.. _examples: ========================================== Examples ========================================== .. contents:: :local: Example analyses ------------------ Each example analysis is a published study by the `Bloom lab`_. Each analysis is in its own subdirectory `in the examples folder on GitHub `_. Typically there is a `Jupyter notebook`_ that performs the analysis. Here are the analyses: Doud and Bloom (2016) +++++++++++++++++++++++ - **Summary**: Deep mutational scanning of influenza hemagglutinin using :ref:`bcsubamp`, then estimation of the :ref:`prefs`. - **Citation**: `Doud and Bloom (2016)`_ - **Jupyter notebook**: `Doud2016 example`_ Doud et al (2017) ++++++++++++++++++++++ - **Summary**: Mutational antigenic profiling of influenza hemagglutinin against strain-specific antibodies using :ref:`bcsubamp`, then estimation of the :ref:`diffsel` from each antibody - **Citation**: `Doud et al (2017)`_ - **Jupyter notebook**:`Doud2017 example`_. Dingens et al (2017) ++++++++++++++++++++++ - **Summary**: Mutational antigenic profiling of HIV Env (BF520 strain) against PGT151 antibody using :ref:`bcsubamp`, and then estimation of the :ref:`diffsel`. - **Citation**: `Dingens et al (2017)`_ - **Jupyter notebook**: `Dingens2017 example`_. Doud et al (2018) +++++++++++++++++++ - **Summary**: Mutational antigenic profiling of influenza hemagglutinin against broadly neutralizing and strain-specific antibodies using :ref:`bcsubamp`, then estimation of the :ref:`fracsurvive`. - **Citation**: `Doud et al (2018)`_ - **Jupyter notebook**: `Doud2018 example`_. Haddox et al (2018) +++++++++++++++++++++ - **Summary**: Deep mutational scanning of two HIV Envs using :ref:`bcsubamp`, then comparison of the :ref:`prefs`. - **Citation**: `Haddox et al (2018)`_ - **Jupyter notebook**: `Haddox2018 example`_. Dingens et al (2018) +++++++++++++++++++++ - **Summary**: Mutational antigenic profiling of HIV Env against fusion-peptide antibodies usring :ref:`bcsubamp`, then estimation of the :ref:`diffsel`. - **Citations**: `Dingens et al (2018)`_ - **Jupyter notebook**: `Dingens2018 example`_ Lee et al (2018) +++++++++++++++++ - **Summary**: Deep mutational scanning of H3 influenza hemagglutinin using :ref:`bcsubamp`, then estimation of the :ref:`prefs`. - **Citations**: `Lee et al (2018)`_ - **Jupyter notebook**: `Lee2018 example`_ Running the examples ------------------------------------------------- `Navigate here `_ to access the example analyses and require input data. To run a `Jupyter notebook`_, you need to install ``jupyter``. Most of the notebooks also have other requirements (such as `fastq-dump`_ to download the deep sequencing data from the `Sequence Read Archive`_), and these dependencies are described in the notebooks. To run a notebook interactively, type:: jupyter notebook analysis_notebook.ipynb To run a notebook in command-line mode, run:: jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1 analysis_notebook.ipynb You should **not** open the notebook while it is being run in command-line mode. If you are in the `Bloom lab`_ and using the Hutch server, you can run a notebook via `slurm`_ by creating a file ``run.sbatch`` that looks like this:: #!/bin/sh #SBATCH #PBS -l walltime=24:00:00 jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=-1 analysis_notebook.ipynb and then running the file with:: sbatch -p largenode -c 14 --mem=140000 run.sbatch where the number of CPUs requested with ``-c`` should match the number specified for multi-processor operations in the notebook. .. include:: weblinks.txt