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BioSimulators: a central registry of simulation engines and services for recommending specific tools [article]

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks (+59 others)
2022 arXiv   pre-print
To help investigators find and use simulation tools, we developed BioSimulators (, a central registry of the capabilities of simulation tools and consistent Python, command-line  ...  To help modelers find tools for particular projects, we have also used the registry to develop recommendation services.  ...  To help investigators find appropriate tools, we have also used this registry to develop services for recommending specific algorithms and tools for particular systems and scales.  ... 
arXiv:2203.06732v1 fatcat:z3hje6q3lrapph7kigfwtqk3ai

Emerging Patient-Driven Health Care Models: An Examination of Health Social Networks, Consumer Personalized Medicine and Quantified Self-Tracking

Melanie Swan
2009 International Journal of Environmental Research and Public Health  
A new class of patient-driven health care services is emerging to supplement and extend traditional health care delivery models and empower patient self-care.  ...  The potential exists to both improve traditional health care systems and expand the concept of health care though new services.  ...  A second class of patient-focused health social networks is cause-specific, offering primarily the basic emotional support and information sharing service.  ... 
doi:10.3390/ijerph6020492 pmid:19440396 pmcid:PMC2672358 fatcat:4ug7hubvtfcmtl5phyr7fcvofa

Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility

Jonathan Karr, Rahuman S. Malik-Sheriff, James Osborne, Gilberto Gonzalez-Parra, Eric Forgoston, Ruth Bowness, Yaling Liu, Robin Thompson, Winston Garira, Jacob Barhak, John Rice, Marcella Torres (+6 others)
2022 Frontiers in Systems Biology  
During the COVID-19 pandemic, mathematical modeling of disease transmission has become a cornerstone of key state decisions.  ...  This document summarizes these discussions, presents difficulties, and mentions existing efforts towards future solutions that will allow future model utility and integration.  ...  The group thanks him for his efforts. Additional thanks to Tomas Helikar who participated in discussions. Thanks to the MSM viral pandemic working group.  ... 
doi:10.3389/fsysb.2022.822606 fatcat:7orhjcczd5bljhghmzgxb6rfh4

Bioexcel Deliverable 2.3 - User Feedback And Future Roadmap

Adam Hospital, Josep Lluís Gelpí, Jose A. Dianes, Pau Andrio, Darren J. White, Emiliano Ippoliti, Adrien Melquiond, Vytautas Gapsys
2017 Zenodo  
User experience will be the main focus for the cloud portal that is expected to offer a growing number of tools and deployable VMs in the coming months.  ...  Future roadmaps for the BioExcel Cloud Portal and for the workflows and computational infrastructures are presented, which showcase the work planned for the rest of the project.  ...  ELIXIR tools registries and EDAM ontology In the first period of the BioExcel project, all of the tools collected in the catalogue of tools presented in D2.1 were registered in ELIXIR Tools & Data Service  ... 
doi:10.5281/zenodo.1060946 fatcat:i4exxpnhpbaqnglrltelddzw6a

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

Daniel S. Katz, Sou-Cheng T. Choi, Kyle E. Niemeyer, James Hetherington, Frank Löffler, Dan Gunter, Ray Idaszak, Steven R. Brandt, Mark A. Miller, Sandra Gessing, Nick D. Jones, Nic Weber (+9 others)
2016 Journal of Open Research Software  
The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to  ...  For each group, we include a point of contact and a landing page that can be used by those who want to join that group's future activities.  ...  Any opinion, finding, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ... 
doi:10.5334/jors.118 fatcat:xhycdlnixrapnj4qwayutzefba

eResearch2020 The Role of e-Infrastructures in the Creation of Global Virtual Research Communities Final Report eResearch2020 Final Report Disclaimer The study team

Tobias Hüsing, Simon Robinson, Fachhochschule Nordwestschweiz, Franz Barjak, Oliver Bendel, Gordon Wiegand, Kathryn Eccles, Eric Meyer, Ralph Schroeder, Zack Kertcher, Erica Coslor
2010 unpublished
supply of backbone connectivity, single-or multi-purpose grids, supercomputer infrastructure, data grids and repositories, tools for visualization, simulation, data management, storage, analysis and collection  ...  , tools for support in relation to methods or analysis, as well as remote access to research instruments and very large research facilities.  ...  Outside of the US and Europe smaller, but by no means negligible efforts are being undertaken for instance in China, Japan, Australia, New Zealand, and Canada.  ... 

Improving Reproducibility and Reuse of Modelling Results in the Life Sciences

Martin Scharm
Research results are complex and include a variety of heterogeneous data.  ...  Second, I present approaches to obtain shareable and reproducible research results. Altogether, my methods and tools foster exchange and reuse of modelling results.  ...  However, for interoperability I recommend an XML serialisation of the Resource Description Framework (RDF, [LS99; RDF14]) in the initial specification, which is stored in a file called metadata.rdf and  ... 
doi:10.18453/rosdok_id00002315 fatcat:xz3ncilw4nhnvgmgond2lpqn3y