biotite
CNApy
| biotite | CNApy | |
|---|---|---|
| 2 | 1 | |
| 557 | 41 | |
| 1.3% | - | |
| 9.0 | 6.5 | |
| 2 days ago | 22 days ago | |
| Python | Python | |
| BSD 3-clause "New" or "Revised" License | Apache License 2.0 |
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
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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).
CNApy
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CNApy – An integrated environment for metabolic network analysis
CNApy is a desktop application for metabolic network analysis. It is a relative young project that aims to provide an integrated environment inspired by tools like CellNetAnalyser (CNA) and DD-DeCaf. In fact it started as a modernization of the CNA UI that allows to use functions from the CNA toolbox. CNApy is implemented in Python and uses Qt for the UI. Under the hood it uses COBRApy to implement the core model.
The project has matured a lot and in the future we would love this project to be sustained on the basis of a broader community.
Anyone that wants to get involved in the project, please let us know! We are looking for all kinds of contributions.
Links:
- [Project page on GitHub](https://github.com/cnapy-org/CNApy)
- [CONTRIBUTING.md](https://github.com/cnapy-org/CNApy/blob/master/CONTRIBUTING....)
What are some alternatives?
Biopython - Official git repository for Biopython (originally converted from CVS)
dash-cytoscape - Interactive network visualization in Python and Dash, powered by Cytoscape.js
3DFI - The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
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
casq - CaSQ: Celldesigner as Sbml-Qual [https://gitlab.inria.fr/soliman/casq/ mirror]