{"id":96,"date":"2021-07-06T18:58:08","date_gmt":"2021-07-06T18:58:08","guid":{"rendered":"http:\/\/10.250.7.211\/?page_id=96"},"modified":"2026-08-10T12:41:43","modified_gmt":"2026-08-10T12:41:43","slug":"tools","status":"publish","type":"page","link":"https:\/\/mgbio.asab.nust.edu.pk\/index.php\/tools\/","title":{"rendered":"Tools"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"96\" class=\"elementor elementor-96\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-26d3ffc elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"26d3ffc\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-5bf7dbd\" data-id=\"5bf7dbd\" data-element_type=\"column\">\n\t\t\t<div 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margin-top:auto;\r\n    padding-top:1rem;\r\n    border-top:1px dashed var(--iblab-line);\r\n  }\r\n  .iblab-link-btn{\r\n    font-family:'Inter',sans-serif;\r\n    font-size:.82rem;\r\n    font-weight:600;\r\n    text-decoration:none;\r\n    display:inline-flex;\r\n    align-items:center;\r\n    gap:.4rem;\r\n    padding:.5rem .85rem;\r\n    border-radius:8px;\r\n    transition:background .2s ease, color .2s ease, transform .2s ease;\r\n  }\r\n  .iblab-link-btn.iblab-primary{\r\n    background:var(--iblab-navy-deep);\r\n    color:#fff;\r\n  }\r\n  .iblab-link-btn.iblab-primary:hover{ background:var(--iblab-navy); color:#fff; transform:translateY(-1px); }\r\n  .iblab-link-btn.iblab-secondary{\r\n    background:transparent;\r\n    color:var(--iblab-navy);\r\n    border:1px solid var(--iblab-line);\r\n  }\r\n  .iblab-link-btn.iblab-secondary:hover{ border-color:var(--iblab-navy-mid); background:var(--iblab-navy-soft); }\r\n  .iblab-link-btn svg{ width:12px; height:12px; }\r\n\r\n  \/* coming soon cards muted *\/\r\n  .iblab-card.iblab-soon-card{\r\n    background:repeating-linear-gradient(135deg, var(--iblab-paper-raise), var(--iblab-paper-raise) 10px, #fbfaf7 10px, #fbfaf7 20px);\r\n  }\r\n  .iblab-card.iblab-soon-card h3{ color:var(--iblab-ink-soft); }\r\n  .iblab-card.iblab-soon-card::before{ background:var(--iblab-amber); }\r\n  .iblab-card.iblab-soon-card .iblab-card-icon{ background:var(--iblab-amber-soft); }\r\n\r\n  @media (max-width:780px){\r\n    .iblab-page{ padding:3rem 1.4rem 4rem; }\r\n    .iblab-grid{ grid-template-columns:1fr; }\r\n  }\r\n<\/style>\r\n\r\n<div class=\"iblab-wrap\">\r\n<div class=\"iblab-page\">\r\n\r\n  <!-- ============ HERO ============ -->\r\n  <section class=\"iblab-hero\">\r\n    <div class=\"iblab-hero-eyebrow\"><span class=\"iblab-dot\"><\/span> Open-Access Research Software<\/div>\r\n    <h1>Tools &amp; <em>Databases<\/em><\/h1>\r\n    <p class=\"iblab-lede\">A collection of bioinformatics platforms, machine-learning pipelines, and curated databases developed by the Integrative Biology Laboratory to accelerate reverse vaccinology, antimicrobial resistance surveillance, and pathogen genomics.<\/p>\r\n  <\/section>\r\n\r\n  <!-- ============ DATABASES ============ -->\r\n  <section class=\"iblab-section\" id=\"iblab-databases\">\r\n    <div class=\"iblab-section-head\">\r\n      <h2><span class=\"iblab-tag-index\">\u00a71<\/span> Databases<\/h2>\r\n      <span class=\"iblab-count\">3 resources<\/span>\r\n    <\/div>\r\n    <p class=\"iblab-section-sub\">Curated, searchable repositories of antimicrobial peptide and resistance-associated sequence data, built for reuse across the AMR research community.<\/p>\r\n\r\n    <div class=\"iblab-grid\">\r\n\r\n      <!-- AbAMPdb -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"M4 6C4 4.9 7.6 4 12 4C16.4 4 20 4.9 20 6C20 7.1 16.4 8 12 8C7.6 8 4 7.1 4 6Z\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M4 6V18C4 19.1 7.6 20 12 20C16.4 20 20 19.1 20 18V6\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M4 12C4 13.1 7.6 14 12 14C16.4 14 20 13.1 20 12\" stroke=\"#003380\" stroke-width=\"1.6\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-db\">Database<\/span>\r\n        <\/div>\r\n        <h3>AbAMPdb<\/h3>\r\n        <p>A dedicated repository of antibacterial peptides curated for structural and functional annotation, supporting discovery of novel antimicrobial candidates against drug-resistant pathogens.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <a class=\"iblab-link-btn iblab-secondary\" href=\"https:\/\/doi.org\/10.1093\/database\/baae096\" target=\"_blank\" rel=\"noopener\">Publication<\/a>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/abampdb.mgbio.tech\" target=\"_blank\" rel=\"noopener\">Access Database<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n      <!-- ESKAPE AMPdb -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"M4 6C4 4.9 7.6 4 12 4C16.4 4 20 4.9 20 6C20 7.1 16.4 8 12 8C7.6 8 4 7.1 4 6Z\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M4 6V18C4 19.1 7.6 20 12 20C16.4 20 20 19.1 20 18V6\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M4 12C4 13.1 7.6 14 12 14C16.4 14 20 13.1 20 12\" stroke=\"#003380\" stroke-width=\"1.6\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-db\">Database<\/span>\r\n        <\/div>\r\n        <h3>ESKAPE AMPdb<\/h3>\r\n        <p>An antimicrobial peptide database focused specifically on the ESKAPE pathogen group, compiling sequence, structural, and activity data to guide peptide-based therapeutic design.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/mgbio.asab.nust.edu.pk\/eskapeamp\/\" target=\"_blank\" rel=\"noopener\">Access Database<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n      <!-- PAAMPdb -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"M4 6C4 4.9 7.6 4 12 4C16.4 4 20 4.9 20 6C20 7.1 16.4 8 12 8C7.6 8 4 7.1 4 6Z\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M4 6V18C4 19.1 7.6 20 12 20C16.4 20 20 19.1 20 18V6\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M4 12C4 13.1 7.6 14 12 14C16.4 14 20 13.1 20 12\" stroke=\"#003380\" stroke-width=\"1.6\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-db\">Database<\/span>\r\n        <\/div>\r\n        <h3>PAAMPdb<\/h3>\r\n        <p>A curated database of antimicrobial peptides derived from <em>Pseudomonas aeruginosa<\/em>, providing sequence and activity information for research on this high-priority pathogen.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <span class=\"iblab-badge iblab-publication\">Publication in progress<\/span>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/mgbio.asab.nust.edu.pk\/paampdb\/\" target=\"_blank\" rel=\"noopener\">Access Database<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n    <\/div>\r\n  <\/section>\r\n\r\n  <!-- ============ TOOLS ============ -->\r\n  <section class=\"iblab-section\" id=\"iblab-tools\">\r\n    <div class=\"iblab-section-head\">\r\n      <h2><span class=\"iblab-tag-index\">\u00a72<\/span> Tools &amp; Pipelines<\/h2>\r\n      <span class=\"iblab-count\">6 platforms<\/span>\r\n    <\/div>\r\n    <p class=\"iblab-section-sub\">Computational pipelines spanning reverse vaccinology, pangenome analysis, and machine-learning-driven resistance profiling.<\/p>\r\n\r\n    <div class=\"iblab-grid\">\r\n\r\n      <!-- VacSol-ML(ESKAPE) -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"M12 3V7\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><path d=\"M6 8L9 12\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><path d=\"M18 8L15 12\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><circle cx=\"12\" cy=\"15\" r=\"6\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M9.5 15L11 16.5L14.5 13\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-tool\">Vaccine Design<\/span>\r\n        <\/div>\r\n        <h3>VacSol-ML (ESKAPE)<\/h3>\r\n        <p>A machine-learning-enhanced reverse vaccinology pipeline that prioritizes vaccine target candidates specifically across ESKAPE pathogen proteomes.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <a class=\"iblab-link-btn iblab-secondary\" href=\"https:\/\/doi.org\/10.1016\/j.vaccine.2024.126204\" target=\"_blank\" rel=\"noopener\">Publication<\/a>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/mgbio.asab.nust.edu.pk\/vaccines\/eskapeml_upload\/\" target=\"_blank\" rel=\"noopener\">Launch Tool<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n      <!-- B-vac -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"M12 3V7\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><path d=\"M6 8L9 12\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><path d=\"M18 8L15 12\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><circle cx=\"12\" cy=\"15\" r=\"6\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M9.5 15L11 16.5L14.5 13\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-tool\">Vaccine Design<\/span>\r\n        <\/div>\r\n        <h3>B-vac<\/h3>\r\n        <p>A bacterial vaccine target prediction platform that integrates subtractive genomics with reverse vaccinology to shortlist high-confidence antigen candidates.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <a class=\"iblab-link-btn iblab-secondary\" href=\"https:\/\/doi.org\/10.1038\/s41598-025-01201-0\" target=\"_blank\" rel=\"noopener\">Publication<\/a>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/samavinasir.github.io\/b-vac\/\" target=\"_blank\" rel=\"noopener\">Launch Tool<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n      <!-- B-Pan -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><circle cx=\"12\" cy=\"12\" r=\"3\" stroke=\"#003380\" stroke-width=\"1.6\"\/><circle cx=\"12\" cy=\"4.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"18.5\" cy=\"8.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"18.5\" cy=\"15.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"12\" cy=\"19.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"5.5\" cy=\"15.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"5.5\" cy=\"8.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><path d=\"M12 9V6M14.5 10.5L17 9M14.5 13.5L17 15M12 15V18M9.5 13.5L7 15M9.5 10.5L7 9\" stroke=\"#003380\" stroke-width=\"1.3\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-tool\">Pangenome Tool<\/span>\r\n        <\/div>\r\n        <h3>B-Pan<\/h3>\r\n        <p>An integrated pangenome analysis pipeline that characterizes genomic diversity through core\/accessory genome identification, COG functional annotation, and phylogenetic reconstruction.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <span class=\"iblab-badge iblab-publication\">Publication in progress<\/span>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/samavinasir.github.io\/B-Pan\/\" target=\"_blank\" rel=\"noopener\">Launch Tool<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n      <!-- VacSol -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><path d=\"M12 3V7\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><path d=\"M6 8L9 12\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><path d=\"M18 8L15 12\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\"\/><circle cx=\"12\" cy=\"15\" r=\"6\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M9.5 15L11 16.5L14.5 13\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-tool\">Vaccine Design<\/span>\r\n        <\/div>\r\n        <h3>VacSol<\/h3>\r\n        <p>The lab's original reverse vaccinology pipeline, automating subtractive proteomics to identify vaccine and drug target candidates from bacterial genomes.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <a class=\"iblab-link-btn iblab-secondary\" href=\"https:\/\/doi.org\/10.1186\/s12859-017-1540-0\" target=\"_blank\" rel=\"noopener\">Publication<\/a>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/sourceforge.net\/projects\/vacsol\/\" target=\"_blank\" rel=\"noopener\">Launch Tool<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n      <!-- PanRV -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><circle cx=\"12\" cy=\"12\" r=\"3\" stroke=\"#003380\" stroke-width=\"1.6\"\/><circle cx=\"12\" cy=\"4.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"18.5\" cy=\"8.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"18.5\" cy=\"15.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"12\" cy=\"19.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"5.5\" cy=\"15.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><circle cx=\"5.5\" cy=\"8.5\" r=\"1.6\" stroke=\"#003380\" stroke-width=\"1.4\"\/><path d=\"M12 9V6M14.5 10.5L17 9M14.5 13.5L17 15M12 15V18M9.5 13.5L7 15M9.5 10.5L7 9\" stroke=\"#003380\" stroke-width=\"1.3\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-tool\">Pangenome Tool<\/span>\r\n        <\/div>\r\n        <h3>PanRV<\/h3>\r\n        <p>A pangenome-driven reverse vaccinology pipeline that combines core and accessory genome analysis to pinpoint conserved, immunogenic vaccine targets.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <a class=\"iblab-link-btn iblab-secondary\" href=\"https:\/\/doi.org\/10.1186\/s12859-019-2713-9\" target=\"_blank\" rel=\"noopener\">Publication<\/a>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/sourceforge.net\/projects\/panrv2\/\" target=\"_blank\" rel=\"noopener\">Launch Tool<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n      <!-- ResPred.AI -->\r\n      <div class=\"iblab-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><rect x=\"4\" y=\"4\" width=\"16\" height=\"16\" rx=\"3\" stroke=\"#003380\" stroke-width=\"1.6\"\/><path d=\"M8 15L10.5 11L13 13.5L16 9\" stroke=\"#003380\" stroke-width=\"1.6\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-tool\">AMR Prediction<\/span>\r\n        <\/div>\r\n        <h3>ResPred.AI<\/h3>\r\n        <p>An AI-driven prediction engine that profiles antimicrobial resistance signatures directly from genomic data to support rapid surveillance and clinical decision-making.<\/p>\r\n        <div class=\"iblab-card-links\">\r\n          <span class=\"iblab-badge iblab-publication\">Publication in progress<\/span>\r\n          <a class=\"iblab-link-btn iblab-primary\" href=\"https:\/\/mgbio.asab.nust.edu.pk\/respred\" target=\"_blank\" rel=\"noopener\">Launch Tool<\/a>\r\n        <\/div>\r\n      <\/div>\r\n\r\n    <\/div>\r\n  <\/section>\r\n\r\n  <!-- ============ COMING SOON ============ -->\r\n  <section class=\"iblab-section\" id=\"iblab-coming-soon\">\r\n    <div class=\"iblab-section-head\">\r\n      <h2><span class=\"iblab-tag-index\">\u00a73<\/span> In Development<\/h2>\r\n      <span class=\"iblab-count\">1 resource<\/span>\r\n    <\/div>\r\n    <p class=\"iblab-section-sub\">Currently under construction.  Check back for release announcements.<\/p>\r\n\r\n    <div class=\"iblab-grid\">\r\n\r\n      <!-- B-vac.AI -->\r\n      <div class=\"iblab-card iblab-soon-card\">\r\n        <div class=\"iblab-card-top\">\r\n          <div class=\"iblab-card-icon\">\r\n            <svg viewBox=\"0 0 24 24\" fill=\"none\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"><circle cx=\"12\" cy=\"12\" r=\"7.5\" stroke=\"#b8863a\" stroke-width=\"1.6\"\/><path d=\"M12 8V12L14.5 14.5\" stroke=\"#b8863a\" stroke-width=\"1.6\" stroke-linecap=\"round\" stroke-linejoin=\"round\"\/><\/svg>\r\n          <\/div>\r\n          <span class=\"iblab-badge iblab-soon\">Coming Soon<\/span>\r\n        <\/div>\r\n        <h3>B-vac.AI<\/h3>\r\n        <p>A next-generation, machine-learning-based vaccine development tool built to accelerate target discovery across WHO-priority pathogens.<\/p>\r\n        <div class=\"iblab-card-links\"><\/div>\r\n      <\/div>\r\n\r\n    <\/div>\r\n  <\/section>\r\n\r\n<\/div>\r\n<\/div>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Open-Access Research Software Tools &amp; 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