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Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks [chapter]

Rajeev Alur, Calin Belta, Franjo Ivančić, Vijay Kumar, Harvey Rubin, Jonathan Schug, Oleg Sokolsky, Jonathan Webb
2002 Lecture Notes in Computer Science  
In this paper we introduce our new tool BIOSKETCHPAD that allows visual programming and modeling of biological regulatory networks.  ...  The tool allows biologists to create dynamic models of networks using a menu of icons, arrows, and pop-up menus, and translates the input model into CHARON, a modeling language for modular design of interacting  ... 
doi:10.1007/3-540-36265-7_67 fatcat:zhruok426vacdbfgb2tixgigty

Formal Methods for the Synthesis of Biomolecular Circuits (Dagstuhl Seminar 18082)

Yaakov Benenson, Neil Dalchau, Heinz Koeppl, Oded Maler, Michael Wagner
2018 Dagstuhl Reports  
This report documents the program and the outcomes of Dagstuhl Seminar 18082 "Formal Methods for the Synthesis of Biomolecular Circuits".  ...  This was often achieved with the help of two ingredients, a library of previously well-characterized parts and some computational modeling.  ...  In a future work I plan to incorporate stochastic simulations exploiting a recently developed method for efficient simulation of stochastic gene regulatory networks, based on a Partial Integro-Differential  ... 
doi:10.4230/dagrep.8.2.88 dblp:journals/dagstuhl-reports/BenensonDKM18 fatcat:gh3poeii3ndmffhuiax3bf2pfu

Python Unleashed on Systems Biology [article]

Christopher R. Myers, Ryan N. Gutenkunst, James. P. Sethna
2007 arXiv   pre-print
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics,  ...  visualization, and parallel programming.  ...  Acknowledgments We would like to thank Fergal Casey, Joshua Waterfall, and Robert Kuczenski for their help in developing and testing SloppyCell, and we would like to acknowledge the insights of Kevin Brown  ... 
arXiv:0704.3259v1 fatcat:jbm63j22evgpflsdunudngvwbe

SynBioSS-Aided Design of Synthetic Biological Constructs [chapter]

Yiannis N. Kaznessis
2011 Methods in Enzymology  
We present walkthrough examples of using SynBioSS to design, model, and simulate synthetic gene regulatory networks.  ...  SynBioSS-based modeling of biomolecular ensembles that interact away from the thermodynamic limit and not necessarily at steady state affords for a theoretical framework that is generally applicable to  ...  R01GM086865), and the University of Minnesota Biotechnology Institute.  ... 
doi:10.1016/b978-0-12-385120-8.00006-1 pmid:21601676 pmcid:PMC4820535 fatcat:3vlyw5nby5barajfamogkgmt7i

Python Unleashed on Systems Biology

Christopher R. Myers, Ryan N. Gutenkunst, James P. Sethna
2007 Computing in science & engineering (Print)  
A central component of the emerging field of systems biology is the modeling and simulation of complex biomolecular networks, which describe the dynamics of regulatory, signaling, metabolic, and developmental  ...  Naturally, tools for inferring networks from experimental data, simulating network behavior, estimating model parameters, and quantifying model uncertainties are all necessary to this endeavor.  ...  Parallel Programming in SloppyCell Because of the sloppy structure of complex biomolecular networks, it's important not to just simulate a model for one set of parameters but to do so over large families  ... 
doi:10.1109/mcse.2007.60 fatcat:otsjsldp4zatpgheb5drgil2ci

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

Lily A. Chylek, Leonard A. Harris, Chang-Shung Tung, James R. Faeder, Carlos F. Lopez, William S. Hlavacek
2013 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Rule-based modeling was developed to address the limitations of traditional approaches for modeling chemical kinetics in cell signaling systems.  ...  These systems consist of multiple interacting biomolecules (e.g., proteins), which themselves consist of multiple parts (e.g., domains, linear motifs, and sites of phosphorylation).  ...  BIOMOLECULAR INTERACTION NETWORKS: COMPLEX, DYNAMIC, AND MODULAR Complex networks of interacting biomolecules are ubiquitous in cells, and form the regulatory machinery controlling fundamental biological  ... 
doi:10.1002/wsbm.1245 pmid:24123887 pmcid:PMC3947470 fatcat:yjrs7ohxr5afdfjrgxfbcaggo4

Optimization meets systems biology

Yong Wang, Xiang-Sun Zhang, Luonan Chen
2010 BMC Systems Biology  
The OSB2009 was organized by Chinese Academy of Sciences, Shanghai University, and University of Tokyo.  ...  We also thank the Academy of Mathematics and Systems Science (AMSS), Shanghai University, and National Natural Science  ...  For example, linear programming and convex programming have been widely developed to reconstruct gene regulatory network, transcriptional regulatory network, protein interaction network, conditional specific  ... 
doi:10.1186/1752-0509-4-s2-s1 pmid:20840723 pmcid:PMC2982683 fatcat:37asyohoy5f3vpuydvcgwdozme

Modelling techniques for biomolecular networks [article]

Gerhard Mayer
2020 arXiv   pre-print
We also give a short overview about the mathematical frameworks for modelling of logical networks and list available software packages for logical modelling.  ...  First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail.  ...  Also programming libraries for accessing and writing SBML files [151] and for simulation of SBML models [152] are available.  ... 
arXiv:2003.00327v1 fatcat:ldcslhpgdrhfpavwypbx2c6qxu

Data Retrieval and Visualization for Setting Research Priorities in Biomedical Research [chapter]

Hailin Chen, Vincent VanBure
2011 Knowledge-Oriented Applications in Data Mining  
Visualization of biomolecular interactions with cognoscente Cognoscente is a querying and visualization tool for drawing biomolecular interaction networks from documented interaction knowledge, and currently  ...  Kauffman noted that the case of K~2 was appropriate for modelling gene regulatory networks, especially in an evolutionary context (Kauffman, 1969) .  ...  Data Retrieval and Visualization for Setting Research Priorities in Biomedical Research, Knowledge-Oriented Applications in Data Mining, Prof.  ... 
doi:10.5772/14077 fatcat:vatae3f6snhmlk22afdedowzbe

Topological and system-level protein interaction network (PIN) analyses to deduce molecular mechanism of curcumin

Anupam Dhasmana, Swati Uniyal, Anukriti, Vivek Kumar Kashyap, Pallavi Somvanshi, Meenu Gupta, Uma Bhardwaj, Meena Jaggi, Murali M. Yallapu, Shafiul Haque, Subhash C. Chauhan
2020 Scientific Reports  
STRING and Cytoscape programs.  ...  The precise mode of action of curcumin and its impact on system level protein networks are still not well studied.  ...  Shailendra Gupta and Prof. Olaf Wolkenhauer from University of Rostock, Germany for providing the motivation and guidance for this study. The author, Dr.  ... 
doi:10.1038/s41598-020-69011-0 pmid:32694520 fatcat:jlv336lvajctfogxbeqrrich7u

ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming

Osama Shiraz Shah, Muhammad Faizyab Ali Chaudhary, Hira Anees Awan, Fizza Fatima, Zainab Arshad, Bibi Amina, Maria Ahmed, Hadia Hameed, Muhammad Furqan, Shareef Khalid, Amir Faisal, Safee Ullah Chaudhary
2018 Scientific Reports  
Boolean modelling of biological networks is a well-established technique for abstracting dynamical biomolecular regulation in cells.  ...  Boolean modelling paradigm has been widely employed as a suitable strategy for evaluating the system level outcomes of such biomolecular networks [16] [17] [18] [19] .  ...  Discussion Computational modelling and simulation of biomolecular networks has provided significant assistance in decoding regulatory mechanisms underpinning cellular life.  ... 
doi:10.1038/s41598-018-22031-3 pmid:29476134 pmcid:PMC5824948 fatcat:iykklnnucrdkxcgrj7dzrnhan4

Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics [article]

Mahnoor Naseer Gondal, Safee Ullah Chaudhary
2021 bioRxiv   pre-print
(iii) associated simulation software for development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-driven in silico clinical oncology  ...  Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multiscale biomolecular cancer data, (ii) systems biology models developed using this data,  ...  E-Cell can be employed to model biochemical regulations and genetic processes using biomolecular regulatory networks in cells.  ... 
doi:10.1101/2021.05.17.444410 fatcat:vbfvmtb5irdapglgkmh5na73je

Taming Data

Alan Aderem, Ilya Shmulevich
2008 Cell Host and Microbe  
In summary, Queck et al. present for the first time RNAIII-independent target gene regulation of the agr locus in S. aureus.  ...  Note, however, that the direct, AgrA-mediated activation of psm genes is much stronger than RNAIII-dependent repression, and that the mechanism of the latter is as yet unknown.  ...  and simulating biomolecular networks (Bonneau et al., 2007; Ramsey et al., 2008) .  ... 
doi:10.1016/j.chom.2008.09.011 pmid:18854235 pmcid:PMC3074406 fatcat:rdridyt245gk7ab25dqs6wo3sm

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single Gene

Issa Coulibaly, Grier P. Page
2008 International Journal of Plant Genomics  
Here, we highlight selected tools and resources for gene class level ontology analysis (Section 2), gene coexpression analysis (Section 3), gene network analysis (Section 4), biological pathway analysis  ...  This prior knowledge is stored in various public and private databases and covers several aspects of gene function and biological information.  ...  GNA (Genetic Network Analyzer): http://www-helix.inrialpes.fr/article122.html GNA is a freely available software used for modeling and simulating genetic regulatory networks from gene expression data and  ... 
doi:10.1155/2008/893941 pmid:18615189 pmcid:PMC2443398 fatcat:nvqj4qu6tfhatghnzofvebf7sm

Fuzzy modeling of metabolic maps in MetNetDB

J.A. Dickerson, Pan Du, E. Wurtele, Jie Li
2004 IEEE Annual Meeting of the Fuzzy Information, 2004. Processing NAFIPS '04.  
FCModeler, a publicly available software package is designed to enable the biologist to visualize and model metabolic and regulatory network maps in plants.  ...  Metabolic networks combine metabolism and regulation. These complex networks are difficult to understand and visualize due to the diverse types of information that need to be represented.  ...  ACKNOWLEDGMENT We thank Lucas Mueller and TAIR for helpful advice and for making the AraCyc pathways publicly available. Thank you to our Metabolic Networking project collaborators: Dr.  ... 
doi:10.1109/nafips.2004.1336272 fatcat:fb5takeg4fhrvocgde6x4kbhbu
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