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Reproducibility in systems biology modelling

An excerpt from the recently published paper "Reproducibility in Systems Biology Modelling". https://www.biorxiv.org/content/10.1101/2020.08.07.239855v1 "The reproducibility crisis has emerged as an important concern across many fields of science including life science, since many published results failed to reproduce. Systems biology modeling, which involves mathematical representation of biological processes to study complex system behaviour, was expected to [...]

2021-02-11T23:54:15-08:00October 12th, 2020|News|
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Executable Simulation Model of the Liver

Dr. Matthias König from Institute for Theoretical Biology, Institute of Biology, Humboldt-University, Berlin, Germany has published a very interesting paper, "Executable Simulation Model of the Liver". He highlights the challenges of reproducibility in computational modeling.

2021-02-11T19:54:53-08:00October 12th, 2020|Front Page News, News|
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New IMAG Multi-scale Modeling Working Group

Inviting interested researchers to join a new Interagency Modeling and Analysis Group (IMAG) – Multi-scale Modeling Consortium (MSM) Working Group (WG) entitled MULTISCALE MODELING AND VIRAL PANDEMICS. The ongoing COVID-19 pandemic has provided a striking example of the real-world importance of mathematical and computational modeling. Though significant work has been done on epidemiology models, we [...]

2020-10-09T21:23:32-07:00October 9th, 2020|Front Page News, News|
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COMBINE 2020 To Take Place Virtually Oct. 5-9

The Combine 2020 schedule has been released for this year's online virtual meeting. Due to the current COVID-19 situation, COMBINE 2020 will be an online (virtual) meeting from October 5th (Monday) to October 9th (Friday). Organizers are providing a robust schedule that takes into account all time zones around the world, a real 24 hour [...]

2023-01-08T12:26:35-08:00September 25th, 2020|Front Page News, News|
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A compiler for biological networks on silicon chips

From the September 2020 PLoS Computational Biology the peer-reviewed article "A compiler for biological networks on silicon chips". https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008063 Author summary: We present a “silicon compiler” that is capable of translating biochemical models encoded in the SBML standard into specialized analog cytomorphic hardware and transfer function–level simulations of such hardware. We show how the compiler [...]

2021-02-14T21:00:08-08:00September 25th, 2020|Front Page News, News|
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ObjTables

https://youtu.be/OJmqtJey4zg ObjTables is a community initiative to make supplementary spreadsheets to journal articles - one of the most common methods for sharing scientific data  -  more reusable. The long-term goal is to create an ecosystem of reusable data for comparative and integrative research. ObjTables combines the ease of use of spreadsheets (XLSX file [...]

2022-07-26T19:31:46-07:00July 31st, 2020|Front Page News, News, Software, TR&D 1 - Software|
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Datanator

Danator is an integrated database of molecular data designed to facilitate integrative analysis of multiple cellular subsystems. To help investigators overcome the lack of complete data about every molecule and reaction in every organism, Datanator includes tools for building "clouds" of data that include data about chemically similar molecules and reactions in phylogenetically similar [...]

2022-07-26T19:33:39-07:00July 31st, 2020|Front Page News, News, Software, TR&D 1 - Software|
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PLOS Announces Reproducibility Modeling Pilot with CRBM

PLOS Computational Biology has announced the official launch of their Reproducibility Modelling pilot, in collaboration with the Center for Reproducible Biomedical Modelling, The aim is to support improved reproducibility of systems biology or physiology-based models that are submitted to PLOS Computational Biology. Authors with relevant models in their manuscript will be able to take part in [...]

2020-10-09T21:23:33-07:00May 5th, 2020|Front Page News, News|
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Publishers Make COVID-19-Related Research Available to Everyone

The scholarly publishing community is responding with positive support to global leaders' request for making COVID-19 related research available to everyone. The CRBM also supports this unprecedented effort to share research that can help foster positive solutions in this moment of global need. We believe sharing such research across peer-review journals and all outlets will [...]

2020-10-09T21:23:33-07:00March 16th, 2020|Front Page News, News|
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Call to Action to the Tech Community on New Machine Readable COVID-19 Dataset

Researchers across all sectors have joined in the request from the White House and have formed CORD-19, the COVID-19 Open Research Dataset. "This valuable new resource is the fruit of unselfish collaboration and now offers the opportunity to find answers to important questions about COVID-19,” said Dr. Dewey Murdick, Director of Data Science at Georgetown [...]

2020-10-09T21:23:33-07:00March 16th, 2020|Front Page News, News|
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