Biopython
Numba
Biopython | Numba | |
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31 | 124 | |
4,171 | 9,452 | |
1.1% | 1.1% | |
9.6 | 9.9 | |
1 day ago | 6 days ago | |
Python | Python | |
GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" License |
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Biopython
- Invitación a proyecto - Biopython en Español
- Biopython – Python Tools for Computational Molecular Biology
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comparing the similarity between a set of protein sequences
Usearch will do all-against-all comparisons, cluster sequences, and produce alignments for each cluster. You can set the clustering threshold (proportion of residues identical). The alignments are in fasta format, which is pretty standard. If all you want is basic similarity it might be easiest to just write something that calculates normalized Hamming distances (typically called p-distances in the molecular evolution literature) between pairs of sequences. I suspect the biopython fasta reader (you can install biopython from https://biopython.org/) will be good enough.
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u/Responsible-Gas3852 comments on "Why is Cancer so Hard to Cure?"
Yes, the computing tool for biological computation.
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My boss is considering letting me take a programming course if I have some good reasons why.
Beside that their core lectures to non-computer scientists are public (survey), workshops by software carpentry move around the globe. Maybe your intent to seed hands-on knowledge is in similar tune before heading for biopython, bioperl, bioawk. It doesn't hurt to tap into resources initially written for non-labrats either, e.g. about regular expressions by programming historian.
- Can you run ScanProsite locally?
- How to iterate over the whole GRCh38 genome with python?
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Help they’re turning me into a programmer
Well, what language do you want to learn? What is your background so far? Assuming it is more on the side of biology, software carpentry's Python may eventually lead to biopython? Though there equally is a chance for AWK (Hack the planet's text! and bioawk...
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Biology related exercices and "challenges" to train by myself
I think you mind find something of a community around BioPython, which might be helpful. Just looking at the capabilities will probably be instructive as well.
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Joining the Open Source Development Course
Python is the main programming language I use nowadays. In particular numpy and pandas are of course extremely useful. I also use biopython package - a collection of software tools for biological computation written in Python by an international group of researchers and developers.
Numba
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Mojo🔥: Head -to-Head with Python and Numba
Around the same time, I discovered Numba and was fascinated by how easily it could bring huge performance improvements to Python code.
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Is anyone using PyPy for real work?
Simulations are, at least in my experience, numba’s [0] wheelhouse.
[0]: https://numba.pydata.org/
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Any data folks coding C++ and Java? If so, why did you leave Python?
That's very cool. Numba introduces just-in-time compilation to Python via decorators and its sole reason for being is to turn everything it can into abstract syntax trees.
- Using Matplotlib with Numba to accelerate code
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Python Algotrading with Machine Learning
A super-fast backtesting engine built in NumPy and accelerated with Numba.
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PYTHON vs OCTAVE for Matlab alternative
Regarding speed, I don't agree this is a good argument against Python. For example, it seems no one here has yet mentioned numba, a Python JIT compiler. With a simple decorator you can compile a function to machine code with speeds on par with C. Numba also allows you to easily write cuda kernels for GPU computation. I've never had to drop down to writing C or C++ to write fast and performant Python code that does computationally demanding tasks thanks to numba.
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Codon: Python Compiler
Just for reference,
* Nuitka[0] "is a Python compiler written in Python. It's fully compatible with Python 2.6, 2.7, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, and 3.11."
* Pypy[1] "is a replacement for CPython" with builtin optimizations such as on the fly JIT compiles.
* Cython[2] "is an optimising static compiler for both the Python programming language and the extended Cython programming language... makes writing C extensions for Python as easy as Python itself."
* Numba[3] "is an open source JIT compiler that translates a subset of Python and NumPy code into fast machine code."
* Pyston[4] "is a performance-optimizing JIT for Python, and is drop-in compatible with ... CPython 3.8.12"
[0] https://github.com/Nuitka/Nuitka
[1] https://www.pypy.org/
[2] https://cython.org/
[3] https://numba.pydata.org/
[4] https://github.com/pyston/pyston
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This new programming language has the potential to make python (the dominant language for AI) run 35,000X faster.
For the benefit of future readers: https://numba.pydata.org/
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Two-tier programming language
Taichi (similar to numba) is a python library that allows you to write high speed code within python. So your program consists of slow python that gets interpreted regularly, and fast python (fully type annotated and restricted to a subset of the language) that gets parallellized and jitted for CPU or GPU. And you can mix the two within the same source file.
- Numba Supports Python 3.11
What are some alternatives?
RDKit - The official sources for the RDKit library
NetworkX - Network Analysis in Python
biotite - A comprehensive library for computational molecular biology
jax - Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
bioconda-recipes - Conda recipes for the bioconda channel.
Dask - Parallel computing with task scheduling
Pandas - Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
cupy - NumPy & SciPy for GPU
PyDy - Multibody dynamics tool kit.
Pyjion - Pyjion - A JIT for Python based upon CoreCLR
weblogo - WebLogo 3: Sequence Logos redrawn
SymPy - A computer algebra system written in pure Python