24 papers · ranked by Valyu relevance
Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost + 12 more
'Felipe da Veiga Leprevost' 'Hervé Ménager' 'Dan Søndergaard' 'Hannes Röst' 'Timo Sachsenberg' "Brian O'Connor" 'Fábio Madeira' 'Victoria Dominguez Del Angel' 'Michael R. Crusoe' 'Susheel Varma' 'Daniel Blankenberg' 'Rafael C. Jimenez' '' 'Yasset Perez-Riverol'] Software Containers are changing the way scientists and…
Ryan Dale, Björn Grüning, Andreas Sjödin, Jillian Rowe + 147 more
We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager, Conda. Currently, Bioconda offers a collection of over 2900 software tools, which are continuously maintained, updated, and extended by a growing global…
Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor + 16 more
'Richard J. Abdill' 'Neha Rajkumar' 'Nathan LaPierre' 'Jaqueline Brito' 'Andre M. Ribeiro-dos-Santos' 'Can Fırtına' 'Nour Almadhoun' 'Varuni Sarwal' 'Eleazar Eskin' 'Qiyang Hu' 'Derek Ryan Strong' 'Byoung-Do' 'Kim Kim' 'Malak Abedalthagafi' 'Onur Mutlu' 'Serghei Mangul'] Mohammed Alser1 , Sharon Waymost 2 , Ram…
Vahid Jalili, Dave Clements, Björn Grüning, Daniel Blankenberg + 1 more
A growing number of biomedical methods and protocols are being disseminated as open-source software packages. When put in concert with other packages, they can execute in-depth and comprehensive computational pipelines. Therefore, their integration with other software packages plays a prominent role in their adoption…
Michael Banck
Started in 1993, the Debian project is one of the oldest Free Software projects. Due to its volunteer nature, specialists from all fields contribute to the Debian GNU/Linux distribution, which includes more than 30000 packages. The Debian packaging policy, its advanced package management system and the conservative…
Eva Maxfield Brown, Stephan Druskat, Laurent Hébert-Dufresne, James Howison + 5 more
Despite the importance of scientific software for research, it is often not formally recognized nor rewarded. This is especially true for foundational libraries, which are hidden below packages visible to the users (and thus doubly hidden, since even the packages directly used in research are frequently not visible in…
Shian Su, Vincent J. Carey, Lori Shepherd, Matthew Ritchie + 2 more
The Bioconductor project, a large collection of open source software for the comprehension of large-scale biological data, continues to grow with new packages added each week, motivating the development of software tools focused on exposing package metadata to developers and users. The resulting BiocPkgTools package…
Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon + 9 more
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both…
Federico D. Sacerdoti
This paper describes a practical method of developing custom HPC software products using a store of libraries and tools independent from the OS called a "garden". All dependencies from the product to libraries of the underlying OS distribution are carefully severed, isolating the package from instability due to system…
Sergio Pablo-García, Raúl Pérez-Soto, Albert Sabadell-Rendón, Diego Garay-Ruiz + 2 more
In the study of chemical reactions, visualizing reaction networks is pivotal for identifying crucial compounds and reactions. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity.…
Farid Zakaria, Tom Scogland, S.J. Gamblin, Carlos Maltzahn
In this paper, we explore the mechanisms available for packaging software to find its own dependencies in the context of a taxonomy of software distribution, and discuss their benefits and pitfalls. We discuss workarounds for some common problems caused by using these composed stacks and introduce Shrinkwrap: A…
Harshitha Menon, Konstantinos Parasyris, Tom Scogland, S.J. Gamblin
Modern software is incredibly complex. A typical application may comprise hundreds or thousands of reusable components. Automated package managers can help to maintain a consistent set of dependency versions, but ultimately the solvers in these systems rely on constraints generated by humans. At scale, small errors add…
Francesco Strozzi, Roel Janssen, Ricardo Wurmus, Michael R. Crusoe + 7 more
'George Githinji' 'Paolo Di Tommaso' 'Dominique Belhachemi' 'Steffen Möller' 'Geert Smant' 'Joep de Ligt' 'Pjotr Prins'] Biological, clinical, and pharmacological research now often involves analyses of genomes, transcriptomes, proteomes, and interactomes, within and between individuals and across species. Due to large…
Piyush Agrawal, Rajesh Kumar, Salman Sadullah Usmani, Anjali Dhall + 9 more
In past number of web-based resources has been developed in the field of Bioinformatics. These resources are heavily used by scientific community to provide solution for challenges faced by experimental researchers particularly in the field of biomedical sciences. There are number of challenges in utilizing full…
Yu Liu, Xue-Wei Dong, Gang Li
A simple, flexible packaging system for EPICS modules and related software is implemented at HEPS, which also produces reusable modular IOC executables that can be composed to replace many multi-device IOC applications. A configuration convention is suggested that helps to implement easily maintainable multi-IOC…
G. Amádio, Benda Xu
—Providing users of HPC systems with a wide variety of up to date software packages is a challenging task. Large software stacks built from source are difficult to manage, requiring powerful package management tools. The Portage package manager from Gentoo is a highly flexible tool that offers a mature solution to this…
Serghei Mangul, Thiago Mosqueiro, Richard J. Abdill, Dat Duong + 13 more
'Keith Mitchell' 'Varuni Sarwal' 'Brian Hill' 'Jaqueline Brito' 'Russell Jared Littman' 'Benjamin Statz' 'Angela Ka-Mei Lam' 'Gargi Dayama' 'Laura Grieneisen' 'Lana S. Martin' 'Jonathan Flint' 'Eleazar Eskin' 'Ran Blekhman'] Developing new software tools for analysis of large-scale biological data is a key component of…
Anupam Ojha, Lane Votapka, Gary Huber, Shang Gao + 1 more
SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) is a powerful and versatile software tool designed to computationally estimate the kinetics and thermodynamics of complex molecular processes, particularly emphasizing the process of receptor-ligand binding and unbinding. We present a suite of tutorials for…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
Alejandro Santana-Bonilla, Raquel Lopez-Rios De Castro, Peike Sun, Robert Ziolek + 1 more
Machine learning methods offer the opportunity to design new functional materials on an unprecedented scale however building the large, diverse databases of molecules on which to train such methods remains a daunting task. Automated computational chemistry modelling workflows are therefore becoming essential tools in…
Andreas Prlić, Hilmar Lapp
As a member of the PLOS family, PLOS Computational Biology promotes open and unrestricted access to scientific publications and the research products that support them. For PLOS Computational Biology, this specifically includes computational methods and the software that implements them. To foster a culture of open…
Joao Aires-de-Sousa
GUIDEMOL is a Python computer program based on the RDKit software to process molecular structures and calculate molecular descriptors with a graphical user interface using the tkinter package. It can calculate descriptors already implemented in RDKit as well as grid representations of 3D molecular structures using the…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
Kirill Zinovjev, Marc W. van der Kamp
X-ray crystallography allows detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. However, crystal structures provide little more than a static picture of proteinligand interactions, whereas dynamical…