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<!DOCTYPE html>
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<div class="intro-lead-in">Notebook environment for both interactive data analysis and batch data processing</div>
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<li class="active"><a href="index.html#content">Introduction</a> </li>
<li><a href="running.html#content">Running SoS</a> </li>
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<p>Script of Scripts (SoS) is a computational environment for the development and execution of scripts in multiple languages for daily computational research. It can be used to develop scripts to analyze data interactively in a Jupyter environment, and, with minimal effort, convert the scripts to a workflow that analyzes a large amount of data in batch mode.</p>
<p align="center">
<img src="https://vatlab.github.io/sos-docs/doc/media/SoS_Notebook_and_Workflow.png">
</p><p>SoS consists of a ployglot notebook that allows the use of multiple kernels in one Jupyter notebook, and a workflow system that is designed for daily computational research. Basically,</p>
<ul>
<li><a href="https://github.com/vatlab/sos-notebook">SoS Polyglot Notebook</a> is a <a href="https://jupyter.org/">Jupyter Notebook</a> with a SoS kernel.</li>
<li>SoS Notebook serves as a super kernel to all other Jupyter kernels and allows the <a href="https://vatlab.github.io/blog/post/sos-notebook/">use of multiple kernels in one Jupyter notebook</a>.</li>
<li><a href="https://github.com/vatlab/SoS">SoS Workflow System</a> is a Python based workflow system that is designed to be readable, sharable, and <a href="https://vatlab.github.io/blog/post/sos-workflow-engine/">suitable for daily data analysis</a>.</li>
<li>SoS Workflow System can be used from command line or use SoS Notebook as its IDE.</li>
</ul>
<p>The figure is linked to a <a href="https://www.youtube.com/watch?v=U75eKosFbp8">youtube video</a> for a <a href="https://github.com/vatlab/JupyterCon2018">presentation on SoS during the 2018 JupyterCon</a>, which introduces both SoS Notebook and SoS Workflow System and can be a good starting point for you to learn SoS. The SoS Workflow part starts at <a href="https://www.youtube.com/watch?v=U75eKosFbp8#t=20m">20min</a>.</p>
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<h1 id="Multi-language-Jupyter-Notebook">Multi-language Jupyter Notebook<a class="anchor-link" href="#Multi-language-Jupyter-Notebook"></a></h1>
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<p>As an <strong>interactive environment</strong> and <strong>notebook tool</strong> that promotes <a href="https://en.wikipedia.org/wiki/Literate_programming">literate programming</a>, SoS
allows you to perform and record your analysis in different languages in a single <a href="http://jupyter.org/">Jupyter notebook</a>, with seamless integration
of multiple Jupyter kernels (e.g. python, and <a href="https://github.com/IRkernel/IRkernel">R</a>). The ability to exchange data between live jupyter kernels allows you to use the most appropriate languages for different parts of your analyses.</p>
<p>SoS can work with all <a href="https://github.com/jupyter/jupyter/wiki/Jupyter-kernels">Jupyter kernels</a> and currently provides native support (with data exchange) for the following languages:</p>
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<td><img src="img/Bash.png" alt="Bash"></td>
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<td bgcolor="#E6EEFF">Bash</td>
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<tr>
<td><img src="img/JavaScript.png" alt="JavaScript"></td>
</tr>
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<td bgcolor="#c8e1ae">JavaScript</td>
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</table>
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<td><img src="img/Julia.png" alt="Julia"></td>
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<td bgcolor="#ebd8eb">Julia</td>
</tr>
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<td><img src="img/Matlab.png" alt="MATLAB"></td>
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<td><img src="img/Ruby.png" alt="Ruby"></td>
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<td bgcolor="#e8c2be">Ruby</td>
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<td><img src="img/Octave.png" alt="Octave"></td>
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<td bgcolor="#dff8fb">Octave</td>
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<td><img src="img/Python.png" alt="Python"></td>
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<td bgcolor="#FFF177">Python 2</td>
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<td><img src="img/Python3.png" alt="Python3"></td>
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<td bgcolor="#ffd91a">Python 3</td>
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<td><img src="img/R.png" alt="R"></td>
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<td bgcolor="#DCDCDA">R</td>
</tr>
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<tr>
<td><img src="img/SAS.png" alt="SAS"></td>
</tr>
<tr>
<td bgcolor="#9CD4F9">SAS</td>
</tr>
</table>
</div>
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<table>
<tr>
<td><img src="img/scilab.png" alt="Scilab"></td>
</tr>
<tr>
<td bgcolor="#e8c2be">Scilab</td>
</tr>
</table>
</div>
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<table>
<tr>
<td><img src="img/Stata.jpg" alt="Stata"></td>
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<tr>
<td bgcolor="#CAE8F3">Stata</td>
</tr>
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<td><img src="img/TypeScript.png" alt="TypeScript"></td>
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<td bgcolor="#56A6DC">TypeScript</td>
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<td><img src="img/zsh.png" alt="Zsh"></td>
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<td bgcolor="#E6EEFA">Zsh</td>
</tr>
</table>
</div>
</div>
</div><p>Other langauges can be supported through third-party langauge modules. Please feel free to submit a PR if you would like to list your language modules below:</p>
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<td><img src="img/c++.png" alt="C++11"></td>
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<td bgcolor="#F80000"><a href="https://pypi.org/project/sos-java/">C++11</a></td>
</tr>
</table>
</div>
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<table>
<tr>
<td><img src="img/c++.png" alt="C++14"></td>
</tr>
<tr>
<td bgcolor="#D5CCFF"><a href="https://github.com/LabShare/sos-xeus-cling">C++14</a></td>
</tr>
</table>
</div>
<div class="col-md-2">
<table>
<tr>
<td><img src="img/c++.png" alt="C++17"></td>
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<tr>
<td bgcolor="#EAE6FF"><a href="https://github.com/LabShare/sos-xeus-cling">C++17</a></td>
</tr>
</table>
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<table>
<tr>
<td><img src="img/Java.png" alt="Java"></td>
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<tr>
<td bgcolor="#E6EEFF">Java</td>
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<h1 id="A-workflow-system-designed-for-daily-data-analysis">A workflow system designed for daily data analysis<a class="anchor-link" href="#A-workflow-system-designed-for-daily-data-analysis"></a></h1>
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<p>Most workflow systems have rigorous interfaces and syntaxes for specification of computational tasks. Inevitably, re-factoring codes for these pipeline platforms results in notably different implementations of their non-pipeline counterparts. Therefore, overuse of pipelines, particularly in the early stages of projects, decreases productivity, as researchers are forced to redirect their focus from scientific problems to engineering details. For these reasons, <a href="https://www.nature.com/articles/nbt.2740"><strong>pipelineitis is a nasty disease</strong></a> and prevents the use of workflow tools for exploratory data analysis.</p>
<p>The SoS workflow system is designed for daily data analysis. SoS is extended from Python 3.6 with a minimal ammount of extra syntax. It also follows an incremental design so that you can literally convert your scripts into a workflow in seconds, while allowing the use of more advanced features as needs arise.</p>
<p align="center">
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006843"><img src="https://vatlab.github.io/sos-docs/doc/media/sos_wf_figure1.png" width="70%"></a>
</p>
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<h1 id="Mixed-Style-Workflows">Mixed Style Workflows<a class="anchor-link" href="#Mixed-Style-Workflows"></a></h1><p>SoS follows your definition of workflow that allows you to define workflows in both foward and makefile style, even a mixture of both. More specifically, you can define workflows as ordered steps that would be executed sequentially step by step to process specified input files; or as a set of makefile-style rules that would be executed to generated specified output files; or as a sequence of steps with help from makefile-style steps. SoS automatically analyzes the input and output of steps and execute workflows using a dynamic DAG (Directed Acyclic Graph) that would be expanded and shrinked during the execution.</p>
<p align="center">
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006843"><img src="https://vatlab.github.io/sos-docs/doc/media/sos_wf_figure2.png" width="70%"></a>
</p>
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<h1 id="Remote-execution-made-easy">Remote execution made easy<a class="anchor-link" href="#Remote-execution-made-easy"></a></h1>
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<p>One of the major obstacles for reproducible data analysis is the fact that large workflows need to exploit remote computational resources, which usually involves logging to remote systems, creating system-specific wrapper scripts, submitting jobs and collecting results are the jobs are done. With SoS' remote execution model, all these steps are simplified so that you can submit tasks to different remote hosts and cluster systems, all from your local desktop or laptop.</p>
<p align="center">
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006843"><img src="https://vatlab.github.io/sos-docs/doc/media/sos_wf_figure3.png" width="70%"></a>
</p>
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<h1 id="Finally,-a-workflow-system-that-is-readable">Finally, a workflow system that is readable<a class="anchor-link" href="#Finally,-a-workflow-system-that-is-readable"></a></h1>
</div>
</div>
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<p>The SoS workflow system can be embeded to SoS notebooks and be <a href="https://vatlab.github.io/sos-docs/doc/user_guide/sos_in_notebook.html">executed both from command line or from within the notebook</a>. This allows SoS notebooks to include scientific narratives, workflow descriptions, sample input and output, along with the embedded workflows, which makes them much more readable, therefore much easier to share than other workflow systems, and becomes a perfect medium for the sharing of analytic procedures for daily data analysis.</p>
<p align="center">
<iframe src="https://vatlab.github.io/sos-docs/doc/examples/RNASeqGTEx.html" width="70%" height="600px"></iframe>
</p>
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