bionetgen (@bionetgen) profile picture

bionetgen

@bionetgen

Open-source rule-based modeling and simulation software for computational systems biology.

bionetgen.org
Joined October 2011
  • Tweets61
  • Following44
  • Followers87
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bionetgen retweeted
SysMod (@cosi_sysmod) profile picture
SysMod@cosi_sysmod13 Jul 2022
Congratulations 👏👏👏 to the awardees of this year’s SysMod poster prizes at #ISMB2022 🥁 ➢ 3ʳᵈ: Shaimaa Bakr @stanford_ee ➢ 2ⁿᵈ: Kang Jin @CincyInformatix ➢ 1ˢᵗ: Caroline I. Larkin @PittTweet
Prize Name: 1st Best Poster Award winners name and affiliation: Caroline I. Larkin, University of Pittsburgh Award winner title of abstract: A Mechanistic Model of Alphavirus Replication within a Mammalian Host Cell

ALT Prize Name: 1st Best Poster Award winners name and affiliation: Caroline I. Larkin, University of Pittsburgh Award winner title of abstract: A Mechanistic Model of Alphavirus Replication within a Mammalian Host Cell

Prize Name: 2nd Best Poster Award winners name and affiliation: Kang Jin, Cincinnati Children’s Hospital Medical Center Award winner title of abstract: CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data

ALT Prize Name: 2nd Best Poster Award winners name and affiliation: Kang Jin, Cincinnati Children’s Hospital Medical Center Award winner title of abstract: CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data

Prize Name: 3rd Best Poster Award winners name and affiliation: Shaimaa Bakr, Stanford University Award winner title of abstract: Identifying key multifunctional components shared by critical cancer and normal liver pathways via sparseGMM

ALT Prize Name: 3rd Best Poster Award winners name and affiliation: Shaimaa Bakr, Stanford University Award winner title of abstract: Identifying key multifunctional components shared by critical cancer and normal liver pathways via sparseGMM

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New news story from @nanoHUBnews on our #COVID19 multiscale modeling coalition. Such an amazing team to coalesce in such a short time! Please give it a look! nanohub.org/covid19sim @SMB_MathBiology @smb_imin
Image from Paul Macklin (@MathCancer)
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bionetgen retweeted
Jim Faeder (@DoctorF) profile picture
Jim Faeder@DoctorF23 Apr 2020
The 2002 Cell Modeling Virtual Workshop featuring #mcell @bionetgen @cellorganizer will take place June 22-26, 2020. Registration is available here: bit.ly/2yDDSq1. #cellbiology #modeling
Image from Jim Faeder (@DoctorF)
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bionetgen retweeted
Jim Faeder (@DoctorF) profile picture
Jim Faeder@DoctorF30 Oct 2018
New @arxiv preprint on spatial network-free simulation of biochemical systems: arxiv.org/abs/1810.12244. Congratulations to @jjtapia and @bionetgen and @mcellteam!
MCell-R: A particle-resolution network-free spatial modeling framework

MCell-R: A particle-resolution network-free spatial modeling framework

Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model...

arxiv.org
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bionetgen retweeted
Jim Faeder (@DoctorF) profile picture
Jim Faeder@DoctorF15 Feb 2018
Just created a new @bionetgen channel on YouTube: youtube.com/channel/UCn_W9_6…

BioNetGen

Instructional videos on using the BioNetGen software to build, simulate, and analyzed detailed models of biological processes and networks. RuleBender is the graphical interface for BioNetGen. For...

youtube.com
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Replying to @DoctorF
I tapped your wires @DoctorF
Remember to get your vote in for @DoctorF for SBML editor. Voting closes *tonight* at midnight PST, 9pm EST. Vote at goo.gl/forms/iW7RBjjZSvdjGsQ…
Our own @DoctorF has been nominated for @sbmlnews Editor. Vote for him at goo.gl/forms/iW7RBjjZSvdjGsQ…. Voting ends Dec 31. Vote for Jim!
bionetgen retweeted
Jim Faeder (@DoctorF) profile picture
Jim Faeder@DoctorF3 Aug 2016
Application note on BioNetGen 2.2 was just published in Bioinformatics. bioinformatics.oxfordjournal…
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The supplementary text at arxiv.org/abs/1507.03572 includes links to documentation pages and the new BNG Quick Reference Guide.
Check out a preprint of our new manuscript describing added features in BioNetGen 2.2 at arxiv.org/abs/1507.03572.
We're extremely happy to announce the release of BNG 2.2.6-stable. Try the new SBML import and model viz tools at bionetgen.org/index.php/Down….
Image from bionetgen (@bionetgen)
We're happy to announce the release of BioNetGen 2.2.6-testing, now with SBML import and model viz tools. Get it at bionetgen.org/index.php/BioN….
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The BioNetGen source code has migrated to Github. Find it at github.com/RuleWorld/bionetg….
GitHub - RuleWorld/bionetgen: Rule-based modeling framework

GitHub - RuleWorld/bionetgen: Rule-based modeling framework

Rule-based modeling framework. Contribute to RuleWorld/bionetgen development by creating an account on GitHub.

github.com
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Ever wonder what's the difference between BNGL and Kappa? See a list of differences at bionetgen.org/index.php/Kapp….
Try out our new experimental SBML-to-BNGL translator at ratomizer.appspot.com/transl…. Also look for it in the upcoming BNG 2.2.6 release.
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New paper on particle/population simulation using BioNetGen/NFsim just published in PLOS Computational Biology: ploscompbiol.org/article/inf…
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Check out the new and improved BioNetGen Actions and Arguments Guide, the most comprehensive listing compiled to date docs.google.com/a/cornell.ed…
BNG_actions_and_args

BNG_actions_and_args

docs.google.com
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If you haven't seen the RuleBender video tutorial be sure to check it out at youtube.com/watch?v=xe3PtOlJ….
Working with RuleBender 2.0

Working with RuleBender 2.0

A brief introduction to using RuleBender 2.0 (www.rulebender.org). ...

youtube.com
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