Journal of Integrative Bioinformatics最新文献_第9页

OMEX metadata specification (version 1.2). OMEX元数据规范(1.2版)。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-10-20 DOI: 10.1515/jib-2021-0020

John H Gennari, Matthias König, Goksel Misirli, Maxwell L Neal, David P Nickerson, Dagmar Waltemath

{"title":"OMEX metadata specification (version 1.2).","authors":"John H Gennari, Matthias König, Goksel Misirli, Maxwell L Neal, David P Nickerson, Dagmar Waltemath","doi":"10.1515/jib-2021-0020","DOIUrl":"https://doi.org/10.1515/jib-2021-0020","url":null,"abstract":"A standardized approach to annotating computational biomedical models and their associated files can facilitate model reuse and reproducibility among research groups, enhance search and retrieval of models and data, and enable semantic comparisons between models. Motivated by these potential benefits and guided by consensus across the COmputational Modeling in BIology NEtwork (COMBINE) community, we have developed a specification for encoding annotations in Open Modeling and EXchange (OMEX)-formatted archives. This document details version 1.2 of the specification, which builds on version 1.0 published last year in this journal. In particular, this version includes a set of initial model-level annotations (whereas v 1.0 described exclusively annotations at a smaller scale). Additionally, this version uses best practices for namespaces, and introduces omex-library.org as a common root for all annotations. Distributing modeling projects within an OMEX archive is a best practice established by COMBINE, and the OMEX metadata specification presented here provides a harmonized, community-driven approach for annotating a variety of standardized model representations. This specification acts as a technical guideline for developing software tools that can support this standard, and thereby encourages broad advances in model reuse, discovery, and semantic analyses.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8560343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39534730","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: 7

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. 模拟实验描述标记语言(SED-ML): 1级语言规范第4版。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-10-05 DOI: 10.1515/jib-2021-0021

Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König

{"title":"The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.","authors":"Lucian P Smith, Frank T Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias König","doi":"10.1515/jib-2021-0021","DOIUrl":"https://doi.org/10.1515/jib-2021-0021","url":null,"abstract":"Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expands these capabilities to cover additional types of models, model languages, parameter estimations, simulations and analyses of models, and analyses and visualizations of simulation results. To facilitate consistent practices across the community, Level 1 Version 4 also more clearly describes the use of SED-ML constructs, and includes numerous concrete validation rules. SED-ML is supported by a growing ecosystem of investigators, model languages, and software tools, including eight languages for constraint-based, kinetic, qualitative, rule-based, and spatial models, over 20 simulation tools, visual editors, model repositories, and validators. Additional information about SED-ML is available at https://sed-ml.org/.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8560344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40324428","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: 5

Big data in the healthcare system: a synergy with artificial intelligence and blockchain technology. 医疗系统中的大数据:与人工智能和区块链技术的协同作用。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-08-18 DOI: 10.1515/jib-2020-0035

Reyes-González Juan Pablo, Díaz-Peregrino Roberto, Soto-Ulloa Victor, Galvan-Remigio Isabel, Castillo Paul, Ogando-Rivas Elizabeth

{"title":"Big data in the healthcare system: a synergy with artificial intelligence and blockchain technology.","authors":"Reyes-González Juan Pablo, Díaz-Peregrino Roberto, Soto-Ulloa Victor, Galvan-Remigio Isabel, Castillo Paul, Ogando-Rivas Elizabeth","doi":"10.1515/jib-2020-0035","DOIUrl":"https://doi.org/10.1515/jib-2020-0035","url":null,"abstract":"In the last decades big data has facilitating and improving our daily duties in the medical research and clinical fields; the strategy to get to this point is understanding how to organize and analyze the data in order to accomplish the final goal that is improving healthcare system, in terms of cost and benefits, quality of life and outcome patient. The main objective of this review is to illustrate the state-of-art of big data in healthcare, its features and architecture. We also would like to demonstrate the different application and principal mechanisms of big data in the latest technologies known as blockchain and artificial intelligence, recognizing their benefits and limitations. Perhaps, medical education and digital anatomy are unexplored fields that might be profitable to investigate as we are proposing. The healthcare system can be revolutionized using these different technologies. Thus, we are explaining the basis of these systems focused to the medical arena in order to encourage medical doctors, nurses, biotechnologies and other healthcare professions to be involved and create a more efficient and efficacy system.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9135137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39326687","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: 15

In silico gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment. 在硅基因敲除预测使用蝙蝠算法和最小化代谢调节的混合。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-08-04 DOI: 10.1515/jib-2020-0037

Mei Yen Man, Mohd Saberi Mohamad, Yee Wen Choon, Mohd Arfian Ismail

{"title":"In silico gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment.","authors":"Mei Yen Man, Mohd Saberi Mohamad, Yee Wen Choon, Mohd Arfian Ismail","doi":"10.1515/jib-2020-0037","DOIUrl":"https://doi.org/10.1515/jib-2020-0037","url":null,"abstract":"Microorganisms commonly produce many high-demand industrial products like fuels, food, vitamins, and other chemicals. Microbial strains are the strains of microorganisms, which can be optimized to improve their technological properties through metabolic engineering. Metabolic engineering is the process of overcoming cellular regulation in order to achieve a desired product or to generate a new product that the host cells do not usually need to produce. The prediction of genetic manipulations such as gene knockout is part of metabolic engineering. Gene knockout can be used to optimize the microbial strains, such as to maximize the production rate of chemicals of interest. Metabolic and genetic engineering is important in producing the chemicals of interest as, without them, the product yields of many microorganisms are normally low. As a result, the aim of this paper is to propose a combination of the Bat algorithm and the minimization of metabolic adjustment (BATMOMA) to predict which genes to knock out in order to increase the succinate and lactate production rates in Escherichia coli (E. coli).","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8573224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39277083","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

On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection. 淀粉样蛋白序列的边界:PDB_Amyloid集合中平行β片的前缀分析。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-07-26 DOI: 10.1515/jib-2020-0043

Kristóf Takács, Vince Grolmusz

{"title":"On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection.","authors":"Kristóf Takács, Vince Grolmusz","doi":"10.1515/jib-2020-0043","DOIUrl":"https://doi.org/10.1515/jib-2020-0043","url":null,"abstract":"The Protein Data Bank (PDB) today contains more than 174,000 entries with the 3-dimensional structures of biological macromolecules. Using the rich resources of this repository, it is possible identifying subsets with specific, interesting properties for different applications. Our research group prepared an automatically updated list of amyloid- and probably amyloidogenic molecules, the PDB_Amyloid collection, which is freely available at the address http://pitgroup.org/amyloid. This resource applies exclusively the geometric properties of the steric structures for identifying amyloids. In the present contribution, we analyze the starting (i.e., prefix) subsequences of the characteristic, parallel beta-sheets of the structures in the PDB_Amyloid collection, and identify further appearances of these length-5 prefix subsequences in the whole PDB data set. We have identified this way numerous proteins, whose normal or irregular functions involve amyloid formation, structural misfolding, or anti-coagulant properties, simply by containing these prefixes: including the T-cell receptor (TCR), bound with the major histocompatibility complexes MHC-1 and MHC-2; the p53 tumor suppressor protein; a mycobacterial RNA polymerase transcription initialization complex; the human bridging integrator protein BIN-1; and the tick anti-coagulant peptide TAP.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1515/jib-2020-0043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39217075","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: 3

Synthetic biology open language visual (SBOL Visual) version 2.3. 合成生物学开放语言可视化(SBOL可视化)2.3版。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-06-08 DOI: 10.1515/jib-2020-0045

Hasan Baig, Pedro Fontanarossa, Vishwesh Kulkarni, James McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Shyam Bhakta, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Robert Sidney Cox, Angel Goñi Moreno, Thomas Gorochowski, Raik Grunberg, Jihwan Lee, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novere, Zachary Palchick, Matthew Pocock, Nicholas Roehner, Herbert Sauro, James Scott-Brown, John T Sexton, Guy-Bart Stan, Jeffrey J Tabor, Logan Terry, Marta Vazquez Vilar, Christopher A Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris Myers

{"title":"Synthetic biology open language visual (SBOL Visual) version 2.3.","authors":"Hasan Baig, Pedro Fontanarossa, Vishwesh Kulkarni, James McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Shyam Bhakta, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Robert Sidney Cox, Angel Goñi Moreno, Thomas Gorochowski, Raik Grunberg, Jihwan Lee, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novere, Zachary Palchick, Matthew Pocock, Nicholas Roehner, Herbert Sauro, James Scott-Brown, John T Sexton, Guy-Bart Stan, Jeffrey J Tabor, Logan Terry, Marta Vazquez Vilar, Christopher A Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris Myers","doi":"10.1515/jib-2020-0045","DOIUrl":"https://doi.org/10.1515/jib-2020-0045","url":null,"abstract":"People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level \"interactions with interactions,\" such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new \"unspecified interaction\" glyph is added for visualizing interactions whose nature is unknown, the \"insulator\" glyph is deprecated in favor of a new \"inert DNA spacer\" glyph, and the polypeptide region glyph is recommended for showing 2A sequences.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1515/jib-2020-0045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39071280","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: 2

Exploratory and discriminant analysis of plant phenolic profiles obtained by UV-vis scanning spectroscopy. 对紫外-可见扫描光谱法获得的植物酚谱进行探索和判别分析。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-06-04 DOI: 10.1515/jib-2019-0056

Monique Souza, Jucinei José Comin, Rodolfo Moresco, Marcelo Maraschin, Claudinei Kurtz, Paulo Emílio Lovato, Cledimar Rogério Lourenzi, Fernanda Kokowicz Pilatti, Arcângelo Loss, Shirley Kuhnen

{"title":"Exploratory and discriminant analysis of plant phenolic profiles obtained by UV-vis scanning spectroscopy.","authors":"Monique Souza, Jucinei José Comin, Rodolfo Moresco, Marcelo Maraschin, Claudinei Kurtz, Paulo Emílio Lovato, Cledimar Rogério Lourenzi, Fernanda Kokowicz Pilatti, Arcângelo Loss, Shirley Kuhnen","doi":"10.1515/jib-2019-0056","DOIUrl":"10.1515/jib-2019-0056","url":null,"abstract":"Some species of cover crops produce phenolic compounds with allelopathic potential. The use of math, statistical and computational tools to analyze data obtained with spectrophotometry can assist in the chemical profile discrimination to choose which species and cultivation are the best for weed management purposes. The aim of this study was to perform exploratory and discriminant analysis using R package specmine on the phenolic profile of Secale cereale L., Avena strigosa L. and Raphanus sativus L. shoots obtained by UV-vis scanning spectrophotometry. Plants were collected at 60, 80 and 100 days after sowing and at 15 and 30 days after rolling in experiment in Brazil. Exploratory and discriminant analysis, namely principal component analysis, hierarchical clustering analysis, t-test, fold-change, analysis of variance and supervised machine learning analysis were performed. Results showed a stronger tendency to cluster phenolic profiles according to plant species rather than crop management system, period of sampling or plant phenologic stage. PCA analysis showed a strong distinction of S. cereale L. and A. strigosa L. 30 days after rolling. Due to the fast analysis and friendly use, the R package specmine can be recommended as a supporting tool to exploratory and discriminatory analysis of multivariate data.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8573236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38992260","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

Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions. 结构关系匹配:一种识别rna结构模式及其相互作用的算法。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-05-31 DOI: 10.1515/jib-2020-0039

Michela Quadrini

{"title":"Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions.","authors":"Michela Quadrini","doi":"10.1515/jib-2020-0039","DOIUrl":"https://doi.org/10.1515/jib-2020-0039","url":null,"abstract":"RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA-RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA-RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2021-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1515/jib-2020-0039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39031294","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

Cross-evaluation of social mining for classification of depressed online personas. 抑郁在线人物角色分类的社会挖掘交叉评价。

IF 1.9

Journal of Integrative Bioinformatics Pub Date : 2021-05-20 DOI: 10.1515/jib-2020-0051

Alina Trifan, José Luis Oliveira

引用次数: 2

Cardiac well-being indexes: a decision support tool to monitor cardiovascular health. 心脏健康指数：监测心血管健康的决策支持工具。

IF 1.5

Journal of Integrative Bioinformatics Pub Date : 2021-03-29 DOI: 10.1515/jib-2020-0040

Ana Duarte, Orlando Belo

引用次数: 0