Gene Ontology Meta Annotator for Plants (GOMAP)

AbstractAnnotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipeline’s availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on $$F_{max}$$ F max ) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/. A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/.

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Gene Ontology Meta Annotator for Plants

10.1101/809988 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kokulapalan Wimalanathan ◽

Carolyn J. Lawrence-Dill

Keyword(s):

Gene Ontology ◽

Go Annotation ◽

Plant Genomes ◽

Link Type ◽

Gene Structures ◽

And Performance ◽

Genome Assemblies ◽

Genome Scale ◽

Per Gene

AbstractAnnotating gene structures and functions to genome assemblies is a must to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most pervasively used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. GOMAP, the Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation for plant genomes. GOMAP’s methods have been shown to expand and improve the number of genes annotated and annotations assigned per gene as well as the quality (based on F-score) of GO assignments in maize. Here we report on the pipeline’s availability and performance for annotating large, repetitive plant genomes and describe how to deploy GOMAP to annotate additional plant genomes. We containerized GOMAP to increase portability and reproducibility, and optimized its performance for HPC environments. GOMAP has been used to annotate multiple maize lines, and is currently being deployed to annotate other species including wheat, rice, barley, cotton, soy, and others. Instructions along with access to the GOMAP Singularity container are freely available online at https://gomap-singularity.readthedocs.io/en/latest/. A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/gomap-datasets/.

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BiSCoT: Improving large eukaryotic genome assemblies with optical maps

10.1101/674721 ◽

2019 ◽

Cited By ~ 1

Author(s):

Benjamin Istace ◽

Caroline Belser ◽

Jean-Marc Aury

Keyword(s):

Human Genome ◽

Fasta File ◽

Plant Genomes ◽

Link Type ◽

Long Reads ◽

Entire Chromosome ◽

Long Read ◽

Optical Maps ◽

Genome Assemblies

ABSTRACTMotivationLong read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and organization of contigs into scaffolds is not always optimal.ResultsWe developed BiSCoT (Bionano SCaffolding COrrection Tool), a tool that post-processes files generated during a Bionano scaffolding in order to produce an assembly of greater contiguity and quality. BiSCoT was tested on a human genome and four publicly available plant genomes sequenced with Nanopore long reads and improved significantly the contiguity and quality of the assemblies. BiSCoT generates a fasta file of the assembly as well as an AGP file which describes the new organization of the input assembly.AvailabilityBiSCoT and improved assemblies are freely available on Github at http://www.genoscope.cns.fr/biscot and Pypi at https://pypi.org/project/biscot/.

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Genome Warehouse: A Public Repository Housing Genome-scale Data

10.1101/2021.02.10.430367 ◽

2021 ◽

Author(s):

Meili Chen ◽

Yingke Ma ◽

Song Wu ◽

Xinchang Zheng ◽

Hongen Kang ◽

...

Keyword(s):

Genome Assembly ◽

Public Repository ◽

Genome Sequences ◽

Link Type ◽

Genome Data ◽

Research Activities ◽

Wide Range ◽

Genome Assemblies ◽

Genome Scale ◽

Scale Data

AbstractThe Genome Warehouse (GWH) is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission, storage, release, and sharing. As one of the core resources in the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB, https://bigd.big.ac.cn/), GWH accepts both full genome and partial genome (chloroplast, mitochondrion, and plasmid) sequences with different assembly levels, as well as an update of existing genome assemblies. For each assembly, GWH collects detailed genome-related metadata including biological project and sample, and genome assembly information, in addition to genome sequence and annotation. To archive high-quality genome sequences and annotations, GWH is equipped with a uniform and standardized procedure for quality control. Besides basic browse and search functionalities, all released genome sequences and annotations can be visualized with JBrowse. By December 2020, GWH has received 17,264 direct submissions covering a diversity of 949 species, and has released 3370 of them. Collectively, GWH serves as an important resource for genome-scale data management and provides free and publicly accessible data to support research activities throughout the world. GWH is publicly accessible at https://bigd.big.ac.cn/gwh/.

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BiSCoT: improving large eukaryotic genome assemblies with optical maps

PeerJ ◽

10.7717/peerj.10150 ◽

2020 ◽

Vol 8 ◽

pp. e10150

Author(s):

Benjamin Istace ◽

Caroline Belser ◽

Jean-Marc Aury

Keyword(s):

Human Genome ◽

Fasta File ◽

Plant Genomes ◽

Link Type ◽

Long Reads ◽

Entire Chromosome ◽

Long Read ◽

Optical Maps ◽

Genome Assemblies

Motivation Long read sequencing and Bionano Genomics optical maps are two techniques that, when used together, make it possible to reconstruct entire chromosome or chromosome arms structure. However, the existing tools are often too conservative and organization of contigs into scaffolds is not always optimal. Results We developed BiSCoT (Bionano SCaffolding COrrection Tool), a tool that post-processes files generated during a Bionano scaffolding in order to produce an assembly of greater contiguity and quality. BiSCoT was tested on a human genome and four publicly available plant genomes sequenced with Nanopore long reads and improved significantly the contiguity and quality of the assemblies. BiSCoT generates a fasta file of the assembly as well as an AGP file which describes the new organization of the input assembly. Availability BiSCoT and improved assemblies are freely available on GitHub at http://www.genoscope.cns.fr/biscot and Pypi at https://pypi.org/project/biscot/.

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MetaNetX/MNXref - unified namespace for metabolites and biochemical reactions in the context of metabolic models

10.1101/2020.09.15.297507 ◽

2020 ◽

Author(s):

Sébastien Moretti ◽

Van Du T. Tran ◽

Florence Mehl ◽

Mark Ibberson ◽

Marco Pagni

Keyword(s):

Metabolic Network ◽

Intrinsic Properties ◽

Biochemical Reactions ◽

Online Services ◽

Major Improvement ◽

Sparql Endpoint ◽

Link Type ◽

Cross Links ◽

Genome Scale

ABSTRACTMetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).

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ORT: A workflow linking genome-scale metabolic models with reactive transport codes

10.1101/2021.03.02.433463 ◽

2021 ◽

Author(s):

Rebecca L. Rubinstein ◽

Mikayla A. Borton ◽

Haiyan Zhou ◽

Michael Shaffer ◽

David W. Hoyt ◽

...

Keyword(s):

Simple Model ◽

Reactive Transport ◽

River System ◽

Supplementary Information ◽

Metagenomic Data ◽

Test Case ◽

Modeling Tools ◽

Natural Systems ◽

Link Type ◽

Genome Scale

AbstractMotivationAdvanced modeling tools are available for ‘omics-based metabolic modeling and for reactive transport modeling, but there is a disconnect between these methods, which hinders linking models across scales. Microbial processes strongly impact many natural systems, and so better capture of microbial dynamics could greatly improve simulations of these systems.ResultsOur approach, ORT, applied to environmental metagenomic data from a river system predicted nitrogen cycling patterns with site-specific insight into chemical and biological drivers of nitrification and denitrification processes.Availability and ImplementationLive interactive models are available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data is available at NCBI via BioProject ID PRJNA576070. The code for ORT (written in Python 3) is available at https://github.com/subsurfaceinsights. The KBase narrative used for the test case is publicly available at https://narrative.kbase.us/narrative/[email protected] or [email protected] informationSupplementary data are available online.

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LIGHTING AND PERFORMANCE: AN ANALYSIS ON LIGHTING EFFICIENCY OF ARCHITECTURE STUDIO

Malaysian Journal of Sustainable Environment ◽

10.24191/myse.v1i1.5563 ◽

2019 ◽

Vol 1 (1) ◽

pp. 92

Author(s):

Fazidah Hanim Husain

Keyword(s):

Learning Environment ◽

Comfort Level ◽

Artificial Lighting ◽

Level Measurement ◽

Acceptable Range ◽

Creative Learning ◽

Illuminance Level ◽

And Performance ◽

Effect Of Light

Lighting is one of the key elements in any space and building infrastructure. Good design for an area in the building requires sufficient light that contributes to the efficiency of the activities. The correct method allows natural light to transmit, reduce heat and glare in providing a conducive learning environment. Light plays a significant influence to the quality of space and contributes focus of the students in an architecture studio. Previous research has shown that the effect of light also controlled emotions, behavior, and mood of the students. The operations of artificial lighting that have been used most of the time in an architecture studio during day and night may create lavishness and inadequacy at the same time. Therefore, this paper focuses on the identifying the quality of light for the architecture studio in UiTM (Perak), to instill a creative learning environment. Several methodologies adopted in this study such as illuminance level measurement using lux meter (LM-8100), and a questionnaire survey in gauging the lighting comfort level from students’ perspective. The study revealed that the illuminance level in the architecture studio is insufficient and not in the acceptable range stated in the Malaysian: Standards 1525:2007 and not evenly distributed. The study also concluded that the current studio environment is not condusive and appears monotonous.

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Strategic threats to energy security as risks of quality of people's life

National Interests Priorities and Security ◽

10.24891/ni.16.4.730 ◽

2020 ◽

Vol 16 (4) ◽

pp. 730-744

Author(s):

V.I. Loktionov

Keyword(s):

Quality Of Life ◽

Energy Security ◽

Well Being ◽

Scientific Methods ◽

Analysis And Synthesis ◽

General Scientific ◽

And Performance ◽

Economic Well Being ◽

The Way

Subject. The article reviews the way strategic threats to energy security influence the quality of people's life. Objectives. The study unfolds the theory of analyzing strategic threats to energy security by covering the matter of quality of people's life. Methods. To analyze the way strategic threats to energy security spread across cross-sectoral commodity and production chains and influences quality of people's living, I applied the factor analysis and general scientific methods of analysis and synthesis. Results. I suggest interpreting strategic threats to energy security as risks of people's quality of life due to a reduction in the volume of energy supply. I identified mechanisms reflecting how the fuel and energy complex and its development influence the quality of people's life. The article sets out the method to assess such quality-of-life risks arising from strategic threats to energy security. Conclusions and Relevance. In the current geopolitical situation, strategic threats to energy security cause long-standing adverse consequences for the quality of people's life. If strategic threats to energy security are further construed as risk of quality of people's life, this will facilitate the preparation and performance of a more effective governmental policy on energy, which will subsequently raise the economic well-being of people.

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Return on Invesment (ROI) of Software Product: A Systematic Literature Review

Jurnal ULTIMA InfoSys ◽

10.31937/si.v6i1.279 ◽

2015 ◽

Vol 6 (1) ◽

pp. 50-57

Author(s):

Rizqa Raaiqa Bintana ◽

Putri Aisyiyah Rakhma Devi ◽

Umi Laili Yuhana

Keyword(s):

Return On Investment ◽

Assessment Criteria ◽

Software Product ◽

And Performance ◽

Rational Consideration ◽

Actual Return ◽

The Cost ◽

Investment Models ◽

The Impact

The quality of the software can be measured by its return on investment. Factors which may affect the return on investment (ROI) is the tangible factors (such as the cost) dan intangible factors (such as the impact of software to the users or stakeholder). The factor of the software itself are assessed through reviewing, testing, process audit, and performance of software. This paper discusses the consideration of return on investment (ROI) assessment criteria derived from the software and its users. These criteria indicate that the approach may support a rational consideration of all relevant criteria when evaluating software, and shows examples of actual return on investment models. Conducted an analysis of the assessment criteria that affect the return on investment if these criteria have a disproportionate effort that resulted in a return on investment of a software decreased. Index Terms - Assessment criteria, Quality assurance, Return on Investment, Software product

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The Four Branches of the Mabinogi, ed. and trans. by Matthieu Boyd, with the modernization assistance of Stacie Lents. Peterborough, Ont.: Broadview Press, 2017, 119 pp., 5 b/w ill, 1 map.

Mediaevistik ◽

10.3726/med012018_401 ◽

2018 ◽

Vol 31 (1) ◽

pp. 401-401

Author(s):

Albrecht Classen

Keyword(s):

Undergraduate Students ◽

Twelfth Century ◽

English Translation ◽

English Version ◽

Personal Names ◽

University Teachers ◽

Link Type ◽

Welsh Literature

Welsh medievalists have long recognized the canonical quality of The Four Branches of the Mabinogi (late eleventh or early twelfth century), resulting in a long series of editions and translations. William Owen Pughe was the first to offer a modern English translation in 1795. The <?page nr="402"?>recent translation by Will Parker (2005) is available now online at: <ext-link ext-link-type="uri" xlink:href="http://www.mabinogi.net/translations.htm">http://www.mabinogi.net/translations.htm</ext-link>, and I suspect that many university teachers happily rely on this one because of its easy accessibility and clarity of the English version. Now, Matthieu Boyd, who teaches at Fairleigh Dickinson University (Florham Campus, Madison, MD), offers a new rendering, which is specifically targeting undergraduate students. This explains his strategy to modernize the medieval Welsh as much as possible, and to turn this marvelous text into an enjoyable read even for contemporary students, without moving too far away from the original. This modernization was carried out with the assistance of his colleague, the playwright Stacie Lents. This entails, for instance, that even some of the medieval names are adapted. Many times the conservative reader might feel uncomfortable when words and phrases such as “to shit,” “to egg on,” “to nip at the heels,” or “Manawydan & Co” (60–61) appear. The adaptation of personal names is not carried out systematically, but the overall impression of this translation is certainly positive, making the study of this masterpiece of medieval Welsh literature to a real pleasure.

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