scholarly journals Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i534-i541
Author(s):  
Marwan Abdellah ◽  
Nadir Román Guerrero ◽  
Samuel Lapere ◽  
Jay S Coggan ◽  
Daniel Keller ◽  
...  
Keyword(s):  
Visual Analysis ◽  
Interactive Visualization ◽  
Application Programming Interface ◽  
Supplementary Information ◽  
Vascular Networks ◽  
Substantial Impact ◽  
Domain Specific ◽  
Brain Vasculature ◽  
Application Programming ◽  
Background Mode

Abstract Motivation Accurate morphological models of brain vasculature are key to modeling and simulating cerebral blood flow in realistic vascular networks. This in silico approach is fundamental to revealing the principles of neurovascular coupling. Validating those vascular morphologies entails performing certain visual analysis tasks that cannot be accomplished with generic visualization frameworks. This limitation has a substantial impact on the accuracy of the vascular models employed in the simulation. Results We present VessMorphoVis, an integrated suite of toolboxes for interactive visualization and analysis of vast brain vascular networks represented by morphological graphs segmented originally from imaging or microscopy stacks. Our workflow leverages the outstanding potentials of Blender, aiming to establish an integrated, extensible and domain-specific framework capable of interactive visualization, analysis, repair, high-fidelity meshing and high-quality rendering of vascular morphologies. Based on the initial feedback of the users, we anticipate that our framework will be an essential component in vascular modeling and simulation in the future, filling a gap that is at present largely unfulfilled. Availability and implementation VessMorphoVis is freely available under the GNU public license on Github at https://github.com/BlueBrain/VessMorphoVis. The morphology analysis, visualization, meshing and rendering modules are implemented as an add-on for Blender 2.8 based on its Python API (application programming interface). The add-on functionality is made available to users through an intuitive graphical user interface, as well as through exhaustive configuration files calling the API via a feature-rich command line interface running Blender in background mode. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Malware Analysis Using Visualized Image Matrices

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
KyoungSoo Han ◽  
BooJoong Kang ◽  
Eul Gyu Im
Keyword(s):  
Visual Analysis ◽  
Application Programming Interface ◽  
Malware Analysis ◽  
Analysis Method ◽  
Execution Traces ◽  
Similarity Calculation ◽  
Application Programming ◽  
Representative Image ◽  
Programming Interface

This paper proposes a novel malware visual analysis method that contains not only a visualization method to convert binary files into images, but also a similarity calculation method between these images. The proposed method generates RGB-colored pixels on image matrices using the opcode sequences extracted from malware samples and calculates the similarities for the image matrices. Particularly, our proposed methods are available for packed malware samples by applying them to the execution traces extracted through dynamic analysis. When the images are generated, we can reduce the overheads by extracting the opcode sequences only from the blocks that include the instructions related to staple behaviors such as functions and application programming interface (API) calls. In addition, we propose a technique that generates a representative image for each malware family in order to reduce the number of comparisons for the classification of unknown samples and the colored pixel information in the image matrices is used to calculate the similarities between the images. Our experimental results show that the image matrices of malware can effectively be used to classify malware families both statically and dynamically with accuracy of 0.9896 and 0.9732, respectively.

scholarly journals Diplomatic documents data for international relations: the Freedom of Information Archive Database

2020 ◽  
pp. 073889422093032
Author(s):  
Matthew J Connelly ◽  
Raymond Hicks ◽  
Robert Jervis ◽  
Arthur Spirling ◽  
Clara H Suong
Keyword(s):  
International Relations ◽  
Language Processing ◽  
Application Programming Interface ◽  
Us Foreign Policy ◽  
Freedom Of Information ◽  
Domain Specific ◽  
Government Documents ◽  
The Usa ◽  
Application Programming ◽  
Programming Interface

We introduce the Freedom of Information Archive (FOIArchive) Database, a collection of over 3 million documents about state diplomacy. Substantively, our database focusses on the USA and provides opportunities to analyze previously classified (or publicly unavailable) corpora of internal government documents which include the raw—often full—text of those documents. We also provide within-country diplomatic records for the USA, UK, and Brazil. The full span of the data is 1620–2013, but it is mainly from the twentieth century. Our database allows scholars to view text and associated statistics online and to download and view customized datasets via an application programming interface. We provide extensive metadata about the documents, including the countries and persons they mention, and their topics and classification levels. The metadata includes information we extracted with domain-specific, customized natural language processing tools. To demonstrate the potential of this data, we use it to design and validate a new index for “country importance” in the context of US foreign policy priorities.

scholarly journals MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature

2020 ◽  
Author(s):  
Benjamin Elsworth ◽  
Tom R Gaunt
Keyword(s):  
Language Processing ◽  
Application Programming Interface ◽  
Biomedical Literature ◽  
Supplementary Information ◽  
Modern Natural ◽  
Application Programming ◽  
The Subject ◽  
Processing Algorithms ◽  
Literature Based Discovery ◽  
Programming Interface

ABSTRACT Summary The field of literature-based discovery is growing in step with the volume of literature being produced. From modern natural language processing algorithms to high quality entity tagging, the methods and their impact are developing rapidly. One annotation object that arises from these approaches, the subject–predicate–object triple, is proving to be very useful in representing knowledge. We have implemented efficient search methods and an application programming interface, to create fast and convenient functions to utilize triples extracted from the biomedical literature by SemMedDB. By refining these data, we have identified a set of triples that focus on the mechanistic aspects of the literature, and provide simple methods to explore both enriched triples from single queries, and overlapping triples across two query lists. Availability and Implementation: https://melodi-presto.mrcieu.ac.uk/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals EpyNN: Educational python for Neural Networks

2021 ◽  
Author(s):  
Florian Malard ◽  
Laura Danner ◽  
Emilie Rouzies ◽  
Jesse G Meyer ◽  
Ewen Lescop ◽  
...  
Keyword(s):  
Neural Networks ◽  
Graphical Representation ◽  
Source Code ◽  
Application Programming Interface ◽  
Supplementary Information ◽  
Practical Implementation ◽  
Data Preparation ◽  
Link Type ◽  
Application Programming ◽  
Programming Interface

AbstractSummaryArtificial Neural Networks (ANNs) have achieved unequaled performance for numerous problems in many areas of Science, Business, Public Policy, and more. While experts are familiar with performance-oriented software and underlying theory, ANNs are difficult to comprehend for non-experts because it requires skills in programming, background in mathematics and knowledge of terminology and concepts. In this work, we release EpyNN, an educational python resource meant for a public willing to understand key concepts and practical implementation of scalable ANN architectures from concise, homogeneous and idiomatic source code. EpyNN contains an educational Application Programming Interface (API), educational workflows from data preparation to ANN training and a documentation website setting side-by-side code, mathematics, graphical representation and text to facilitate learning and provide teaching material. Overall, EpyNN provides basics for python-fluent individuals who wish to learn, teach or develop from scratch.AvailabilityEpyNN documentation is available at https://epynn.net and repository can be retrieved from https://github.com/synthaze/epynn.ContactStéphanie Olivier-Van-Stichelen, [email protected] InformationSupplementary files and listings.

scholarly journals BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

2020 ◽  
Author(s):  
Nowlan H Freese ◽  
Karthik Raveendran ◽  
Chaitanya Kintali ◽  
Srishti Tiwari ◽  
Pawan Bole ◽  
...  
Keyword(s):  
Visual Analytics ◽  
Web Application ◽  
Visual Analysis ◽  
Genomic Data ◽  
Application Programming Interface ◽  
Genome Browser ◽  
Rna Seq ◽  
Web Based ◽  
Science Gateways ◽  
Application Programming

AbstractBackgroundVisualization of genomic data is a key step in validating methods and results. Web-based science gateways such as CyVerse provide storage and analysis tools for genomic data but often lack visualization capability. Desktop visualization tools like Integrated Genome Browser (IGB) enable highly interactive data visualization but are difficult to deploy in science gateways. Developing ways for gateways to interoperate with pre-existing external tools like IGB would enhance their value to users.ResultsWe developed BioViz Connect, a new web application that connects CyVerse and IGB using the CyVerse Terrain Application Programming Interface (API). Using BioViz Connect, users can (i) stream their CyVerse data to IGB for visualization, (ii) add IGB specific metadata such as genome version and track appearance to CyVerse data, and (iii) run compute-intensive visual analytics functions to create new visualizations for IGB. To demonstrate BioViz Connect, we present an example visual analysis of RNA-Seq data from Arabidopsis thaliana plants undergoing heat and desiccation stresses. The example shows how researchers can seamlessly analyze and visualize their CyVerse data in IGB. BioViz Connect is accessible from https://bioviz.org.ConclusionsBioViz Connect demonstrates a new way to integrate science gateways with desktop applications using APIs.

Unipept CLI 2.0: adding support for visualizations and functional annotations

2020 ◽  
Vol 36 (14) ◽  
pp. 4220-4221 ◽  
Author(s):  
Pieter Verschaffelt ◽  
Philippe Van Thienen ◽  
Tim Van Den Bossche ◽  
Felix Van der Jeugt ◽  
Caroline De Tender ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Web Application ◽  
Application Programming Interface ◽  
Supplementary Information ◽  
Functional Annotations ◽  
New Information ◽  
Interactive Visualizations ◽  
Application Programming ◽  
Version 2.0 ◽  
The Individual

Abstract Summary Unipept is an ecosystem of tools developed for fast metaproteomics data-analysis consisting of a web application, a set of web services (application programming interface, API) and a command-line interface (CLI). After the successful introduction of version 4 of the Unipept web application, we here introduce version 2.0 of the API and CLI. Next to the existing taxonomic analysis, version 2.0 of the API and CLI provides access to Unipept’s powerful functional analysis for metaproteomics samples. The functional analysis pipeline supports retrieval of Enzyme Commission numbers, Gene Ontology terms and InterPro entries for the individual peptides in a metaproteomics sample. This paves the way for other applications and developers to integrate these new information sources into their data processing pipelines, which greatly increases insight into the functions performed by the organisms in a specific environment. Both the API and CLI have also been expanded with the ability to render interactive visualizations from a list of taxon ids. These visualizations are automatically made available on a dedicated website and can easily be shared by users. Availability and implementation The API is available at http://api.unipept.ugent.be. Information regarding the CLI can be found at https://unipept.ugent.be/clidocs. Both interfaces are freely available and open-source under the MIT license. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Tibanna: software for scalable execution of portable pipelines on the cloud

2019 ◽  
Vol 35 (21) ◽  
pp. 4424-4426 ◽  
Author(s):  
Soohyun Lee ◽  
Jeremy Johnson ◽  
Carl Vitzthum ◽  
Koray Kırlı ◽  
Burak H Alver ◽  
...  
Keyword(s):  
Open Source Software ◽  
Source Code ◽  
Software Tool ◽  
Application Programming Interface ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Description Language ◽  
Amazon Web Services ◽  
Application Programming ◽  
Programming Interface

Abstract Summary We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network. Availability and implementation Source code is available on GitHub at https://github.com/4dn-dcic/tibanna. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A Proposed Criteria for Evaluting Cloud based Systems

2014 ◽  
Vol 13 (3) ◽  
pp. 4281-4290
Author(s):  
Sururah Apinke Bello
Keyword(s):  
Cloud Computing ◽  
Open Systems ◽  
Application Programming Interface ◽  
Domain Specific ◽  
Starting Point ◽  
Cloud Providers ◽  
Level Information ◽  
Application Programming ◽  
And Performance ◽  
High Level

A number of Cloud Providers have sprung up with different offers ranging from providing instances that looks much like physical hardware to application domain-specific offers. This study intends to propose a set of review criteria to evaluate existing Cloud computing providers to high level information about this emerging way of IT provisioning. Existing Cloud providers in the Iaas, Paas and SaaS were considered using, Architecture, Application Programming Interface, User Interface, Security, Fault tolerance and Scalability, Software implementation, Monitoring, Payment and Performance. This study is to assist Cloud users and researchers in making important decision in using Cloud Systems. The study exposed a refined method of further classification of Cloud based System. The classification will enable users to know open systems that are readily available for research, commercial systems for big projects and also be a good starting point for new comers into Cloud Computing environment.

scholarly journals Showcase Browsing with Texttiles 2.0 and BubbleLines

2012 ◽  
Vol 3 (2) ◽  
Author(s):  
Alejandro Giacometti ◽  
Stan Ruecker ◽  
Carlos Fioirentino
Keyword(s):  
User Study ◽  
Interactive Visualization ◽  
Application Programming Interface ◽  
Search Results ◽  
Text Collections ◽  
Application Programming ◽  
Visualization Tools ◽  
Multiple Documents ◽  
Programming Interface

In this article, we argue that it is possible to effectively expand interactions with a subset of a collection of text files by using an online interface based on rich-prospect browsing principles, coupled with task-specific visualization tools. In this context, we will present the revisions carried out to create the next iteration of the Texttiles browser, based on results from a user study in 2009. These changes have produced a much more flexible platform for showcasing significant items in text collections, based on user selections of display details, arrangement of items into groups, and annotation marks. In addition, we introduce BubbleLines, an interactive visualization that sits on the Texttiles 2.0 Application Programming Interface (API) and allows users to see search results across multiple documents simultaneously.

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