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Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates). Please follow, star, and fork to get the latest functions.

PenSimPy

PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation. This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.

PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration, dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid, phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.

Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes. A web application based on PenSimPy can be found here.

Installation

PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself. Once fastodeint is installed, you can install PenSimPy by the following command

pip install pensimpy

Examples

See the examples directory

About

The Python implementation of IndPenSim

Resources

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1 star

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates).
Please follow, star, and fork to get the latest functions.
PenSimPy 
PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation.
This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.
PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration,
dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid,
phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used
Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.
Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes.
A web application based on PenSimPy can be found here.
Installation
PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself.
Once fastodeint is installed, you can install PenSimPy by the following command
pip install pensimpy

Examples
See the examples directory
About
The Python implementation of IndPenSim
Resources
Readme
License
Activity
Stars
1 star
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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alt text
Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates).
Please follow, star, and fork to get the latest functions.
PenSimPy 
PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation.
This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.
PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration,
dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid,
phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used
Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.
Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes.
A web application based on PenSimPy can be found here.
Installation
PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself.
Once fastodeint is installed, you can install PenSimPy by the following command
pip install pensimpy

Examples
See the examples directory
About
The Python implementation of IndPenSim
Resources
Readme
License
Activity
Stars
1 star
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
alt text
Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates).
Please follow, star, and fork to get the latest functions.
PenSimPy 
PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation.
This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.
PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration,
dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid,
phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used
Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.
Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes.
A web application based on PenSimPy can be found here.
Installation
PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself.
Once fastodeint is installed, you can install PenSimPy by the following command
pip install pensimpy

Examples
See the examples directory
About
The Python implementation of IndPenSim
Resources
Readme
License
Activity
Stars
1 star
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
alt text
Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates).
Please follow, star, and fork to get the latest functions.
PenSimPy 
PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation.
This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.
PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration,
dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid,
phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used
Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.
Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes.
A web application based on PenSimPy can be found here.
Installation
PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself.
Once fastodeint is installed, you can install PenSimPy by the following command
pip install pensimpy

Examples
See the examples directory
About
The Python implementation of IndPenSim
Resources
Readme
License
Activity
Stars
1 star
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
alt text
Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates).
Please follow, star, and fork to get the latest functions.
PenSimPy 
PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation.
This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.
PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration,
dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid,
phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used
Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.
Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes.
A web application based on PenSimPy can be found here.
Installation
PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself.
Once fastodeint is installed, you can install PenSimPy by the following command
pip install pensimpy

Examples
See the examples directory
About
The Python implementation of IndPenSim
Resources
Readme
License
Activity
Stars
1 star
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
alt text
Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates).
Please follow, star, and fork to get the latest functions.
PenSimPy 
PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation.
This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.
PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration,
dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid,
phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used
Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.
Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes.
A web application based on PenSimPy can be found here.
Installation
PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself.
Once fastodeint is installed, you can install PenSimPy by the following command
pip install pensimpy

Examples
See the examples directory
About
The Python implementation of IndPenSim
Resources
Readme
License
Activity
Stars
1 star
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
alt text
Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates).
Please follow, star, and fork to get the latest functions.
PenSimPy 
PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation.
This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.
PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration,
dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid,
phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used
Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.
Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes.
A web application based on PenSimPy can be found here.
Installation
PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself.
Once fastodeint is installed, you can install PenSimPy by the following command
pip install pensimpy

Examples
See the examples directory
About
The Python implementation of IndPenSim
Resources
Readme
License
Activity
Stars
1 star
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages