Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 14 de 14
Filtrar
1.
Bioinformatics ; 39(1)2023 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-36645249

RESUMEN

SUMMARY: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022. AVAILABILITY AND IMPLEMENTATION: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Gráficos por Computador , Bibliotecas , Programas Informáticos , Navegador Web , Documentación
2.
Nucleic Acids Res ; 48(D1): D489-D497, 2020 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-31647099

RESUMEN

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.


Asunto(s)
Bases de Datos Factuales , Redes y Vías Metabólicas , Programas Informáticos , Genoma Humano , Genómica/métodos , Humanos , Metabolómica/métodos
3.
Nano Lett ; 21(12): 5209-5216, 2021 06 23.
Artículo en Inglés | MEDLINE | ID: mdl-34110166

RESUMEN

The ability to rapidly diagnose, track, and disseminate information for SARS-CoV-2 is critical to minimize its spread. Here, we engineered a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. Our device achieved a clinical sensitivity of 90% and specificity of 100% for SARS-CoV-2, as compared to 34% and 100%, respectively, for lateral flow assays in a head-to-head comparison. The lateral flow assay misdiagnosed ∼2 out of 3 SARS-CoV-2 positive patients. Our quantum dot barcode device has ∼3 times greater clinical sensitivity because it is ∼140 times more analytically sensitive than lateral flow assays. Our device can diagnose SARS-CoV-2 at different sampling dates and infectious severity. We developed a databasing app to provide instantaneous results to inform patients, physicians, and public health agencies. This assay and device enable real-time surveillance of SARS-CoV-2 seroprevalence and potential immunity.


Asunto(s)
COVID-19 , Puntos Cuánticos , Humanos , Inmunoensayo , SARS-CoV-2 , Sensibilidad y Especificidad , Estudios Seroepidemiológicos , Teléfono Inteligente
4.
Nucleic Acids Res ; 46(W1): W60-W64, 2018 07 02.
Artículo en Inglés | MEDLINE | ID: mdl-29912392

RESUMEN

GeneMANIA (http://genemania.org) is a flexible user-friendly web site for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query gene list, GeneMANIA finds functionally similar genes using a wealth of genomics and proteomics data. In this mode, it weights each functional genomic dataset according to its predictive value for the query. Another use of GeneMANIA is gene function prediction. Given a single query gene, GeneMANIA finds genes likely to share function with it based on their interactions with it. Enriched Gene Ontology categories among this set can point to the function of the gene. Nine organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Escherichia coli, Homo sapiens, Mus musculus, Rattus norvegicus and Saccharomyces cerevisiae). Hundreds of data sets and hundreds of millions of interactions have been collected from GEO, BioGRID, IRefIndex and I2D, as well as organism-specific functional genomics data sets. Users can customize their search by selecting specific data sets to query and by uploading their own data sets to analyze. We have recently updated the user interface to GeneMANIA to make it more intuitive and make more efficient use of visual space. GeneMANIA can now be used effectively on a variety of devices.


Asunto(s)
Bases de Datos Genéticas , Genómica , Internet , Programas Informáticos , Algoritmos , Animales , Arabidopsis/genética , Drosophila melanogaster/genética , Ontología de Genes , Redes Reguladoras de Genes/genética , Humanos , Ratones , Ratas , Saccharomyces cerevisiae/genética , Pez Cebra/genética
5.
Amino Acids ; 51(2): 263-272, 2019 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-30288604

RESUMEN

Consecutive multicomponent reactions have been applied for the synthesis of novel pseudo-peptides bearing dithiocarbamate and N,X-heterocyclic groups (X = S, O) in only one structure. The first multicomponent reaction includes the synthesis of dithiocarbamates using an amine or amino acid, CS2 and an electrophile. The second MCR is synthesis of Asinger imines using 2-chloroisobutyraldehyde, NaXH (X = S, O), ketone and ammonia. The final MCR is Ugi reaction to afford the corresponding three-dimensional pseudo-peptides. Various Asinger imines, carboxylic acids and isocyanides were applied in this protocol to provide diversities of pseudo-peptides in high to excellent yields.


Asunto(s)
Ácidos Carboxílicos/química , Cianuros/química , Compuestos Heterocíclicos/química , Iminas/síntesis química , Péptidos/síntesis química , Tiocarbamatos/química , Tiocarbamatos/síntesis química , Glicina/química , Difracción de Rayos X
6.
Org Biomol Chem ; 16(37): 8292-8304, 2018 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-30221304

RESUMEN

The first trapping of N-acyliminium ions by in situ generated carbaminic acid (product of carbon dioxide (CO2) and amine) is reported. This catalyst-free reaction provides a convenient and feasible approach to prepare N-acyl thia- and oxazolidinyl carbamates with good functional-group compatibility and high efficiency under green conditions. Furthermore, the multicomponent method features a broad substrate scope, facile product diversification, smooth scale-up and notable potential for polymer applications.

7.
Bioinformatics ; 32(2): 309-11, 2016 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-26415722

RESUMEN

UNLABELLED: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. AVAILABILITY AND IMPLEMENTATION: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. CONTACT: gary.bader@utoronto.ca.


Asunto(s)
Gráficos por Computador , Programas Informáticos , Navegador Web , Biología Computacional , Humanos , Lenguajes de Programación , Mapas de Interacción de Proteínas
8.
Nucleic Acids Res ; 41(Web Server issue): W115-22, 2013 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-23794635

RESUMEN

GeneMANIA (http://www.genemania.org) is a flexible user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query gene list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. GeneMANIA can also be used in a function prediction setting: given a query gene, GeneMANIA finds a small set of genes that are most likely to share function with that gene based on their interactions with it. Enriched Gene Ontology categories among this set can sometimes point to the function of the gene. Seven organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens, Rattus norvegicus and Saccharomyces cerevisiae), and hundreds of data sets have been collected from GEO, BioGRID, IRefIndex and I2D, as well as organism-specific functional genomics data sets. Users can customize their search by selecting specific data sets to query and by uploading their own data sets to analyze.


Asunto(s)
Genes , Programas Informáticos , Algoritmos , Animales , Redes Reguladoras de Genes , Humanos , Internet , Ratones , Ratas
9.
Nucleic Acids Res ; 38(Web Server issue): W214-20, 2010 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-20576703

RESUMEN

GeneMANIA (http://www.genemania.org) is a flexible, user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist.


Asunto(s)
Genes , Programas Informáticos , Algoritmos , Animales , Redes Reguladoras de Genes , Genes/fisiología , Genómica , Humanos , Internet , Ratones
10.
Bioinformatics ; 26(18): 2347-8, 2010 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-20656902

RESUMEN

UNLABELLED: Cytoscape Web is a web-based network visualization tool-modeled after Cytoscape-which is open source, interactive, customizable and easily integrated into web sites. Multiple file exchange formats can be used to load data into Cytoscape Web, including GraphML, XGMML and SIF. AVAILABILITY AND IMPLEMENTATION: Cytoscape Web is implemented in Flex/ActionScript with a JavaScript API and is freely available at http://cytoscapeweb.cytoscape.org/.


Asunto(s)
Internet , Programas Informáticos
11.
Front Endocrinol (Lausanne) ; 12: 706504, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34354672

RESUMEN

Background: In previous studies, we reported the beneficial impact of two lipoxygenase-inhibitors, Baicalein and Zileuton, on osteoporotic bone in a postmenopausal rat model. Whereas subcutaneous Baicalein predominantly improved cortical bone, Zileuton enhanced vertebral and femoral trabecular bone. In this study, we aimed to reveal whether the oral administration of Baicalein caused similar effects on bone and whether a combined administration of Baicalein and Zileuton could act synergistically to ameliorate the formerly reported effects in the musculoskeletal system. Methods: We treated ovariectomized (OVX) female Sprague-Dawley rats either with Baicalein (10mg/kg BW), Zileuton (10mg/kg BW) or a combination of both (each 10mg/kg BW) for 13 weeks and compared with untreated OVX and NON-OVX groups (n=12-16 rats per group). Lumbar vertebral bodies and femora were analyzed. Tibiae were osteotomized, plate-stabilized (at week 8 after OVX) and likewise analyzed by biomechanical, histological, micro-computed tomographical and ashing tests. The skeletal muscle structure was analyzed. Results: Oral administration of Baicalein did not confirm the reported favorable cortical effects in neither vertebra nor femur. Zileuton showed a beneficial effect on trabecular vertebra, while the femur was negatively affected. Callus formation was enhanced by all treatments; however, its density and biomechanical properties were unaltered. Lipoxygenase inhibition did not show a beneficial effect on skeletal muscle. The combination therapy did not ameliorate OVX-induced osteoporosis but induced even more bone loss. Conclusions: The preventive anti-osteoporotic treatments with two lipoxygenase inhibitors applied either alone or in combination showed no benefit for the musculoskeletal system in estrogen deficient rats.


Asunto(s)
Enfermedades Óseas Metabólicas/tratamiento farmacológico , Estrógenos/deficiencia , Inhibidores de la Lipooxigenasa/farmacología , Lipooxigenasas/química , Sistema Musculoesquelético/efectos de los fármacos , Osteoporosis/tratamiento farmacológico , Animales , Enfermedades Óseas Metabólicas/enzimología , Enfermedades Óseas Metabólicas/etiología , Enfermedades Óseas Metabólicas/patología , Femenino , Flavanonas/farmacología , Hidroxiurea/análogos & derivados , Hidroxiurea/farmacología , Osteoporosis/enzimología , Osteoporosis/etiología , Osteoporosis/patología , Ratas , Ratas Sprague-Dawley
12.
Elife ; 102021 12 03.
Artículo en Inglés | MEDLINE | ID: mdl-34860157

RESUMEN

Making the knowledge contained in scientific papers machine-readable and formally computable would allow researchers to take full advantage of this information by enabling integration with other knowledge sources to support data analysis and interpretation. Here we describe Biofactoid, a web-based platform that allows scientists to specify networks of interactions between genes, their products, and chemical compounds, and then translates this information into a representation suitable for computational analysis, search and discovery. We also report the results of a pilot study to encourage the wide adoption of Biofactoid by the scientific community.


Asunto(s)
Biología Computacional/métodos , Genómica/métodos , Biología Computacional/instrumentación , Bases de Datos Factuales , Genómica/instrumentación , Proyectos Piloto
13.
Org Lett ; 17(23): 5866-9, 2015 Dec 04.
Artículo en Inglés | MEDLINE | ID: mdl-26571048

RESUMEN

A novel Cu-mediated rearrangement reaction based on bisamides containing a thiazolidine substructure opens the possibility for diastereoselective synthesis toward a tricyclic annulated and bridged heterocyclic system. The required precursors are easily synthesizable by a two-step synthetic pathway using the concept of sequential multicomponent reactions, i.e. the Asinger and Ugi reactions. Due to this synthesis strategy, a number of unique tricyclic heterocycles, characterized by high diversity, are synthesized in an effective manner.

14.
Elife ; 42015 Jul 08.
Artículo en Inglés | MEDLINE | ID: mdl-26153621

RESUMEN

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.


Asunto(s)
Disciplinas de las Ciencias Biológicas/métodos , Biología Computacional/métodos , Programas Informáticos
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA