software.html

<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>Software — Contextual Dynamics Lab</title>
    <link rel="stylesheet" href="css/style.css">
    <link rel="icon" type="image/x-icon" href="favicon.ico">
</head>
<body>
    <!-- Header -->
    <header class="site-header">
        <div class="header-inner">
            <a href="index.html" class="logo">
                <img src="images/CDL_Avatar.png" alt="Contextual Dynamics Lab">
                <span class="logo-text">contextual dynamics lab</span>
            </a>
            <nav class="main-nav">
                <ul>
                    <li><a href="index.html">contextual dynamics lab</a></li>
                    <li class="dropdown">
                        <span class="dropdown-toggle">about</span>
                        <ul class="dropdown-menu">
                            <li><a href="research.html">research</a></li>
                            <li><a href="people.html">people</a></li>
                            <li><a href="news.html">news</a></li>
                        </ul>
                    </li>
                    <li><a href="publications.html">publications</a></li>
                    <li><a href="software.html">software</a></li>
                    <li><a href="contact.html">contact</a></li>
                </ul>
                <div class="social-icons">
                    <a href="https://github.com/organizations/ContextLab" target="_blank" title="GitHub">
                        <svg viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg">
                            <path d="M12 0C5.37 0 0 5.37 0 12c0 5.31 3.435 9.795 8.205 11.385.6.105.825-.255.825-.57 0-.285-.015-1.23-.015-2.235-3.015.555-3.795-.735-4.035-1.41-.135-.345-.72-1.41-1.23-1.695-.42-.225-1.02-.78-.015-.795.945-.015 1.62.87 1.845 1.23 1.08 1.815 2.805 1.305 3.495.99.105-.78.42-1.305.765-1.605-2.67-.3-5.46-1.335-5.46-5.925 0-1.305.465-2.385 1.23-3.225-.12-.3-.54-1.53.12-3.18 0 0 1.005-.315 3.3 1.23.96-.27 1.98-.405 3-.405s2.04.135 3 .405c2.295-1.56 3.3-1.23 3.3-1.23.66 1.65.24 2.88.12 3.18.765.84 1.23 1.905 1.23 3.225 0 4.605-2.805 5.625-5.475 5.925.435.375.81 1.095.81 2.22 0 1.605-.015 2.895-.015 3.3 0 .315.225.69.825.57A12.02 12.02 0 0024 12c0-6.63-5.37-12-12-12z"/>
                        </svg>
                    </a>
                    <a href="http://x.com/contextmemlab/" target="_blank" title="X (Twitter)">
                        <svg viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg">
                            <path d="M18.244 2.25h3.308l-7.227 8.26 8.502 11.24H16.17l-5.214-6.817L4.99 21.75H1.68l7.73-8.835L1.254 2.25H8.08l4.713 6.231zm-1.161 17.52h1.833L7.084 4.126H5.117z"/>
                        </svg>
                    </a>
                    <a href="mailto:contextualdynamics@gmail.com" title="Email">
                        <svg viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg">
                            <path d="M20 4H4c-1.1 0-2 .9-2 2v12c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V6c0-1.1-.9-2-2-2zm0 4l-8 5-8-5V6l8 5 8-5v2z"/>
                        </svg>
                    </a>
                </div>
            </nav>
        </div>
    </header>

    <!-- Main Content -->
    <main class="main-content">
        <div class="page-header">
            <h1>software</h1>
            <h3>We like sharing resources and helping everyone to do their best science.</h3>
            <p class="page-intro">Check out the links below (or follow our <a href="https://github.com/ContextLab" target="_blank">GitHub repository</a>) to enjoy our lab's handy software tools. We always like to hear about the cool new ways our tools are being applied, so feel free to <a href="contact.html">send us a note</a> about how they're contributing to your work!</p>
            <p class="jump-links"><a href="#python">python</a> | <a href="#javascript">javascript</a> | <a href="#swift">swift</a> | <a href="#kotlin">kotlin</a> | <a href="#matlab">matlab</a></p>
        </div>

        <hr>

        <section id="python" class="content-section software-section">
            <h2><img src="images/software/python-icon.png" alt="python">python code</h2>

            <div class="software-list mt-20">
                <p><strong>CDL Slides.</strong> Our lab's software package for creating themed slides and posters. [<a href="https://github.com/ContextLab/cdl-slides" target="_blank">GitHub</a>]</p>

                <p><strong>Claude History Surfer.</strong> Easily navigate your Claude Code prompt history. [<a href="https://github.com/ContextLab/claude-history-surfer" target="_blank">GitHub</a>]</p>

                <p><strong>Claude Skill Compounder.</strong> A Claude Code hook that continually asks Claude to spin off insights and discoveries into new skills. [<a href="https://github.com/ContextLab/claude-skill-compounder" target="_blank">GitHub</a>]</p>

                <p><strong>Knowledge Map Renderer.</strong> Construct Blender-based renders of knowledge maps. [<a href="https://github.com/ContextLab/knowledge-map-renders" target="_blank">GitHub</a>]</p>

                <p><strong>Clustrix.</strong> Clustrix is a Python package that enables seamless distributed computing on clusters. With a simple decorator, you can execute any Python function remotely on cluster resources while automatically handling dependency management, environment setup, and result collection. [<a href="https://github.com/ContextLab/clustrix" target="_blank">GitHub</a>]</p>

                <p><strong>llmXive.</strong> An LLM-driven system for automating scientific discovery. [<a href="https://github.com/ContextLab/llmXive" target="_blank">GitHub</a>] [<a href="https://context-lab.com/llmXive" target="_blank">Demo</a>]</p>

                <p><strong>Chatify.</strong> Add an LLM-based "teaching assistant" to Jupyter notebooks. [<a href="https://github.com/ContextLab/chatify" target="_blank">GitHub</a>]</p>

                <p><strong>Davos.</strong> Manage project dependencies for notebook-based projects. [<a href="https://github.com/ContextLab/davos" target="_blank">GitHub</a>]</p>

                <p><strong>DataWrangler.</strong> Format and clean data, with a special focus on applying natural language processing models to text data. [<a href="https://github.com/ContextLab/data-wrangler" target="_blank">GitHub</a>]</p>

                <p><strong>Abstract2Paper.</strong> Auto-generate an entire paper from a prompt or abstract. [<a href="https://github.com/ContextLab/abstract2paper" target="_blank">GitHub</a>]</p>

                <p><strong>Timecorr Toolbox.</strong> Estimate dynamic high-order correlations in multivariate timeseries data. [<a href="https://github.com/ContextLab/timecorr" target="_blank">GitHub</a>]</p>

                <p><strong>SuperEEG Toolbox.</strong> Infer full-brain activity patterns from a small(ish) number of ECoG electrodes using Gaussian process regression. [<a href="https://github.com/ContextLab/supereeg" target="_blank">GitHub</a>]</p>

                <p><strong>Quail.</strong> Analyze and visualize free recall data. [<a href="https://github.com/ContextLab/quail" target="_blank">GitHub</a>]</p>

                <p><strong>HyperTools.</strong> Visualize and manipulate high-dimensional data. (Way better than the MATLAB version!) [<a href="https://github.com/ContextLab/hypertools" target="_blank">GitHub</a>]</p>

                <p><strong>BrainIAK Toolbox.</strong> Collaboration with the <a href="https://pni.princeton.edu/" target="_blank">Princeton Neuroscience Institute</a> and <a href="http://www.intel.com/content/www/us/en/research/intel-research.html" target="_blank">Intel Labs</a> to implement a bunch of useful brain analysis tools, including Hierarchical Topographic Factor Analysis. [<a href="https://github.com/IntelPNI/brainiak" target="_blank">GitHub</a>]</p>

                <p><strong>CDL-bibliography.</strong> The bibliography management system used by the Contextual Dynamics Lab. [<a href="https://github.com/ContextLab/CDL-bibliography" target="_blank">GitHub</a>]</p>
            </div>

            <p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
        </section>

        <hr>

        <section id="javascript" class="content-section software-section">
            <h2><img src="images/software/javascript-icon.png" alt="javascript">javascript code</h2>

            <div class="software-list mt-20">
                <p><strong>Thunderbird Snooze.</strong> Thunderbird plugin that adds a "snooze message" feature similar to Gmail. [<a href="https://github.com/ContextLab/thunderbird-snooze" target="_blank">GitHub</a>]</p>

                <p><strong>Dream Stream.</strong> Android and web-based application for delivering sleep-stage triggered cues to guide lucid dreaming. [<a href="https://github.com/ContextLab/dream-stream" target="_blank">GitHub</a>] [<a href="https://context-lab.com/dream-stream/" target="_blank">Demo</a>]</p>

                <p><strong>Knowledge Mapper.</strong> Map out an approximation of everything you know by answering multiple-choice quiz questions. [<a href="https://github.com/ContextLab/mapper" target="_blank">GitHub</a>] [<a href="https://context-lab.com/mapper/" target="_blank">Demo</a>]</p>

                <p><strong>Scheduler.</strong> A self-hosted appointment scheduling system like YouCanBook.me or Calendly, but free, open-source, and fully under your control. [<a href="https://github.com/ContextLab/scheduler" target="_blank">GitHub</a>] [<a href="https://cdl-scheduler.readthedocs.io/" target="_blank">Docs</a>]</p>

                <p><strong>LLM Geometry Visualizer.</strong> Understand LLMs using geometric approaches and visualizations. [<a href="https://github.com/ContextLab/llm-geometry" target="_blank">GitHub</a>] [<a href="https://context-lab.com/llm-geometry" target="_blank">Demo</a>]</p>

                <p><strong>Fourier Control Theory.</strong> An interactive demo showing that a robot arm whose joints spin at constant rates is a Fourier series, and vice versa. [<a href="https://github.com/ContextLab/fourier-control-theory" target="_blank">GitHub</a>] [<a href="https://context-lab.com/fourier-control-theory" target="_blank">Demo</a>]</p>

                <p><strong>Sky Viewer.</strong> Enter a date, location, direction, and time of day, and get back an animated visualization of the stars. [<a href="https://github.com/ContextLab/sky-viewer" target="_blank">GitHub</a>] [<a href="https://context-lab.com/sky-viewer" target="_blank">Demo</a>]</p>

                <p><strong>Dino Trivia.</strong> A two-player dinosaur trivia game. [<a href="https://github.com/ContextLab/dino-trivia" target="_blank">GitHub</a>] [<a href="https://context-lab.com/dino-trivia" target="_blank">Demo</a>]</p>

                <p><strong>Claude Context Bar.</strong> A Claude Code mod that draws the context window as a stacked bar under the prompt. [<a href="https://github.com/ContextLab/claude-context-bar" target="_blank">GitHub</a>]</p>

                <p><strong>LLM Demos.</strong> A collection of interactive language model demonstrations. [<a href="https://github.com/ContextLab/llm-course/tree/main/demos" target="_blank">GitHub</a>] [<a href="https://context-lab.com/llm-course/demos/" target="_blank">Demo</a>]</p>

                <p><strong>autoFR.</strong> A verbal free recall experiment that incorporates automatic speech-to-text processing, ready-to-run on Amazon Mechanical Turk. [<a href="https://github.com/ContextLab/autoFR" target="_blank">GitHub</a>]</p>
            </div>

            <p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
        </section>

        <hr>

        <section id="swift" class="content-section software-section">
            <h2><img src="images/software/swift-icon.png" alt="swift">swift code</h2>

            <div class="software-list mt-20">
                <p><strong>Markdown Buddy.</strong> MacOS Finder Quick View plugin for displaying markdown and other text-based files with syntax highlighting and high-quality rendering. [<a href="https://github.com/ContextLab/md-buddy" target="_blank">GitHub</a>]</p>
            </div>

            <p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
        </section>

        <hr>

        <section id="kotlin" class="content-section software-section">
            <h2><img src="images/software/kotlin-icon.png" alt="kotlin">kotlin code</h2>

            <div class="software-list mt-20">
                <p><strong>Android Scholar.</strong> Android Google Scholar application. [<a href="https://github.com/ContextLab/android-scholar" target="_blank">GitHub</a>]</p>
            </div>

            <p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
        </section>

        <hr>

        <section id="matlab" class="content-section software-section">
            <h2><img src="images/software/matlab-icon.png" alt="matlab">matlab code</h2>

            <div class="software-list mt-20">
                <p><strong>Hyperplot Tools.</strong> Plot and manipulate high-dimensional data. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/56623" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Hierarchical Topographic Factor Analysis.</strong> Efficiently identify functional brain networks in fMRI data. [<a href="https://app.box.com/s/elcxpst2n0q6elpuzndj" target="_blank">Download</a>]</p>

                <p><strong>MATLAB Ipsum.</strong> Generate filler text using MATLAB. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/43428" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Easy resample.</strong> Simple interface for interpolating or resampling a 1D signal. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/43320" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Chuck Close-ify.</strong> Automatically create artwork in Chuck Close's iconic style based on existing photographs. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/38770" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Plot fMRI images.</strong> Quick and easy method for generating 2D and 3D brain plots. [<a href="https://github.com/ContextLab/brain-plots" target="_blank">GitHub</a>] [<a href="http://www.mathworks.com/matlabcentral/fileexchange/36139" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Generate synthetic fMRI data.</strong> Generate synthetic data for testing fMRI analyses and models. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/36125" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Sane pColor.</strong> Create 2D images that don't look blurry in OS X's Preview PDF viewer. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/35601" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Attach.</strong> MATLAB implementation of the attach function in R. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/35436" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Get tight subplot handles.</strong> Allows user to exert finer control over subplot spacing in MATLAB. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/35435" target="_blank">MATLAB Central File Exchange</a>]</p>

                <p><strong>Slices.</strong> Efficiently slice a tensor along the n<sup>th</sup> dimension. [<a href="http://www.mathworks.com/matlabcentral/fileexchange/35439" target="_blank">MATLAB Central File Exchange</a>]</p>
            </div>

            <p class="back-to-top">^ <a href="#top">REINSTATE CONTEXT (BACK TO TOP)</a> ^</p>
        </section>
    </main>

    <!-- Footer Navigation -->
    <nav class="footer-nav">
        <div class="footer-nav-inner">
            <button class="mobile-menu-toggle" aria-label="Toggle menu">
                <span></span>
                <span></span>
                <span></span>
            </button>
            <a href="index.html" class="logo">
                <img src="images/CDL_Avatar.png" alt="CDL">
            </a>
            <ul>
                <li><a href="index.html">contextual dynamics lab</a></li>
                <li class="dropdown">
                    <span class="dropdown-toggle">about</span>
                    <ul class="dropdown-menu">
                        <li><a href="research.html">research</a></li>
                        <li><a href="people.html">people</a></li>
                        <li><a href="news.html">news</a></li>
                    </ul>
                </li>
                <li><a href="publications.html">publications</a></li>
                <li class="active"><a href="software.html">software</a></li>
                <li><a href="contact.html">contact</a></li>
            </ul>
        </div>
    </nav>

    <script src="js/main.js"></script>
    <script data-goatcounter="https://context-lab.goatcounter.com/count"
            async src="//gc.zgo.at/count.js"></script>
</body>
</html>