biotite
A comprehensive library for computational molecular biology (by biotite-dev)
3DFI
The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space. (by PombertLab)
| biotite | 3DFI | |
|---|---|---|
| 2 | 2 | |
| 557 | 16 | |
| 1.3% | - | |
| 9.0 | 2.8 | |
| 2 days ago | about 2 months ago | |
| Python | Perl | |
| BSD 3-clause "New" or "Revised" License | MIT 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.
biotite
Posts with mentions or reviews of biotite.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-04-28.
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Journey into bioinformatics
For bioinformatics in Python, the BioPython library (https://biopython.org/) is commonly used. An alternative to this package is Biotite (https://www.biotite-python.org/), a package I am maintaining.
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What bioinformatics software can i give my contribute?
If you like programming in Python, you could contribute to Biotite (https://www.biotite-python.org/). You may have a look at the open issues at https://github.com/biotite-dev/biotite/issues or the projects at https://github.com/biotite-dev/biotite/projects. If you are interested in a project, you can get in contact via Mail or our Discord channel (https://discord.gg/cUjDguF).
3DFI
Posts with mentions or reviews of 3DFI.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-01-03.
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I did my bachelor's and Masters in Biomedical Sciences. I got admitted into a PhD project in protein engineering where the first year I will be doing protein structure modeling and prediction (possibly using RosettaFold). I have 0 experience. Where should I start?
Not to self promote, but my lab and I developed a pipeline to help with the 3D structure prediction process, and works with a number of these tools. You can find it at https://github.com/PombertLab/3DFI.
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I managed to get Googles deepmind Alphafold running. I modeled segment of DNA from M.Genitalia and also compared it to the much less accurate method of homology modeling that was used in days past.
The pipeline: https://github.com/PombertLab/3DFI
What are some alternatives?
When comparing biotite and 3DFI you can also consider the following projects:
Biopython - Official git repository for Biopython (originally converted from CVS)
ColabFold - Making Protein folding accessible to all!
seqtk - Toolkit for processing sequences in FASTA/Q formats
Clairvoyante - Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
CNApy - An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!