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Seeding Structured Data by Default via Open Source Library Systems [chapter]

Dan Scott
2014 Lecture Notes in Computer Science  
However, some agile open source library systems have begun closing this gap by publishing structured data that uses the schema.org vocabulary to describe the bibliographic data, make offers for items available  ...  Finally, we discuss the impact that "the power of the default" publishing of structured data could have on discoverability of library offerings on the Semantic Web.  ...  Our efforts to enable library systems to publish structured data by default focused on two mature open source library systems (Koha and Evergreen), and one mature open source discovery system: VuFind.  ... 
doi:10.1007/978-3-319-07443-6_44 fatcat:omiigp7ccbardg7wpirsoo2lgu

Utopia: A Comprehensive and Collaborative Modeling Framework for Complex and Evolving Systems

Lukas Riedel, Benjamin Herdeanu, Harald Mack, Yunus Sevinchan, Julian Weninger
2020 Journal of Open Source Software  
Utopia includes a C++ library for model implementations and data writing and a Python frontend for simulation control, data analysis, and plotting.  ...  This makes Utopia a valuable tool for both research in and teaching of complex and evolving systems. Utopia is available as Docker image from DockerHub 1 or can be compiled from source.  ...  Acknowledgements We gratefully acknowledge the contributions by Narek Baghumian, Lorenzo Biasi, Unai Fischer Abaigar, Christian Kobrow, Fabian Krautgasser, Daniel Lake, Hendrik Leusmann, Peter  ... 
doi:10.21105/joss.02165 fatcat:sbsfy46au5g5dilv337zya7qqq

AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization

Jacob O. Spiegel, Jacob D. Durrant
2020 Journal of Cheminformatics  
We here present AutoGrow4, an open-source program for semi-automated computer-aided drug discovery.  ...  AutoGrow4 uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds.  ...  The default fragment libraries included with AutoGrow4 were derived from a subset of the ZINC database (https :// zinc.docki ng.org/).  ... 
doi:10.1186/s13321-020-00429-4 pmid:33431021 fatcat:dhavkga3lnehzc3fhwtnjtvpi4

FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models

Anders S. Christensen, Thomas Hamelryck, Jan H. Jensen
2014 PeerJ  
The generated peptides can then be geometry optimized by the MMFF94 molecular mechanics force field via convenient functions inside the library.  ...  FragBuilder is freely available at https://github.com/jensengroup/fragbuilder/ under the terms of the BSD open source license. 1 PeerJ PrePrints | http://dx.doi.org/10.7287/peerj.preprints.169v3 | CC-BY  ...  The random seed can be set explicitly via the fragbuilder.set seed() function. If no seed is supplied the seeding will be random.  ... 
doi:10.7717/peerj.277 pmid:24688855 pmcid:PMC3961104 fatcat:4fna6e65f5azvixdhszuxrv7da

Enhancing reproducibility and collaboration via management of R package cohorts [article]

Gabriel Becker, Cory Barr, Robert Gentleman, Michael Lawrence
2015 arXiv   pre-print
It introduces the package manifest as a central data structure for representing version specific, decentralized package cohorts.  ...  We provide a high-level interface for creating and switching between side-by-side package libraries derived from manifests.  ...  Availability We have released our switchr, switchrGist, and GRANBase packages under the Artistic 2.0 open-source software license.  ... 
arXiv:1501.02284v2 fatcat:vpdgdksn2nhcxahvgawnxg5k7a

Enhancing Reproducibility and Collaboration via Management of R Package Cohorts

Gabriel Becker, Cory Barr, Robert Gentleman, Michael Lawrence
2017 Journal of Statistical Software  
It introduces the package manifest as a central data structure for representing versionspecific, decentralized package cohorts.  ...  We provide a high-level interface for creating and switching between side-by-side package libraries derived from manifests.  ...  to explicitly including the package sources themselves (the approach pursued by Ushey et al. 2016 with their packrat system).  ... 
doi:10.18637/jss.v082.i01 fatcat:hzeoc3zzpjem7ojoybzsi2o7o4

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

Vishwesh Venkatraman, Thomas H. Colligan, George T. Lesica, Daniel R. Olson, Jeremiah Gaiser, Conner J. Copeland, Travis J. Wheeler, Amitava Roy
2022 Frontiers in Pharmacology  
As an example of performance, our pipeline required ∼40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ∼3.7 billion candidate molecules.  ...  Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation  ...  To identify library-sourced compounds similar to the de novo seeds produced by AutoGrow4, 1024-bit ECFP4 fingerprints (O'Boyle and Sayle, 2016) are computed for all ~3.7 billion library compounds.  ... 
doi:10.3389/fphar.2022.874746 pmid:35559261 pmcid:PMC9086895 fatcat:ik4aemqlxvhbnpplbcxzwguk4u

A RESTful API for Accessing Microbial Community Data for MG-RAST

Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer (+1 others)
2015 PLoS Computational Biology  
By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools  ...  This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects.  ...  By opening MG-RAST up via a web services API (application programmers interface) we have enabled a programmatic way for others to use their bioinformatics tools with MG-RAST data.  ... 
doi:10.1371/journal.pcbi.1004008 pmid:25569221 pmcid:PMC4287624 fatcat:jhgiyh24qrhflmok3fsm44j6yi

QCOR: A Language Extension Specification for the Heterogeneous Quantum-Classical Model of Computation [article]

Tiffany M. Mintz, Alexander J. Mccaskey, Eugene F. Dumitrescu, Shirley V. Moore, Sarah Powers, Pavel Lougovski
2019 arXiv   pre-print
Motivated by the lack of such a model, we introduce a language extension specification, called QCOR, that enables single-source quantum-classical programming.  ...  Programs written using the QCOR library and directives based language extensions can be compiled to produce functional hybrid binary executables.  ...  This research used quantum computing system resources supported by the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research program office.  ... 
arXiv:1909.02457v1 fatcat:dvavkdnyozbmlk2fee3cqzg3ia

Stochastic Perturbations of Tabular Features for Non-Deterministic Inference with Automunge [article]

Nicholas J. Teague
2022 arXiv   pre-print
We offer the Automunge library for tabular preprocessing as a resource for the practice, which includes options to integrate random sampling or entropy seeding with the support of quantum circuits, representing  ...  sourced from the operating system.  ...  Automunge Automunge (Teague, 2021b ) is an open source python library, available now for pip install, built on top of Pandas (McKinney, 2010) , Numpy (Harris et al., 2020) , SciKitlearn (Pedregosa  ... 
arXiv:2202.09248v2 fatcat:rjdhtjjzlnej7nkvdtlbpuel5e

ViSTA FlowLib - A Framework for Interactive Visualization and Exploration of Unsteady Flows in Virtual Environments [article]

M. Schirski, A. Gerndt, T. Van Reimersdahl, T. Kuhlen, P. Adomeit, O. Lang, S. Pischinger, C. Bischof
2003 ICAT-EGVE 2014 - International Conference on Artificial Reality and Telexistence and Eurographics Symposium on Virtual Environments  
This is done by connecting dedicated sub-modules with clearly defined responsibilities through appropriate interfaces, whilst implementing sensible default behavior.  ...  In the past a lot of work has been invested in various aspects of an interactive visualization of CFD simulation data.  ...  - It is an extension library of our cross-platform virtual reality toolkit ViSTA 22 and uses the open-source Visualization Toolkit (VTK) 23 for a variety of visualization algorithms.  ... 
doi:10.2312/egve/ipt_egve2003/077-086 fatcat:yvxgk7s7j5gl5eepjlx6a7nbqm

Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser [article]

Yuri Kochnev, Erich Hellemann, Kevin C Cassidy, Jacob D Durrant
2019 bioRxiv   pre-print
Webina will be a useful open-source tool for the research and educational communities. A working version of the app can be accessed free of charge from http://durrantlab.com/webina.  ...  Webina is a JavaScript/WebAssembly library that runs AutoDock Vina entirely in a web browser. To use Webina, users need only visit a Webina-enabled webpage.  ...  We use Webpack, an open-source module bundler, to organize and assemble all custom and third-party libraries 98 and files (https://webpack.js.org/).  ... 
doi:10.1101/2019.12.18.881789 fatcat:b2w3tmxktnhalfl5vped4n5vju

PyKale: Knowledge-Aware Machine Learning from Multiple Sources in Python [article]

Haiping Lu, Xianyuan Liu, Robert Turner, Peizhen Bai, Raivo E Koot, Shuo Zhou, Mustafa Chasmai, Lawrence Schobs
2021 arXiv   pre-print
We present Pykale - a Python library for knowledge-aware machine learning on graphs, images, texts, and videos to enable and accelerate interdisciplinary research.  ...  We demonstrate its interdisciplinary nature via examples in bioinformatics, knowledge graph, image/video recognition, and medical imaging.  ...  We also thank early users of our library and their helpful feedback.  ... 
arXiv:2106.09756v1 fatcat:mnuxoz26mbdexn5cobnpqhkmyi

Integrative Functional Statistics in Logic Programming [chapter]

Nicos Angelopoulos, Vítor Santos Costa, João Azevedo, Jan Wielemaker, Rui Camacho, Lodewyk Wessels
2013 Lecture Notes in Computer Science  
Furthermore it can be used to open up new application areas for logic programming and AI techniques such as bioinformatics, computational biology, text mining, psychology and neuro sciences, where R has  ...  Programs utilising the library syntax are elegant and succinct with intuitive semantics and clear integration.  ...  The R environment [15] is an open source software package for statistical data analysis.  ... 
doi:10.1007/978-3-642-45284-0_13 fatcat:apjn37e5azd4rh67hnjzpajwzq

Web-based Visualization Platform for Geospatial Data

Martin Hecher, Christoph Traxler, Gerd Hesina, Anton Fuhrmann
2015 Proceedings of the 6th International Conference on Information Visualization Theory and Applications  
Via a simple configuration file the system can be configured for different stakeholder use cases, by defining desired data sources and available viewer modules.  ...  The implemented software is based on open source libraries and uses modern web technologies to provide a platform-independent, pluginfree user experience.  ...  ACKNOWLEDGEMENTS The V-MANIP project was funded by the European Space Agency in Frascati, Italy (ESA/ESRIN) under the reference AO/1-7193/12/I-AM.  ... 
doi:10.5220/0005359503110316 dblp:conf/grapp/HecherTHFF15 fatcat:ifbaflfg4nfnbdfblsw43rvgzm
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