Fully Integrated Software-Defined Networking (SDN) Testbed Using Open-Source Platforms

AbstractCas-mediated genome editing has enabled researchers to perform mutagenesis experiments with relative ease. Effective genome editing requires tools for guide RNA selection, off-target prediction, and genotyping assay design. While independent tools exist for these functions, there is still a need for a comprehensive platform to design, view, evaluate, store, and catalogue guides and their associated primers. The Finding Optimizing and Reporting Cas Targets (FORCAST) application integrates existing open source tools such as JBrowse, Primer3, BLAST, bwa, and Silica to create a complete allele design and quality assurance pipeline. FORCAST is a fully integrated software that allows researchers performing Cas-mediated genome editing to generate, visualize, store, and share information related to guides and their associated experimental parameters. It is available from a public GitHub repository and as a Docker image, for ease of installation and portability.

Download Full-text

Scalable OneM2M IoT Open-Source Platform Evaluated in an SDN Optical Network Controller Scenario

Sensors ◽

10.3390/s22020431 ◽

2022 ◽

Vol 22 (2) ◽

pp. 431

Author(s):

Martina Troscia ◽

Andrea Sgambelluri ◽

Francesco Paolucci ◽

Piero Castoldi ◽

Paolo Pagano ◽

...

Keyword(s):

Open Source ◽

Optical Networks ◽

Optical Network ◽

Software Defined Networking ◽

Production Network ◽

Adequate Level ◽

Network Controller ◽

Iot Devices ◽

Control Application ◽

The Way

Software Defined Networking represents a mature technology for the control of optical networks, though all open controller implementations present in the literature still lack the adequate level of maturity and completeness to be considered for (pre)-production network deployments. This work aims at experimenting on, assessing and discussing the use of the OneM2M open-source platform in the context of optical networks. Network elements and devices are implemented as IoT devices, and the control application is built on top of an OneM2M-compliant server. The work concretely addresses the scalability and flexibility performances of the proposed solution, accounting for the expected growth of optical networks. The two experiment scenarios show promising results and confirm that the OneM2M platform can be adopted in such a context, paving the way to other researches and studies.

Download Full-text

Software-Defined Networking: Open-Source Alternatives for Small to Medium Sized

Advanced Information Networking and Applications - Lecture Notes in Networks and Systems ◽

10.1007/978-3-030-75078-7_20 ◽

2021 ◽

pp. 188-199

Author(s):

Paul Thornley ◽

Maryam Bagheri

Keyword(s):

Open Source ◽

Software Defined Networking

Download Full-text

MxDC & MxLIVE:Software for Macromolecular Crystallography Experiments at the CLS

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314092079 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C792-C792

Author(s):

Kathryn Janzen ◽

Michel Fodje ◽

Shaun Labiuk ◽

James Gorin ◽

Pawel Grochulski

Keyword(s):

Data Processing ◽

Anomalous Dispersion ◽

Data Sets ◽

Macromolecular Crystallography ◽

Fully Integrated ◽

Level Of Automation ◽

Multiple Wavelength ◽

Experiment Management ◽

High Level ◽

Integrated Software

The Canadian Macromolecular Crystallography Facility (CMCF) is a suite of two beamlines 08ID-1 and 08B1-1. Beamline 08B1-1 is a bending-magnet beamline for high-throughput macromolecular crystallography enabling Multiple-Wavelength Anomalous Dispersion (MAD) and Single-Wavelength Anomalous Dispersion (SAD) experiments with a high level of automation. We have developed an integrated software system with modules for beamline control, experiment management, and automated data processing for both on-side and remote users. The experiment management module, also known as MxLIVE (Macromolecular Crystallography Laboratory Information Virtual Environment) is responsible for managing the storage of information about samples, sample shipments, experiment requests, experiment results and data sets. It provides a web-based interface for users to submit sample information and experiment requests, track shipments en route to the CLS and review experiment results and data sets as they are completed on site, and for beamline staff to manage Mail-In data acquisition sessions, reducing the need for user travel to the synchrotron. The beamline control module includes a user-friendly interface for data collection, MxDC (Macromolecular Crystallography Data Collector). MxDC is fully integrated with beamline hardware as well as software applications such as MxLIVE and AutoProcess, an innovative data processing pipeline. This makes MxDC a hub for all experiment-focused activities at CMCF beamlines, including sample auto-mounting, centering and screening crystals, diffraction experiments, and automated data reduction.

Download Full-text

Demonstration of Software Defined Network Services Utilizing Quantum Key Distribution Fully Integrated with Standard Telecommunication Network

Quantum Reports ◽

10.3390/quantum2030032 ◽

2020 ◽

Vol 2 (3) ◽

pp. 453-458

Author(s):

Diego R. Lopez ◽

Vicente Martin ◽

Victor Lopez ◽

Fernando de la Iglesia ◽

Antonio Pastor ◽

...

Keyword(s):

Quantum Key Distribution ◽

Telecommunication Network ◽

Software Defined Networking ◽

Key Distribution ◽

Network Services ◽

Software Defined Network ◽

Fully Integrated ◽

Production Facilities

We present a demonstration of software defined networking (SDN) services utilizing quantum key distribution (QKD) technology, fully integrated with standard telecommunication network connecting production facilities of Telefonica in Madrid. All communications “co-propagate” over the same fiber infrastructure.

Download Full-text

MOSGA: Modular Open-Source Genome Annotator

Bioinformatics ◽

10.1093/bioinformatics/btaa1003 ◽

2020 ◽

Author(s):

Roman Martin ◽

Thomas Hackl ◽

Georges Hattab ◽

Matthias G Fischer ◽

Dominik Heider

Keyword(s):

Open Source ◽

Source Code ◽

Supplementary Information ◽

Web Interface ◽

Fully Integrated ◽

Sequencing Technologies ◽

A Genome ◽

Wide Range ◽

User Friendly ◽

Eukaryotic Genomes

Abstract Motivation The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies—a crucial step toward unlocking the biology of the organism of interest—has remained a complex challenge that often requires advanced bioinformatics expertise. Results Here, we present MOSGA (Modular Open-Source Genome Annotator), a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. Availability and implementation We provide MOSGA as a web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga: latest. Source code can be found at https://gitlab.com/mosga/mosga Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text

Correction to: Software-Defined Networking: Open-Source Alternatives for Small to Medium Sized Enterprises

Advanced Information Networking and Applications - Lecture Notes in Networks and Systems ◽

10.1007/978-3-030-75078-7_71 ◽

2021 ◽

pp. C1-C1

Author(s):

Paul Thornley ◽

Maryam Bagheri

Keyword(s):

Open Source ◽

Software Defined Networking

Download Full-text

Application of Supply Chain Management through SAP in Agriculture of SAARC Nations

Strategic Infrastructure Development for Economic Growth and Social Change - Advances in Business Strategy and Competitive Advantage ◽

10.4018/978-1-4666-7470-7.ch023 ◽

2015 ◽

pp. 347-359

Author(s):

Somnath Chaudhuri

Keyword(s):

Supply Chain ◽

Supply Chain Management ◽

Software Package ◽

Agricultural Sector ◽

Vital Role ◽

Economic Conditions ◽

Successful Implementation ◽

Chain Management ◽

Fully Integrated ◽

Integrated Software

The prime source of income of the different countries in the SAARC region comes from the agricultural sector. Currently, this sector is facing several challenges in this entire region, threatening its growth and sustainability. Hence, if the policymakers need to improve the economic conditions of the nations, then the only way to do that is to improve the agricultural sectors of this region. This can be achieved by successful implementation of Supply Chain Management (SCM). This chapter is concerned with the concept of SCM and how it can play a vital role in developing the agricultural sectors in the SAARC countries. Another aspect of this chapter is concerned with the effectiveness of the application of SCM in agriculture; it can be implemented by using a fully integrated software package like SAP ERP. By the application of this IT software package, SCM can be made more efficient and lead to time and inventory reduction.

Download Full-text