u-track
Multiple-particle tracking designed to (1) track dense particle fields, (2) close gaps in particle trajectories resulting from detection failure, and (3) capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events (by DanuserLab)
Biopython
Official git repository for Biopython (originally converted from CVS) (by biopython)
| u-track | Biopython | |
|---|---|---|
| 1 | 31 | |
| 43 | 4,194 | |
| - | 1.8% | |
| 3.7 | 9.6 | |
| 13 days ago | 7 days ago | |
| MATLAB | Python | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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.
u-track
Posts with mentions or reviews of u-track.
We have used some of these posts to build our list of alternatives
and similar projects.
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Recording the movement of beetles in a video
The general task you should look up is particle tracking. There are a number of packages out there that do this. Here's one that I've used https://github.com/DanuserLab/u-track
Biopython
Posts with mentions or reviews of Biopython.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-12.
- 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?
When comparing u-track and Biopython you can also consider the following projects:
Kassiopeia - Simulation of electric and magnetic fields and particle tracking
RDKit - The official sources for the RDKit library
bio-sequence
biotite - A comprehensive library for computational molecular biology
cellpose - a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
bioconda-recipes - Conda recipes for the bioconda channel.
pipes-ordered-zip
Numba - NumPy aware dynamic Python compiler using LLVM
heatitup
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
PyDy - Multibody dynamics tool kit.
weblogo - WebLogo 3: Sequence Logos redrawn