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Top 7 Python Biology Projects
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deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
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OpenWorm
Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
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Project mention: The baffling intelligence of a single cell: The story of E. coli chemotaxis | news.ycombinator.com | 2024-03-21So I have three thoughts about this.
The first is cell specialization, particularly neurons. It seems like nature really came up with a universal neuron. There aren't neurons for eyesight vs thinking, etc. They've experimented with this on frogs where they've reweired the optic nerve to a different part ofd the brain and the frog seems to see just fine. They've even added an eye and the frog seems to cope and use it just fine.
The second is the OpenWorm project [1]. This is an attempt to simulate a relatively simple organism with IIRC ~280 neurons. Despite lots of effort, the simulated version just doesn't match up to the real thing. In artificial neural networks we have a stupidly simplified model of neurons that tends to get reduced to a binary signal and an activation function. Thius can do a lot but it's clearly wholly inadequate for any realistic modelling. The protein interactions in a cell are mind-bogglingly complex.
The third is the three-body problem. To summarize, we have a general solution for the grvity interactions of two bodies. Add one more and we don't. We have classes of solutions but no general solution. This is why JPL needs to use supercomputers to calculate flight plans with a relatively low number of bodies. We see a relatively simple set of interactions lead to massive complexity with protein folding. I imagine that it just won't be computationally viable to simulate even a single realistic cell given all th einteractions that go on. We're simply left to make estimations.
[1]: https://openworm.org/
I found This repo. Not the domain expert here though. I do feel like classes will help you as the state of your simulation gets complicated.
NOTE:
The open source projects on this list are ordered by number of github stars.
The number of mentions indicates repo mentiontions in the last 12 Months or
since we started tracking (Dec 2020).
Python Biology related posts
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The baffling intelligence of a single cell: The story of E. coli chemotaxis
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Money Bubble
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Mind-reading devices are revealing the brain's secrets
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Thousands of AI Authors on the Future of AI
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Discussion Thread
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Openworm – a biological simulation of a worm with 302 neurons
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Openworm – a biological simulation of a worm with 302 neurons
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www.influxdata.com | 9 May 2024
Index
What are some of the best open-source Biology projects in Python? This list will help you:
| Project | Stars | |
|---|---|---|
| 1 | deepchem | 5,140 |
| 2 | OpenWorm | 2,264 |
| 3 | ncbi-genome-download | 891 |
| 4 | chemicalx | 700 |
| 5 | seagull | 173 |
| 6 | betse | 51 |
| 7 | biology | 13 |
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