New, Chemical View of Ecosystems
https://www.quantamagazine.org/a-new-chemical-view-of-ecosystems-20250305
Rare and powerful compounds, known as keystone molecules, can build a web of invisible interactions among species.
3/8 
For the first time (or do update us), we've modelled dynamic, plant gene circuits with absolute units for both RNA and protein copies per cell.
You can compare our mathematical models directly to your biochemical data. Over time, both approaches should benefit! #SystemsBiology
4/8 
Those absolute units mean that we can predict the DNA-binding dissociation constants (Kd) of our clock transcription factors in vivo, for example.
After some tricky calibration, we estimated comparable Kd values in vitro from our earlier data and the literature, extending the method to any promoter sequence (more on this later).
So, did they match?
Hi all #Python enthusiasts!
I'm looking for someone who has time now to conduct a review of a piece of software for Journal of Open Source Software (JOSS). Details are here:
https://github.com/openjournals/joss-reviews/issues/7491
The review process is quite simple - you get a checklist and you run some tests. It's all open, on GitHub.
This account is for the bioinformatics team at FHML, Maastricht University. You can find some of them on Mastodon:
- Susan Coort: @susancoort
- Marvin Martens: @Marvin
- Egon Willighagen: @egonw
But also some of the projects we have been involved in:
- BridgeDb: @bridgedb
- WikiPathways: @wikipathways
- ELIXIR Europe: @elixir_europe
Molecular causality in the advent of foundation models https://www.embopress.org/doi/full/10.1038/s44320-024-00041-w #artificialintelligence #bioinformatics #systemsbiology #causality
open PhD vacancy with Dr Friederike Ehrhart:
"Rare Epilepsies disease networks"
"Within this collaborative project, we are looking for a PhD candidate with either a background in bioinformatics, data sciences, systems biology with a demonstratable experience in biomedical or life sciences, or a background in life sciences/biomedical sciences with a demonstratable experience in data analysis, #bioinformatics or #SystemsBiology "
More information: https://vacancies.maastrichtuniversity.nl/job/Maastricht-PhD-Candidate-Rare-Epilepsies-disease-networks/799514102/
looking forward to #BioSB2024 next week
BioSB is the Dutch national meeting around #bioinformatics and #systemsBiology
Leute. Ich hab sooooooooooo was geiles entdeckt.
Kennt ihr schon https://www.olivetin.app/ ?
Damit kann man #Shell Tools eine #WebGUI verpassen. 
Ok, das würde sich auch mit #Shiny von #rstats umsetzen lassen. Aber dennoch.
Für unsere Beschäftigten, die eher Windows gewohnt sind kann ich so Shell Tools leichter zugänglich machen. Das ist so toll.
Für #Schulen sicher auch einen Blick wert. :3
#FediLZ #Science #bioinformatics #systemsbiology
#olivetin #bash #Linux
My colleague Andreas Dräger at the University of Tübingen in Germany has a postdoc opening in his group. They do computational systems biology. Deadline is Dec. 31, 2023. Excellent German language skills are a prerequisite. For more information, please refer to the official job posting: https://uni-tuebingen.de/de/171129
Mark your calendars for the next HARMONY (Hackathon on Resources for Modeling in Biology), to be held at the University College London during April 8–11, 2024. A placeholder page is up now: https://co.mbine.org/events/
#SystemsBiology #ComputationalBiology #Biology #Bioinformatics #SyntheticBiology
The UCI Center for Complex Biological Systems is hosting a short course on Systems Biology foundations in February–March, 2024.
https://ccbs.uci.edu/education/fasb-sc/
#SystemsBiology #ComputatonalBiology #CellBiology #Bioinformatics #Biology
COPASI 4.41 (Build 283) has been released.
https://copasi.org/News/2023/11/21/Release/
This new version resolves a number of bugs and improves the GUI startup time. Downloads available at https://copasi.org/Download/
Hello! #introductions
I'm a #ComputationalBiologist (1st #biochemist, then #ComputerScientist). I'm faculty at UConn Health. I'm interested in many scientific areas such as #SystemsBiology, #ComputationalModeling and #Simulation, #IronMetabolism, #NonlinearDynamics, #SoftwareDevelopment. I'm one of the authors of the @copasi simulation software and its predecessor Gepasi (thus my handle). I care about #OpenAccess & #OpenSource. I am also interested in #photography, #Linux, and #EVs.
Fungi: Web of Life Trailer (IMAX movie, narrated by Björk, presented by Merlin Sheldrake)
https://youtu.be/YCf7YywIBZ8?feature=shared
"The film is about the ways that fungi have shaped life on Earth for over a billion years, and how we might partner with them to adapt to the radical change of our times.
It's narrated by Björk, who speaks the story with inimitable magic and sensitivity.
It features astonishing fungal time lapse photography from some of the best fungal photographers working today, including Steve Axford (@planet_fungi on the birdsite), Patrick Hickey, and Wim van Egmond. Much of this footage depicts aspects of fungal life that have never been captured in such high spatial and temporal resolution before.
The film will be trickling into IMAX cinemas across Europe and North America over the latter part of 2023 and into 2024, and may already be playing at a theatre near you."
Looking for paper leads on: a genetic network w/ attractor states linked to brains
I'm fond of the approaches in this paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2571012/
The gist here is to model a genetic network as a dynamical system with two attractor states (in this case, it's leukemia and the states are apoptosis on-versus-off).
I'm looking for leads to papers that apply this type of approach to model genetic networks (not neural circuits) that have something a bit more to do with the brain; ideally not cancer.
(This is not my field). Huntington's? Fragile X? Anything neuron related?
Thanks in advance!
(3/3)
#Physiology: https://biologists.social/@biorxiv_physio
#PlantBiology: https://biologists.social/@biorxiv_plants
#ScientificCommunication (#SciComm) and #Education: https://biologists.social/@biorxiv_scicomm
#SyntheticBiology: https://biologists.social/@biorxiv_synthbio
Ok. Gerade fällt mir doch was ein, über was ich sprechen könnte. 
Aber mit dem Wissen...nunja. Praktisch könnt ihr das im Alltag nicht anwenden oder so. 
Hätte jemensch Interesse an Biologischen Netzwerken? Also so die Basics und Konzepte?
Ich finde ja den Aufruf nett, mehr Talks zu halten und so.
Aber ich trau mich nicht, nicht weil ich nicht reden könnte oder so, sondern weil ich mich für nicht kompetent genug halte um ein Thema würdig zu vertreten. That's it. 
Selbst Themen aus meinem beruflichen Bereich. Ich hab da leider hohe Ansprüche an mich selbst. Sry. 
Ich mach zwar viel mit Omics und #systemsbiology, aber Talks wird es dazu keine von mir geben. Sry. 
Ben West - 
