CytoCopasi: A Chemical Systems Biology Target and Drug Discovery Visual Data Analytics Platform

IF 4.4 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Bioinformatics Pub Date : 2023-12-09 DOI:10.1093/bioinformatics/btad745
Hikmet Emre Kaya, Kevin J Naidoo
{"title":"CytoCopasi: A Chemical Systems Biology Target and Drug Discovery Visual Data Analytics Platform","authors":"Hikmet Emre Kaya, Kevin J Naidoo","doi":"10.1093/bioinformatics/btad745","DOIUrl":null,"url":null,"abstract":"Motivation Target discovery and drug evaluation for diseases with complex mechanisms call for a streamlined chemical systems analysis platform. Currently available tools lack the emphasis on reaction kinetics, access to relevant databases, and algorithms to visualize perturbations on a chemical scale providing quantitative details as well streamlined visual data analytics functionality. Results CytoCopasi, a Maven-based application for Cytoscape that combines the chemical systems analysis features of COPASI with the visualization and database access tools of Cytoscape and its plugin applications has been developed. The diverse functionality of CytoCopasi through ab initio model construction, model construction via pathway and parameter databases KEGG and BRENDA is presented. The comparative systems biology visualization analysis toolset is illustrated through a drug competence study on the cancerous RAF/MEK/ERK pathway. Availability The COPASI files, simulation data, native libraries, and the manual are available on https://github.com/scientificomputing/CytoCopasi Supplementary information Supplementary data is available at Bioinformatics online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"29 1","pages":""},"PeriodicalIF":4.4000,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btad745","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0

Abstract

Motivation Target discovery and drug evaluation for diseases with complex mechanisms call for a streamlined chemical systems analysis platform. Currently available tools lack the emphasis on reaction kinetics, access to relevant databases, and algorithms to visualize perturbations on a chemical scale providing quantitative details as well streamlined visual data analytics functionality. Results CytoCopasi, a Maven-based application for Cytoscape that combines the chemical systems analysis features of COPASI with the visualization and database access tools of Cytoscape and its plugin applications has been developed. The diverse functionality of CytoCopasi through ab initio model construction, model construction via pathway and parameter databases KEGG and BRENDA is presented. The comparative systems biology visualization analysis toolset is illustrated through a drug competence study on the cancerous RAF/MEK/ERK pathway. Availability The COPASI files, simulation data, native libraries, and the manual are available on https://github.com/scientificomputing/CytoCopasi Supplementary information Supplementary data is available at Bioinformatics online.
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
CytoCopasi:化学系统生物学目标和药物发现可视化数据分析平台
动机 针对机制复杂的疾病进行目标发现和药物评估,需要一个简化的化学系统分析平台。目前可用的工具缺乏对反应动力学的重视、对相关数据库的访问以及在化学尺度上可视化扰动的算法,无法提供定量细节和简化的可视化数据分析功能。结果 CytoCopasi 是一个基于 Maven 的 Cytoscape 应用程序,它将 COPASI 的化学系统分析功能与 Cytoscape 及其插件应用程序的可视化和数据库访问工具相结合。介绍了 CytoCopasi 的多种功能,包括自证模型构建、通过路径和参数数据库 KEGG 和 BRENDA 构建模型。通过对癌症 RAF/MEK/ERK 通路的药物能力研究,说明了比较系统生物学可视化分析工具集。可用性 COPASI 文件、模拟数据、原生库和手册可在 https://github.com/scientificomputing/CytoCopasi 上获取 补充信息 补充数据可在 Bioinformatics online 上获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
Bioinformatics
Bioinformatics 生物-生化研究方法
CiteScore
11.20
自引率
5.20%
发文量
753
审稿时长
2.1 months
期刊介绍: The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.
期刊最新文献
MEHunter: Transformer-based mobile element variant detection from long reads Metabolic syndrome may be more frequent in treatment-naive sarcoidosis patients. Coracle—A Machine Learning Framework to Identify Bacteria Associated with Continuous Variables CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1