive Circuits for Edge Computing: A review

The volume, veracity, variability, and velocity of data produced from the ever-increasing network of sensors connected to Internet pose challenges for power management, scalability, and sustainability of cloud computing infrastructure. Increasing the data processing capability of edge computing devices at lower power requirements can reduce several overheads for cloud computing solutions. This paper provides the review of neuromorphic CMOS-memristive architectures that can be integrated into edge computing devices. We discuss why the neuromorphic architectures are useful for edge devices and show the advantages, drawbacks and open problems in the field of neuro-memristive circuits for edge computing

Principles of Neuromorphic Photonics

In an age overrun with information, the ability to process reams of data has become crucial. The demand for data will continue to grow as smart gadgets multiply and become increasingly integrated into our daily lives. Next-generation industries in artificial intelligence services and high-performance computing are so far supported by microelectronic platforms. These data-intensive enterprises rely on continual improvements in hardware. Their prospects are running up against a stark reality: conventional one-size-fits-all solutions offered by digital electronics can no longer satisfy this need, as Moore's law (exponential hardware scaling), interconnection density, and the von Neumann architecture reach their limits. With its superior speed and reconfigurability, analog photonics can provide some relief to these problems; however, complex applications of analog photonics have remained largely unexplored due to the absence of a robust photonic integration industry. Recently, the landscape for commercially-manufacturable photonic chips has been changing rapidly and now promises to achieve economies of scale previously enjoyed solely by microelectronics. The scientific community has set out to build bridges between the domains of photonic device physics and neural networks, giving rise to the field of \emph{neuromorphic photonics}. This article reviews the recent progress in integrated neuromorphic photonics. We provide an overview of neuromorphic computing, discuss the associated technology (microelectronic and photonic) platforms and compare their metric performance. We discuss photonic neural network approaches and challenges for integrated neuromorphic photonic processors while providing an in-depth description of photonic neurons and a candidate interconnection architecture. We conclude with a future outlook of neuro-inspired photonic processing.Comment: 28 pages, 19 figure

Special Session on Industry 4.0

No abstract available