Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
Keywords
Repository
Glycan Analysis and Glycoinformatics Library for Python
Basic Info
Statistics
- Stars: 36
- Watchers: 9
- Forks: 14
- Open Issues: 9
- Releases: 4
Topics
Metadata Files
README.md
glypy Glycan Analysis and Glycoinformatics Library for Python
Glycobiology is the study of the biological functions, properties, and structures of carbohydrate biomolecules, also called glycans. These large, tree-like molecules are complex, having a wide variety of building blocks as well as modifications and substitutions on those building blocks.
[glypy]{role="mod"} is a Python library providing code for reading, writing, and manipulating glycan structures, glycan compositions, monosaccharides, and their substituents. It also includes interfaces to popular glycan structure databases, GlyTouCan and UnicarbKB using [SPARQL]{role="term"} queries and an RDF-object mapper.
Example Use Cases
- Traverse structures using either canonical or residue-level rule ordering.
- Operate on monosaccharide and substituents as nodes and bonds as edges.
- Add, remove, and modify these structures to alter glycan properties.
- Identify substructures and motifs, classifying glycans.
- Evaluate structural similarities with one of several ordering and comparator methods.
- Plot tree structures with MatPlotLib, rendering using a configurable symbol nomenclature, such as SNFG, CFG, or IUPAC. Layout using vector graphics for lossless scaling.
- Calculate the mass of a native or derivatized glycan.
- Generate glycosidic and cross ring cleavage fragments for a collection of glycan structures for performing MS/MS database search.
Perform substructure similarity searches with exact ordering or topological comparison and exact or fuzzy per-residue matching to classify a structure as an N-linked glycan.
Annotate MS spectra with glycan structures, labeling which peaks
: matched a database entry.
Download all N-Glycans from GlyTouCan
Find all glycans in a list which contain a particular subtree, or
: find common subtrees in a database of glycans, performing treelet enrichment analysis.
- Synthesize all possible glycans using a set of enzymes starting from
: a set of seed structures.
Citing
If you use [glypy]{role="mod"} in a publication please cite:
Klein, J., & Zaia, J. (2019). glypy - An open source glycoinformatics library. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.9b00367
Owner
- Name: Joshua Klein
- Login: mobiusklein
- Kind: user
- Location: Boston
- Repositories: 87
- Profile: https://github.com/mobiusklein
GitHub Events
Total
- Issues event: 3
- Watch event: 5
- Issue comment event: 9
- Push event: 35
- Pull request event: 1
- Create event: 5
Last Year
- Issues event: 3
- Watch event: 5
- Issue comment event: 9
- Push event: 35
- Pull request event: 1
- Create event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Joshua Klein | m****n@g****m | 649 |
| Michael Marty | m****0@g****m | 1 |
| azure-pipelines[bot] | a****] | 1 |
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 23
- Total pull requests: 5
- Average time to close issues: 5 months
- Average time to close pull requests: about 12 hours
- Total issue authors: 9
- Total pull request authors: 3
- Average comments per issue: 2.7
- Average comments per pull request: 0.4
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 2
- Pull requests: 3
- Average time to close issues: 3 days
- Average time to close pull requests: about 1 hour
- Issue authors: 2
- Pull request authors: 2
- Average comments per issue: 3.5
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- mobiusklein (10)
- bobaoai (5)
- tiskapot (2)
- NessimRaou (1)
- edwardsnj (1)
- aokinobu (1)
- michaelgoetze (1)
- tomdstanton (1)
- michaelmarty (1)
Pull Request Authors
- mobiusklein (3)
- dependabot[bot] (2)
- michaelmarty (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 567 last-month
- Total dependent packages: 2
- Total dependent repositories: 7
- Total versions: 33
- Total maintainers: 1
pypi.org: glypy
A Glycoinformatics Toolkit
- Homepage: https://github.com/mobiusklein/glypy
- Documentation: https://glypy.readthedocs.io/
- License: Apache Software License
-
Latest release: 1.0.17
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- Cython *
- SPARQLWrapper *
- matplotlib *
- nbsphinx *
- rdflib *
- sphinx >=4.0.2
- SPARQLWrapper *
- dill *
- hjson >=1.5
- lxml *
- matplotlib >=2.0
- rdflib *
- requests *
- six >=1.9
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/checkout v2 composite
- actions/download-artifact v3 composite
- actions/setup-python v2 composite
- actions/upload-artifact v3 composite