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
• INSTALLATION
• TUTORIALS
• SIMULATION WORKFLOW
• CHANGE LOG
• LICENSE

REFERENCE

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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

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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

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• An example with 3 genomes
• Recreating Fig 1 from Lueders et al., 2004

SIMULATION_WORKFLOW

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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

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• Free software: MIT license