asherichia.github.io/lab-programmes.html at main · asherichia/asherichia.github.io · GitHub

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<!DOCTYPE html>
<html lang="en">
<head>
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  <title>Dr Ash Otter - Lab Programmes</title>
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</head>
<body data-auto-init-microbe data-microbe-obstacles=".tool-card" data-microbe-food-count="80" data-microbe-spawn-x="0.2" data-microbe-spawn-y="0.5">
  <canvas class="background-canvas" id="canvas"></canvas>

  <!-- Main page container -->
  <div class="page-container">
    <!-- Navigation -->
    <div class="nav-container">
      <div class="nav-links">
        <a href="index.html" class="nav-btn">
          <i class="fas fa-home"></i> Home
        </a>
        <a href="research-experience.html" class="nav-btn">
          <i class="fas fa-flask"></i> Research
        </a>
      </div>
    </div>

    <!-- Header section -->
    <div class="header-section">
      <h1 class="page-title">Lab Programmes</h1>
      <p class="page-subtitle">Assortment of random tools for the lab/bioinformatics/data analysis, all to make life a bit easier and more straightforward</p>
      <p class="page-description">
        See         <a href="https://github.com/asherichia">Github</a> for further details.
      </p>
    </div>

    <!-- Programmes container -->
    <div class="programmes-container">
      <div class="programmes-grid">


              <!-- Luminex Data Extractor Programme -->
        <div class="programme-card">
          <div class="card-image-container">
            <div class="status-badge beta">Beta</div>
            <div class="card-title-overlay">
              <div class="card-title">Luminex Data Extractor</div>
              <div class="card-subtitle">Automated data analysis direct from CSV exports</div>
            </div>
          </div>
          <div class="card-content">
            <p class="card-description">
              Standalone HTML application for processing of Luminex data CSV files and analysis relative to standards. Provides automated analyte (bead) detection, efficiency calculations on standards, interpolation, hook/low quality standards, and visual plots.
            </p>
            <div class="programme-features">
              <div class="features-title">Key Features:</div>
              <div class="feature-item">Process direct from Luminex exports</div>
              <div class="feature-item">Standard curve validation through 4PL curve, with sample interpolation</div>
              <div class="feature-item">Hook effect and low quality standards</div>
              <div class="feature-item">Efficiency calculations and interpolation</div>
            </div>
            <a href="https://asherichia.github.io/LuminexDataExtractor_HTML/LuminexExtractorAnalyser.html" target="_blank" class="launch-btn">
              Launch Tool <i class="fas fa-external-link-alt"></i>
            </a>
          </div>
        </div>

                <!-- Luminex Data Extractor Programme -->
        <div class="programme-card">
          <div class="card-image-container">
            <div class="status-badge beta">Beta</div>
            <div class="card-title-overlay">
              <div class="card-title">Hamilton Parser</div>
              <div class="card-subtitle">Data parsing for Hamilton</div>
            </div>
          </div>
          <div class="card-content">
            <p class="card-description">
              Standalone HTML application for merging Hamilton Decapper and Hamilton liquid handling export files.
            </p>
            <div class="programme-features">
              <div class="features-title">Key Features:</div>
              <div class="feature-item">Combines multiple Hamilton export files into one unified file</div>

            </div>
            <a href="https://asherichia.github.io/HamiltonParser/hamilton_parser.html" target="_blank" class="launch-btn">
              Launch Tool <i class="fas fa-external-link-alt"></i>
            </a>
          </div>
        </div>

        <!-- Alanine Scanning Programme -->
        <div class="programme-card">
          <div class="card-image-container">
            <div class="status-badge beta">Beta</div>
            <div class="card-title-overlay">
              <div class="card-title">Alanine Scanning</div>
              <div class="card-subtitle">Protein FASTA sequence mutagenesis tool</div>
            </div>
          </div>
          <div class="card-content">
            <p class="card-description">
              Python bioinformatics tool for systematic alanine scanning mutagenesis analysis along a FASTA sequence to generate comprehensive amino acid substitution and sequences. Useful for downstream synthesis/bioinformatics structure-function studies.
            </p>
            <div class="programme-features">
              <div class="features-title">Key Features:</div>
              <div class="feature-item">FASTA sequence input</div>
              <div class="feature-item">Systematic amino acid replacement, single, double and triple mutants</div>
              <div class="feature-item">Replaces naturally occurring Ala with Gly</div>
              <div class="feature-item">Python</div>
            </div>
            <a href="https://github.com/asherichia/AlanineScanning" target="_blank" class="launch-btn">
              Launch Tool <i class="fas fa-external-link-alt"></i>
            </a>
          </div>
        </div>

        <!-- Plate barcode scan parser -->
        <div class="programme-card">
          <div class="card-image-container">
           <div class="status-badge beta">Beta</div>
            <div class="card-title-overlay">
              <div class="card-title">File parser for plates</div>
              <div class="card-subtitle">Tool for assigning samples to 96/384 well plate layouts</div>
            </div>
          </div>
          <div class="card-content">
            <p class="card-description">
              Allows the assigning of imported sample lists (TXT or CSV) to either 96 or 384 well plate layouts. Can be used with plain lists, partially completed well locations, or fully mapped lists to produce standardised output files.
            </p>
            <div class="programme-features">
              <div class="features-title">Key Features:</div>
              <div class="feature-item">96 or 384 well layouts</div>
              <div class="feature-item">Automatic well detection/assignment</div>
              <div class="feature-item">Plate visualisation once assigned</div>
              <div class="feature-item">HTML in browser use</div>
            </div>
            <a href="https://asherichia.github.io/PlateFileParser/PlateParser.html" target="_blank" class="launch-btn">
              Launch Tool <i class="fas fa-external-link-alt"></i>
            </a>
          </div>
        </div>


        <!-- CAULDRON Programme -->
        <div class="programme-card">
          <div class="card-image-container">
            <div class="status-badge beta">Beta</div>
            <div class="card-title-overlay">
              <div class="card-title">CAULDRON</div>
              <div class="card-subtitle">Curve Analysis Using Luminex Data for IC50 and neutRalisatiON</div>
            </div>
          </div>
          <div class="card-content">
            <p class="card-description">
              A web-based tool for analyzing neutralization assays using Luminex immunoassay data. Process dilution series to calculate IC50 values through 4-parameter logistic curve fitting.
            </p>
            <div class="programme-features">
              <div class="features-title">Key Features:</div>
              <div class="feature-item">Upload data → Configure dilutions → Run analysis → Get IC50 results</div>
              <div class="feature-item">4-parameter logistic curve fitting for dose-response analysis</div>
              <div class="feature-item">Neutralization assay processing with dilution series support</div>
              <div class="feature-item">Streamlined workflow for IC50 calculation</div>
            </div>
            <a href="https://asherichia.github.io/Cauldron-Tool/LuminexInhibitionAnalyzer.html" target="_blank" class="launch-btn">
              Launch Tool <i class="fas fa-external-link-alt"></i>
            </a>
          </div>
        </div>

        <!-- IQC Monitor Programme -->
        <div class="programme-card">
          <div class="card-image-container">
            <div class="status-badge beta">Beta</div>
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              <div class="card-title">IQC HTML tracker</div>
              <div class="card-subtitle">Quality Control Dashboard</div>
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              React.js quality control monitoring dashboard for laboratory processes.
              Features Levy-Jennings plots, statistical process control charts,
              and real-time data visualization with TailwindCSS styling.
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              <div class="feature-item">Levy-Jennings plotting</div>
              <div class="feature-item">CSV data import with PapaParse</div>
              <div class="feature-item">Interactive Recharts visualization</div>
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