12 papers · ranked by Valyu relevance
M. Eric Irrgang, Jennifer M. Hays, Peter M. Kasson
Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are…
Dilawar Singh, Steven S. Andrews
Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ applicaton programming interface (API), which were convenient, but limited extensibility. We added a Python API to Smoldyn…
M. Eric Irrgang, Caroline Davis, Peter M. Kasson
Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS…
Matteo Valerio, Alessandro Inno, Stefania Gori
Python 36 was chosen as the programming language for pyBioPortal, given its growing popularity in bioinformatics and compatibility with all major operating systems. The version of Python used for development is 3.9, which ensures stability and support in the more recent versions of Python, as version 2 has not been…
Sachin Gavali, Julie Cowart, Chuming Chen, Karen E Ross + 2 more
'Cecilia Arighi' 'Cathy H Wu'] Title: Abstract iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and…
Aziz Khan, Anthony Mathelier
JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to…
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…
Erik Huckvale, Hunter N.B. Moseley
The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and…
Erick Martins Ratamero, Kiya Govek, Julio Mateos Langerak, Fernando Cervantes Sanchez + 1 more
Many research laboratories need to manage, process, and analyze the increasingly large volumes and complexity of data being produced by state-of-the-art bioimaging platforms. OMERO is a popular open-source client-server application that provides a unified interface for managing and working with bioimages and their…
Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz
'Morris A. Swertz'] Background Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science.…
Tianze Cao, Qian Li, Yuexia Huang, Anshui Li
Background The visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learning, Python is currently the most popular programming language. The…
Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner + 3 more
Authentication is the process of identifying a client when the server is provided with a login and password (credentials) that match an authorised individual’s information within an authentication service. We encourage API developers to use common authentication methods such as OAuth 2.0 , JsonWebToken , and Basic…