13 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…
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…
Venkata Chandrasekhar, Nisha Sharma, Jonas Schaub, Christoph Steinbeck + 1 more
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management.…
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…
Gergely Zahoránszky-Kőhalmi, Brandon Walker, Nathan Miller, Brett Yang + 11 more
The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication, we identified the need for the development of an Application Programming Interface (API) that could promote biomedical data integration…
Authors not listed
The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions…
Helle W. van den Maagdenberg, Martin Šícho, David Alencar Araripe, Sohvi Luukkonen + 9 more
Building reliable and robust quantitative structure-property relationship (QSPR) models is a challenging task. First, the experimental data needs to be obtained, analyzed and curated. Second, the number of available methods is continuously growing and evaluating different algorithms and methodologies can be arduous.…
Authors not listed
The widespread adoption of open-source cheminformatics toolkits remains constrained by technical implementation barriers, including complex installation procedures, dependency management, and integration challenges. Here, we present Cheminformatics Microservice V3, a significant update to the existing platform that…
Martin Šícho, Xuhan Liu, Daniel Svozil, Gerard van Westen
This manuscript describes the development and architecture of the GenUI software platform for integration of molecular generators. The source code for the components of the platform is available in the following repositories: https://github.com/martin-sicho/genui https://github.com/martin-sicho/genui-gui…
Sterling G. Baird, Taylor D. Sparks
Closed-loop Spectroscopy Lab: Light-mixing Demo (CLSLab:Light) is a teaching and prototyping platform for autonomous scientific discovery. It consists of a set of LEDs and a light sensor while encapsulating key principles for "self-driving" (i.e., autonomous) research laboratories, including sending commands, receiving…