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BioSimulators paper just published in Nucleic Acids Research

We're glad to share information from a new paper just published in Nucleic Acids Research: BioSimulators: a central registry of simulation engines and services for recommending specific tools. https://academic.oup.com/.../doi/10.1093/nar/gkac331/6582178. “BioSimulators provide streamlined abilities to find, obtain, and use simulation tools for a broad range of modeling frameworks, formats, and algorithms, to help make systems biology, [...]

2022-05-10T20:48:12-07:00May 10th, 2022|Front Page News, News|

2022 Network Modeling Virtual Summer School & Symposium

Click to download Flyer You are invited to attend a week-long summer school on network modeling, which will conclude with a symposium of research and modeling tool talks to demonstrate how the skills you learn are being used in research settings. This summer school is designed to take beginner and intermediate level modelers [...]

2022-07-28T17:43:46-07:00May 6th, 2022|Front Page News, News|

2022 PhysiCell Workshop Hackathon Registration is Open

Applications for the 2022 PhysiCell workshop/hackathon are now OPEN! This virtual course will teach concepts of agent-based biological simulations, through our open-source PhysiCell package. Sessions include integrating intracellular models, such as Boolean networks, systems of reactions (SBML), flux balance models, and pre-trained deep neural network surrogate models. The organizers also plan to introduce a new [...]

2022-05-02T19:50:32-07:00April 26th, 2022|Front Page News, News|

Read The Center’s First Biannual Newsletter!

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 [...]

2024-07-05T20:41:54-07:00March 12th, 2022|Front Page News, News|

IMAG Webinar on Team Mindset takes place March 3rd

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 [...]

2022-07-26T16:06:09-07:00February 11th, 2022|Front Page News, News|

Peer Community Journal

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 [...]

2021-11-30T17:24:18-08:00November 29th, 2021|Front Page News, News|

Biologically Informed Models of Combination Therapies: January 24-28, 2022

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 [...]

2021-11-22T16:56:01-08:00November 22nd, 2021|Front Page News, News|

Pre-Print: SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models

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 [...]

2021-11-18T23:41:10-08:00October 11th, 2021|Front Page News, News|

Data Integration in Logic-based Models of Biological Mechanisms

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 [...]

2021-10-04T18:35:18-07:00September 27th, 2021|Front Page News, News|

Supporting Computational Reproducibility Through Code Review

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.

2021-08-25T23:22:52-07:00August 23rd, 2021|Front Page News, News|
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