scholarly journals simuG: a general-purpose genome simulator

2018 ◽  
Author(s):  
Jia-Xing Yue ◽  
Gianni Liti
Keyword(s):  
General Purpose ◽  
Bioinformatics Analyses ◽  
Full Spectrum ◽  
Genomic Variants ◽  
Link Type ◽  
Wide Range ◽  
Simulation Based ◽  
Testing Data

AbstractSummarySimulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a light-weighted tool for simulating the full-spectrum of genomic variants. The simplicity and versatility of simuG makes it a unique general purpose genome simulator for a wide-range of simulation-based applications.Availability and implementationCode in Perl along with user manual and testing data is available at https://github.com/yjx1217/simuG. This software is free for use under the MIT license.

scholarly journals simuG: a general-purpose genome simulator

2019 ◽  
Vol 35 (21) ◽  
pp. 4442-4444 ◽  
Author(s):  
Jia-Xing Yue ◽  
Gianni Liti
Keyword(s):  
Copy Number Variants ◽  
General Purpose ◽  
Supplementary Information ◽  
Nucleotide Polymorphisms ◽  
Bioinformatics Analyses ◽  
Full Spectrum ◽  
Single Nucleotide ◽  
Genomic Variants ◽  
Wide Range ◽  
Simulation Based

Abstract Summary Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Deletions, copy number variants, inversions and translocations) for any organisms (including human). The simplicity and versatility of simuG make it a unique general-purpose genome simulator for a wide-range of simulation-based applications. Availability and implementation Code in Perl along with user manual and testing data is available at https://github.com/yjx1217/simuG. This software is free for use under the MIT license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals FastTrack: An open-source software for tracking varying numbers of deformable objects

2021 ◽  
Vol 17 (2) ◽  
pp. e1008697
Author(s):  
Benjamin Gallois ◽  
Raphaël Candelier
Keyword(s):  
Open Source ◽  
Cell Tracking ◽  
Ad Hoc ◽  
Ground Truth ◽  
General Purpose ◽  
Two Dimensions ◽  
Deformable Objects ◽  
Tracking Accuracy ◽  
Link Type ◽  
Wide Range

Analyzing the dynamical properties of mobile objects requires to extract trajectories from recordings, which is often done by tracking movies. We compiled a database of two-dimensional movies for very different biological and physical systems spanning a wide range of length scales and developed a general-purpose, optimized, open-source, cross-platform, easy to install and use, self-updating software called FastTrack. It can handle a changing number of deformable objects in a region of interest, and is particularly suitable for animal and cell tracking in two-dimensions. Furthermore, we introduce the probability of incursions as a new measure of a movie’s trackability that doesn’t require the knowledge of ground truth trajectories, since it is resilient to small amounts of errors and can be computed on the basis of an ad hoc tracking. We also leveraged the versatility and speed of FastTrack to implement an iterative algorithm determining a set of nearly-optimized tracking parameters—yet further reducing the amount of human intervention—and demonstrate that FastTrack can be used to explore the space of tracking parameters to optimize the number of swaps for a batch of similar movies. A benchmark shows that FastTrack is orders of magnitude faster than state-of-the-art tracking algorithms, with a comparable tracking accuracy. The source code is available under the GNU GPLv3 at https://github.com/FastTrackOrg/FastTrack and pre-compiled binaries for Windows, Mac and Linux are available at http://www.fasttrack.sh.

scholarly journals Simulation-Based Power-Loss Optimization of General-Purpose High-Voltage SiC MOSFET Circuit Under High-Frequency Operation

IEEE Access ◽  
2021 ◽  
Vol 9 ◽  
pp. 23786-23794
Author(s):  
Abhishek Kar ◽  
Mitiko Miura-Mattausch ◽  
Mainak Sengupta ◽  
Dondee Navaroo ◽  
Hideyuki Kikuchihara ◽  
...  
Keyword(s):  
High Voltage ◽  
High Frequency ◽  
Power Loss ◽  
General Purpose ◽  
Simulation Based ◽  
High Frequency Operation

scholarly journals A Generalization Performance Study Using Deep Learning Networks in Embedded Systems

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1031
Author(s):  
Joseba Gorospe ◽  
Rubén Mulero ◽  
Olatz Arbelaitz ◽  
Javier Muguerza ◽  
Miguel Ángel Antón
Keyword(s):  
Deep Learning ◽  
Embedded Systems ◽  
Embedded System ◽  
General Purpose ◽  
Learning Networks ◽  
Performance Study ◽  
Learning Techniques ◽  
Wide Range ◽  
Learning Architectures

Deep learning techniques are being increasingly used in the scientific community as a consequence of the high computational capacity of current systems and the increase in the amount of data available as a result of the digitalisation of society in general and the industrial world in particular. In addition, the immersion of the field of edge computing, which focuses on integrating artificial intelligence as close as possible to the client, makes it possible to implement systems that act in real time without the need to transfer all of the data to centralised servers. The combination of these two concepts can lead to systems with the capacity to make correct decisions and act based on them immediately and in situ. Despite this, the low capacity of embedded systems greatly hinders this integration, so the possibility of being able to integrate them into a wide range of micro-controllers can be a great advantage. This paper contributes with the generation of an environment based on Mbed OS and TensorFlow Lite to be embedded in any general purpose embedded system, allowing the introduction of deep learning architectures. The experiments herein prove that the proposed system is competitive if compared to other commercial systems.

scholarly journals An information theoretic approach to link prediction in multiplex networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Seyed Hossein Jafari ◽  
Amir Mahdi Abdolhosseini-Qomi ◽  
Masoud Asadpour ◽  
Maseud Rahgozar ◽  
Naser Yazdani
Keyword(s):  
Real World ◽  
Link Prediction ◽  
Large Scale ◽  
Similarity Measures ◽  
Prediction Method ◽  
General Purpose ◽  
Fast Method ◽  
Theoretic Approach ◽  
Multiplex Networks ◽  
Wide Range

AbstractThe entities of real-world networks are connected via different types of connections (i.e., layers). The task of link prediction in multiplex networks is about finding missing connections based on both intra-layer and inter-layer correlations. Our observations confirm that in a wide range of real-world multiplex networks, from social to biological and technological, a positive correlation exists between connection probability in one layer and similarity in other layers. Accordingly, a similarity-based automatic general-purpose multiplex link prediction method—SimBins—is devised that quantifies the amount of connection uncertainty based on observed inter-layer correlations in a multiplex network. Moreover, SimBins enhances the prediction quality in the target layer by incorporating the effect of link overlap across layers. Applying SimBins to various datasets from diverse domains, our findings indicate that SimBins outperforms the compared methods (both baseline and state-of-the-art methods) in most instances when predicting links. Furthermore, it is discussed that SimBins imposes minor computational overhead to the base similarity measures making it a potentially fast method, suitable for large-scale multiplex networks.

scholarly journals Towards an accurate description of perovskite ferroelectrics: exchange and correlation effects

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Simuck F. Yuk ◽  
Krishna Chaitanya Pitike ◽  
Serge M. Nakhmanson ◽  
Markus Eisenbach ◽  
Ying Wai Li ◽  
...  
Keyword(s):  
Density Functional ◽  
General Purpose ◽  
Correlation Effects ◽  
Lattice Constants ◽  
Bulk Solids ◽  
Wide Range ◽  
Exchange Enhancement ◽  
Experimental Values ◽  
Similar Accuracy ◽  
Ferroelectric Oxides

Abstract Using the van der Waals density functional with C09 exchange (vdW-DF-C09), which has been applied to describing a wide range of dispersion-bound systems, we explore the physical properties of prototypical ABO 3 bulk ferroelectric oxides. Surprisingly, vdW-DF-C09 provides a superior description of experimental values for lattice constants, polarization and bulk moduli, exhibiting similar accuracy to the modified Perdew-Burke-Erzenhoff functional which was designed specifically for bulk solids (PBEsol). The relative performance of vdW-DF-C09 is strongly linked to the form of the exchange enhancement factor which, like PBEsol, tends to behave like the gradient expansion approximation for small reduced gradients. These results suggest the general-purpose nature of the class of vdW-DF functionals, with particular consequences for predicting material functionality across dense and sparse matter regimes.

SYSTEMC IMPLEMENTATION AND PERFORMANCE EVALUATION OF A DECOUPLED GENERAL-PURPOSE MATRIX PROCESSOR

2010 ◽  
Vol 20 (02) ◽  
pp. 103-121 ◽  
Author(s):  
MOSTAFA I. SOLIMAN ◽  
ABDULMAJID F. Al-JUNAID
Keyword(s):  
Performance Evaluation ◽  
Matrix Multiplication ◽  
General Purpose ◽  
System Level ◽  
Memory Latency ◽  
Single Chip ◽  
Wide Range ◽  
Matrix Unit ◽  
And Performance ◽  
Vector Matrix

Technological advances in IC manufacturing provide us with the capability to integrate more and more functionality into a single chip. Today's modern processors have nearly one billion transistors on a single chip. With the increasing complexity of today's system, the designs have to be modeled at a high-level of abstraction before partitioning into hardware and software components for final implementation. This paper explains in detail the implementation and performance evaluation of a matrix processor called Mat-Core with SystemC (system level modeling language). Mat-Core is a research processor aiming at exploiting the increasingly number of transistors per IC to improve the performance of a wide range of applications. It extends a general-purpose scalar processor with a matrix unit. To hide memory latency, the extended matrix unit is decoupled into two components: address generation and data computation, which communicate through data queues. Like vector architectures, the data computation unit is organized in parallel lanes. However, on parallel lanes, Mat-Core can execute matrix-scalar, matrix-vector, and matrix-matrix instructions in addition to vector-scalar and vector-vector instructions. For controlling the execution of vector/matrix instructions on the matrix core, this paper extends the well known scoreboard technique. Furthermore, the performance of Mat-Core is evaluated on vector and matrix kernels. Our results show that the performance of four lanes Mat-Core with matrix registers of size 4 × 4 or 16 elements each, queues size of 10, start up time of 6 clock cycles, and memory latency of 10 clock cycles is about 0.94, 1.3, 2.3, 1.6, 2.3, and 5.5 FLOPs per clock cycle; achieved on scalar-vector multiplication, SAXPY, Givens, rank-1 update, vector-matrix multiplication, and matrix-matrix multiplication, respectively.

scholarly journals RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Danying Shao ◽  
Nabeel Ahmed ◽  
Nishant Soni ◽  
Edward P. O’Brien
Keyword(s):  
Integer Programming ◽  
Web Application ◽  
Stop Codon ◽  
Ribosome Profiling ◽  
Programming Method ◽  
Analysis Tool ◽  
Site Location ◽  
Link Type ◽  
Wide Range ◽  
A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

Evaluation of Composted Sewage Sludge/Straw Mixture for Horticultural Utilization

1989 ◽  
Vol 21 (8-9) ◽  
pp. 889-897 ◽  
Author(s):  
J. M. Lopez-Real ◽  
E. Witter ◽  
F. N. Midmer ◽  
B. A. O. Hewett
Keyword(s):  
Collaborative Research ◽  
Slow Release ◽  
General Purpose ◽  
Exchange Capacity ◽  
Soluble Salts ◽  
Slow Release Fertilizer ◽  
Wide Range ◽  
Sludge Cake ◽  
Bulk Volume ◽  
Composted Sewage Sludge

Collaborative research between Southern Water and Wye College, University of London, has led to the development of a static aerated pile composting process for the treatment of dewatered activated sludge cake/straw mixtures. The process reduces bulk volume of the sludge producing an environmentally acceptable, stabilised, odour and pathogen-free product. Characteristics of the compost make it a suitable general purpose medium for container grown plants, providing the salt concentration is reduced by washing the compost prior to planting. Compared with peat the compost has a higher bulk density, a lower waterholding capacity, a lower cation exchange capacity, a high content of soluble salts, and a higher content of plant nutrients. A compost mixture was successfully developed in the growing trials containing equal quantities of compost, Sphagnum peat, and horticultural vermiculite. The compost has been used successfully to grow a wide range of plants. Plants grown in mixtures based on the compost were in general similar to those grown in peat-based growing media. The compost is a valuable soil conditioner and slow release fertilizer.

scholarly journals A FIJI Macro for quantifying pattern in extracellular matrix

2019 ◽  
Author(s):  
Esther Wershof ◽  
Danielle Park ◽  
David J Barry ◽  
Robert P Jenkins ◽  
Antonio Rullan ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Quantitative Analysis ◽  
Comprehensive Description ◽  
Link Type ◽  
Wide Range ◽  
Automated Pipeline ◽  
Imagej Plugin

AbstractDiverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

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