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.

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

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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

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• 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

• 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 ilastik/ilastik-conda-recipes#17
• scipy MKL issues
  • See BVLC/caffe#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.

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.

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

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

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

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

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• Free software: MIT license