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About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all \u003cpre\u003e\u003ccode\u003e 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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About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

Resources

Readme
License

Contributing

Contributing
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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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Current releaseGitHub DiscussionsZenodoMATLAB File Exchange

About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

Resources

Readme
License

Contributing

Contributing
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131 stars

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13 watching

Forks

62 forks
Report repository

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, '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 \u003e 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
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Current releaseGitHub DiscussionsZenodoMATLAB File Exchange

About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

Resources

Readme
License

Contributing

Contributing
Activity
Custom properties

Stars

131 stars

Watchers

13 watching

Forks

62 forks
Report repository

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, '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
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Current releaseGitHub DiscussionsZenodoMATLAB File Exchange

About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

Resources

Readme
License

Contributing

Contributing
Activity
Custom properties

Stars

131 stars

Watchers

13 watching

Forks

62 forks
Report repository

Releases

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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
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About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

Resources

Readme
License

Contributing

Contributing
Activity
Custom properties

Stars

131 stars

Watchers

13 watching

Forks

62 forks
Report repository

Releases

Used by

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
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About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

Resources

Readme
License

Contributing

Contributing
Activity
Custom properties

Stars

131 stars

Watchers

13 watching

Forks

62 forks
Report repository

Releases

Used by

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About RAVEN 2

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for MATLAB that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Documentation

The information about downloading, installing and developing RAVEN is included in the Wiki. The source code documentation is also available online.

Cite Us

If you use RAVEN 2 in your scientific work, please cite:

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ. (2018) RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput Biol 14(10): e1006541. doi:10.1371/journal.pcbi.1006541.

Starting with RAVEN v2.3.1, all the releases are also archived in Zenodo, for you to cite the specific version of RAVEN that you used in your study

If you use ftINIT in your scientific work, please cite:

Gustafsson J, Anton M, Roshanzamir F, Jörnsten R, Kerkhoven EJ, Robinson JL, Nielsen J. (2023) Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proc Natl Acad Sci 120(6): e2217868120. doi:10.1073/pnas.2217868120

For crediting supporting work, please cite doi:10.1002/msb.145122 (tInit); doi:10.1371/journal.pcbi.1000859 (randomsampling). For crediting RAVEN 1, cite doi:10.1371/journal.pcbi.1002980. For more details, see wiki#cite-us.

Contact Us

Use GitHub Discussions for support, to ask questions or leave comments.

Contributing

Contributions are always welcome! Please read the Contributor guidelines to get started.

About

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

sysbiochalmers.github.io/RAVEN/

Topics

constraint-based-modelinggap-fillinggenome-scale-modelshuman-metabolismmetabolic-engineeringmetabolic-modelsmetabolic-reconstructionsysbiosystems-biology

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