14 papers · ranked by Valyu relevance
Noel M O'Boyle, Chris Morley, Geoffrey R Hutchison
Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We…
Yury V. Zaytsev, Abigail Morrison
NEST is a simulator for large-scale networks of spiking point neuron models (Gewaltig and Diesmann, [11]). Originally, simulations were controlled via the Simulation Language Interpreter (SLI), a built-in scripting facility implementing a language derived from PostScript (Adobe Systems, Inc., [1]). The introduction of…
Yangyang Li, Rendong Yang
Background With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern…
Martin Larralde, Georg Zeller, Can Alkan
Protein similarity search and annotation is a key part of biological sequence analysis, allowing for the discovery of protein function from sequence data. Improving on Position-Specific Scoring Matrices that were used historically to search for motifs, Profile Hidden Markov Models (pHMMs) were introduced in HMMER () to…
Pierre Fernique, Christophe Pradal, Nick Higham
Most of Python and R scientific packages incorporate compiled scientific libraries to speed up the code and reuse legacy libraries. While several semi-automatic solutions exist to wrap these compiled libraries, the process of wrapping a large library is cumbersome and time consuming. In this paper, we introduce…
Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost + 1 more
'Martin Zacharias'] Background Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application. Results We present an object-oriented…
Hugo Cornelis, Armando L. Rodriguez, Allan D. Coop, James M. Bower + 1 more
The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and…
Laurent Gautier
Background Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has relative strong points, making some languages better suited than others for a given task to be…
Kirill Batmanov, Jan Delabie, Junbai Wang
Most of somatic mutations in cancer occur outside of gene coding regions. These mutations may disrupt the gene regulation by affecting protein-DNA interaction. A study of these disruptions is important in understanding tumorigenesis. However, current computational tools process DNA sequence variants individually, when…
Kristopher J. L. Irizarry, Randall L. Bryden
Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved…
David Miguel Susano Pinto, Mick A. Phillips, Nicholas Hall, Julio Mateos-Langerak + 5 more
'Julio Mateos-Langerak' 'Danail Stoychev' 'Tiago Susano Pinto' 'Martin J. Booth' 'Ilan Davis' 'Ian M. Dobbie'] Title: ABSTRACT Custom-built microscopes often require control of multiple hardware devices and precise hardware coordination. It is also desirable to have a solution that is scalable to complex systems and…
João Victor da Silva Guerra, Helder Veras Ribeiro-Filho, Gabriel Ernesto Jara, Leandro Oliveira Bortot + 2 more
Background Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the increasing availability of biostructural data due to advances in structural determination and…
Eilif Muller, James A. Bednar, Markus Diesmann, Marc-Oliver Gewaltig + 2 more
'Michael Hines' 'Andrew P. Davison'] This Research Topic of Frontiers in Neuroinformatics is dedicated to the memory of Rolf Kötter (1961-2010), who was the Frontiers Associate Editor responsible for this Research Topic, and who gave us considerable support and encouragement during the process of conceiving and…
Sebastian Bassi, Fran Lewitter
Usually enclosed by quotes (') or double quotes ("). Triple quotes (''') are used to delimit multiline strings. Strings are immutable. Once created they can't be modified. String methods are available at [http://www.python.org/doc/2.5/lib/string-methods.html](). For example: >>> s0='A regular string' Defined as an…