scholarly journals WAVES: a Web Application for Versatile Enhanced bioinformatic Services

2018 ◽  
Author(s):  
Marc Chakiachvili ◽  
Sylvain Milanesi ◽  
Anne-Muriel Arigon Chifolleau ◽  
Vincent Lefort
Keyword(s):  
Web Services ◽  
General Public ◽  
Web Application ◽  
Source Code ◽  
Web Pages ◽  
Tool Integration ◽  
Web Framework ◽  
Bioinformatic Tool ◽  
Restful Web Services ◽  
General Public License

AbstractSummary: WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.Availability and implementation: WAVES was developed with Django, a Python-based web framework. It was designed as a reusable web application. It is fully portable, as only a Python installation is required to run Django. It is licensed under GNU General Public License. Source code, documentation with examples and demo are available from http://www.atgc-montpellier.fr/waves/.Contact:[email protected]

scholarly journals Implementation Model of Source Code Generator

2011 ◽  
Vol 7 (2) ◽  
pp. 71
Author(s):  
Ivan Magdalenić ◽  
Danijel Radošević ◽  
Dragutin Kermek
Keyword(s):  
Web Services ◽  
Web Application ◽  
Source Code ◽  
Data Retrieval ◽  
Active Role ◽  
Information Discovery ◽  
Code Generator ◽  
Implementation Model ◽  
On Demand ◽  
Dynamic Generation

The on demand generation of source code and its execution is essential if computers are expected to play an active role in information discovery and retrieval. This paper presents a model of implementation of a source code generator, whose purpose is to generate source code on demand. Theimplementation of the source code generator is fully configurable and its adoption to a new application is done by changing the generator configuration and not the generator itself. The advantage of using the source code generator is rapid and automatic development of a family of application once necessary program templates and generator configuration are made. The model of implementation of the source code generator is general and implemented source code generator can be used in differentareas. We use a source code generator for dynamic generation of ontology supported Web services for data retrieval and for building of different kind of web application.

Analyses of Evolving Legacy Software into Secure Service-Oriented Software using Scrum and a Visual Model

2013 ◽  
pp. 196-217
Author(s):  
Sam Chung ◽  
Conrado Crompton ◽  
Yan Bai ◽  
Barbara Endicott-Popovsky ◽  
Seung-Ho Baeg ◽  
...  
Keyword(s):  
Web Services ◽  
Web Application ◽  
Software Reengineering ◽  
Software Application ◽  
Legacy Software ◽  
Web Technologies ◽  
Model Driven ◽  
Service Oriented ◽  
Modernization Process ◽  
Restful Web Services

This chapter explores using service-oriented computing to reengineer non-secure legacy software applications to create new secure target applications. Two objectives of this chapter are: (1) to analyze the architectural changes required in order to adopt new web technologies and cope with resultant vulnerabilities in source code; and (2) to measure the level of effort required to modernize software by adopting new web technologies and adding security countermeasures. To meet these objectives, a model-driven Scrum for Service-Oriented Software Reengineering (mScrum4SOSR) methodology was chosen and applied to a reengineering project. Scrum is employed to manage the reengineering project, as well as to measure implementation effort related to the modernization process. Further, a re-documentation technique called 5W1H Re-Doc is used to re-document the non-secure software application at a high level of abstraction in order to help project participants comprehend what is needed to identify candidate services for service-oriented reengineering. Case studies with and without security features are created for different types of applications - a desktop graphical user interface, a web application, a web services application, a restful web services application, and an enterprise service bus application.

scholarly journals GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

2019 ◽  
Author(s):  
Pierre-Alain Chaumeil ◽  
Aaron J Mussig ◽  
Philip Hugenholtz ◽  
Donovan H Parks
Keyword(s):  
General Public ◽  
Source Code ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Computationally Efficient ◽  
Taxonomic Assignments ◽  
General Public License

Abstract Summary The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10,156 bacterial and archaeal metagenome-assembled genomes. Availability GTDB-Tk is implemented in Python and licensed under the GNU General Public License v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk Supplementary information Supplementary data are available at Bioinformatics online.

From requirements to source code: a Model-Driven Engineering approach for RESTful web services

2016 ◽  
Vol 24 (4) ◽  
pp. 791-838 ◽  
Author(s):  
Christoforos Zolotas ◽  
Themistoklis Diamantopoulos ◽  
Kyriakos C. Chatzidimitriou ◽  
Andreas L. Symeonidis
Keyword(s):  
Web Services ◽  
Source Code ◽  
Model Driven Engineering ◽  
Model Driven ◽  
Engineering Approach ◽  
Restful Web Services

scholarly journals ARBitR: an overlap-aware genome assembly scaffolder for linked reads

2020 ◽  
Author(s):  
Markus Hiltunen ◽  
Martin Ryberg ◽  
Hanna Johannesson
Keyword(s):  
Genome Assembly ◽  
General Public ◽  
Source Code ◽  
Draft Genome ◽  
Supplementary Information ◽  
Genomic Sequencing ◽  
Supplementary Data ◽  
Genome Assemblies ◽  
General Public License

Abstract Summary Linked genomic sequencing reads contain information that can be used to join sequences together into scaffolds in draft genome assemblies. Existing software for this purpose performs the scaffolding by joining sequences with a gap between them, not considering potential overlaps of contigs. We developed ARBitR to create scaffolds where overlaps are taken into account and show that it can accurately recreate regions where draft assemblies are broken. Availability and implementation ARBitR is written and implemented in Python3 for Unix-based operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License v3. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CircularLogo: A lightweight web application to visualize intra-motif dependencies

2017 ◽  
Author(s):  
Zhenqing Ye ◽  
Tao Ma ◽  
Michael T. Kalmbach ◽  
Surendra Dasari ◽  
Jean-Pierre A. Kocher ◽  
...  
Keyword(s):  
Binding Sites ◽  
Web Application ◽  
Source Code ◽  
Sequence Logo ◽  
Rna Motifs ◽  
Biomolecular Structure ◽  
Web Based ◽  
Link Type ◽  
Web Framework ◽  
Interactive Application

AbstractBackgroundThe sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization.ResultWe developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies. Applying CircularLogo to HNF6 binding sites and tRNA sequences demonstrated its ability to show intra-motif dependencies and intuitively reveal biomolecular structure. CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program’s source code and user’s manual are freely available at http://circularlogo.sourceforge.net. CircularLogo web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html.ConclusionCircularLogo is an innovative web application that is specifically designed to visualize and interactively explore intra-motif dependencies.

Analyses of Evolving Legacy Software into Secure Service-Oriented Software using Scrum and a Visual Model

2014 ◽  
pp. 1764-1786
Author(s):  
Sam Chung ◽  
Conrado Crompton ◽  
Yan Bai ◽  
Barbara Endicott-Popovsky ◽  
Seung-Ho Baeg ◽  
...  
Keyword(s):  
Web Services ◽  
Web Application ◽  
Software Reengineering ◽  
Software Application ◽  
Legacy Software ◽  
Web Technologies ◽  
Model Driven ◽  
Service Oriented ◽  
Modernization Process ◽  
Restful Web Services

This chapter explores using service-oriented computing to reengineer non-secure legacy software applications to create new secure target applications. Two objectives of this chapter are: (1) to analyze the architectural changes required in order to adopt new web technologies and cope with resultant vulnerabilities in source code; and (2) to measure the level of effort required to modernize software by adopting new web technologies and adding security countermeasures. To meet these objectives, a model-driven Scrum for Service-Oriented Software Reengineering (mScrum4SOSR) methodology was chosen and applied to a reengineering project. Scrum is employed to manage the reengineering project, as well as to measure implementation effort related to the modernization process. Further, a re-documentation technique called 5W1H Re-Doc is used to re-document the non-secure software application at a high level of abstraction in order to help project participants comprehend what is needed to identify candidate services for service-oriented reengineering. Case studies with and without security features are created for different types of applications - a desktop graphical user interface, a web application, a web services application, a restful web services application, and an enterprise service bus application.

scholarly journals DeepRec: An Open-source Toolkit for Deep Learning based Recommendation

2019 ◽  
Author(s):  
Shuai Zhang ◽  
Yi Tay ◽  
Lina Yao ◽  
Bin Wu ◽  
Aixin Sun
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Programming Languages ◽  
Recommender Systems ◽  
General Public ◽  
Source Code ◽  
Recommendation Algorithms ◽  
New Models ◽  
Rating Prediction ◽  
General Public License

Deep learning based recommender systems have been extensively explored in recent years. However, the large number of models proposed each year poses a big challenge for both researchers and practitioners in reproducing the results for further comparisons. Although a portion of papers provides source code, they adopted different programming languages or different deep learning packages, which also raises the bar in grasping the ideas. To alleviate this problem, we released the open source project: \textbf{DeepRec}. In this toolkit, we have implemented a number of deep learning based recommendation algorithms using Python and the widely used deep learning package - Tensorflow. Three major recommendation scenarios: rating prediction, top-N recommendation (item ranking) and sequential recommendation, were considered. Meanwhile, DeepRec maintains good modularity and extensibility to easily incorporate new models into the framework. It is distributed under the terms of the GNU General Public License. The source code is available at github: https://github.com/cheungdaven/DeepRec

scholarly journals Next Generation HGVS Nomenclature Checker

2021 ◽  
Author(s):  
Mihai Lefter ◽  
Jonathan K Vis ◽  
Martijn Vermaat ◽  
Johan T den Dunnen ◽  
Peter E M Taschner ◽  
...  
Keyword(s):  
Open Source ◽  
Human Genome ◽  
General Public ◽  
Scientific Literature ◽  
Source Code ◽  
Genetic Diagnostics ◽  
Clinical Genetic ◽  
Human Genome Variation Society ◽  
Open Source Project ◽  
General Public License

ABSTRACT Motivation Unambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature, and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Results Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in approximately 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for approximately 7% of cases, Mutalyzer was able to automatically correct the description. Availability Mutalyzer is an Open Source project under the GNU Affero General Public License. The source code is available on GitHub (https://github.com/mutalyzer/mutalyzer) and a running instance is available at: https://mutalyzer.nl.

scholarly journals ARBitR: An overlap-aware genome assembly scaffolder for linked reads

2020 ◽  
Author(s):  
Markus Hiltunen ◽  
Martin Ryberg ◽  
Hanna Johannesson
Keyword(s):  
Genome Assembly ◽  
General Public ◽  
Source Code ◽  
Draft Genome ◽  
Supplementary Information ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Long Read ◽  
Genome Assemblies ◽  
General Public License

Abstract10X Genomics Chromium linked reads contain information that can be used to link sequences together into scaffolds in draft genome assemblies. Existing software for this purpose perform the scaffolding by joining sequences together with a gap between them, not considering potential contig overlaps. Such overlaps can be particularly prominent in genome drafts assembled from long-read sequencing data where an overlap-layout-consensus (OLC) algorithm has been used. Ignoring overlapping contig ends may result in genes and other features being incomplete or fragmented in the resulting scaffolds. We developed the application ARBitR to generate scaffolds from genome drafts using 10X Chromium data, with a focus on minimizing the number of gaps in resulting scaffolds by incorporating an OLC step to resolve junctions between linked contigs. We tested the performance of ARBitR on three published and simulated datasets and compared to the previously published tools ARCS and ARKS. The results revealed that ARBitR performed similarly considering contiguity statistics, and the advantage of the overlapping step was revealed by fewer long and short variants in ARBitR produced scaffolds, in addition to a higher proportion of completely assembled LTR retrotransposons. We expect ARBitR to have broad applicability in genome assembly projects that utilize 10X Chromium linked reads.Availability and implementationARBitR is written and implemented in Python3 for Unix-like operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License [email protected] informationavailable online

Sign in / Sign up

Export Citation Format

Share Document