The Center's first biannual newsletter is now available! The newsletter describes the CRBM's recent progress in the creation of new tools, its outreach efforts to the larger community, as well as ongoing partnerships with journals for more reproducible science. It also features Lucian Smith, one of the main authors behind SED-ML and parody songwriter [...]
Dr. L. Michelle Bennett is currently serving as the Chief Collaboration Officer of LMBennett Consulting where she focuses on helping individuals, teams and organizations create the capacity for more productive partnerships and innovation in team science. Diversity in team science has emerged as a critical element in successful research outcomes, especially in computational [...]
BioSimulations is a free platform for sharing and re-using biomodels, simulations, simulation results, and visualizations of simulation results. BioSimulations supports a wide range of frameworks (e.g., logical, Flux-Balance Analysis (FBA), continuous kinetic, discrete kinetic), simulation algorithms (e.g., FBA, SSA), model formats (e.g., SBML), and tools (e.g., COBRApy, COPASI, tellurium). BioSimulations, developed by Jonathan Karr, [...]
runBioSimulations is a free tool for running a wide range of biological simulations. Through the BioSimulators registry of biosimulation tools, runBioSimulations supports a broad range of modeling frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), modeling formats (e.g., SBML, SED-ML), and simulation tools (e.g., COBRApy, COPASI). run.biosimulations.org
BioSimulators is a free registry of biosimulation tools. The registry includes tools for a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and model formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). Many of the simulation tools provide Python packages, command-line programs, and Docker images with consistent interfaces. Together, BioSimulators makes it [...]
We're glad to share information about Peer Community Journal, a community-based, diamond open-access journal that publishes only articles recommended by @PeerCommunityIn. Pear Community Journal was created and funded by the not-for-profit and non-commercial “Peer Community In” organization, publishes PCI-recommended articles in open access, without further peer review, at no cost to the authors. The evaluation of [...]
Combination Therapies for Cancer Treatments - Ideas Lab The National Cancer Institute’s Division of Cancer Biology (NCI DCB) and IBM Research are partnering to build a Community of Accelerated Discovery composed of a multi-disciplinary group of researchers focused on the discovery implications of clinical translation of biologically informed combination therapies for cancer. The over-arching goal [...]
Distribution of knowledge resources of the four element types, obtained from 1,000 BioModels.Only seven most frequently used knowledge resources were specified. Annotations were collected either by thesbotermattribute or thegetAnnotationString()method. In annotation strings, those with eitherbqbiol:isorbqbiol:isVersionOftag were selected. SBO and GO consisted more than 50% of all annotations found. In thefollowing analyses, we used the [...]
Recently published in Current Opinions in Systems Biology: Discrete, logic-based models are increasingly used to describe biological mechanisms. Initially introduced to study gene regulation, these models evolved to cover various molecular mechanisms, such as signaling, transcription factor cooperativity, and even metabolic processes. The abstract nature and amenability of discrete models to robust mathematical analyses make [...]
Code is at the heart of computational social and behavioral science. To increase code reliability and reproducibility, Nature Human Behavior is implementing formal peer review of the code behind computational models whenever they are essential to published research. They ask authors to prepare and store their code with readability, transparency, and future replicability in mind.
