@bionetgen profile picture
bionetgen @bionetgen

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

Joined October 2011
  • Tweets 61
  • Following 44
  • Followers 88
2 Photos and videos
bionetgen retweeted
SysMod@cosi_sysmod
13 Jul 2022
Congratulations šŸ‘šŸ‘šŸ‘ to the awardees of this yearā€™s SysMod poster prizes at #ISMB2022 šŸ„ āž¢ 3Ź³įµˆ: Shaimaa Bakr @stanford_ee āž¢ 2āæįµˆ: Kang Jin @CincyInformatix āž¢ 1Ė¢įµ—: 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 Childrenā€™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 Childrenā€™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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bionetgen retweeted
Paul Macklin@MathCancer
24 Apr 2020
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
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bionetgen retweeted
Jim Faeder@DoctorF
23 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
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bionetgen retweeted
Jim Faeder@DoctorF
30 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

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
15 Feb 2018
Just created a new @bionetgen channel on YouTube: youtube.com/channel/UCn_W9_6ā€¦

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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bionetgen@bionetgen
9 Mar 2017
Replying to @DoctorF
I tapped your wires @DoctorF
bionetgen@bionetgen
31 Dec 2016
Remember to get your vote in for @DoctorF for SBML editor. Voting closes *tonight* at midnight PST, 9pm EST. Vote at goo.gl/forms/iW7RBjjZSvdjGsQā€¦
bionetgen@bionetgen
18 Dec 2016
Our own @DoctorF has been nominated for @sbmlnews Editor. Vote for him at goo.gl/forms/iW7RBjjZSvdjGsQā€¦. Voting ends Dec 31. Vote for Jim!
bionetgen retweeted
Jim Faeder@DoctorF
3 Aug 2016
Application note on BioNetGen 2.2 was just published in Bioinformatics. bioinformatics.oxfordjournalā€¦

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bionetgen@bionetgen
14 Jul 2015
The supplementary text at arxiv.org/abs/1507.03572 includes links to documentation pages and the new BNG Quick Reference Guide.
bionetgen@bionetgen
14 Jul 2015
Check out a preprint of our new manuscript describing added features in BioNetGen 2.2 at arxiv.org/abs/1507.03572.
bionetgen@bionetgen
14 Jul 2015
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/Downā€¦.
bionetgen@bionetgen
8 May 2015
bionetgen@bionetgen
7 Apr 2015
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/BioNā€¦.
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bionetgen@bionetgen
7 Apr 2015
The BioNetGen source code has migrated to Github. Find it at github.com/RuleWorld/bionetgā€¦.

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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bionetgen@bionetgen
26 Aug 2014
Ever wonder what's the difference between BNGL and Kappa? See a list of differences at bionetgen.org/index.php/Kappā€¦.
bionetgen@bionetgen
17 Jul 2014
Try out our new experimental SBML-to-BNGL translator at ratomizer.appspot.com/translā€¦. Also look for it in the upcoming BNG 2.2.6 release.
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bionetgen@bionetgen
11 Apr 2014
New paper on particle/population simulation using BioNetGen/NFsim just published in PLOS Computational Biology: ploscompbiol.org/article/infā€¦
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bionetgen@bionetgen
21 Jun 2013
Check out the new and improved BioNetGen Actions and Arguments Guide, the most comprehensive listing compiled to date docs.google.com/a/cornell.edā€¦

BNG_actions_and_args

docs.google.com
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bionetgen@bionetgen
13 Jun 2013
If you haven't seen the RuleBender video tutorial be sure to check it out at youtube.com/watch?v=xe3PtOlJā€¦.

Working with RuleBender 2.0

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

youtube.com
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