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sipsim

A toolset for simulating high resolution stable isotope probing data

https://github.com/nick-youngblut/sipsim

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 4 committers (75.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

A toolset for simulating high resolution stable isotope probing data

Basic Info
  • Host: GitHub
  • Owner: nick-youngblut
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 231 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created about 9 years ago · Last pushed almost 8 years ago
Metadata Files
Readme License

README.md

Build Status

SIPSim

SIPSim is a toolset for simulating data from high resolution stable isotope probing (HR-SIP) experiments.

Note: currently SIPSim is only Python 2.7 compatable, mainly because MFEprimer is used for simulating sequences from genomes. We recommend using an anaconda environment, which will also help with installing the dependencies.

Sections

REFERENCE

[top]

If you use SIPSim, please cite:

Youngblut, Nicholas D., Samuel E. Barnett, and Daniel H. Buckley. 2018. "SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments." Frontiers in Microbiology 9: 570. doi: 10.3389/fmicb.2018.00570

INSTALLATION

[top]

DEPENENCIES

  • SIPSim_pymix

    • This is a modified version of pymix
      • It has been modified to fix bugs resulting from the integration with SIPSim

  • MFEprimer_linux

    • This is a modified version of MFEprimer-2.0
    • It has been modified for installation into a linux environment via python setup.py install

Dependency install issues (using Anaconda)

  • boost-python
    • install via conda or see boost.org on other methods to install
    • Note: there's currently no official conda channel for boost-python
  • scipy libgrfortran issues
    • See https://github.com/ilastik/ilastik-build-conda/issues/17
  • scipy MKL issues
    • See https://github.com/BVLC/caffe/issues/3884
    • MKL can be shut down. See this blog post
    • This can be done by: conda install nomkl
    • NOTE: OpenBlas will try to use all threads. To limit threads, use export OMP_NUM_THREADS=N, where N is the number of threads to use.

Installation of SIPSim

Clone the repo

See the "before_install:" and "install:" sections in .travis.yml file for installation instructions. If the travisCI tests are passing, then these instructions should work on a linux machine.

Installation of SIPSimR

SIPSimR contains R scripts for data analysis and plotting of data produced by SIPSim. See the SIPSimR README for more information.

TUTORIALS

[top]

SIMULATION_WORKFLOW

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simulation pipeline

CHANGELOG

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v0.3

  • Added many unit tests and created SIPSim-specific dependency packages.

v0.2

  • Restructered SIPSim to be fully installable via setup.py. This involved spliting the software into 3 repositories (SIPSim, SIPSimR, and MFEprimer-linux).

LICENSE

[top]

  • Free software: MIT license

Owner

  • Name: Nick Youngblut
  • Login: nick-youngblut
  • Kind: user
  • Location: South San Francisco
  • Company: Federation Bio

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 296
  • Total Committers: 4
  • Avg Commits per committer: 74.0
  • Development Distribution Score (DDS): 0.155
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nick Youngblut n****2@c****u 250
Nicholas Youngblut n****t@t****e 40
Sam Barnett s****9@c****u 5
Nick Youngblut n****2@g****m 1
Committer Domains (Top 20 + Academic)
cornell.edu: 2 tuebingen.mpg.de: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
View more stats
Top Authors
Issue Authors
  • fred-herritsch (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 7 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 1
pypi.org: sipsim

Simulate High Resolution Stable Isotope Probing Datasets

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 7 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Forks count: 29.8%
Average: 29.8%
Stargazers count: 31.9%
Downloads: 55.6%
Maintainers (1)
nick_youngblut
Last synced: 11 months ago