Journal of Integrative Bioinformatics最新文献

{"title":"Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool.","authors":"Alexandre Oliveira,&nbsp;Emanuel Cunha,&nbsp;Fernando Cruz,&nbsp;João Capela,&nbsp;João C Sequeira,&nbsp;Marta Sampaio,&nbsp;Cláudia Sampaio,&nbsp;Oscar Dias","doi":"10.1515/jib-2022-0014","DOIUrl":"https://doi.org/10.1515/jib-2022-0014","url":null,"abstract":"<p><p>Genome-scale metabolic models (GEMs) are essential tools for <i>in silico</i> phenotype prediction and strain optimisation. The most straightforward GEMs reconstruction approach uses published models as templates to generate the initial draft, requiring further curation. Such an approach is used by BiGG Integration Tool (BIT), available for <i>merlin</i> users. This tool uses models from BiGG Models database as templates for the draft models. Moreover, BIT allows the selection between different template combinations. The main objective of this study is to assess the draft models generated using this tool and compare them BIT, comparing these to CarveMe models, both of which use the BiGG database, and curated models. For this, three organisms were selected, namely <i>Streptococcus thermophilus</i>, <i>Xylella fastidiosa</i> and <i>Mycobacterium tuberculosis.</i> The models' variability was assessed using reactions and genes' metabolic functions. This study concluded that models generated with BIT for each organism were differentiated, despite sharing a significant portion of metabolic functions. Furthermore, the template seems to influence the content of the models, though to a lower extent. When comparing each draft with curated models, BIT had better performances than CarveMe in all metrics. Hence, BIT can be considered a fast and reliable alternative for draft reconstruction for bacteria models.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40344291","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}

{"title":"A device and an app for the diagnosis and self-management of tinnitus.","authors":"Pierpaolo Vittorini,&nbsp;Pablo Chamoso,&nbsp;Fernando De la Prieta","doi":"10.1515/jib-2022-0004","DOIUrl":"https://doi.org/10.1515/jib-2022-0004","url":null,"abstract":"<p><p>Tinnitus is an annoying ringing in the ears, in varying shades and intensities. Tinnitus can affect a person's overall health and social well-being (e.g., sleep problems, trouble concentrating, anxiety, depression and inability to work). The diagnostic procedure of tinnitus usually consists of three steps: an audiological examination, psychoacoustic measurement, and a disability evaluation. All steps are performed by physicians, who use specialised hardware/software and administer questionnaires. This paper presents a system, to be used by patients, for the diagnosis and self-management of tinnitus. The system is made up of an app and a device. The app is responsible for executing - through the device - a part of the required audiological and psychoacoustic examinations, as well as administering questionnaires that evaluate disability. The paper reviews the quality of the automated audiometric reporting and the user experience provided by the app. Descriptive and inferential statistics were used to support the findings. The results show that automated reporting is comparable with that of physicians and that user experience was improved by re-designing and re-developing the acufenometry of the app. As for the user experience, two experts in Human-Computer Interaction evaluated the first version of the app: their agreement was good (Cohen's <i>K</i> = 0.639) and the average rating of the app was 1.43/2. Also patients evaluated the app in its initial version: the satisfactory tasks (audiometry and questionnaires) were rated as 4.31/5 and 4.65/5. The unsatisfactory task (acufenometry) was improved and the average rating increased from 2.86/5 to 3.96/5 (<i>p</i> = 0.0005). Finally, the general usability of the app was increased from the initial value of 73.6/100 to 85.4/100 (<i>p</i> = 0.0003). The strengths of the project are twofold. Firstly, the automated reporting feature, which - to the best of our knowledge - is the first attempt in this area. Secondly, the overall app usability, which was evaluated and improved during its development. In summary, the conclusion drawn from the conducted project is that the system works as expected, and despite some weaknesses, also the replication of the device would not be expensive, and it can be used in different scenarios.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9534487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33447017","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}

{"title":"KaIDA: a modular tool for assisting image annotation in deep learning.","authors":"Marcel P Schilling, Svenja Schmelzer, Lukas Klinger, Markus Reischl","doi":"10.1515/jib-2022-0018","DOIUrl":"10.1515/jib-2022-0018","url":null,"abstract":"<p><p>Deep learning models achieve high-quality results in image processing. However, to robustly optimize parameters of deep neural networks, large annotated datasets are needed. Image annotation is often performed manually by experts without a comprehensive tool for assistance which is time- consuming, burdensome, and not intuitive. Using the here presented modular Karlsruhe Image Data Annotation (KaIDA) tool, for the first time assisted annotation in various image processing tasks is possible to support users during this process. It aims to simplify annotation, increase user efficiency, enhance annotation quality, and provide additional useful annotation-related functionalities. KaIDA is available open-source at https://git.scc.kit.edu/sc1357/kaida.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9800041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9094039","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}

{"title":"Evaluating molecular representations in machine learning models for drug response prediction and interpretability.","authors":"Delora Baptista, João Correia, Bruno Pereira, Miguel Rocha","doi":"10.1515/jib-2022-0006","DOIUrl":"10.1515/jib-2022-0006","url":null,"abstract":"<p><p>Machine learning (ML) is increasingly being used to guide drug discovery processes. When applying ML approaches to chemical datasets, molecular descriptors and fingerprints are typically used to represent compounds as numerical vectors. However, in recent years, end-to-end deep learning (DL) methods that can learn feature representations directly from line notations or molecular graphs have been proposed as alternatives to using precomputed features. This study set out to investigate which compound representation methods are the most suitable for drug sensitivity prediction in cancer cell lines. Twelve different representations were benchmarked on 5 compound screening datasets, using DeepMol, a new chemoinformatics package developed by our research group, to perform these analyses. The results of this study show that the predictive performance of end-to-end DL models is comparable to, and at times surpasses, that of models trained on molecular fingerprints, even when less training data is available. This study also found that combining several compound representation methods into an ensemble can improve performance. Finally, we show that a <i>post hoc</i> feature attribution method can boost the explainability of the DL models.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521826/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33438674","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}

{"title":"Design X Bioinformatics: a community-driven initiative to connect bioinformatics and design.","authors":"Björn Sommer,&nbsp;Daisuke Inoue,&nbsp;Marc Baaden","doi":"10.1515/jib-2022-0037","DOIUrl":"https://doi.org/10.1515/jib-2022-0037","url":null,"abstract":"<p><p>Bioinformatics applies computer science approaches to the analysis of biological data. It is widely known for its genomics-based analysis approaches that have supported, for example, the 1000 Genomes Project. In addition, bioinformatics relates to many other areas, such as analysis of microscopic images (e.g., organelle localization), molecular modelling (e.g., proteins, biological membranes), and visualization of biological networks (e.g., protein-protein interaction networks, metabolism). Design is a highly interdisciplinary field that incorporates aspects such as aesthetic, economic, functional, philosophical, and/or socio-political considerations into the creative process and is usually determined by context. While visualization plays a critical role in bioinformatics, as reflected in a number of conferences and workshops in the field, design in bioinformatics-related research contexts in particular is not as well studied. With this special issue in conjunction with an international workshop, we aim to bring together bioinformaticians from different fields with designers, design researchers, and medical and scientific illustrators to discuss future challenges in the context of bioinformatics and design.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9377699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40527885","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}

{"title":"A hybrid of Bees algorithm and regulatory on/off minimization for optimizing lactate and succinate production.","authors":"Mohd Izzat Yong,&nbsp;Mohd Saberi Mohamad,&nbsp;Yee Wen Choon,&nbsp;Weng Howe Chan,&nbsp;Hasyiya Karimah Adli,&nbsp;Khairul Nizar Syazwan Wsw,&nbsp;Nooraini Yusoff,&nbsp;Muhammad Akmal Remli","doi":"10.1515/jib-2022-0003","DOIUrl":"https://doi.org/10.1515/jib-2022-0003","url":null,"abstract":"<p><p>Metabolic engineering has expanded in importance and employment in recent years and is now extensively applied particularly in the production of biomass from microbes. Metabolic network models have been employed extravagantly in computational processes developed to enhance metabolic production and suggest changes in organisms. The crucial issue has been the unrealistic flux distribution presented in prior work on rational modelling framework adopting Optknock and OptGene. In order to address the problem, a hybrid of Bees Algorithm and Regulatory On/Off Minimization (BAROOM) is used. By employing <i>Escherichia coli</i> as the model organism, the most excellent set of genes in <i>E. coli</i> that can be removed and advance the production of succinate can be decided. Evidences shows that BAROOM outperforms alternative strategies used to escalate in succinate production in model organisms like <i>E. coli</i> by selecting the best set of genes to be removed.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40518181","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}

{"title":"Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.","authors":"Simon Orozco-Arias,&nbsp;Mariana S Candamil-Cortes,&nbsp;Paula A Jaimes,&nbsp;Estiven Valencia-Castrillon,&nbsp;Reinel Tabares-Soto,&nbsp;Gustavo Isaza,&nbsp;Romain Guyot","doi":"10.1515/jib-2021-0036","DOIUrl":"https://doi.org/10.1515/jib-2021-0036","url":null,"abstract":"<p><p>Transposable elements are mobile sequences that can move and insert themselves into chromosomes, activating under internal or external stimuli, giving the organism the ability to adapt to the environment. Annotating transposable elements in genomic data is currently considered a crucial task to understand key aspects of organisms such as phenotype variability, species evolution, and genome size, among others. Because of the way they replicate, LTR retrotransposons are the most common transposable elements in plants, accounting in some cases for up to 80% of all DNA information. To annotate these elements, a reference library is usually created, a curation process is performed, eliminating TE fragments and false positives and then annotated in the genome using the homology method. However, the curation process can take weeks, requires extensive manual work and the execution of multiple time-consuming bioinformatics software. Here, we propose a machine learning-based approach to perform this process automatically on plant genomes, obtaining up to 91.18% F1-score. This approach was tested with four plant species, obtaining up to 93.6% F1-score (<i>Oryza granulata</i>) in only 22.61 s, where bioinformatics methods took approximately 6 h. This acceleration demonstrates that the ML-based approach is efficient and could be used in massive sequencing projects.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9521825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40498603","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}

{"title":"Colors in the representation of biological structures.","authors":"Monica Zoppè","doi":"10.1515/jib-2022-0021","DOIUrl":"10.1515/jib-2022-0021","url":null,"abstract":"<p><p>Among the many properties of proteins, sugars, nucleic acids, membranes and other cellular components, color is not present. At the same time, we humans have a natural ability of recognizing and appreciating colors, and use them generously, with the aim of both delivering information and pleasing the eyes. In this article, I suggest how we can conciliate these two situations, with the contribution of biologists, artists, and computer graphics and perception experts. The concept can be developed in a series of initiatives involving the community, including discussion sessions, technical challenges, experimental studies and outreach activities.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2022-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9377705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40562034","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}

{"title":"Design considerations for representing systems biology information with the Systems Biology Graphical Notation.","authors":"Falk Schreiber,&nbsp;Tobias Czauderna","doi":"10.1515/jib-2022-0024","DOIUrl":"https://doi.org/10.1515/jib-2022-0024","url":null,"abstract":"<p><p>Visual representations are commonly used to explore, analyse, and communicate information and knowledge in systems biology and beyond. Such visualisations not only need to be accurate but should also be aesthetically pleasing and informative. Using the example of the Systems Biology Graphical Notation (SBGN) we will investigate design considerations for graphically presenting information from systems biology, in particular regarding the use of glyphs for types of information, the style of graph layout for network representation, and the concept of bricks for visual network creation.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9377698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40470351","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}

{"title":"Design - a new way to look at old molecules.","authors":"Davide Spalvieri,&nbsp;Anne-Marine Mauviel,&nbsp;Matthieu Lambert,&nbsp;Nicolas Férey,&nbsp;Sophie Sacquin-Mora,&nbsp;Matthieu Chavent,&nbsp;Marc Baaden","doi":"10.1515/jib-2022-0020","DOIUrl":"https://doi.org/10.1515/jib-2022-0020","url":null,"abstract":"<p><p>We discuss how design enriches molecular science, particularly structural biology and bioinformatics. We present two use cases, one in academic practice and the other to design for outreach. The first case targets the representation of ion channels and their dynamic properties. In the second, we document a transition process from a research environment to general-purpose designs. Several testimonials from practitioners are given. By describing the design process of abstracted shapes, exploded views of molecular structures, motion-averaged slices, 360-degree panoramic projections, and experiments with lit sphere shading, we document how designers help make scientific data accessible without betraying its meaning, and how a creative mind adds value over purely data-driven visualizations. A similar conclusion was drawn for public outreach, as we found that comic-book-style drawings are better suited for communicating science to a broad audience.</p>","PeriodicalId":53625,"journal":{"name":"Journal of Integrative Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2022-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9377703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40563696","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}