BacArena

R package for simulation and analysis of microbial communities

[BacArena @_BacArena]

The official BacArena paper: Individual-based metabolic modeling of heterogeneous microbes in complex communities https://t.co/n2iBVzhCYM

[johannes zimmermann @_jozimmermann]

I'm quite happy to share the news that the gapseq paper just got published: https://t.co/fdNYRCsGAy. It's about a novel method for metabolic pathway prediction and metabolic model reconstruction.

[BacArena @_BacArena]

@marouenbg challenging indeed... In the past, the 'gene-for-x' search was often flawed. At least, it is 'polygenic' nowadays 😆 But gwas is only correlating gene loci. Where is the environment in this? The old 'heretic' Lewontin on this 'naive current prejudice': https://t.co/AIxZoor8nK

[BacArena @_BacArena]

new feature to import matlab models into BacArena
https://t.co/yksbI3AC2k

[Systems Biologist @SystemBiology]

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
https://t.co/rz0VopTYRM

[Joseph Moran @MoranLabChem]

Our latest in @nature: Fe2+ promotes a one-pot reaction network that resembles the Krebs cycle and amino acid synthesis, starting from just pyruvate and glyoxylate Congrats @KamilaMuchowska and @ajaanubahu! @unistra @CNRS @INC_CNRS https://t.co/4RxAzpfVFu

[Babak Momeni @bmomeni]

Our paper on coexistence within microbial communities is now published in @NatureComms. We use empirically inspired assumptions in our model to simulate how interactions take place through the chemical environment. Collective work of great undergrad and grad students in the lab.

[BacArena @_BacArena]

New tutorial on how to use BacArena to switch from an anaerobic to aerobic environment after some time: https://t.co/wsWSLkQ8Aj

[BacArena @_BacArena]

On the impact of the tumor environment: BacArena simulations helped to identify metabolic phenotypes in #PancreaticCancer depending on the #liver micromilieu https://t.co/J7YrL50dXg #inflammation #cancer #cancerecology #systemsbiology

[Alma Dal Co @Alma_DalCo]

At which spatial scale do cells interact inside microbial communities?
Here how we measure it!

From Martin Ackermann's talk #SPP1617conference. More in our preprint: https://t.co/HXBeKCU1tm from @MicSysEcoLab and former member @simon_vanvliet.

[Camilo Barbosa @cbarbosap88]

Latest preprint from the Schulenburg group together with @RoderichRoemhi1! Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa https://t.co/CZozomLzwQ

[Quantitative Biology (Neurons and Cognition) @BioPapers]

The Chaos Decision Tree Algorithm: A Fully Automated Tool for the Experimental Study of Chaotic Dynamics. https://t.co/GHfwpe86xC

[BacArena @_BacArena]

In a new study, we used BacArena to explain the context-dependency of metabolic interactions by an extracellular invertase in the #microbiome of C. elegans https://t.co/FExklwtCn4 #microbialecology #crossfeeding

[Host-microbe papers @host_microbe]

Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease https://t.co/iCPEqDkLk2

[BacArena @_BacArena]

very interesting paper by @jeffchengore about rules shaping microbial interactions #microbialecology #populationdynamics https://t.co/pRO7v3ppE3

[Quantitative Biology (Neurons and Cognition) @BioPapers]

Essential guidelines for computational method benchmarking. https://t.co/Yplz9GfjG1

[Akos T. Kovacs @EvolvedBiofilm]

Simple organizing principles in microbial communities

Curr Opin Microbiol by @jeffchengore

https://t.co/eEOl93o4pR

[BacArena @_BacArena]

new #BacArena tutorial on microbial crossfeeding in a wester diet gut community
https://t.co/8IprUmdmik
#systemsbiology #microbialecology #crossfeeding

[(((Dan Graur))) ダン דן גראור 🇮🇱🇺🇸🇺🇦✌️�� @DanGraur]

Long before there was ⁦@23andMe⁩ there was Luigi Cavalli-Sforza https://t.co/SJtA4qmxts