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Journal articles on the topic 'Programmation interface'

Author: Grafiati
Published: 4 June 2021
Last updated: 2 February 2022

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1

Laugier, C. "Les apports respectifs des langages symboliques et de la cao en programmation des robots." Robotica 6, no. 3 (July 1988): 243–53. http://dx.doi.org/10.1017/s0263574700004355.

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SUMMARYA high-level robot programming language constitutes a general purpose interface for accessing the basic functional capabilities of a robot. On the other hand, CAD facilities give the possibility of using a subset of these capabilities in an easier fashion. In this paper, we show how a robot programming language and CAD facilities can be combined to obtain a robot programming system satisfying the need for generality, and allowing an easy connection with the basic robot programming functions. Such a connection is based on a “complete” simulator providing facilities for executing robot control programs on a graphic display, for describing manipulation tasks using interactive graphic tools, for simulating the physical world and its perception through sensors, and for displaying three-dimensional scenes as shaded pictures.
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2

Vandergucht, David. "ZFOREST : UN PROTOTYPE DE PLATEFORME WEB DE COVISUALISATION LIDAR, RASTER ET VECTEUR À GRANDE ÉCHELLE." Revue Française de Photogrammétrie et de Télédétection 1, no. 211-212 (December 30, 2020): 129–42. http://dx.doi.org/10.52638/rfpt.2015.551.

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En recherche comme en exploitation forestière, la donnée Lidar aéroportée apporte des clefs de compréhension surla structure du terrain, de la forêt et par extension, des informations sur la biomasse aérienne. Mais pour être utile, cette donnée Lidar doit couvrir de vastes étendues tout en étant très résolue spatialement. Ces caractéristiques se traduisent par de grands volumes de données très difficiles à visualiser, manipuler et étudier sans l’aide de logiciels très onéreux.Dans le cadre du projet ANR FORESEE, nous avons développé un logiciel web, de visualisation mixte nuage de pointsLidar / surface 3D issue d’un Modèle Numérique de Terrain / carte / photographie aérienne et terrestre / donnée vectorielle : la plateforme zForest. Ce logiciel, qui s’adresse aux chercheurs en télédétection et à terme aux exploitants forestiers, permet la navigation à grande échelle dans des données massives et leur exploration, du niveau de détail le plus large (la région) jusqu’au plus fin (l’arbre). Cet outil permet la mesure, l’annotation et l’extraction des données. Il propose également une interface de programmation web (API) permettant à d’autres outils du marché d’utiliser ses données sources. zForest étant une plateforme web, elle est disponible sans installation sur tous les navigateurs internet récents, facilitant son accessibilité et son déploiement.
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GUO, JUNXIA, and HAO HAN. "ANALYSIS AND DESIGN OF PROGRAMMATIC INTERFACES FOR INTEGRATION OF DIVERSE WEB CONTENTS." International Journal of Software Engineering and Knowledge Engineering 23, no. 10 (December 2013): 1487–511. http://dx.doi.org/10.1142/s0218194013500472.

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The technology that integrates various types of Web contents to build a new Web application through end-user programming is widely used nowadays. However, the Web contents do not have a uniform interface for accessing the data and computation. Most of the general Web users access information on the Web through applications until now. Hence, designing a uniform and flexible programmatic interface for integration of different Web contents is unavoidable. In this paper, we propose an approach that can be used to analyze Web applications automatically and reuse the information of Web applications through the programmatic interface we designed. Our approach can support the flexible integration of Web applications, Web services and Web feeds. In our experiments, we use a large number of Web pages from different types of Web applications and achieve the integration by the proposed programmatic interfaces. The experimental results show that our approach brings to the end-users a flexible and user-friendly programming environment.
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4

Vitvar, Tomas, Steve Vinoski, and Cesare Pautasso. "Programmatic Interfaces for Web Applications." IEEE Internet Computing 16, no. 4 (July 2012): 11–14. http://dx.doi.org/10.1109/mic.2012.86.

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5

Fortin, J. P., R. Moussa, C. Bocquillon, and J. P. Villeneuve. "Hydrotel, un modèle hydrologique distribué pouvant bénéficier des données fournies par la télédétection et les systèmes d'information géographique." Revue des sciences de l'eau 8, no. 1 (April 12, 2005): 97–124. http://dx.doi.org/10.7202/705215ar.

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Les processus hydrologiques variant dans l'espace et dans le temps en fonction de la variabilité spatio-temporelle des entrées météorologiques et de l'occupation du sol ainsi que de la variabilité spatiale de la topographie et de la nature du terrain, un modèle conçu pour bénéficier des données provenant de la télédétection et des SIG a été développé. Les principaux objectifs poursuivis étaient: l'application au plus grand nombre de bassins possible, une sélection d'algorithmes permettant de tenir compte des données disponibles, un minimum d'étalonnage, la facilité de transfert d'un bassin à l'autre, la programmation des algorithmes sur micro-ordinateur avec une interface très conviviale. La structure d'écoulement à l'intérieur d'un bassin versant est obtenue de manière informatisée à partir d'une discrétisation des altitudes rencontrées dans la zone d'intérêt, en mailles carrées de dimensions données, d'où l'on tire les pentes et les orientations de chaque maille, puis le bassin versant en amont de la maille identifiée comme exutoire, le réseau hydrographique, les sous-bassins versants et, finalement, les unités hydrologiques relativement homogènes (UHRH), définies sur la base de ces sous-bassins, en les regroupant ou les divisant au besoin. Un logiciel spécifique pour ce faire a été développé: PHYSITEL. Selon la conception très modulaire adoptée pour HYDROTEL, chaque sous-modèle offre généralement plus d'une option de simulation, afin de tenir compte des données disponibles sur le bassin versant traité. Les simulations peuvent être réalisées en considérant comme unité de simulation du bilan hydrologique vertical les mailles originales constituant le bassin ou les UHRH. Des exemples de simulation des débits à l'aide du modèle HYDROTEL sur divers bassins versants situés au Canada (Québec, Ontario, Colombie-Britannique) et dans le sud de la France sont présentés. Ces simulations indiquent que les différents algorithmes du modèle réagissent bien et qu'il est possible de considérer son application sur des bassins très divers situés sous des conditions climatiques variées. Des tests plus poussés sont en cours afin de mieux cerner la sensibilité des divers algorithmes aux données d'entrée ainsi que leur interchangeabilité.
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6

Broman, David. "Interactive Programmatic Modeling." ACM Transactions on Embedded Computing Systems 20, no. 4 (June 2021): 1–26. http://dx.doi.org/10.1145/3431387.

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Modeling and computational analyses are fundamental activities within science and engineering. Analysis activities can take various forms, such as simulation of executable models, formal verification of model properties, or inference of hidden model variables. Traditionally, tools for modeling and analysis have similar workflows: (i) a user designs a textual or graphical model or the model is inferred from data, (ii) a tool performs computational analyses on the model, and (iii) a visualization tool displays the resulting data. This article identifies three inherent problems with the traditional approach: the recomputation problem, the variable inspection problem, and the model expressiveness problem. As a solution, we propose a conceptual framework called Interactive Programmatic Modeling. We formalize the interface of the framework and illustrate how it can be used in two different domains: equation-based modeling and probabilistic programming.
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7

Staton, Ann Q. "The interface of communication and instruction: Conceptual considerations and programmatic manifestations." Communication Education 38, no. 4 (October 1989): 364–71. http://dx.doi.org/10.1080/03634528909378777.

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8

Zou, Xiao Jia, Xiang Dong You, Hao Pan, Xu Zhang, and Qian Luo. "User Interface Design and Implementation for Electricity Operation Information System Based on Android." Applied Mechanics and Materials 602-605 (August 2014): 3630–34. http://dx.doi.org/10.4028/www.scientific.net/amm.602-605.3630.

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In this paper, we mainly explore how to design and implement the user interfaces of Electricity Operation Information System based on Android. The paper extends its process as the following four aspects---requirements analysis, UI design, interaction design and programmatic implementation. In response to user actions fluidly and friendly, we add modules to handle exceptions. In the end, we give a briefly test on the system UI to ensure it run smoothly and make less mistakes. There are limited studies focusing on the flow design of UI combined with programmatic implementation. The UI design and implementation methodology has good reference at the early stage of developing an application, especially on Android platforms.
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Larraondo, Pablo R., Sean Pringle, Jian Guo, Joseph Antony, and Ben Evans. "GSio: A programmatic interface for delivering Big Earth data-as-a-service." Big Earth Data 1, no. 1-2 (November 30, 2017): 173–90. http://dx.doi.org/10.1080/20964471.2017.1397898.

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10

Kim, Sunghwan, Paul A. Thiessen, Tiejun Cheng, Bo Yu, and Evan E. Bolton. "An update on PUG-REST: RESTful interface for programmatic access to PubChem." Nucleic Acids Research 46, W1 (April 30, 2018): W563—W570. http://dx.doi.org/10.1093/nar/gky294.

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11

Anguita, Alberto, Miguel García-Remesal, Diana de la Iglesia, and Victor Maojo. "NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases." BioMed Research International 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/983805.

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RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.
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12

Dass, Gaurhari, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A. Grüning, Henning Hermjakob, and Yasset Perez-Riverol. "The omics discovery REST interface." Nucleic Acids Research 48, W1 (May 6, 2020): W380—W384. http://dx.doi.org/10.1093/nar/gkaa326.

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Abstract The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org/ws/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.
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13

Alexander, Adam, Ahmed El-Aassar, John MacDonald, and Anjoli Martin. "Technical Approaches to Developing a Highway Noise Programmatic Agreement." Transportation Research Record: Journal of the Transportation Research Board 2673, no. 1 (January 2019): 102–9. http://dx.doi.org/10.1177/0361198118822282.

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There are many instances in which noise studies were completed for projects that were not likely to result in noise impacts. In this paper, the authors provide an analysis from their conducted study, validating a programmatic agreement (PA) intended to reduce the need for unnecessary noise analyses. The technical study considered a range of average daily traffic volumes between 500 and 28,000. The parameters of the PA rely solely on calculated noise levels at specified traffic volume, mix, speed, and roadway designs using the FHWA Traffic Noise Model (TNM®) version 2.5 to develop a series of TNM cases, testing impact thresholds at various speed and slope conditions. Using this data, the authors developed a regression model to enable the PA expansion and provide answers for a finer grid of traffic volume. Using the regression model results, the authors will develop a graphical user interface to assess project eligibility for the PA.
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14

Gopaulakrishnan, Shweta, Samuela Pollack, BJ Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, and Vincent Carey. "restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor." F1000Research 8 (January 7, 2019): 21. http://dx.doi.org/10.12688/f1000research.17518.1.

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Bioconductor's SummarizedExperiment class unites numerical assay quantifications with sample- and experiment-level metadata. SummarizedExperiment is the standard Bioconductor class for assays that produce matrix-like data, used by over 200 packages. We describe the restfulSE package, a deployment of this data model that supports remote storage. We illustrate use of SummarizedExperiment with remote HDF5 and Google BigQuery back ends, with two applications in cancer genomics. Our intent is to allow the use of familiar and semantically meaningful programmatic idioms to query genomic data, while abstracting the remote interface from end users and developers.
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15

Vejnar, Charles E., and Antonio J. Giraldez. "LabxDB: versatile databases for genomic sequencing and lab management." Bioinformatics 36, no. 16 (June 5, 2020): 4530–31. http://dx.doi.org/10.1093/bioinformatics/btaa557.

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Abstract Summary Experimental laboratory management and data-driven science require centralized software for sharing information, such as lab collections or genomic sequencing datasets. Although database servers such as PostgreSQL can store such information with multiple-user access, they lack user-friendly graphical and programmatic interfaces for easy data access and inputting. We developed LabxDB, a versatile open-source solution for organizing and sharing structured data. We provide several out-of-the-box databases for deployment in the cloud including simple mutant or plasmid collections and purchase-tracking databases. We also developed a high-throughput sequencing (HTS) database, LabxDB seq, dedicated to storage of hierarchical sample annotations. Scientists can import their own or publicly available HTS data into LabxDB seq to manage them from production to publication. Using LabxDB’s programmatic access (REST API), annotations can be easily integrated into bioinformatics pipelines. LabxDB is modular, offering a flexible framework that scientists can leverage to build new database interfaces adapted to their needs. Availability and implementation LabxDB is available at https://gitlab.com/vejnar/labxdb and https://labxdb.vejnar.org for documentation. LabxDB is licensed under the terms of the Mozilla Public License 2.0. Supplementary information Supplementary data are available at Bioinformatics online.
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16

Farrell, Damien. "epitopepredict: a tool for integrated MHC binding prediction." Gigabyte 2021 (February 24, 2021): 1–14. http://dx.doi.org/10.46471/gigabyte.13.

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A key step in the cellular adaptive immune response is the presentation of antigens to T cells. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics, which allows in silico screening of peptides before experiments are performed. With the availability of whole genomes for many microbial species it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open-source license from https://github.com/dmnfarrell/epitopepredict
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Lee, Kyongryun, Florian Hahne, Deepayan Sarkar, and Robert Gentleman. "iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor." Advances in Bioinformatics 2009 (November 12, 2009): 1–3. http://dx.doi.org/10.1155/2009/103839.

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Flow cytometry (FCM) has become an important analysis technology in health care and medical research, but the large volume of data produced by modern high-throughput experiments has presented significant new challenges for computational analysis tools. The development of an FCM software suite in Bioconductor represents one approach to overcome these challenges. In the spirit of the R programming language (Tree Star Inc., “FlowJo”), these tools are predominantly console-driven, allowing for programmatic access and rapid development of novel algorithms. Using this software requires a solid understanding of programming concepts and of the R language. However, some of these tools|in particular the statistical graphics and novel analytical methods|are also useful for nonprogrammers. To this end, we have developed an open source, extensible graphical user interface (GUI) iFlow, which sits on top of the Bioconductor backbone, enabling basic analyses by means of convenient graphical menus and wizards. We envision iFlow to be easily extensible in order to quickly integrate novel methodological developments.
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18

Novichkov, P. S., T. S. Brettin, E. S. Novichkova, P. S. Dehal, A. P. Arkin, I. Dubchak, and D. A. Rodionov. "RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics." Nucleic Acids Research 40, W1 (June 14, 2012): W604—W608. http://dx.doi.org/10.1093/nar/gks562.

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19

Kaleb, Klara, Alex Warwick Vesztrocy, Adrian Altenhoff, and Christophe Dessimoz. "Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python." F1000Research 8 (January 10, 2019): 42. http://dx.doi.org/10.12688/f1000research.17548.1.

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The Orthologous Matrix (OMA) is a well-established resource to identify orthologs among many genomes. Here, we present two recent additions to its programmatic interface, namely a REST API, and user-friendly R and Python packages called OmaDB. These should further facilitate the incorporation of OMA data into computational scripts and pipelines. The REST API can be freely accessed at https://omabrowser.org/api. The R OmaDB package is available as part of Bioconductor at http://bioconductor.org/packages/OmaDB/, and the omadb Python package is available from the Python Package Index (PyPI) at https://pypi.org/project/omadb/.
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20

Kaleb, Klara, Alex Warwick Vesztrocy, Adrian Altenhoff, and Christophe Dessimoz. "Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python." F1000Research 8 (March 29, 2019): 42. http://dx.doi.org/10.12688/f1000research.17548.2.

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The Orthologous Matrix (OMA) is a well-established resource to identify orthologs among many genomes. Here, we present two recent additions to its programmatic interface, namely a REST API, and user-friendly R and Python packages called OmaDB. These should further facilitate the incorporation of OMA data into computational scripts and pipelines. The REST API can be freely accessed at https://omabrowser.org/api. The R OmaDB package is available as part of Bioconductor at http://bioconductor.org/packages/OmaDB/, and the omadb Python package is available from the Python Package Index (PyPI) at https://pypi.org/project/omadb/.
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21

Matalonga, Leslie, Carles Hernández-Ferrer, Davide Piscia, Enzo Cohen, Isabel Cuesta, Daniel Danis, Anne-Sophie Denommé-Pichon, et al. "Solving patients with rare diseases through programmatic reanalysis of genome-phenome data." European Journal of Human Genetics 29, no. 9 (June 1, 2021): 1337–47. http://dx.doi.org/10.1038/s41431-021-00852-7.

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AbstractReanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP’s Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics.
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Letunic, Ivica, and Peer Bork. "Interactive Tree Of Life (iTOL) v4: recent updates and new developments." Nucleic Acids Research 47, W1 (April 1, 2019): W256—W259. http://dx.doi.org/10.1093/nar/gkz239.

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Abstract The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.
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23

Abdulrehman, D., P. T. Monteiro, M. C. Teixeira, N. P. Mira, A. B. Lourenco, S. C. dos Santos, T. R. Cabrito, et al. "YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface." Nucleic Acids Research 39, Database (October 23, 2010): D136—D140. http://dx.doi.org/10.1093/nar/gkq964.

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Sellés Vidal, Lara, Rafael Ayala, Guy-Bart Stan, and Rodrigo Ledesma-Amaro. "rfaRm: An R client-side interface to facilitate the analysis of the Rfam database of RNA families." PLOS ONE 16, no. 1 (January 15, 2021): e0245280. http://dx.doi.org/10.1371/journal.pone.0245280.

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rfaRm is an R package providing a client-side interface for the Rfam database of non-coding RNA and other structured RNA elements. The package facilitates the search of the Rfam database by keywords or sequences, as well as the retrieval of all available information about specific Rfam families, such as member sequences, multiple sequence alignments, secondary structures and covariance models. By providing such programmatic access to the Rfam database, rfaRm enables genomic workflows to incorporate information about non-coding RNA, whose potential cannot be fully exploited just through interactive access to the database. The features of rfaRm are demonstrated by using it to analyze the SARS-CoV-2 genome as an example case.
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Kim, Sunghwan, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, et al. "PubChem in 2021: new data content and improved web interfaces." Nucleic Acids Research 49, no. D1 (November 5, 2020): D1388—D1395. http://dx.doi.org/10.1093/nar/gkaa971.

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Abstract PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Ратов, Д. В. "Object adaptation of Drag and Drop technology for web-system interface components." ВІСНИК СХІДНОУКРАЇНСЬКОГО НАЦІОНАЛЬНОГО УНІВЕРСИТЕТУ імені Володимира Даля, no. 4(268) (June 10, 2021): 7–12. http://dx.doi.org/10.33216/1998-7927-2021-268-4-7-12.

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Today, in the development of information systems, cloud technologies are often used for remote computing and data processing. There are web technologies, and on their basis, libraries and frameworks have been developed for creating web applications and user interfaces designed for the operation of information systems in browsers. Ready-made JavaScript libraries have been developed to add drag and drop functionality to a web application. However, in some situations, the library may not be available, or there may be overhead or dependencies that the project does not need to use it. In such situations, an alternative solution provides the functionality of APIs available in modern browsers. The article discusses the current state of the methods of the Drag and Drop mechanism and proposes a programmatic way to improve the interface by creating a class for dragging and dropping elements when organizing work in multi-user information web systems. Drag and Drop is a convenient way to improve the interface. Grabbing an element with the mouse and moving it visually simplifies many operations: from copying and moving documents, as in file managers, to placing orders in online store services. The HTML drag and drop API uses the DOM event model to retrieve information about a dragged element and update that element after the drag. Using JavaScript event handlers, it is possible to turn any element of the web system into a drag-and-drop element or drop target. To solve this problem, a JavaScript object was developed with methods that allow you to create a copy of any object and handle all events of this object aimed at organizing the Drag and Drop mechanism. Basic algorithm of Drag and Drop technology based on processing mouse events. The software implementation is considered and the results of the practical use of object adaptation of the Drag and Drop technology for the interface components of the web system - the medical information system MedSystem, in which the application modules have the implementation of the dispatcher and the interactive window interface are presented. In the "Outpatient clinic" module, the Drag and Drop mechanism is used when working with the "Appointment sheet". In the "Hospital" module of the MedSystem medical information system, the Drag and Drop mechanism is used in the "List of doctor's appointments". The results of using object adaptation of Drag and Drop technology have shown that this mechanism organically fits into existing technologies for building web applications and has sufficient potential to facilitate and automate work in multi-user information systems and web services.
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Fishenden, Jerry. "Sounds of Time and Place." Leonardo 50, no. 1 (February 2017): 12–19. http://dx.doi.org/10.1162/leon_a_01362.

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The author describes various aural techniques developed as part of the origination of the sonic content of compositions themed on palimpsests of time and place. Field-based recordings, authentic and synthetic impulse responses, convolution reverb and the use of third-party sounds retrieved via open programmatic interfaces are considered. The role of usability feedback is also discussed, specifically its beneficial impact on informing the development both of the compositions and the techniques they utilize. An initial mobile phone application is described, together with continuing work to develop additional mobile experiences.
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Piovesan, Damiano, Marco Necci, Nahuel Escobedo, Alexander Miguel Monzon, András Hatos, Ivan Mičetić, Federica Quaglia, et al. "MobiDB: intrinsically disordered proteins in 2021." Nucleic Acids Research 49, no. D1 (November 25, 2020): D361—D367. http://dx.doi.org/10.1093/nar/gkaa1058.

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Abstract The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users.
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Hoarfrost, Adrienne, Nick Brown, C. Titus Brown, and Carol Arnosti. "Sequencing data discovery with MetaSeek." Bioinformatics 35, no. 22 (June 21, 2019): 4857–59. http://dx.doi.org/10.1093/bioinformatics/btz499.

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Abstract Summary Sequencing data resources have increased exponentially in recent years, as has interest in large-scale meta-analyses of integrated next-generation sequencing datasets. However, curation of integrated datasets that match a user’s particular research priorities is currently a time-intensive and imprecise task. MetaSeek is a sequencing data discovery tool that enables users to flexibly search and filter on any metadata field to quickly find the sequencing datasets that meet their needs. MetaSeek automatically scrapes metadata from all publicly available datasets in the Sequence Read Archive, cleans and parses messy, user-provided metadata into a structured, standard-compliant database and predicts missing fields where possible. MetaSeek provides a web-based graphical user interface and interactive visualization dashboard, as well as a programmatic API to rapidly search, filter, visualize, save, share and download matching sequencing metadata. Availability and implementation The MetaSeek online interface is available at https://www.metaseek.cloud/. The MetaSeek database can also be accessed via API to programmatically search, filter and download all metadata. MetaSeek source code, metadata scrapers and documents are available at https://github.com/MetaSeek-Sequencing-Data-Discovery/metaseek/.
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Chudoba, B., E. Haney, L. Gonzalez, A. Omoragbon, and A. Oza. "Strategic forecasting in uncertain environments: hypersonic cruise vehicle research and development case study." Aeronautical Journal 119, no. 1211 (January 2015): 45–65. http://dx.doi.org/10.1017/s0001924000010241.

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AbstractThe exponentially increasing amount of information accumulated from past to current engineering projects has created an environment where repurposing existing data to support new projects is paramount to sustainable success. Strategic planning and early design decisions, specifically, occur in decision-making environments that require information support capabilities that lie outside of traditional engineering analyses. In order to advance towards a more complete planning environment, a pragmatic methodology has been developed for modern aerospace data and information collection, categorisation, and utilisation with a focus on current efforts in hypersonic vehicle research and development. The main thrust has been to provide insights into financial and technical trends that support objective programmatic and planning decision-making. The end-product is a suite of graphical decision-making interfaces, linked through a unified hypersonic database. The graphical interfaces are capable of highlighting the key project drivers along varying levels of categorisation and refinement. Aided by these newly developed data and information support interfaces covering past and present hypersonic efforts, the planner’s forecasting assessment of present and future hypersonic research and development efforts is pragmatically enriched towards a more complete managerial program-planning framework.
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Howe, Kevin L., Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu Akanni, James Allen, Jorge Alvarez-Jarreta, et al. "Ensembl Genomes 2020—enabling non-vertebrate genomic research." Nucleic Acids Research 48, no. D1 (October 10, 2019): D689—D695. http://dx.doi.org/10.1093/nar/gkz890.

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Abstract Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.
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Ramirez-Gonzalez, Ricardo H., Richard M. Leggett, Darren Waite, Anil Thanki, Nizar Drou, Mario Caccamo, and Robert Davey. "StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics." F1000Research 2 (November 15, 2013): 248. http://dx.doi.org/10.12688/f1000research.2-248.v1.

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Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages.
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Ramirez-Gonzalez, Ricardo H., Richard M. Leggett, Darren Waite, Anil Thanki, Nizar Drou, Mario Caccamo, and Robert Davey. "StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics." F1000Research 2 (February 19, 2014): 248. http://dx.doi.org/10.12688/f1000research.2-248.v2.

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Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages.
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34

Eckes, Annemarie H., Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, et al. "Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data." F1000Research 6 (April 12, 2017): 465. http://dx.doi.org/10.12688/f1000research.11301.1.

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The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data. Trait data associated with Brassica research and breeding experiments conducted on Brassica crops, used as vegetables, for livestock fodder and biofuels, is hosted on the site, together with information on the experimental plant materials used, as well as trial design. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for scientists and breeders. BIP opens up the opportunity to apply big data analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.
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35

Howe, Kevin L., Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, et al. "Ensembl 2021." Nucleic Acids Research 49, no. D1 (November 2, 2020): D884—D891. http://dx.doi.org/10.1093/nar/gkaa942.

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Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
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36

Ramos, Stephen J. "Materiality in the Seam Space: Sketches for a Transitional Port City Dome District." Urban Planning 6, no. 3 (July 27, 2021): 210–22. http://dx.doi.org/10.17645/up.v6i3.4082.

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Biomass material volatility generates new opportunities for port-city relationships. Alternative energy markets require specialized port facilities to handle new bulk commodities like biomass. Wood pellets, a type of biomass, present warehousing challenges due to combustion danger. The industrial response to this risk has generated new storage forms for port regions. The return to bulk cargo reintroduces materiality as a focus for port city research, which had generally been regarded as a peripheral concern since the advent of the shipping container. The container had come to represent a borderless, ‘fast capitalism’ throughput model, but research on port ‘accidents’ has complicated this reductive globalization narrative. The programmatic dynamism of wood pellet dome structures suggests new spatially-porous possibilities for an interstitial border space at the port-city interface with material commonalities and hybrid potentials for resilient logistics and civic facilities. In contrast to container cargo unitization, the dome signifies the standardization of the coastal/riparian port environment. Dome structures can help ports plan for the complex challenges of cargo material behaviors and increasing extreme weather events. The article begins with wood pellet materiality to then explore programmatic possibilities that industrial construction technology generates. Conceptually, this joins the proposal of port as ‘seam space’ with port-city resilience planning and the porosity celebrated in recent urbanism literature. Scaling up from wood pellet materiality to an interstitial port-city district, the article contributes to calls for increased attention to materiality as a means to envision new urban agendas.
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Shapiro, Kenneth. "Human-Animal Studies: Remembering the Past, Celebrating the Present, Troubling the Future." Society & Animals 28, no. 7 (November 25, 2020): 797–833. http://dx.doi.org/10.1163/15685306-bja10029.

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Abstract This is the third in a series of reports on the state of the field of Human-Animal Studies. In the introductory section, major terms in the prevailing definition of the field—Human-Animal Studies is the interdisciplinary study of human-animal relationships—are unpacked and critically analyzed. Subsequent sections deal with the field’s past, present, and possible futures. A schematic history of the field considers both scholarly contributions and programmatic inroads in the academy. The current state of the field section describes its breadth in terms of publication venues, disciplines that interface with it, and the variety of methods employed. It also offers a description of several common strategies that critique the received view of the categorical divide between human and other animal beings. The final section highlights both the potential of and anticipated roadblocks to each of several future trajectories.
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38

Altenhoff, Adrian M., Natasha M. Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy, David Dylus, Tarcisio M. de Farias, et al. "The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces." Nucleic Acids Research 46, no. D1 (November 2, 2017): D477—D485. http://dx.doi.org/10.1093/nar/gkx1019.

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39

Eckes, Annemarie H., Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, et al. "Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data." F1000Research 6 (November 15, 2017): 465. http://dx.doi.org/10.12688/f1000research.11301.2.

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The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data. The site hosts trait data associated with brassica research and breeding experiments conducted on brassica crops, that are used as oilseeds, vegetables, livestock forage and fodder and for biofuels. A key feature is the explicit management of meta-data describing the provenance and relationships between experimental plant materials, as well as trial design and trait descriptors. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies for any crop data. A new user interface and programmatic submission/retrieval system helps to simplify data access for researchers, breeders and other end-users. BIP opens up the opportunity to apply integrative, cross-project analyses to data generated by the Brassica Research Community. Here, we present a short description of the current status of the repository.
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40

Rees, Ian, Ed Langley, Wah Chiu, and Steven J. Ludtke. "EMEN2: An Object Oriented Database and Electronic Lab Notebook." Microscopy and Microanalysis 19, no. 1 (January 29, 2013): 1–10. http://dx.doi.org/10.1017/s1431927612014043.

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AbstractTransmission electron microscopy and associated methods, such as single particle analysis, two-dimensional crystallography, helical reconstruction, and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source.
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41

Oh, Sehyun, Jasmine Abdelnabi, Ragheed Al-Dulaimi, Ayush Aggarwal, Marcel Ramos, Sean Davis, Markus Riester, and Levi Waldron. "HGNChelper: identification and correction of invalid gene symbols for human and mouse." F1000Research 9 (December 21, 2020): 1493. http://dx.doi.org/10.12688/f1000research.28033.1.

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Gene symbols are recognizable identifiers for gene names but are unstable and error-prone due to aliasing, manual entry, and unintentional conversion by spreadsheets to date format. Official gene symbol resources such as HUGO Gene Nomenclature Committee (HGNC) for human genes and the Mouse Genome Informatics project (MGI) for mouse genes provide authoritative sources of valid, aliased, and outdated symbols, but lack a programmatic interface and correction of symbols converted by spreadsheets. We present HGNChelper, an R package that identifies known aliases and outdated gene symbols based on the HGNC human and MGI mouse gene symbol databases, in addition to common mislabeling introduced by spreadsheets, and provides corrections where possible. HGNChelper identified invalid gene symbols in the most recent Molecular Signatures Database (mSigDB 7.0) and in platform annotation files of the Gene Expression Omnibus, with prevalence ranging from ~3% in recent platforms to 30-40% in the earliest platforms from 2002-03. HGNChelper is installable from CRAN.
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42

CHIU, DICKSON K. W., DANNY KOK, ALEX K. C. LEE, and S. C. CHEUNG. "INTEGRATING LEGACY SITES INTO WEB SERVICES WITH WEBXCRIPT." International Journal of Cooperative Information Systems 14, no. 01 (March 2005): 25–44. http://dx.doi.org/10.1142/s0218843005001006.

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Despite the recent uprising of the Web Services technology for programmatic interfaces of business-to-business (B2B) E-commerce services (e-services) over the Internet, most existing sites can only support human interactions with Hypertext Markup Language (HTML) through web browsers. Automating third-party client access into Web Services generally requires developing sophisticated programs to simulate human access by handling HTML pages. However, these HTML interfaces vary across web sites, and are often subject to changes. Client maintenance is therefore tedious and expensive. Even for the site owner, it may still require much effort in redeveloping the underlying presentation and application logics. This motivates our study for the requirement and the formulation of a conceptual model for such automation. Based on the requirement, we develop a novel approach to automating dialogs with web-based services (particularly for cross-organizational processes), using a high-level script language, called WebXcript language. The language provides features for HTML forms-based dialogues and eXtended Markup Language (XML) messaging. The XML syntax of WebXcript further enables convenient user authoring and easy engine development with extensively available XML tools. It supports expected responses and exception handling. We further propose a wrapper architecture based on WebXcript to integrate legacy sites into Web Services, where Web Service Definition Language (WSDL) interfaces are generated from high-level mappings from database or WebXcript parameter definitions. We demonstrate the applicability of our approach with examples in integrating distributed information, online ordering, and XML messaging, together with discussions on our experiences and the advantages of our approach.
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43

Kahsay, Robel, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, et al. "GlyGen data model and processing workflow." Bioinformatics 36, no. 12 (April 23, 2020): 3941–43. http://dx.doi.org/10.1093/bioinformatics/btaa238.

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Abstract Summary Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization and dissemination project for carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources. Availability and implementation GlyGen web portal is freely available to access at https://glygen.org. The data portal, web services, SPARQL endpoint and GitHub repository are also freely available at https://data.glygen.org, https://api.glygen.org, https://sparql.glygen.org and https://github.com/glygener, respectively. All code is released under license GNU General Public License version 3 (GNU GPLv3) and is available on GitHub https://github.com/glygener. The datasets are made available under Creative Commons Attribution 4.0 International (CC BY 4.0) license. Supplementary information Supplementary data are available at Bioinformatics online.
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Selama, Okba, Phillip James, Farida Nateche, Elizabeth M. H. Wellington, and Hocine Hacène. "The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database." BioMed Research International 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/240175.

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Databases are an essential tool and resource within the field of bioinformatics. The primary aim of this study was to generate an overview of global bacterial biodiversity and biogeography using available data from the two largest public online databases, NCBI Nucleotide and GBIF. The secondary aim was to highlight the contribution each geographic area has to each database. The basis for data analysis of this study was the metadata provided by both databases, mainly, the taxonomy and the geographical area origin of isolation of the microorganism (record). These were directly obtained from GBIF through the online interface, whileE-utilitiesandPythonwere used in combination with a programmatic web service access to obtain data from the NCBI Nucleotide Database. Results indicate that the American continent, and more specifically the USA, is the top contributor, while Africa and Antarctica are less well represented. This highlights the imbalance of exploration within these areas rather than any reduction in biodiversity. This study describes a novel approach to generating global scale patterns of bacterial biodiversity and biogeography and indicates that theProteobacteriaare the most abundant and widely distributed phylum within both databases.
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Hoksza, David, Piotr Gawron, Marek Ostaszewski, Ewa Smula, and Reinhard Schneider. "MINERVA API and plugins: opening molecular network analysis and visualization to the community." Bioinformatics 35, no. 21 (April 25, 2019): 4496–98. http://dx.doi.org/10.1093/bioinformatics/btz286.

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Abstract Summary The complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform’s visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network. Availability and implementation Plugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.
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46

Van Londen, G. J., Jill Weiskopf Brufsky, and Ira Russell Parker. "The University of Pittsburgh CancerCenter Primary Care Provider Workforce Integration Initiative: An institutional model—Design, process, status, and implications." Journal of Clinical Oncology 34, no. 3_suppl (January 20, 2016): 41. http://dx.doi.org/10.1200/jco.2016.34.3_suppl.41.

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41 Background: Due to increasing numbers of individuals diagnosed with cancer, a burgeoning cohort of cancer survivors with significant medical co-morbidities, and oncology workforce “supply-demand” challenges, the optimal integration of Primary Care Providers (PCPs) into the comprehensive cancer care paradigm is of timely importance. The objective is to describe those specific planning and implementation issues impacting the establishment of a cancer care delivery model targeting the interface between Oncology and Primary Care. Methods: The University of Pittsburgh CancerCenter PCP Workforce Integration Initiative received authorization to proceed in December of 2014. Immediate actions were then undertaken: 1) Establishment of an “Advisory/Working Group” [Fifteen stakeholders representing the interests of Oncology, Patient Advocacy, Nursing, Primary Care (Family Medicine, Geriatric Medicine, Internal Medicine, and Gynecology); Administration, Information Technology, and Research]; 2) Conduct of focus groups and individual, fact-finding conversations; 3) Programmatic planning of a “pilot” intervention; and 4) Planning of a full-day, continuing medical/nursing education symposium focusing upon the specific training and empowerment needs of PCPs with regard to their evolving roles in the comprehensive cancer care paradigm (November/2015). Results: Focus groups demonstrated an overall acknowledgement of the importance of the issue and a willingness to participate. Specific identification of those unique provider roles and competencies necessary to address a patient’s individual “survivorship” risk profile and the development of a system to best enhance communication and information exchange among the providers and patients were made evident. The results of a survey (knowledge, attitudes, beliefs, and practices) conducted to the attendees of the Symposium will be discussed. Conclusions: To best optimize the interface between Oncologists and PCPs with regard to best practices cancer care, well-planned competency training and “system development” will be necessary.
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Singh, Sameer. "Minecraft as a Platform for Project-Based Learning in AI." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 09 (April 3, 2020): 13504–5. http://dx.doi.org/10.1609/aaai.v34i09.7070.

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Undergraduate courses that focus on open-ended, project-based learning teach students how to define concrete goals, transfer conceptual understanding of algorithms to code, and evaluate/analyze/present their solution. However, AI, along with machine learning, is getting increasingly varied in terms of both the approaches and applications, making it challenging to design project courses that span a sufficiently wide spectrum of AI. For these reasons, existing AI project courses are restricted to a narrow set of approaches (e.g. only reinforcement learning) or applications (e.g. only computer vision).In this paper, we propose to use Minecraft as the platform for teaching AI via project-based learning. Minecraft is an open-world sandbox game with elements of exploration, resource gathering, crafting, construction, and combat, and is supported by the Malmo library that provides a programmatic interface to the player observations and actions at various levels of granularity. In Minecraft, students can design projects to use approaches like search-based AI, reinforcement learning, supervised learning, and constraint satisfaction, on data types like text, audio, images, and tabular data. We describe our experience with an open-ended, undergraduate AI projects course using Minecraft that includes 82 different projects, covering themes that ranged from navigation, instruction following, object detection, combat, and music/image generation.
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48

Birgmeier, Johannes, Maximilian Haeussler, Cole A. Deisseroth, Ethan H. Steinberg, Karthik A. Jagadeesh, Alexander J. Ratner, Harendra Guturu, et al. "AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature." Science Translational Medicine 12, no. 544 (May 20, 2020): eaau9113. http://dx.doi.org/10.1126/scitranslmed.aau9113.

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The diagnosis of Mendelian disorders requires labor-intensive literature research. Trained clinicians can spend hours looking for the right publication(s) supporting a single gene that best explains a patient’s disease. AMELIE (Automatic Mendelian Literature Evaluation) greatly accelerates this process. AMELIE parses all 29 million PubMed abstracts and downloads and further parses hundreds of thousands of full-text articles in search of information supporting the causality and associated phenotypes of most published genetic variants. AMELIE then prioritizes patient candidate variants for their likelihood of explaining any patient’s given set of phenotypes. Diagnosis of singleton patients (without relatives’ exomes) is the most time-consuming scenario, and AMELIE ranked the causative gene at the very top for 66% of 215 diagnosed singleton Mendelian patients from the Deciphering Developmental Disorders project. Evaluating only the top 11 AMELIE-scored genes of 127 (median) candidate genes per patient resulted in a rapid diagnosis in more than 90% of cases. AMELIE-based evaluation of all cases was 3 to 19 times more efficient than hand-curated database–based approaches. We replicated these results on a retrospective cohort of clinical cases from Stanford Children’s Health and the Manton Center for Orphan Disease Research. An analysis web portal with our most recent update, programmatic interface, and code is available at AMELIE.stanford.edu.
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Kok, Kasper. "The grammatical potential of co-speech gesture." Functions of Language 23, no. 2 (October 6, 2016): 149–78. http://dx.doi.org/10.1075/fol.23.2.01kok.

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In recent years, consensus has been growing that certain co-speech gestures must be incorporated in grammatical theory. Contrary to traditional beliefs, gestural expression has been found to be systematic in various ways, to exhibit some degree of compositional structure and to be to a certain extent language-specific. Most current work on the gesture-grammar interface is, nonetheless, rather programmatic in character or lacks an appropriate theoretical framework. This paper shows that Functional Discourse Grammar (FDG) provides a promising model for understanding the grammar-gesture relationship in a more comprehensive and detailed way than has thus far been achieved. It first evaluates how a FDG perspective on language structure aligns with the ways gestures have been studied. Then it demonstrates that various types of co-speech manual gestures can be classified (perhaps even exhaustively) according to the pragmatic and semantic layers recognized in FDG. On the basis of this survey, a first sketch of a multi-channel (speech-gesture) version of FDG’s architecture is presented. Finally, some challenges are put forward that arise when taking the multimodal grammar enterprise seriously. Altogether, the content of this paper suggests that a multimodal perspective on grammar can be mutually beneficial for functionally oriented linguists and gesture researchers.
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Mi, Huaiyu, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, and Paul D. Thomas. "PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API." Nucleic Acids Research 49, no. D1 (December 8, 2020): D394—D403. http://dx.doi.org/10.1093/nar/gkaa1106.

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Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all domains of life. The evolutionary classification is based on a library of over 15,000 phylogenetic trees, and the functional classifications include Gene Ontology terms and pathways. Here, we analyze the current coverage of genes from genomes in different taxonomic groups, so that users can better understand what to expect when analyzing a gene list using PANTHER tools. We also describe extensive improvements to PANTHER made in the past two years. The PANTHER Protein Class ontology has been completely refactored, and 6101 PANTHER families have been manually assigned to a Protein Class, providing a high level classification of protein families and their genes. Users can access the TreeGrafter tool to add their own protein sequences to the reference phylogenetic trees in PANTHER, to infer evolutionary context as well as fine-grained annotations. We have added human enhancer-gene links that associate non-coding regions with the annotated human genes in PANTHER. We have also expanded the available services for programmatic access to PANTHER tools and data via application programming interfaces (APIs). Other improvements include additional plant genomes and an updated PANTHER GO-slim.
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