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Julia for Biologists [article]

Elisabeth Roesch, Joe G. Greener, Adam L. MacLean, Huda Nassar, Christopher Rackauckas, Timothy E. Holy, Michael P.H. Stumpf
2021 arXiv   pre-print
Collecting, curating, processing, and analysing large genomic and imaging data sets poses major computational challenges, as does simulating larger and more realistic models in systems biology.  ...  Here we discuss how a relative newcomer among computer programming languages -- Julia -- is poised to meet the current and emerging demands in the computational biosciences, and beyond.  ...  into new Julia projects via language specific packages ( Figure 4 , Integration of non-Julia code).  ... 
arXiv:2109.09973v1 fatcat:csx5wnzcc5datpxyckhzcri6le

THE ERATO SYSTEMS BIOLOGY WORKBENCH: ENABLING INTERACTION AND EXCHANGE BETWEEN SOFTWARE TOOLS FOR COMPUTATIONAL BIOLOGY

M. HUCKA, A. FINNEY, H. M. SAURO, H. BOLOURI, J. DOYLE, H. KITANO
2001 Biocomputing 2002  
In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows these heterogeneous application components-written in diverse programming languages and running on  ...  Researchers in computational biology today make use of a large number of different software packages for modeling, analysis, and data manipulation and visualization.  ...  The Systems Biology Workbench has benefitted from the input of many people.  ... 
doi:10.1142/9789812799623_0042 fatcat:mgt3ogab5jfmxmrzoxav4xukbu

Improving Collaboration by Standardization Efforts in Systems Biology

Andreas Dräger, Bernhard Ø. Palsson
2014 Frontiers in Bioengineering and Biotechnology  
; SBGN-ML, systems biology graphical notation mark-up language; SBML, systems biology mark-up language; SBOL, synthetic biology open language; SBRML, systems biology result mark-up language; SBW, systems  ...  ; PDE, partial differential equation; PharmML, pharmacometrics mark-up language; PHML, physiological hierarchy mark-up language; RDF, resource description framework; SBGN, systems biology graphical notation  ...  Systems biology mark-up language The Systems Biology Mark-up Language Hucka et al., 2003 Hucka et al., , 2004 2 is a hierarchical XML-based format consisting of several lists of components, such as compartments  ... 
doi:10.3389/fbioe.2014.00061 pmid:25538939 pmcid:PMC4259112 fatcat:yvsizmtklreanfa6oybwaifccm

PEtab—Interoperable specification of parameter estimation problems in systems biology

Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos (+18 others)
2021 PLoS Computational Biology  
Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing  ...  Yet, there has been—so far—no broadly supported format for the specification of parameter estimation problems in systems biology.  ...  In particular the Systems Biology Markup Language (SBML) [11] , CellML [12] and the BioNet-Gen Language (BNGL) [13] are widely used.  ... 
doi:10.1371/journal.pcbi.1008646 pmid:33497393 fatcat:dkmsqgoywfejroj6nt4pgebcoi

PEtab – interoperable specification of parameter estimation problems in systems biology [article]

Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos (+17 others)
2020 arXiv   pre-print
Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing  ...  Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology.  ...  Similarly, the 47 XML-based Systems Biology Results Markup Language (SBRML) was designed to 48 associate models with experimental data and share simulation experiment results in a 49 machine-readable way  ... 
arXiv:2004.01154v4 fatcat:zuo6hkdfnnb6nosphcz2s7j2gu

Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration

Herbert M. Sauro, Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, Hiroaki Kitano
2003 Omics  
Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation.  ...  In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms-to  ...  ACKNOWLEDGMENTS This work was initially funded by the Japan Science and Technology Corporation under the ERATO Kitano Systems Biology Project.  ... 
doi:10.1089/153623103322637670 pmid:14683609 fatcat:n72kaisq25g35psxqb3zmzyeqy

The IUPS human physiome project

Peter Hunter, Peter Robbins, Denis Noble
2002 Pflügers Archiv: European Journal of Physiology  
A major goal of the project is to use computational modelling to analyse integrative biological function in terms of underlying structure and molecular mechanisms.  ...  To support that goal the project is establishing web-accessible physiological databases dealing with model-related data, including bibliographic information, at the cell, tissue, organ and organ system  ...  The markup languages ensure that models are encoded in a consistent form and allows simulation packages to import the models in a standard format.  ... 
doi:10.1007/s00424-002-0890-1 pmid:12397380 fatcat:4fnlhyzjnrfnxa5hfza62rei3a

Simulation tools for biochemical networks: evaluation of performance and usability

A. Pettinen, T. Aho, O.-P. Smolander, T. Manninen, A. Saarinen, K.-L. Taattola, O. Yli-Harja, M.-L. Linne
2004 Bioinformatics  
Results: We examine selected simulation tools that are intended for the simulation of biochemical systems.  ...  Numerous simulation tools have been developed for numerical simulation of the behavior of a system described in mathematical form. However, there exist only a few evaluation studies of these tools.  ...  Most simulation tools have an integrated design tool, or models can be implemented via specific script or markup language (similar to programming languages).  ... 
doi:10.1093/bioinformatics/bti018 pmid:15358616 fatcat:crlwhsijhbdibcotcqkjfm3lhe

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

Szymon Stoma, Martina Fröhlich, Susanne Gerber, Edda Klipp
2011 BMC Bioinformatics  
Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems.  ...  availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology  ...  It would be also crucial to support import and export of SBML (Systems Biology Markup Language) files. For the latter, a prior establishment of a standard for spatial modeling would be required.  ... 
doi:10.1186/1471-2105-12-126 pmid:21527030 pmcid:PMC3114743 fatcat:5d6zgm52wjbc3lx6ilyhoni4aq

JWS Online Cellular Systems Modelling and Microbiology

J. L. Snoep
2003 Microbiology  
Introduction Rapid developments in the relatively new disciplines of 'bioinformatics', 'computational biology' and 'systems biology' have led to a marked increase in the use of kinetic models in the study  ...  SBML compatibility is already integrated into several metabolic modelling packages, for example, SCAMP (Sauro, 1993) , GEPASI (Mendes, 1997) and JARNAC (Sauro, 2000) .  ... 
doi:10.1099/mic.0.c0124-0 pmid:14600216 fatcat:yijwcsizmnewxk46krpqiw27am

Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective

Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
2021 npj Systems Biology and Applications  
AbstractReuse of mathematical models becomes increasingly important in systems biology as research moves toward large, multi-scale models composed of heterogeneous subcomponents.  ...  For this reason, we compare existing suitable languages in detail and demonstrate their benefits for a modular model of the human cardiac conduction system written in Modelica.  ...  biology.  ... 
doi:10.1038/s41540-021-00182-w pmid:34083542 fatcat:isocg5rzuzgodf5oycp7nypesu

Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations

Etienne Lord, Mickael Leclercq, Alix Boc, Abdoulaye Baniré Diallo, Vladimir Makarenkov, Simon Joly
2012 PLoS ONE  
As Armadillo is an open-source project, it allows scientists to develop their own modules as well as to integrate existing computer applications.  ...  In this paper we introduce Armadillo v1.1, a novel workflow platform dedicated to designing and conducting phylogenetic studies, including comprehensive simulations.  ...  Moreover, when conducting their experiments and simulations, computational biologists have to cope with programs' limitations and data integration issues [1] .  ... 
doi:10.1371/journal.pone.0029903 pmid:22253821 pmcid:PMC3256230 fatcat:3bn34nd4prbn7fca3vbsty63qe

LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2

Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini, R. Angus Silver
2014 Frontiers in Neuroinformatics  
We establish that LEMS can be used to define models from systems biology and map them to neuroscience-domain specific simulators, enabling models to be shared between these traditionally separate disciplines  ...  However, published models are currently implemented using a diverse set of modeling approaches, simulation tools, and computer languages making them inaccessible and difficult to reproduce.  ...  The language contains a variety of biological concepts that are widely implemented in systems biology simulation tools such as reactants, products and well stirred compartments.  ... 
doi:10.3389/fninf.2014.00079 pmid:25309419 pmcid:PMC4174883 fatcat:3mu57iygjzfploomyu3ltd7f4y

Common Data Format for Program Sharing and Integration [chapter]

Elda Rossi, Andrew Emerson, Stefano Evangelisti
2003 Lecture Notes in Computer Science  
"namespaces" (i.e. mark-up language definitions) within the same document.  ...  However, in recent years developments in the evolution of the creation of documents destined for the WEB has led to a new formalism termed XML (eXstensible Mark-up Language) [11] .  ... 
doi:10.1007/3-540-44862-4_34 fatcat:t4yocbf64jcr3pfdku7gqow3nu

Hierarchical approaches for systems modeling in cardiac development

Russell A. Gould, Lina M. Aboulmouna, Jeffrey D. Varner, Jonathan T. Butcher
2013 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Lastly, we conclude with some important future directions for cardiac systems modeling.  ...  In this review, we discuss relevant in vivo and in vitro experimental approaches, compare different computational frameworks for systems modeling, and the latest information about systems modeling of cardiac  ...  of systems languages to facilitate data representation and interoperability, and (3) robust integrative software tools available for systems biology research.  ... 
doi:10.1002/wsbm.1217 pmid:23463736 pmcid:PMC3625506 fatcat:gclrs7tjn5flji35w3bvnpkvza
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