基因笔记本，一个用于比较基因组学的协作笔记本。

GeneNoteBook, a collaborative notebook for comparative genomics.

机构信息

Laboratory of Molecular Biology, 6708PB Wageningen, The Netherlands.

Bioinformatics Group, Wageningen University, 6708PB Wageningen, The Netherlands.

出版信息

Bioinformatics. 2019 Nov 1;35(22):4779-4781. doi: 10.1093/bioinformatics/btz491.

DOI:10.1093/bioinformatics/btz491

PMID:31199463

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6853645/

Abstract

SUMMARY

Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms.

AVAILABILITY AND IMPLEMENTATION

GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

在生物研究中，对基因组和转录组数据集进行分析和比较已经成为标准程序。然而，对于非模式生物，目前还没有有效的工具可以直观地处理多个基因组及其元数据，并以协作的方式对这些数据进行注释。在这里，我们介绍了 GeneNoteBook：一个用于比较基因组学的基于网络的协作笔记本。GeneNoteBook 允许实验和计算研究人员查询、浏览、可视化和管理多个基因组的生物信息学分析结果。GeneNoteBook 特别适合于非模式生物的分析，因为它允许将新测序的基因组与模式生物的基因组进行比较。

可用性和实现

GeneNoteBook 是一个用 node.js 实现的网络应用程序，依赖于 MongoDB 和 NCBI BLAST。源代码可在 https://github.com/genenotebook/genenotebook 获得。此外，GeneNoteBook 可以通过 Bioconda 和 Docker 镜像进行安装。完整的安装说明和在线文档可在 https://genenotebook.github.io 获得。