As a PLATFORM for SYSTEMS BIOLOGY, the open-source project LIFE123 (https://life123.science) offers a growing set of tools to wrestle with the complications of numerical solutions to complex dynamical systems, such as cycles of biochemical reactions.
ONLY 1/2 OF THE BATTLE, is to offer functions to set up and simulate webs...
CYCLES of reactions are the bread-and-butter of biological networks... Explore them with just a few lines of Python code! (optionally in a 1-click hosted environment 😀 )
Pleased to announce version Beta 21 of the COLLABORATIVE OPEN-SOURCE project LIFE123 (https://life123.science) : Computational Systems Biology, with em...
Pleased to announce version Beta 19 of the COLLABORATIVE OPEN-SOURCE project LIFE123 (https://life123.science) : Computational Systems Biology, with emphasis on Dynamical Models (quantitative reactomics with spatial awareness.)
This new version brings Adaptive Variable Time Resolution for coupled reactions (to ration c...
We know there's tons of troubleshooting information on Twitter so we've spoken with our community council and decided to start up a campaign to start archiving all sorts of experimental resolutions from across #sciencetwitter to add to our "lab-rary" using the tag #scifound. I've provided guidelines below to have an idea of...
Hello everyone
I hope you are fine and doing great. I am a fresh graduate of Microbiology (Food and Nutrition). I want to hunt a postdoc in my research domain (Microbiome, Probiotics, Genomics). As per my research and collected information, the postdoc positions are competitive and the ones with a high number of pertinent ...
From Turing, Complexity to Programming of Biological Circuit Design.
Since the turn of the XXIth century when the term “digital biology” was coined circa 2005, there have been many revisionists that have sparked an interesting discussion of how information technologies and contemporary biology have merged and adapted into ...
Hello fun(gi) friends! Did everyone see the two (!) papers published recently in Cell about the mycobiota profiles of tumors? One was from Rob Knight and Ravid Straussman's groups (https://www.cell.com/cell/pdf/S0092-8674(22)01127-8.pdf) and the other from Iliyan Iliev's group (https://www.cell.com/action/showPdf?pii=S0092-...
Our lab's GPU rig died recently :(
So I decided to dig up some old notes and try GPU basecalling of ONT long reads using Google Colab (sort of reskinned Jupyter notebook).
The ipynb notebook (github) is available via the link below.
PDF copy of the steps and quick write up is available on my lab notebook here
Note that ...
We have an old Opentrons v2 in the lab, and I was finally able to dust it off and try out its python API for a simple environmental sampling dilution prep. Quick note - the exact code on their tutorial page (also for dilution) can be a little hairy for beginners to figure out, due to their code being in pieces (indentation ...

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