osdc-2023-01-public
Biopython
osdc-2023-01-public | Biopython | |
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7 | 31 | |
2 | 4,171 | |
- | 1.2% | |
4.7 | 9.6 | |
about 1 year ago | 5 days ago | |
Python | ||
GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
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osdc-2023-01-public
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Journey Journal
Welcome back dear reader. Let me remind you that I am Silent-Mobius, also known as Alex M. Schapelle, your faithful narrator. As you might remember, I have applied to short journey of sort, whose main orchestrator is @szabgab, under a code name of #OSCD. Despite the fact the journey is still under its first steps, I've been willing to remember it with any possible tool I can have under my utility belt. That is why I've decided, to use #git. Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
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osdc-2023-assignment4
As part of the fourth assignment of the OSDC we had to practice GitHub and create a new project.
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Creating github pages is easy!
I am taking Open Source Development Course given by Gabor Szabo in order to gain a better understanding of this field. In the second session we learned about github pages which is an easy way for building a website. Anyone can do it, even if they don't have programming experience. All you need is a github account!
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Joining the Open Source Development Course
Through a shared colleague, I recently got to know Gabor Szabo. Luckily, he invited me to join his Open Source Development Course.
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Open source developement cource
And he also created a practice website which we can update
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Assignment 2
I have done my second assignment for the Open Source Development course (OSDC). The assignment was to practice markdowns in GitHub.
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.
What are some alternatives?
adeptus-ridiculus
RDKit - The official sources for the RDKit library
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
biotite - A comprehensive library for computational molecular biology
git - A fork of Git containing Windows-specific patches.
bioconda-recipes - Conda recipes for the bioconda channel.
pages-gem - A simple Ruby Gem to bootstrap dependencies for setting up and maintaining a local Jekyll environment in sync with GitHub Pages
Numba - NumPy aware dynamic Python compiler using LLVM
PyDy - Multibody dynamics tool kit.
weblogo - WebLogo 3: Sequence Logos redrawn
statsmodels - Statsmodels: statistical modeling and econometrics in Python