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

2018 ◽  
Author(s):  
Soohyun Lee ◽  
Jeremy Johnson ◽  
Carl Vitzthum ◽  
Koray Kırlı ◽  
Burak H. Alver ◽  
...  
Keyword(s):  
Web Services ◽  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Software Tool ◽  
Application Programming Interface ◽  
Description Language ◽  
Amazon Web Services ◽  
Application Programming ◽  
Programming Interface

AbstractSummaryWe 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.AvailabilitySource code is available on GitHub at https://github.com/4dn-dcic/tibanna.

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 A SEMI-AUTOMATIC PROCEDURE FOR A DEMOGRAPHIC ANALYSIS OF THE FOSS4G DEVELOPERS’ COMMUNITY

2018 ◽  
Vol XLII-4/W8 ◽  
pp. 171-174
Author(s):  
D. Oxoli ◽  
H.-K. Kang ◽  
M. A. Brovelli
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Application Programming Interface ◽  
Demographic Analysis ◽  
Software Applications ◽  
Individual Project ◽  
Application Programming ◽  
Programming Interface ◽  
The Web

<p><strong>Abstract.</strong> The open and direct collaboration at the creation, improvement, and documentation of source code and software applications &amp;ndash; enabled by the web &amp;ndash; is recognized as a peculiarity of the Free and Open Source Software for Geospatial (FOSS4G) projects representing, at the same time, one of their main strengths. With this in mind, it turns out to be interesting to perform an extensive monitoring of both the evolution and the geographical arrangement of the developers’ communities in order to investigate their actual extension, evolution and degree of activity. In this work, a semi-automatic procedure to perform this particular analysis is described. The procedure is mainly based on the use of the GitHub Search Application Programming Interface by means of JavaScript custom modules to perform a census of the users registered with a collaborator role to the repositories of the most popular FOSS4G projects, hosted on the GitHub platform. The collected data is processed and analysed using Python and QGIS. The results &amp;ndash; presented through tables, charts, and thematic maps &amp;ndash; allow describing both dimensions as well as the geographical heterogeneity of the contributing community of each individual project, while enabling to identify the most active countries &amp;ndash; in terms of the number of contributors &amp;ndash; in the development of the most popular FOSS4G. The limits of the analysis, including technical constraints and considerations on the significance of the developers' census, are finally highlighted and discussed.</p>

CellTracker (not only) for dummies

2015 ◽  
Vol 32 (6) ◽  
pp. 955-957 ◽  
Author(s):  
Filippo Piccinini ◽  
Alexa Kiss ◽  
Peter Horvath
Keyword(s):  
Graphical User Interface ◽  
Open Source Software ◽  
Phase Contrast ◽  
Cell Tracking ◽  
Source Code ◽  
Software Tool ◽  
Time Lapse ◽  
Supplementary Information ◽  
Differential Interference Contrast ◽  
User Friendly

Abstract Motivation: Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Availability and implementation: CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

scholarly journals PolishEM: image enhancement in FIB–SEM

2020 ◽  
Vol 36 (12) ◽  
pp. 3947-3948
Author(s):  
Jose-Jesus Fernandez ◽  
Teobaldo E Torres ◽  
Eva Martin-Solana ◽  
Gerardo F Goya ◽  
Maria-Rosario Fernandez-Fernandez
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Focused Ion Beam ◽  
Ion Beam ◽  
Source Code ◽  
Software Tool ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Efficient Processing ◽  
Scanning Electron

Abstract Summary We have developed a software tool to improve the image quality in focused ion beam–scanning electron microscopy (FIB–SEM) stacks: PolishEM. Based on a Gaussian blur model, it automatically estimates and compensates for the blur affecting each individual image. It also includes correction for artifacts commonly arising in FIB–SEM (e.g. curtaining). PolishEM has been optimized for an efficient processing of huge FIB–SEM stacks on standard computers. Availability and implementation PolishEM has been developed in C. GPL source code and binaries for Linux, OSX and Windows are available at http://www.cnb.csic.es/%7ejjfernandez/polishem. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals KOFFI and Anabel 2.0—a new binding kinetics database and its integration in an open-source binding analysis software

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Leo William Norval ◽  
Stefan Daniel Krämer ◽  
Mingjie Gao ◽  
Tobias Herz ◽  
Jianyu Li ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Application Programming Interface ◽  
Extraction Methods ◽  
Binding Kinetics ◽  
Binding Data ◽  
Meta Information ◽  
Application Programming ◽  
Kinetics Of ◽  
Programming Interface

Abstract The kinetics of featured interactions (KOFFI) database is a novel tool and resource for binding kinetics data from biomolecular interactions. While binding kinetics data are abundant in literature, finding valuable information is a laborious task. We used text extraction methods to store binding rates (association, dissociation) as well as corresponding meta-information (e.g. methods, devices) in a novel database. To date, over 270 articles were manually curated and binding data on over 1705 interactions was collected and stored in the (KOFFI) database. Moreover, the KOFFI database application programming interface was implemented in Anabel (open-source software for the analysis of binding interactions), enabling users to directly compare their own binding data analyses with related experiments described in the database.

scholarly journals Automation of Data Consumption by Pluggable Module Software

2021 ◽  
Vol 23 (06) ◽  
pp. 1672-1681
Author(s):  
Vinay Balamurali ◽  
◽  
Prof. Venkatesh S ◽  
Keyword(s):  
Software Design ◽  
Data Science ◽  
Source Code ◽  
Application Programming Interface ◽  
Related Information ◽  
Server Systems ◽  
Data Consumption ◽  
Application Programming ◽  
Using Data ◽  
Programming Interface

Servers are required to monitor the health of the various I/O cards connected to it to alert the required personnel to service these cards. The Data Collection Unit (DCU) is responsible for detecting the I/O cards, sending their inventory as well as monitoring their health. Currently, the keys required to detect these I/O cards are manually coded into the source code. Such a task is highly laborious and time-consuming. To eliminate this manual work, a Software Pluggable Module was devised which would read the I/O card-related information from the I/O component list. This software design aims at using Data Science and OOPS concepts to automate certain tasks on server systems. The proposed methodology is implemented on a Linux system. The software design is modular in nature and extensible to accommodate future requirements. Such an automation framework can be used to track information maintained in Excel Spreadsheets and access them using an Application Programming Interface (API).

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.

Natural mapping between voice commands and APIs

2021 ◽  
Vol 11 (1) ◽  
pp. 135-145
Author(s):  
Matúš Sulír ◽  
Jaroslav Porubän
Keyword(s):  
Control System ◽  
Natural Language ◽  
Source Code ◽  
Application Programming Interface ◽  
Third Party ◽  
Natural Mapping ◽  
Voice Control ◽  
Mapping Process ◽  
Application Programming ◽  
Programming Interface

Abstract After a voice control system transforms audio input into a natural language sentence, its main purpose is to map this sentence to a specific action in the API (application programming interface) that should be performed. This mapping is usually specified after the API is already designed. In this paper, we show how an API can be designed with voice control in mind, which makes this mapping natural. The classes, methods, and parameters in the source code are named and typed according to the terms expected in the natural language commands. When this is insufficient, annotations (attribute-oriented programming) are used to define synonyms, string-to-object maps, or other properties. We also describe the mapping process and present a preliminary implementation called VCMapper. In its evaluation on a third-party dataset, it was successfully used to map all the sentences, while a large portion of the mapping was performed using only naming and typing conventions.

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