GigaByte (Hong Kong, China)最新文献_第4页

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860). 金色鸟翼 Troides aeacus (Felder & Felder, 1860) 染色体级基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-04-25 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.122

引用次数: 0

Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778). 长刺海胆 Diadema setosum (Leske, 1778) 染色体级基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-04-25 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.121

引用次数: 0

Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873). 普通甲壳动物 Liolophura japonica (Lischke, 1873) 染色体级基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-04-25 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.123

引用次数: 0

Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae). 食用果冻真菌 Dacryopinax spathularia（Dacrymycetaceae）的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-04-25 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.120

引用次数: 0

Genome assembly of the milky mangrove Excoecaria agallocha. 牛奶红树林 Excoecaria agallocha 的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-04-25 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.119

引用次数: 0

Bridging Biodiversity and Health: The Global Biodiversity Information Facility's initiative on open data on vectors of human diseases. 连接生物多样性与健康：全球生物多样性信息基金关于人类疾病媒介开放数据的倡议。

GigaByte (Hong Kong, China) Pub Date : 2024-04-11 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.117

Paloma Shimabukuro, Quentin Groom, Florence Fouque, Lindsay Campbell, Theeraphap Chareonviriyaphap, Josiane Etang, Sylvie Manguin, Marianne Sinka, Dmitry Schigel, Kate Ingenloff

{"title":"Bridging Biodiversity and Health: The Global Biodiversity Information Facility's initiative on open data on vectors of human diseases.","authors":"Paloma Shimabukuro, Quentin Groom, Florence Fouque, Lindsay Campbell, Theeraphap Chareonviriyaphap, Josiane Etang, Sylvie Manguin, Marianne Sinka, Dmitry Schigel, Kate Ingenloff","doi":"10.46471/gigabyte.117","DOIUrl":"10.46471/gigabyte.117","url":null,"abstract":"There is an increased awareness of the importance of data publication, data sharing, and open science to support research, monitoring and control of vector-borne disease (VBD). Here we describe the efforts of the Global Biodiversity Information Facility (GBIF) as well as the World Health Special Programme on Research and Training in Diseases of Poverty (TDR) to promote publication of data related to vectors of diseases. In 2020, a GBIF task group of experts was formed to provide advice and support efforts aimed at enhancing the coverage and accessibility of data on vectors of human diseases within GBIF. Various strategies, such as organizing training courses and publishing data papers, were used to increase this content. This editorial introduces the outcome of a second call for data papers partnered by the TDR, GBIF and GigaScience Press in the journal GigaByte. Biodiversity and infectious diseases are linked in complex ways. These links can involve changes from the microorganism level to that of the habitat, and there are many ways in which these factors interact to affect human health. One way to tackle disease control and possibly elimination, is to provide stakeholders with access to a wide range of data shared under the FAIR principles, so it is possible to support early detection, analyses and evaluation, and to promote policy improvements and/or development.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte117"},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11027195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140860840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Snakemake workflows for long-read bacterial genome assembly and evaluation. 用于长读数细菌基因组组装和评估的 Snakemake 工作流程。

GigaByte (Hong Kong, China) Pub Date : 2024-04-01 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.116

Peter Menzel

{"title":"Snakemake workflows for long-read bacterial genome assembly and evaluation.","authors":"Peter Menzel","doi":"10.46471/gigabyte.116","DOIUrl":"10.46471/gigabyte.116","url":null,"abstract":"With the advancement of long-read sequencing technologies and their increasing use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also a need to measure the completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run multiple genome assembly and evaluation programs at once, I developed two workflows for the workflow management system Snakemake, which provide end users with an easy-to-run solution for testing various genome assemblies from their sequencing data. Both workflows use the conda packaging system, so there is no need for manual installation of each program.Availability & implementation: The workflows are available as open source software under the MIT license at github.com/pmenzel/ont-assembly-snake and github.com/pmenzel/score-assemblies.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte116"},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11000499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific. 帝王姬鱼（Holacanthus passer）的全基因组组装和注释有助于深入了解热带东太平洋海洋鱼类的进化。

GigaByte (Hong Kong, China) Pub Date : 2024-03-21 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.115

Remy Gatins, Carlos F Arias, Carlos Sánchez, Giacomo Bernardi, Luis F De León

{"title":"Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific.","authors":"Remy Gatins, Carlos F Arias, Carlos Sánchez, Giacomo Bernardi, Luis F De León","doi":"10.46471/gigabyte.115","DOIUrl":"10.46471/gigabyte.115","url":null,"abstract":"Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: (i) assembled and annotated the nuclear genome of the King Angelfish (Holacanthus passer), and (ii) examined the demographic history of H. passer in the TEP. We generated 43.8 Gb of ONT and 97.3 Gb Illumina reads representing 75× and 167× coverage, respectively. The final genome assembly size was 583 Mb with a contig N50 of 5.7 Mb, which captured 97.5% of the complete Actinoterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs). Repetitive elements accounted for 5.09% of the genome, and 33,889 protein-coding genes were predicted, of which 22,984 were functionally annotated. Our demographic analysis suggests that population expansions of H. passer occurred prior to the last glacial maximum (LGM) and were more likely shaped by events associated with the closure of the Isthmus of Panama. This result is surprising, given that most rapid population expansions in both freshwater and marine organisms have been reported to occur globally after the LGM. Overall, this annotated genome assembly provides a novel molecular resource to study the evolution of Holacanthus angelfishes, while facilitating research into local adaptation, speciation, and introgression in marine fishes.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte115"},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10973836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140320042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular Property Diagnostic Suite for COVID-19 (MPDS^COVID-19): an open-source disease-specific drug discovery portal. 用于 COVID-19 的分子特性诊断套件（MPDSCOVID-19）：一个开源的疾病特异性药物发现门户网站。

GigaByte (Hong Kong, China) Pub Date : 2024-03-14 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.114

Lipsa Priyadarsinee, Esther Jamir, Selvaraman Nagamani, Hridoy Jyoti Mahanta, Nandan Kumar, Lijo John, Himakshi Sarma, Asheesh Kumar, Anamika Singh Gaur, Rosaleen Sahoo, S Vaikundamani, N Arul Murugan, U Deva Priyakumar, G P S Raghava, Prasad V Bharatam, Ramakrishnan Parthasarathi, V Subramanian, G Madhavi Sastry, G Narahari Sastry

{"title":"Molecular Property Diagnostic Suite for COVID-19 (MPDSCOVID-19): an open-source disease-specific drug discovery portal.","authors":"Lipsa Priyadarsinee, Esther Jamir, Selvaraman Nagamani, Hridoy Jyoti Mahanta, Nandan Kumar, Lijo John, Himakshi Sarma, Asheesh Kumar, Anamika Singh Gaur, Rosaleen Sahoo, S Vaikundamani, N Arul Murugan, U Deva Priyakumar, G P S Raghava, Prasad V Bharatam, Ramakrishnan Parthasarathi, V Subramanian, G Madhavi Sastry, G Narahari Sastry","doi":"10.46471/gigabyte.114","DOIUrl":"10.46471/gigabyte.114","url":null,"abstract":"Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDSCOVID-19 was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture of MPDSCOVID-19 effectively employs Galaxy v22.04 features, which are ported on CentOS 7.8 and Python 3.7. MPDSCOVID-19 provides significant updates and the addition of several new tools updated after six years. Tools developed by our group in Perl/Python and open-source tools are collated and integrated into MPDSCOVID-19 using XML scripts. Our MPDS suite aims to facilitate transparent and open innovation. This approach significantly helps bring inclusiveness in the community while promoting free access and participation in software development.Availability & implementation: The MPDSCOVID-19 portal can be accessed at https://mpds.neist.res.in:8085/.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte114"},"PeriodicalIF":0.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10958779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Julearn: an easy-to-use library for leakage-free evaluation and inspection of ML models. Julearn：一个易于使用的库，用于对 ML 模型进行无泄漏评估和检查。

GigaByte (Hong Kong, China) Pub Date : 2024-03-07 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.113

Sami Hamdan, Shammi More, Leonard Sasse, Vera Komeyer, Kaustubh R Patil, Federico Raimondo

{"title":"Julearn: an easy-to-use library for leakage-free evaluation and inspection of ML models.","authors":"Sami Hamdan, Shammi More, Leonard Sasse, Vera Komeyer, Kaustubh R Patil, Federico Raimondo","doi":"10.46471/gigabyte.113","DOIUrl":"10.46471/gigabyte.113","url":null,"abstract":"The fast-paced development of machine learning (ML) and its increasing adoption in research challenge researchers without extensive training in ML. In neuroscience, ML can help understand brain-behavior relationships, diagnose diseases and develop biomarkers using data from sources like magnetic resonance imaging and electroencephalography. Primarily, ML builds models to make accurate predictions on unseen data. Researchers evaluate models' performance and generalizability using techniques such as cross-validation (CV). However, choosing a CV scheme and evaluating an ML pipeline is challenging and, if done improperly, can lead to overestimated results and incorrect interpretations. Here, we created julearn, an open-source Python library allowing researchers to design and evaluate complex ML pipelines without encountering common pitfalls. We present the rationale behind julearn's design, its core features, and showcase three examples of previously-published research projects. Julearn simplifies the access to ML providing an easy-to-use environment. With its design, unique features, simple interface, and practical documentation, it poses as a useful Python-based library for research projects.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte113"},"PeriodicalIF":0.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10940896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140144689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0