Search results for "Source code"
showing 10 items of 61 documents
Development of the BCI Device Controlling C++ Software, Based on Existing Open Source Projects
2021
The possibility of using the BCI open source code for building BCI controlled device, based on small AVR or ARM microcontrollers was considered. Some techniques to extract code snippets from other BCI projects were presented in the case of OpenViBE as the code donor. Problem with obtaining driver source codes for factory BCI devices has been pointed out.
Compiler Driven Automatic Kernel Context Migration for Heterogeneous Computing
2014
Computer systems provide different heterogeneous resources (e.g., GPUs, DSPs and FPGAs) that accelerate applications and that can reduce the energy consumption by using them. Usually, these resources have an isolated memory and a require target specific code to be written. There exist tools that can automatically generate target specific codes for program parts, so-called kernels. The data objects required for a target kernel execution need to be moved to the target resource memory. It is the programmers' responsibility to serialize these data objects used in the kernel and to copy them to or from the resource's memory. Typically, the programmer writes his own serializing function or uses e…
Mapping of BLASTP Algorithm onto GPU Clusters
2011
Searching protein sequence database is a fundamental and often repeated task in computational biology and bioinformatics. However, the high computational cost and long runtime of many database scanning algorithms on sequential architectures heavily restrict their applications for large-scale protein databases, such as GenBank. The continuing exponential growth of sequence databases and the high rate of newly generated queries further deteriorate the situation and establish a strong requirement for time-efficient scalable database searching algorithms. In this paper, we demonstrate how GPU clusters, powered by the Compute Unified Device Architecture (CUDA), OpenMP, and MPI parallel programmi…
Modeling lightning observations from space-based platforms (CloudScat.jl 1.0)
2020
This is an open access article. This work is distributed under the Creative Commons Attribution 4.0 License.
Bill2d - a software package for classical two-dimensional Hamiltonian systems
2015
Abstract We present Bill2d , a modern and efficient C++ package for classical simulations of two-dimensional Hamiltonian systems. Bill2d can be used for various billiard and diffusion problems with one or more charged particles with interactions, different external potentials, an external magnetic field, periodic and open boundaries, etc. The software package can also calculate many key quantities in complex systems such as Poincare sections, survival probabilities, and diffusion coefficients. While aiming at a large class of applicable systems, the code also strives for ease-of-use, efficiency, and modularity for the implementation of additional features. The package comes along with a use…
FINDUS: An Open-Source 3D Printable Liquid-Handling Workstation for Laboratory Automation in Life Sciences
2020
3D-printed laboratory devices can enable ambitious research purposes even at a low-budget level. To follow this trend, here we describe the construction, calibration, and usage of the FINDUS (Fully Integrable Noncommercial Dispensing Utility System). We report the successful 3D printing and assembly of a liquid-handling workstation for less than $400. Using this setup, we achieve reliable and flexible liquid-dispensing automation with relative pipetting errors of less than 0.3%. We show our system is well suited for several showcase applications from both the biology and chemistry fields. In support of the open-source spirit, we make all 3D models, assembly instructions, and source code ava…
Increasing GP Computing Power for Free via Desktop GRID Computing and Virtualization
2009
This paper presents how it is possible to increase the Genetic Programming (GP) Computing Power (CP) for free, via Volunteer Computing (VC), using the well known framework BOINC plus a new ``virtualization'' layer which adds all the benefits from the virtualization paradigm. Two different experiments, employing a standard GP tool and a complex GP system, are performed --with distributed PCs over several cities-- to show the free achieved CP by means of VC, without the necessity of modifying or adapting the original GP source code. The methodology can be easily extended to Evolutionary Algorithms (EAs).
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
2018
Abstract Motivation K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability. Results We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Exper…
ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads
2019
Abstract Motivation Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. Results Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset wit…
Symbolic Reductionist Model for Program Comprehension
2007
This article presents the main features of a novel construction, symbolic analysis, for automatic source code processing. The method is superior to the known methods, because it uses a semiotic, interpretative approach. Its most important processes and characteristics are considered here. We describe symbolic information retrieval and the process of analysis in which it can be used in order to obtain pragmatic information. This, in turn, is useful in understanding a current Java program version when developing a new version.