I currently work on proteogenomic analysis, whose generic features are collected for reproducible research.
module load ceuadmin/ffmpeg
ffmpeg -i jumper21s4.mp4 -ss 8 -t 8 s4.mp4
ffmpeg -i s4.mp4 -f gif s4.gif
ffprobe s4.gif
ffmpeg -i s4.gif -s 640x360 CASP14-t1091.gif
ffmpeg -i CASP14-t1091.gif -vf "drawtext=fontsize=20:text='CASP14-t1091':fontcolor=red:x=25:y=30" CASP14-t1091-text.gif
More information is available from "Critical Assessment of protein Structure Prediction (CASP)", https://predictioncenter.org/casp14/
See also Lin, Z., et al. (2023). Evolutionary-scale prediction of atomic-level protein structure with a language model. Science (New York, N.Y.) 379(6637): 1123-1130, https://doi.org/10.1126/science.ade2574.
The sunflower figure is from CCTV4 covering Baiyin, Gansu province, China.
My repositories at workplace can be accessed from .
@examples.svg
<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.5.2/css/all.min.css" type="text/css"?>
<svg aria-roledescription="flowchart-v2" role="graphics-document document" viewBox="-8 -8 924.6624755859375 233" style="max-width: 100%;" xmlns="http://www.w3.org/2000/svg" width="100%" id="graph-div" height="100%" xmlns:xlink="http://www.w3.org/1999/xlink"><style>#graph-div{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;fill:#333;}#graph-div .error-icon{fill:#552222;}#graph-div .error-text{fill:#552222;stroke:#552222;}#graph-div .edge-thickness-normal{stroke-width:2px;}#graph-div .edge-thickness-thick{stroke-width:3.5px;}#graph-div .edge-pattern-solid{stroke-dasharray:0;}#graph-div .edge-pattern-dashed{stroke-dasharray:3;}#graph-div .edge-pattern-dotted{stroke-dasharray:2;}#graph-div .marker{fill:#333333;stroke:#333333;}#graph-div .marker.cross{stroke:#333333;}#graph-div svg{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;}#graph-div .label{font-family:"trebuchet ms",verdana,arial,sans-serif;color:#333;}#graph-div .cluster-label text{fill:#333;}#graph-div .cluster-label span,#graph-div p{color:#333;}#graph-div .label text,#graph-div span,#graph-div p{fill:#333;color:#333;}#graph-div .node rect,#graph-div .node circle,#graph-div .node ellipse,#graph-div .node polygon,#graph-div .node path{fill:#ECECFF;stroke:#9370DB;stroke-width:1px;}#graph-div .flowchart-label text{text-anchor:middle;}#graph-div .node .katex path{fill:#000;stroke:#000;stroke-width:1px;}#graph-div .node .label{text-align:center;}#graph-div .node.clickable{cursor:pointer;}#graph-div .arrowheadPath{fill:#333333;}#graph-div .edgePath .path{stroke:#333333;stroke-width:2.0px;}#graph-div .flowchart-link{stroke:#333333;fill:none;}#graph-div .edgeLabel{background-color:#e8e8e8;text-align:center;}#graph-div .edgeLabel rect{opacity:0.5;background-color:#e8e8e8;fill:#e8e8e8;}#graph-div .labelBkg{background-color:rgba(232, 232, 232, 0.5);}#graph-div .cluster rect{fill:#ffffde;stroke:#aaaa33;stroke-width:1px;}#graph-div .cluster text{fill:#333;}#graph-div .cluster span,#graph-div p{color:#333;}#graph-div div.mermaidTooltip{position:absolute;text-align:center;max-width:200px;padding:2px;font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:12px;background:hsl(80, 100%, 96.2745098039%);border:1px solid #aaaa33;border-radius:2px;pointer-events:none;z-index:100;}#graph-div .flowchartTitleText{text-anchor:middle;font-size:18px;fill:#333;}#graph-div :root{--mermaid-font-family:"trebuchet ms",verdana,arial,sans-serif;}</style><g><marker orient="auto" markerHeight="12" markerWidth="12" markerUnits="userSpaceOnUse" refY="5" refX="6" viewBox="0 0 10 10" class="marker flowchart" id="graph-div_flowchart-pointEnd"><path style="stroke-width: 1px; stroke-dasharray: 1px, 0px;" class="arrowMarkerPath" d="M 0 0 L 10 5 L 0 10 z"></path></marker><marker orient="auto" markerHeight="12" markerWidth="12" markerUnits="userSpaceOnUse" refY="5" refX="4.5" viewBox="0 0 10 10" class="marker flowchart" id="graph-div_flowchart-pointStart"><path style="stroke-width: 1px; stroke-dasharray: 1px, 0px;" class="arrowMarkerPath" d="M 0 5 L 10 10 L 10 0 z"></path></marker><marker orient="auto" markerHeight="11" markerWidth="11" markerUnits="userSpaceOnUse" refY="5" refX="11" viewBox="0 0 10 10" class="marker flowchart" id="graph-div_flowchart-circleEnd"><circle style="stroke-width: 1px; stroke-dasharray: 1px, 0px;" class="arrowMarkerPath" r="5" cy="5" cx="5"></circle></marker><marker orient="auto" markerHeight="11" markerWidth="11" markerUnits="userSpaceOnUse" refY="5" refX="-1" viewBox="0 0 10 10" class="marker flowchart" id="graph-div_flowchart-circleStart"><circle style="stroke-width: 1px; stroke-dasharray: 1px, 0px;" class="arrowMarkerPath" r="5" cy="5" cx="5"></circle></marker><marker orient="auto" markerHeight="11" markerWidth="11" markerUnits="userSpaceOnUse" refY="5.2" refX="12" viewBox="0 0 11 11" class="marker cross flowchart" id="graph-div_flowchart-crossEnd"><path style="stroke-width: 2px; stroke-dasharray: 1px, 0px;" class="arrowMarkerPath" d="M 1,1 l 9,9 M 10,1 l -9,9"></path></marker><marker orient="auto" markerHeight="11" markerWidth="11" markerUnits="userSpaceOnUse" refY="5.2" refX="-1" viewBox="0 0 11 11" class="marker cross flowchart" id="graph-div_flowchart-crossStart"><path style="stroke-width: 2px; stroke-dasharray: 1px, 0px;" class="arrowMarkerPath" d="M 1,1 l 9,9 M 10,1 l -9,9"></path></marker><g class="root"><g class="clusters"></g><g class="edgePaths"><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-cambridge_ceu LE-internals" id="L-cambridge_ceu-internals-0" d="M656.029,25.063L585.301,31.553C514.574,38.042,373.118,51.021,302.39,60.794C231.662,70.567,231.662,77.133,231.662,80.417L231.662,83.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-cambridge_ceu LE-externals" id="L-cambridge_ceu-externals-0" d="M656.029,28.6L616.718,34.5C577.407,40.4,498.785,52.2,459.474,61.383C420.162,70.567,420.162,77.133,420.162,80.417L420.162,83.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-cambridge_ceu LE-blog" id="L-cambridge_ceu-blog-0" d="M656.029,31.877L629.801,37.231C603.574,42.585,551.118,53.292,530.521,62.929C509.923,72.566,521.184,81.131,526.814,85.414L532.444,89.697"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-internals LE-journal_club" id="L-internals-journal_club-0" d="M159.662,127.165L143.052,131.47C126.442,135.776,93.221,144.388,76.61,151.977C60,159.567,60,166.133,60,169.417L60,172.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-internals LE-scientific_meetings" id="L-internals-scientific_meetings-0" d="M241.232,128L243.276,132.167C245.321,136.333,249.411,144.667,251.455,152.117C253.5,159.567,253.5,166.133,253.5,169.417L253.5,172.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-internals LE-journal_dot" id="L-internals-journal_dot-0" d="M303.662,127.165L320.273,131.47C336.883,135.776,370.104,144.388,386.715,151.977C403.325,159.567,403.325,166.133,403.325,169.417L403.325,172.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-internals LE-github_matters" id="L-internals-github_matters-0" d="M303.662,119.38L340.744,124.983C377.825,130.587,451.987,141.793,489.069,150.68C526.15,159.567,526.15,166.133,526.15,169.417L526.15,172.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-internals LE-csd3" id="L-internals-csd3-0" d="M303.662,116.057L362.327,122.214C420.992,128.371,538.321,140.686,596.985,150.126C655.65,159.567,655.65,166.133,655.65,169.417L655.65,172.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-cambridge_ceu LE-blog" id="L-cambridge_ceu-blog-1" d="M664.297,39L653.108,43.167C641.919,47.333,619.541,55.667,605.197,63.343C590.853,71.019,584.543,78.039,581.388,81.549L578.234,85.058"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-cambridge_ceu LE-github" id="L-cambridge_ceu-github-0" d="M690.589,39L685.018,43.167C679.447,47.333,668.305,55.667,662.734,63.117C657.162,70.567,657.162,77.133,657.162,80.417L657.162,83.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-cambridge_ceu LE-search" id="L-cambridge_ceu-search-0" d="M737.915,39L742.457,43.167C746.998,47.333,756.08,55.667,760.621,63.117C765.162,70.567,765.162,77.133,765.162,80.417L765.162,83.7"></path><path marker-end="url(#graph-div_flowchart-pointEnd)" style="fill:none;" class="edge-thickness-normal edge-pattern-solid flowchart-link LS-cambridge_ceu LE-contact" id="L-cambridge_ceu-contact-0" d="M777.296,36.417L793.774,41.014C810.251,45.611,843.207,54.806,859.685,62.686C876.162,70.567,876.162,77.133,876.162,80.417L876.162,83.7"></path></g><g class="edgeLabels"><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g transform="translate(0, 0)" class="label"><foreignObject height="0" width="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g></g><g class="nodes"><g transform="translate(716.6624984741211, 19.5)" data-id="cambridge_ceu" data-node="true" id="flowchart-cambridge_ceu-174" class="node default default flowchart-label"><rect height="39" width="121.26666259765625" y="-19.5" x="-60.633331298828125" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-53.133331298828125, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="106.26666259765625"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">cambridge-ceu</span></div></foreignObject></g></g><g transform="translate(231.6624984741211, 108.5)" data-id="internals" data-node="true" id="flowchart-internals-175" class="node default default flowchart-label"><rect height="39" width="144" y="-19.5" x="-72" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-64.5, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="129"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/internal/">Internal repositories</a></span></div></foreignObject></g></g><g transform="translate(420.1624984741211, 108.5)" data-id="externals" data-node="true" id="flowchart-externals-177" class="node default default flowchart-label"><rect height="39" width="133" y="-19.5" x="-66.5" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-59, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="118"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/public/">Public repositories</a></span></div></foreignObject></g></g><g transform="translate(557.1624984741211, 108.5)" data-id="blog" data-node="true" id="flowchart-blog-179" class="node default default flowchart-label"><rect height="39" width="41" y="-19.5" x="-20.5" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-13, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="26"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/blog/">Blog</a></span></div></foreignObject></g></g><g transform="translate(60, 197.5)" data-id="journal_club" data-node="true" id="flowchart-journal_club-181" class="node default default flowchart-label"><rect height="39" width="120" y="-19.5" x="-60" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-52.5, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="105"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/CEU-journal-club/">CEU-journal-club</a></span></div></foreignObject></g></g><g transform="translate(253.5, 197.5)" data-id="scientific_meetings" data-node="true" id="flowchart-scientific_meetings-183" class="node default default flowchart-label"><rect height="39" width="167" y="-19.5" x="-83.5" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-76, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="152"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/CEU-scientific-meetings/">CEU-scientific-meetings</a></span></div></foreignObject></g></g><g transform="translate(403.3249969482422, 197.5)" data-id="journal_dot" data-node="true" id="flowchart-journal_dot-185" class="node default default flowchart-label"><rect height="39" width="32.649993896484375" y="-19.5" x="-16.324996948242188" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-8.824996948242188, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="17.649993896484375"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">...</span></div></foreignObject></g></g><g transform="translate(526.1499938964844, 197.5)" data-id="github_matters" data-node="true" id="flowchart-github_matters-187" class="node default default flowchart-label"><rect height="39" width="113" y="-19.5" x="-56.5" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-49, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="98"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/GitHub-matters/">GitHub-matters</a></span></div></foreignObject></g></g><g transform="translate(655.6499938964844, 197.5)" data-id="csd3" data-node="true" id="flowchart-csd3-189" class="node default default flowchart-label"><rect height="39" width="46" y="-19.5" x="-23" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-15.5, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="31"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/csd3/">CSD3</a></span></div></foreignObject></g></g><g transform="translate(657.1624984741211, 108.5)" data-id="github" data-node="true" id="flowchart-github-193" class="node default default flowchart-label"><rect height="39" width="59" y="-19.5" x="-29.5" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-22, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="44"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://github.com/cambridge-ceu/">GitHub</a></span></div></foreignObject></g></g><g transform="translate(765.1624984741211, 108.5)" data-id="search" data-node="true" id="flowchart-search-195" class="node default default flowchart-label"><rect height="39" width="57" y="-19.5" x="-28.5" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-21, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="42"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/search/">Search</a></span></div></foreignObject></g></g><g transform="translate(876.1624984741211, 108.5)" data-id="contact" data-node="true" id="flowchart-contact-197" class="node default default flowchart-label"><rect height="39" width="65" y="-19.5" x="-32.5" ry="0" rx="0" style="" class="basic label-container"></rect><g transform="translate(-25, -12)" style="" class="label"><rect></rect><foreignObject height="24" width="50"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel"><a style="font-size: 25px;font-size:90%" href="https://cambridge-ceu.github.io/contact/">Contact</a></span></div></foreignObject></g></g></g></g></g></svg>
@example.svg