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Pajé, an interactive visualization tool for tuning multi-threaded parallel applications

J. Chassin de Kergommeaux, B. Stein, P.E. Bernard
2000 Parallel Computing  
This paper describes Paj e, an interactive visualization tool for displaying the execution of parallel applications where a potentially large number of communicating threads of various life-times execute  ...  In order to be easily extensible, the architecture of the system was based on components which are connected in a data¯ow graph to produce a given visualization tool.  ...  Acknowledgements Florin Teodorescu designed a prototype thread visualization tool. Philippe Waille implemented the ATHAPASCAN THAPAS CA N tracer.  ... 
doi:10.1016/s0167-8191(00)00010-7 fatcat:rhcfue6yk5cnnktxwnpm47scti

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

Balaguru Ravikumar, Zaid Alam, Gopal Peddinti, Tero Aittokallio
2017 Nucleic Acids Research  
C-SPADE allows the users to visually map the chemical diversity of a screening panel, explore investigational compounds in terms of their similarity to the screening panel, perform polypharmacological  ...  Toward that end, we introduce C-SPADE, an opensource exploratory web-tool for interactive analysis and visualization of drug profiling assays (biochemical, cell-based or cell-free) using compound-centric  ...  ACKNOWLEDGEMENTS We thank our collaborators and colleagues at FIMM for beta-testing of the C-SPADE tool.  ... 
doi:10.1093/nar/gkx384 pmid:28472495 pmcid:PMC5570255 fatcat:izk4ce5ggbgg3gtfim3zpnclqm

InTool Explorer: An Interactive Exploratory Analysis Tool for Versatile Visualizations of Neuroscientific Data

Diana Furcila, Marcos García, Cosmin Toader, Juan Morales, Antonio LaTorre, Ángel Rodríguez, Luis Pastor, Javier DeFelipe, Lidia Alonso-Nanclares
2019 Frontiers in Neuroanatomy  
The main contribution of this tool is to provide a user-designed canvas for data visualization and interaction, to perform specific exploratory tasks according to the user needs.  ...  For this purpose, the tool allows the user to select among different predefined card types.  ...  -Heatmaps: in combination with the correlation test (already implemented), these maps represent a fast tool for crossexamining multivariate data.  ... 
doi:10.3389/fnana.2019.00028 pmid:30914926 pmcid:PMC6421977 fatcat:vvfif554bbakvevsirbgciyzpa

A virtual alternative to molecular model sets: a beginners' guide to constructing and visualizing molecules in open-source molecular graphics software

Siripreeya Phankingthongkum, Taweetham Limpanuparb
2021 BMC Research Notes  
Based on either Avogadro or IQmol, we proposed four sets of tasks for students, building basic molecular geometries, visualizing orbitals and densities, predicting polarity of molecules and matching 3D  ...  The application of molecular graphics software as a simple and free alternative to molecular model sets for introductory-level chemistry learners is presented.  ...  TL thanks the STT46 organizing committee for an invitation to present this work in the "Responsible Chemical Sciences for Future Sustainability" session of the conference at Ramkhamhaeng University on  ... 
doi:10.1186/s13104-021-05461-7 pmid:33597010 fatcat:lh2nmqe4pnclpetarrbwrrne2q

An interactive online atlas of interconnected network maps based on the NaviCell platform

Julio Saez-Rodriguez, Rosa Hernansaiz, Vincent Noël, Inna Kuperstein, Jean-Marie Ravel, Andrei Zinovyev
2021 Zenodo  
With the development of the NaviCell 3.0 web server, there is a complete and automated web-based infrastructure for hosting molecular maps, patient similarity network maps, and multi-omics datasets for  ...  This is the accepted iPC deliverable D4.2 "An interactive online atlas of interconnected network maps based on the NaviCell platform".  ...  One of the most common tools for molecular diagram construction is CellDesigner, which is also useful for manually-curated maps construction and also for visual representation of data-inferred maps.  ... 
doi:10.5281/zenodo.6546372 fatcat:56c3fl5hcraknjxebgpgm3wsly

HomolWat: a web server tool to incorporate 'homologous' water molecules into GPCR structures

Eduardo Mayol, Adrián García-Recio, Johanna K S Tiemann, Peter W Hildebrand, Ramon Guixà-González, Mireia Olivella, Arnau Cordomí
2020 Nucleic Acids Research  
While there are various tools available to predict the positions of internal waters using energy-based methods, the approach of borrowing lacking water molecules from homologous GPCR structures makes HomolWat  ...  Here we present HomolWat, a web application for incorporating water molecules into GPCR structures by using template-based modelling of homologous water molecules obtained from high-resolution structures  ...  ACKNOWLEDGEMENTS The authors thank current and former members of the Laboratori de Medicina Computational for troubleshooting and discussion.  ... 
doi:10.1093/nar/gkaa440 pmid:32484557 fatcat:qlpjmuru45c3jlyk3kjkten43e

CELL SURFACE: FROM MOLECULES TO SHAPE

M Battistelli, S Burattini, E Falcieri
2009 European Journal of Histochemistry  
By adopting tools inspired by the fractal geometry [B.  ...  MECHANICS AND COLOCALIZATION ANALYSIS OF THE PRION PROTEIN THE INTERACTION OF A SINGLE MOLECULE OF FIBRONECTIN WITH A LIVING BACTERIUM B.  ... 
doi:10.4081/837 fatcat:orzqbhzu2vhafbck5vvefek4em

Community-driven roadmap for integrated disease maps

Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M T Fleming, Nicolas Le Novère, Piotr Gawron, Thomas Ligon, Anna Niarakis (+6 others)
2018 Briefings in Bioinformatics  
of tools and modeling maps for predicting drug response.  ...  ; providing technical solutions for complexity management of maps; and Web tools for in-depth exploration of such maps.  ...  Acknowledgements The authors would like to thank the DMC members, whose participation in the discussions in the meeting helped greatly to shape the contents of this article:  ... 
doi:10.1093/bib/bby024 pmid:29688273 fatcat:evg6lluamfg2tn5ygblmxsznea

Small-molecule binding sites to explore protein–protein interactions in the cancer proteome

David Xu, Shadia I. Jalal, George W. Sledge, Samy O. Meroueh
2016 Molecular Biosystems  
The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival.  ...  Gene symbols provided by TCGA were mapped to their respective UniProt IDs using UniProt's mapping tool (http://www.uniprot.org/mapping/).  ...  Binding site annotation PyMOL 80 scripts were generated to create individual sessions for each protein with druggable binding sites.  ... 
doi:10.1039/c6mb00231e pmid:27452673 pmcid:PMC5030169 fatcat:jontwnjcarfivliheezr6ohqlq

MULTI-RESOLUTION APPROACH FOR INTERACTIVELY LOCATING FUNCTIONALLY LINKED ION BINDING SITES BY STEERING SMALL MOLECULES INTO ELECTROSTATIC POTENTIAL MAPS USING A HAPTIC DEVICE [chapter]

OLIVIER DELALANDE, NICOLAS FEREY, BENOIST LAURENT, MARC GUEROULT, BRIGITTE HARTMANN, MARC BAADEN
2009 Biocomputing 2010  
We use interactive steering of charged ions or small molecules in an electrostatic potential map in order to identify potential binding sites.  ...  structure and the probe molecule(s).  ...  Their critical comments enabled us to continually improve the MyPal application.  ... 
doi:10.1142/9789814295291_0023 fatcat:rsc3g257brbcvo7wtkdsqjgacy

Chapter 7 Single-Molecule Fluorescence Microscopy and its Applications to Single-Molecule Sequencing by Cyclic Synthesis [chapter]

Benedict Hebert, Ido Braslavsky
2007 Perspectives in Bioanalysis  
Acknowledgments We would like to acknowledge Timothy Harris from Helicos BioSciences and Stephen Quake from Stanford University for their helpful comments.  ...  While cleavable terminators are a promising tool for SMDS, they still need to be experimentally checked at the single molecule level to be validated as a suitable alternative.  ...  Figure 8 . 8 Sequencing single DNA molecules with FRET. (A) Intensity trace from a single template molecule through the entire session.  ... 
doi:10.1016/s1871-0069(06)02007-6 fatcat:ltnxoo7kyfdhhkbduhoei3egk4

AtlasCBS: a web server to map and explore chemico-biological space

Álvaro Cortés-Cabrera, Antonio Morreale, Federico Gago, Celerino Abad-Zapatero
2012 Journal of Computer-Aided Molecular Design  
New approaches are needed that can help decrease the unsustainable failure in small-molecule drug discovery.  ...  Given a target-ligand database with chemical structures and associated biological affinities/activities for a target, the AtlasCBS server generates two-dimensional, dynamical, representations of its content  ...  topics covered in the Help tab; b) Map viewer: tools for uploading the data from existing databases and for visualizing and analyzing their content; c) Login: required only if the user wants to have private  ... 
doi:10.1007/s10822-012-9587-5 pmid:22798082 fatcat:77gl3abvhzf4vohsnmsq5w2aum

Single-molecule imaging reveals translation of mRNAs localized to stress granules [article]

Daniel Mateju, Bastian Eichenberger, Jan Eglinger, Gregory Roth, Jeffrey Chao
2020 bioRxiv   pre-print
While our data confirms that non-translating mRNAs are preferentially recruited to SGs, we find unequivocal evidence for translation of mRNA localized to SGs.  ...  Here we re-examine this hypothesis using single-molecule imaging of mRNA translation in living cells.  ...  The scatter plot of distance map values and SunTag intensities was plotted for all translating mRNAs in SGs using Prism. 3D visualizations of mRNAs in SGs were created using the Orthogonal Views function  ... 
doi:10.1101/2020.03.31.018093 fatcat:544gsqdjazeopdvpqqxv2wd25e

Exploring biological data: Mappings between ontology- and cluster-based representations

Ilir Jusufi, Andreas Kerren, Falk Schreiber
2013 Information Visualization  
They allow for interactive selection and navigation to explore the data under consideration as well as visual analysis of mappings between ontology-and cluster-based space-filling representations.  ...  This article proposes new visualization methods for this task.  ...  Acknowledgments The authors wish to thank Vladyslav Aleksakhin for implementing the first version of CluMa-GO, Christian Klukas for providing the data sets used in this work, and Christian Klukas and Astrid  ... 
doi:10.1177/1473871612468880 fatcat:tvwy2qjlh5fl5ammtmb2sbwtaa

Visualization of mappings between the gene ontology and cluster trees

Ilir Jusufi, Andreas Kerren, Vladyslav Aleksakhin, Falk Schreiber, Pak Chung Wong, David L. Kao, Ming C. Hao, Chaomei Chen, Robert Kosara, Mark A. Livingston, Jinah Park, Ian Roberts
2012 Visualization and Data Analysis 2012  
This paper proposes a new visualization method for this task.  ...  Ontologies and hierarchical clustering are both important tools in biology and medicine to study high-throughput data such as transcriptomics and metabolomics data.  ...  ACKNOWLEDGMENTS The authors wish to thank Christian Klukas, IPK Gatersleben, Germany, for providing the data sets used in this work as well as for his constructive comments.  ... 
doi:10.1117/12.906700 dblp:conf/vda/JusufiKAS12 fatcat:fasxoqepordg3pfbmgio56n7ja
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