scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources. (by scikit-bio)
PrimesResult
The results of the Dave Plummer's Primes Drag Race (by luizsol)
| scikit-bio | PrimesResult | |
|---|---|---|
| 2 | 6 | |
| 833 | 28 | |
| 0.8% | - | |
| 8.8 | 0.0 | |
| 7 days ago | almost 2 years ago | |
| Python | ||
| BSD 3-clause "New" or "Revised" License | - |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
scikit-bio
Posts with mentions or reviews of scikit-bio.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-09-23.
- What are some of the bioinformatic projects I could do on python as a beginner?
-
Why I Use Nim instead of Python for Data Processing
You make a fair point that using optimized numerical libraries instead of string methods will be ridiculously fast because they're compiled anyway. For example, scikit-bio does just this for their reverse complement operation [1]. However, they use an 8 bit representation since they need to be able to represent the extended IUPAC notation for ambiguous bases, which includes things like the character N for "aNy" nucleotide [2]. One could get creative with a 4 bit encoding and still end up saving space (assuming you don't care about the distinction between upper versus lowercase characters in your sequence [2]). Or, if you know in advance your sequence is unambiguous (unlikely in DNA sequencing-derived data) you could use the 2 bit encoding. When dealing with short nucleotide sequences, another approach is to encode the sequence as an integer. I would love to see a library—Python, Nim, or otherwise—that made using the most efficient encoding for a sequence transparent to the developer.
[1] https://github.com/biocore/scikit-bio/blob/b470a55a8dfd054ae...
[2] https://en.wikipedia.org/wiki/Nucleic_acid_notation
[3]
PrimesResult
Posts with mentions or reviews of PrimesResult.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-01-15.
-
The Sad True
https://github.com/luizsol/PrimesResult People give golang crap for being slower than C. Python is 8.6% of the speed of golang.
-
.NET vs Go vs Node
Possible place to start: https://github.com/luizsol/PrimesResult
-
Best Lisp dialect?
The Performance of CL is much better than Scheme. One example is here https://github.com/luizsol/PrimesResult. Lisp is 11, Chez scheme implementation is 40
-
Why I Use Nim instead of Python for Data Processing
The thing with Python is it's usually pretty easy to optimise quite impressively.
E.g. random example:
Sprinkle some cdef's in your python and suddenly you're faster than c++
https://github.com/luizsol/PrimesResult
https://github.com/PlummersSoftwareLLC/Primes/blob/drag-race...
-
Common Lisp still beats Java, Rust, Julia, Dart in 2021 on benchmarks based on phone number encoding from the famous paper "Lisp as an alternative to Java" from 21 years ago
Sure, but never discount compile time code that can work wonders for your performance (which Rust doesn't really fully have) - https://github.com/luizsol/PrimesResult. Zig is so high up in the results precisely (I'd wager) because of compile time semantics.
- The results of the Dave Plummer's Programming Languages Drag Race.
What are some alternatives?
When comparing scikit-bio and PrimesResult you can also consider the following projects:
nimpylib - Some python standard library functions ported to Nim
sb-simd - A convenient SIMD interface for SBCL.
nimtorch - PyTorch - Python + Nim
Primes - Prime Number Projects in C#/C++/Python
viroiddb - A curated database of all available viroid-like RNA sequences
RecursiveFactorization.jl
biofast - Benchmarking programming languages/implementations for common tasks in Bioinformatics
libpython-clj - Python bindings for Clojure
sb-simd - A convenient SIMD interface for SBCL.
scikit-bio vs nimpylib
PrimesResult vs sb-simd
scikit-bio vs nimtorch
PrimesResult vs Primes
scikit-bio vs viroiddb
PrimesResult vs RecursiveFactorization.jl
scikit-bio vs biofast
PrimesResult vs nimtorch
scikit-bio vs RecursiveFactorization.jl
PrimesResult vs libpython-clj
scikit-bio vs Primes
PrimesResult vs sb-simd