msmbuilder
:building_construction: Statistical models for biomolecular dynamics :building_construction:
Science Score: 20.0%
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
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: arxiv.org, acs.org -
✓Committers with academic emails
15 of 35 committers (42.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
:building_construction: Statistical models for biomolecular dynamics :building_construction:
Basic Info
- Host: GitHub
- Owner: msmbuilder
- License: lgpl-2.1
- Language: Python
- Default Branch: master
- Homepage: http://msmbuilder.org
- Size: 6.91 MB
Statistics
- Stars: 158
- Watchers: 24
- Forks: 95
- Open Issues: 103
- Releases: 0
Topics
Metadata Files
README.md
MSMBuilder
MSMBuilder is a python package which implements a series of statistical models for high-dimensional time-series. It is particularly focused on the analysis of atomistic simulations of biomolecular dynamics. For example, MSMBuilder has been used to model protein folding and conformational change from molecular dynamics (MD) simulations. MSMBuilder is available under the LGPL (v2.1 or later).
Capabilities include:
- Feature extraction into dihedrals, contact maps, and more
- Geometric clustering with a variety of algorithms.
- Dimensionality reduction using time-structure independent component analysis (tICA) and principal component analysis (PCA).
- Markov state model (MSM) construction
- Rate-matrix MSM construction
- Hidden markov model (HMM) construction
- Timescale and transition path analysis.
Check out the documentation at msmbuilder.org and join the mailing list. For a broader overview of MSMBuilder, take a look at our slide deck.
Installation
The preferred installation mechanism for msmbuilder is with conda:
bash
$ conda install -c omnia msmbuilder
If you don't have conda, or are new to scientific python, we recommend that you download the Anaconda scientific python distribution.
Workflow
An example workflow might be as follows:
Set up a system for molecular dynamics, and run one or more simulations for as long as you can on as many CPUs or GPUs as you have access to. There are a lot of great software packages for running MD, e.g OpenMM, Gromacs, Amber, CHARMM, and many others. MSMBuilder is not one of them.
Transform your MD coordinates into an appropriate set of features.
Perform some sort of dimensionality reduction with tICA or PCA. Reduce your data into discrete states by using clustering.
Fit an MSM, rate matrix MSM, or HMM. Perform model selection using cross-validation with the generalized matrix Rayleigh quotient
Owner
- Name: MSMBuilder
- Login: msmbuilder
- Kind: organization
- Email: msmbuilder-user@lists.stanford.edu
- Website: http://msmbuilder.org
- Repositories: 12
- Profile: https://github.com/msmbuilder
Statistical models for biomolecular dynamics
GitHub Events
Total
- Watch event: 5
Last Year
- Watch event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Robert McGibbon | r****o@g****m | 924 |
| Matthew Harrigan | h****n@s****u | 584 |
| Bharath Ramsundar | b****r@g****m | 207 |
| kyleabeauchamp | k****p@g****m | 140 |
| Carlos Hernandez | c****h@s****u | 132 |
| Brooke Husic | b****c@s****u | 125 |
| Mohammad Muneeb Sultan | m****n@g****m | 74 |
| Christian Schwantes | s****r@s****u | 64 |
| msultan | m****n@s****u | 40 |
| Carlos Hernández | c****z@u****m | 34 |
| Peter Eastman | p****n@s****u | 29 |
| Patrick Riley | p****r@g****m | 10 |
| Stephen Liu | s****9@g****m | 10 |
| Jade Shi | j****i@v****u | 8 |
| Jade Shi | j****i@s****u | 8 |
| Nate Stanley | n****y@g****m | 7 |
| brookehus | b****c@g****m | 7 |
| Juan Eiros | j****z@g****m | 6 |
| Robert Arbon | r****n@g****m | 6 |
| skearnes | k****s@s****u | 4 |
| Joshua L. Adelman | j****n@g****m | 4 |
| Nate Stanley | d****e@u****m | 3 |
| Hannah Wayment-Steele | h****1@s****u | 3 |
| Steven Kearnes | s****s@g****m | 2 |
| Unknown | r****n@b****k | 2 |
| Sunhwan Jo | s****j@g****m | 2 |
| Mohammad Sultan | m****b@v****u | 2 |
| gkiss | k****t@g****m | 2 |
| Brooke Husic | b****s@u****m | 1 |
| Brooke Husic | b****c@v****u | 1 |
| and 5 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 79
- Total pull requests: 21
- Average time to close issues: about 2 months
- Average time to close pull requests: 2 months
- Total issue authors: 43
- Total pull request authors: 9
- Average comments per issue: 2.87
- Average comments per pull request: 0.57
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- orthonalmatrix (9)
- sbhakat (6)
- jeiros (6)
- girodat (4)
- ghost (4)
- Nidane (4)
- AlirezaTafazzol (3)
- cxhernandez (3)
- momarzouksobeh (3)
- Avon07 (2)
- brookehus (2)
- asgharrazavi (2)
- vshiv18 (1)
- oni-sama14 (1)
- ahy3nz (1)
Pull Request Authors
- cxhernandez (6)
- brookehus (4)
- nhstanley (3)
- RobertArbon (2)
- rmcgibbo (2)
- sunhwan (1)
- koileee (1)
- HWaymentSteele (1)
- jeiros (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 4
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Total downloads:
- pypi 189 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 11
(may contain duplicates) - Total versions: 26
- Total maintainers: 5
pypi.org: msmbuilder
MSMBuilder: Statistical models for Biomolecular Dynamics
- Homepage: https://github.com/msmbuilder/msmbuilder
- Documentation: https://msmbuilder.readthedocs.io/
- License: GNU Lesser General Public License v2 or later (LGPLv2+)
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Latest release: 3.8.0
published almost 9 years ago
Rankings
Maintainers (4)
pypi.org: testmsm
MSMBuilder: Statistical models for Biomolecular Dynamics
- Homepage: https://github.com/msmbuilder/msmbuilder
- Documentation: https://testmsm.readthedocs.io/
- License: GNU Lesser General Public License v2 or later (LGPLv2+)
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Latest release: 3.8.5
published almost 4 years ago
Rankings
Maintainers (1)
pypi.org: msmbuilder2022
MSMBuilder: Statistical models for Biomolecular Dynamics
- Homepage: https://github.com/msmbuilder/msmbuilder
- Documentation: https://msmbuilder2022.readthedocs.io/
- License: GNU Lesser General Public License v2 or later (LGPLv2+)
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Latest release: 3.8.6
published over 2 years ago
Rankings
Maintainers (1)
conda-forge.org: msmbuilder
MSMBuilder is an application and python library. It builds statistical models for high-dimensional time-series. The particular focus of the package is on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change.
- Homepage: http://msmbuilder.org
- License: LGPLv2.1+
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Latest release: 3.8.0
published over 3 years ago
Rankings
Dependencies
- jinja2 *
- jupyter *
- matplotlib *
- msmb_data *
- msmexplorer *
- nbconvert *
- notebook *
- numpydoc *
- openmm *
- pyparsing *