31,431 Hits in 4.8 sec

An Intuitive Automated Modelling Interface for Systems Biology

Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron
2009 Electronic Proceedings in Theoretical Computer Science  
We introduce a natural language interface for building stochastic pi calculus models of biological systems.  ...  This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy.  ...  To this end, we introduce an intuitive front-end interface language to biological models and a tool for automated translation into Microsoft's stochastic simulation language SPiM [1, 2] , which is a process  ... 
doi:10.4204/eptcs.9.9 fatcat:djlqtwum4vdlhpusotbkffzfsa

Tools for kinetic modeling of biochemical networks

Rui Alves, Fernando Antunes, Armindo Salvador
2006 Nature Biotechnology  
They have intuitive user interfaces, and even those lacking a graphic user interface permit models to be rapidly set up by using a text interface window and a simple syntax.  ...  File-sharing systems over the web also permit remote sharing of models using stand-alone simulators.  ...  It has an intuitive user interface, provides a good assortment of complementary simulation algorithms and is integrated with the Systems Biology Workbench.  ... 
doi:10.1038/nbt0606-667 pmid:16763599 fatcat:us5czy23mzgplnkhdevyjnqgxu

Opportunities for actuated tangible interfaces to improve protein study

Ashlie Brown, Hayes Raffle
2009 Proceedings of the 27th international conference extended abstracts on Human factors in computing systems - CHI EA '09  
Current protein study tools miss fundamental biology concepts because graphical and symbolic interfaces do not allow users to intuitively manipulate complex physical forms.  ...  We outline strategies for actuated tangible user interfaces (TUIs) to improve the study of proteins.  ...  biology-evaluate the concept of actuated models for biology education and research.  ... 
doi:10.1145/1520340.1520344 dblp:conf/chi/BrownR09 fatcat:v3oe3opi5ja5xc3mwuiqrmh3zq

Tangible Augmented Interfaces for Structural Molecular Biology

A. Gillet, M. Sanner, D. Stoffler, A. Olson
2005 IEEE Computer Graphics and Applications  
We have developed an augmented reality (AR) system that lets virtual 3D representations of molecular structures and properties be overlaid on autofabricated models of the molecules (for more information  ...  Current research in molecular biology now focuses on larger assemblies and on more complex interactions, for which the traditional physical molecular models are inadequate.  ...  Projects in VR March/April 2005 We prototyped our current approach to tangible computer interfaces for molecular biology in an inexpensive, portable form, using off-the-shelf components.  ... 
doi:10.1109/mcg.2005.47 pmid:15794144 fatcat:iu2upunz75acbn6uekpiehtkq4

Preface: Intelligent interactive data visualization

Barbara Hammer, Daniel Keim, Neil Lawrence, Guy Lebanon
2013 Data mining and knowledge discovery  
They cannot rely on fully automatic techniques for data analysis and visualization, because effective modeling requires an iterative interaction between computerized processing and human analysis.  ...  for user studies, up to software systems for dedicated application areas such as bioinformatics.  ...  to built time-series models for large heterogeneous spatio-temporal data sets in an interactive data-driven way.  ... 
doi:10.1007/s10618-013-0309-y fatcat:rkf3qrqhzjan5fcwmz35huuthm

Simulating genetic networks made easy: network construction with simple building blocks

S. Vercruysse, M. Kuiper
2004 Bioinformatics  
We present SIM-plex, a genetic network simulator with a very intuitive interface in which a user can easily specify interactions as simple 'if-then' statements.  ...  The simulator is based on the mathematical model of Piecewise Linear Differential Equations (PLDEs). With PLDEs, genetic interactions are approximated as acting in a switch-like manner.  ...  ACKNOWLEDGEMENTS We thank Hidde de Jong for valuable comments. S.V. is indebted to the IWT for a predoctoral fellowship.  ... 
doi:10.1093/bioinformatics/bth478 pmid:15319258 fatcat:2o7vypcqinav7if4trcr2hhzky

Genomic patient information management system

D Dharmiah, M Narasinga Rao, Ravikiran, N Sandeep, V DS Gopal, Allam Appa Rao, GR Sridhar
2010 Genome Biology  
Conclusion The patient information management application has an intuitive user interface and is flexible for further upgradation. © 2010 Sridhar et al; licensee BioMed Central Ltd.  ...  Components We developed a model retrieval "Genomic patient information management system" It caters to the requirements of clinicians and patients by acting as an interface which allows 1) Maintaining  ... 
doi:10.1186/gb-2010-11-s1-p44 fatcat:i2ejs3fyencrjasl3b6uvaqp3a

MOST: a software environment for constraint-based metabolic modeling and strain design

James J. Kelley, Anatoliy Lane, Xiaowei Li, Brahmaji Mutthoju, Shay Maor, Dennis Egen, Desmond S. Lun
2014 Bioinformatics  
MOST (metabolic optimization and simulation tool) is a software package that implements GDBB (genetic design through branch and bound) in an intuitive user-friendly interface with excellike editing functionality  ...  , as well as implementing FBA (flux balance analysis), and supporting systems biology markup language and comma-separated values files.  ...  ACKNOWLEDGEMENTS The authors would like to thank Trent Kroeger for his contributions in starting off the MOST project, and Zhiyuan Zhang for work on FBA.  ... 
doi:10.1093/bioinformatics/btu685 pmid:25677126 fatcat:yfdtffjybzg4tbil7wnxcry36q

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems

Maxwell L. Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari, Ruth Nussinov
2014 PLoS Computational Biology  
Our conclusions have strategic implications for the design of systems biology, synthetic biology, and integrated physiological modeling technologies, as well as communitylevel model curation efforts.  ...  As modelers of complex biological systems, we aim to apply modular production to accelerate our efforts and have therefore investigated several currently available approaches for modular modeling.  ...  Smith for their input on the issue of modular modeling.  ... 
doi:10.1371/journal.pcbi.1003849 pmid:25275523 pmcid:PMC4183381 fatcat:3sb4avxp7ra7tajdynue3denla

The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology

J. Blakes, J. Twycross, F. J. Romero-Campero, N. Krasnogor
2011 Bioinformatics  
The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology.  ...  A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions.  ...  biology models.  ... 
doi:10.1093/bioinformatics/btr571 pmid:21994219 pmcid:PMC3223367 fatcat:mtluk3v7ybechhmkpahu3na6pq

Single crystal pulsed neutron diffraction studies of transition metal hydrogen interactions

A. J. Schultz
2002 Acta Crystallographica Section A Foundations of Crystallography  
Natural and multi-modal interactions with physical objects, offer an expanded view of molecular structure, and an intuitive interface for manipulation and query.  ...  As biology and computation become more enmeshed, issues of software use for the study of complex molecular biological systems become central.  ...  Natural and multi-modal interactions with physical objects, offer an expanded view of molecular structure, and an intuitive interface for manipulation and query.  ... 
doi:10.1107/s0108767302093741 fatcat:qnxr6nyoebfhla37blwlmaz7zi

Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes

P. K. Dhar, T. C. Meng, S. Somani, L. Ye, K. Sakharkar, A. Krishnan, A. B.M. Ridwan, S. H. K. Wah, M. Chitre, Z. Hao
2004 Bioinformatics  
Grid Cellware, an integrated modelling and simulation tool, has been developed to precisely address these niche requirements of the modelling community.  ...  For enchanced computational productivity Grid Cellware uses grid technology with Globus as the middleware.  ...  Intuitive graphical user interface The powerful graphical editor plays an important role in Grid Cellware modelling.  ... 
doi:10.1093/bioinformatics/bti143 pmid:15546936 fatcat:ja4flhxbkbcplird6ms3qitqxm

The solution to overcoming the implementation barrier of Clinical Decision Support Systems [article]

Rianne Fijten
2019 Figshare  
Poster for ESTRO 2019 conference  ...  Conclusion The interface described in this abstract allows for automated generation of model outcomes at a moment's notice with up-to-date information and within the EHR system.  ...  The solution to overcoming the implementation barrier of Clinical Decision Support Systems: EHR-compatible, intuitive interfaces Encouraging the use of decision support systems in routine clinical practice  ... 
doi:10.6084/m9.figshare.7964606.v2 fatcat:gerqsn7ubzfcjlkhpv3rshfzoa

PresentaBALL — A powerful package for presentations and lessons in structural biology

Stefan Nickels, Daniel Stockel, Sabine C. Mueller, Hans-Peter Lenhof, Andreas Hildebrandt, Anna Katharina Dehof
2013 2013 IEEE Symposium on Biological Data Visualization (BioVis)  
But in many scenarios, such as teaching, presentations, and demonstrations, it would be highly preferable to have an intuitive environment for showcasing molecular functionality.  ...  Typically, the graphical interfaces to molecular modeling packages are aimed at domain experts with significant experience and require an extensive learning period.  ...  ACKNOWLEDGEMENTS The authors wish to thank the BALL development team as well as the students Wolfgang Herget, Peter Ebert, Nikola Koch, Markus Konietzko and Jana Panning for work on the web pages and example  ... 
doi:10.1109/biovis.2013.6664344 dblp:conf/biovis/NickelsSMLHD13 fatcat:ljp2zgupyrfptmtyvivayekz44

SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology

Alexander Dörr, Roland Keller, Andreas Zell, Andreas Dräger
2014 Computation  
SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration.  ...  We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2.  ...  Palsson for fruitful discussions, Marcel Kronfeld who helped implementing the connection to EvA2, and the students Max Zwießele and Philipp Stevens for implementing parts of the plot function.  ... 
doi:10.3390/computation2040246 pmid:32211200 pmcid:PMC7093077 fatcat:l7n3wmz74jhu3ki67oan3wug6a
« Previous Showing results 1 — 15 out of 31,431 results