| − | <html lang="en"><head><meta charset="utf-8"/><meta content="width=device-width,initial-scale=1" name="viewport"/><title>Notebook | UIUCiGEM</title><script src="https://2020.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><link href="https://2021.igem.org/Template:UIUC_Illinois/css/contentCSS?action=raw&ctype=text/css" rel="stylesheet"/></head><body><nav class="navbar navbar-expand-xl fixed-top"><div class="container d-flex justify-content-between"><a class="navbar-brand d-lg-inline-block" href="https://2021.igem.org/Team:UIUC_Illinois"><span>iGEM </span>UIUC</a><button aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation" class="navbar-toggler" data-target="#navbarNav" data-toggle="collapse" type="button"><span class="navbar-toggler-icon"></span></button><div class="collapse navbar-collapse" id="navbarNav"><ul class="navbar-nav ml-auto"><li class="nav-item dropdown"><a aria-expanded="false" aria-haspopup="true" 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class="my-4"/></div></header><main><div class="container"><div class="row"><div class="sidebar col-lg-3"><div class="nav" id="contents"><h5>Contents</h5><ul></ul></div></div><div class="content col-lg-9"><article><h1>Headings</h1><h2>Level 2 Heading</h2><h3>Level 3 Heading</h3><h4>Level 4 Heading</h4><h1>Emphasis</h1><p>This is regular text.</p><p><strong>This is bold text.</strong> <strong>This is also bold text.</strong></p><p><em>This is italic text.</em> _This is also italix text.*</p><p><em><strong>This text is bold and italic both.</strong></em> <em><strong>This text is bold and italic both.</strong></em></p><p><s>Strikethrough</s></p><h1>Lists</h1><ol><li>This is item one.</li><li>This is item two.</li><li>It's okay to number every item as 1.<ul><li>This is a nested list.</li><li>Use asterisk for an unordered list,</li><li>Further nesting?</li></ul><ul><li>Plus sign also works.</li></ul><ul><li>And so does minus.</li></ul></li><li><s>Birds aren't real.</s></li></ol><h1>Links</h1><p><a href="https://google.com">Google</a></p><p><a href="https://2021.igem.org/Team:UIUC_Illinois/Notebook/Link-goes-in-parenthesis">Text goes in square brackets</a></p><h1>Blockquote</h1><blockquote><p>This is a blockquote. This continues in the same paragraph.</p><p>To change the paragraph, you have to leave a line.</p></blockquote><blockquote><p>This is another blockquote.</p><p><strong>Pranav Ballaney, 2020</strong></p></blockquote><h1>Images</h1><p>This is a regular paragraph.</p><h4>This is a level 4 heading.</h4><p><a href="google.com">This is a link</a></p><div class="image"><img alt="Caption" src="https://static.igem.org/mediawiki/2021/f/f0/T--UIUC_Illinois--img--Description--josh-withers.jpg" style="width: 100%"/><p>Figure 1: Caption</p></div><p>Back to regular text.</p><h1>Tables</h1><p>This is a regular paragraph, which precedes the table. When you want to insert a table, indent one level back and specify the plugin. Then indent inside again and start writing the table.</p><table><caption id="table1captiongoeshere">Table 1: Caption goes here.</caption><thead><tr><th>This is</th><th>the table</th><th>header row</th></tr></thead><tbody><tr><td>1</td><td>2</td><td>3</td></tr><tr><td>4</td><td>5</td><td>6</td></tr></tbody></table><p>And when you're done, go back to the regular markdown filter.</p><p><strong>Example 2:</strong></p><table><thead><tr><th style="text-align:left">Left aligned</th><th style="text-align:center">Center aligned</th><th style="text-align:right">Right aligned</th></tr></thead><tbody><tr><td style="text-align:left">1</td><td style="text-align:center">2</td><td style="text-align:right">3</td></tr><tr><td style="text-align:left">4</td><td style="text-align:center">5</td><td style="text-align:right">6</td></tr></tbody></table><p><strong>Example 3:</strong></p><table><caption id="table3captiongoeshere">Table 3: Caption goes here.</caption><thead><tr><th></th><th colspan="2" style="text-align:center">Grouping</th></tr><tr><th>First Header</th><th style="text-align:center">Second Header</th><th style="text-align:right">Third Header</th></tr></thead><tbody><tr><td>Content</td><td colspan="2" style="text-align:center"><em>Long Cell</em></td></tr><tr><td>Content</td><td style="text-align:center"><strong>Cell</strong></td><td style="text-align:right">Cell</td></tr><tr><td>New section</td><td style="text-align:center">More</td><td style="text-align:right"><a href="https://google.com">Data</a></td></tr><tr><td>And more</td><td colspan="2" style="text-align:center">With an escaped '|'</td></tr></tbody></table><h1>Definitions</h1><p><dfn>Term ~ Definition</dfn></p><p>This can come <dfn>anywhere in ~ the text</dfn>.</p><h1>MathJax</h1><p>$$\int_{0}^{\infty} e^{-x^2} dx = \frac{\sqrt{\pi}}{2}$$</p><p>$$-\frac{\hbar^2}{2m}\nabla^2\psi + V\psi = E\psi$$</p><p>$$i\hbar\gamma^\mu\partial_\mu\psi = mc\psi$$</p><p>$$y_k = \frac{1}{\sqrt{N}}\sum_{n=0}^{N-1}x_n\omega_N^{kn}$$</p><h1>Citations</h1><p>In text citation for a research article with a DOI. <a href="#citation2">Rosano et al., 2019</a></p><p>In text citation for another research article with a DOI. <a href="#citation1">Allen & Sheridan, 2015</a></p><p>In text citation for a book with no DOI. <a href="#citation3">Ingalls, 2013</a></p><p>In text citation for a website with institutional author. <a href="#citation4">TNAU Agritech Portal, n.d.</a></p><p>In text citation for a website with an author. <a href="#citation5">Author, n.d.</a></p></article><article id="references"><h1>References</h1><ol><li id="citation1"><p class="author">Allen, M. J., & Sheridan, S. C. (2015).</p><cite>Mortality risks during extreme temperature events (ETEs) using a distributed lag non-linear model.</cite><p><span class="journalTitle">International Journal of Biometeorology</span> <span class="journalInfo">62(1), 57-67.</span></p><a class="in-text" href="https://doi.org/10.1007/s00484-015-1117-4" rel="noopener" target="_blank">CrossRef</a><a class="in-text" href="https://scholar.google.com/scholar?q=Mortality risks during extreme temperature events (ETEs) using a distributed lag non-linear model." rel="noopener" target="_blank">Google Scholar</a><a class="in-text" href="#intext1">Back to text</a></li><li id="citation2"><p class="author">Rosano, A., Bella, A., Gesualdo, F., Acampora, A., Pezzotti, P., Marchetti, S., ... & Rizzo, C. (2019).</p><cite>Investigating the impact of influenza on excess mortality in all ages in Italy during recent seasons (2013/14-2016/17 seasons).</cite><p><span class="journalTitle">International Journal of Infectious Diseases</span> <span class="journalInfo">88, 127-134.</span></p><a class="in-text" href="https://doi.org/10.1016/j.ijid.2019.08.003" rel="noopener" target="_blank">CrossRef</a><a class="in-text" href="https://scholar.google.com/scholar?q=Investigating the impact of influenza on excess mortality in all ages in Italy during recent seasons (2013/14-2016/17 seasons)." rel="noopener" target="_blank">Google Scholar</a><a class="in-text" href="#intext2">Back to text</a></li><li id="citation3"><p class="author">Ingalls, B. P. (2013).</p><cite>Mathematical modeling in systems biology: An introduction.</cite><p><span class="details">MIT Press.</span></p><a class="in-text" href="https://books.google.co.in/books?id=OYr6AQAAQBAJ" rel="noopener" target="_blank">Google Books</a><a class="in-text" href="#intext3">Back to text</a></li><li id="citation4"><p class="author"></p><cite>Agriculture: Crop production: Sugarcane. TNAU Agritech Portal.</cite><p><span class="details">(March 15, 2019). Retrieved on June 22, 2020. from </span><a class="in-text" href="https://google.com" rel="noopener" target="_blank">https://google.com</a></p><a class="in-text" href="#intext4">Back to text</a></li><li id="citation5"><p class="author">Author Name. (n.d.).</p><cite>Agriculture: Crop production: Sugarcane. TNAU Agritech Portal.</cite><p><span class="details">Retrieved on June 22, 2020. from </span><a class="in-text" href="https://google.com" rel="noopener" target="_blank">https://google.com</a></p><a class="in-text" href="#intext5">Back to text</a></li></ol></article></div></div></div></main><footer><div class="container"><p>Sample template built using the iGEM Wiki Starter Pack by BITS Goa.</p><p>Code released under the MIT license.</p><p>Based on <a href="https://getbootstrap.com">Bootstrap</a> and themes <a href="https://bootswatch.com/flatly/">Flatly</a> and <a href="https://bootswatch.com/darkly/">Darkly</a> from <a href="https://bootswatch.com/">Bootswatch</a>.</p><p>Some content from the <a href="https://2020.igem.org/Team:Example">iGEM Example Wiki</a>. Images from <a href="https://unsplash.com">Unsplash</a>. Web fonts from <a href="https://fonts.google.com">Google</a>.</p></div></footer><script src="https://2021.igem.org/Template:UIUC_Illinois/content-bundleJS?action=raw&ctype=text/javascript"></script></body></html>
| + | <html lang="en"><head><meta charset="utf-8"/><meta content="width=device-width,initial-scale=1" name="viewport"/><title>Notebook | UIUCiGEM</title><link href="https://2021.igem.org/Template:UIUC_Illinois/css/contentCSS?action=raw&ctype=text/css" rel="stylesheet"/></head><body><nav class="navbar navbar-expand-xl fixed-top"><div class="container d-flex justify-content-between"><a class="navbar-brand" href="https://2021.igem.org/Team:UIUC_Illinois"><i class="navbar-logo"></i></a><button aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation" class="navbar-toggler" data-target="#navbarNav" data-toggle="collapse" type="button"><span class="navbar-toggler-icon"></span></button><div class="collapse navbar-collapse" id="navbarNav"><ul class="navbar-nav ml-auto"><li class="nav-item dropdown"><a aria-expanded="false" aria-haspopup="true" class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" id="navbarTeamDropdown" role="button">Team</a><div 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href="https://2021.igem.org/Team:UIUC_Illinois/Package">Excellence in another area</a><a class="dropdown-item" href="https://2021.igem.org/Team:UIUC_Illinois/Experiments">Experiments</a><a class="dropdown-item" href="https://2021.igem.org/Team:UIUC_Illinois/Model">Model</a><a class="dropdown-item" href="https://2021.igem.org/Team:UIUC_Illinois/Notebook">Notebook</a><a class="dropdown-item" href="https://2021.igem.org/Team:UIUC_Illinois/Partnership">Partnership</a><a class="dropdown-item" href="https://2021.igem.org/Team:UIUC_Illinois/Implementation">Proposed Implementation</a><a class="dropdown-item" href="https://2021.igem.org/Team:UIUC_Illinois/Results">Results</a></div></li><li class="nav-item"><a class="nav-link" href="https://2021.igem.org/Team:UIUC_Illinois/Parts">Parts</a></li><li class="nav-item"><a class="nav-link" href="https://2021.igem.org/Team:UIUC_Illinois/Safety">Safety</a></li><li class="nav-item"><a class="nav-link" href="https://2021.igem.org/Team:UIUC_Illinois/Human_Practices">Human Practices</a></li></ul></div><div class="d-flex" id="themeSwitchWrapper"><i class="far fa-sun"></i><div id="themeSwitch"><label class="switch" for="themeSwitchInput"><input id="themeSwitchInput" type="checkbox"/><span class="slider round"></span></label></div><i class="far fa-moon"></i></div></div></nav><header class="d-flex justify-content-center align-items-center"><div class="container"><h1>Notebook</h1><p class="lead pl-1">Documenting our progress and timeline of our project</p><hr class="my-4"/></div></header><main><div class="container"><div class="row"><div class="sidebar col-lg-3"><div class="nav" id="contents"><h5>Contents</h5><ul></ul></div></div><div class="content col-lg-9"><article><h1>March</h1><h5><a href="https://docs.google.com/presentation/d/1QsMs5O9dXddDGm6dOUSNo-jtgfl_qNP77RfKf1uZuoE/edit?usp=sharing">Week 1</a></h5><ul><li>First team meeting, brainstormed ideas for the project</li></ul><h5><a href="https://docs.google.com/presentation/d/1ct75cn6P3tdHqn7d1uOC8eB6tiNB4VVTNMSjk2wf2tU/edit#slide=id.p">Week 2</a></h5><ul><li>Continuation of Week 1</li></ul><h5><a href="https://docs.google.com/presentation/d/1ewm9bSkwOJqjLO6MO2zrWWgQ-CpccWu5hi2LQyTdNsA/edit#slide=id.p">Week 3</a></h5><ul><li>Narrowed down our project ideas into top two contenders</li></ul><h1>April</h1><h5><a href="https://docs.google.com/presentation/d/16mGN80M4SeKDFyraB4mOoL7qHQRSVn2fe-bXS2BXFjs/edit#slide=id.p">Week 1</a></h5><ul><li>Decided our project topic: Plastic Degradation</li></ul><h5><a href="https://docs.google.com/presentation/d/1mL1wPnVBBH3IET4NTy8y2t0uNuXKPg2HBiFtm1poLEU/edit#slide=id.p">Week 2</a></h5><ul><li>Planned for our project to be composed of a drylab component and a wetlab component</li></ul><h5><a href="https://docs.google.com/presentation/d/1mL1wPnVBBH3IET4NTy8y2t0uNuXKPg2HBiFtm1poLEU/edit#slide=id.p">Week 3</a></h5><ul><li>Brainstormed end goals and tasks for each component of the project</li></ul><h5><a href="https://docs.google.com/presentation/d/1bHYOngWQqoKQGqgpKpaxqRcXzaGb0AudkvwBUNOSSho/edit#slide=id.p">Week 4</a></h5><ul><li>Continuation of Week 3</li></ul><h1>May</h1><h5><a href="https://docs.google.com/presentation/d/11sG14wPYblFdip2gozcdJ6hmnL3QZ9BFtYuw5GUWD2E/edit#slide=id.p">Week 1</a></h5><ul><li>Began literature review for PETase and PET degradation studies</li></ul><h5>Week 2</h5><ul><li>Off week for finals</li></ul><h5><a href="https://docs.google.com/presentation/d/1wH2a9YTCVhDeQHsOzf00dOrrgOYNyrUolY52JRQeexI/edit#slide=id.p">Week 3</a></h5><ul><li>Wetlab: Developed initial protocols</li><li>Drylab: Evaluated different methods of creating a model for new protein sequences</li></ul><h5><a href="https://docs.google.com/presentation/d/1CP6EWY59IrhPJcV3P623Et0aHCNZG_a-Mx6REjDn2Ag/edit#slide=id.p">Week 4</a></h5><ul><li>Continuation of Week 3</li></ul><h1>June</h1><h5><a href="https://docs.google.com/presentation/d/1-hA1KMC0a3G69YG1lB8Ooe7FXrh8YUs1s99g8RfalbI/edit#slide=id.p">Week 1</a></h5><ul><li>Wetlab: Reagents prepared for initial testing of plasmids</li><li>Drylab: Evaluated HMMER and RNN models and their efficacy for sequence analysis and generation</li></ul><h5><a href="https://docs.google.com/presentation/d/1JkmoeHbtuNdLG3UUHCLSfVrMtDNvYVqo0z9oK29NCRY/edit#slide=id.p">Week 2</a></h5><ul><li>Wetlab: Began practice for plasmid transformation and purification</li><li>Drylab: Decided on using an RNN pipeline, researched prior iGEM teams’ computational work with PETase</li></ul><h5><a href="https://docs.google.com/presentation/d/1BklqAkUwnTEajw7hmNL0NIjF3P0AcCJZv8g6I_7HJas/edit#slide=id.ge2014a9313_0_124">Week 3</a></h5><ul><li>Wetlab: Received plasmids, continue work with competent cells</li><li>Drylab: Continued research into previous iGEM work, specifically 2019 iGEM Toronto. Analyzed their pipeline and researched use-cases of UniRep + Docker</li></ul><h5><a href="https://docs.google.com/presentation/d/17E7ev24W4Sl4oF6TSZ0p3ztoG5MlSmeUQrQeONJHdsA/edit#slide=id.p">Week 4</a></h5><ul><li>Wetlab: Performed plasmid purification and Nanodrop analysis, reviewing errors for coming weeks</li><li>Drylab: Compiled initial set of training sequences from literature review. Also performed sequence alignment of Toronto iGEM’s sequences using BLAST</li></ul><h1>July</h1><h5><a href="https://docs.google.com/presentation/d/1bnAyHE6kmmF9FN4Hl38QYyU8d1GjwFQdQ5NUy1l_vPk/edit#slide=id.p">Week 1</a></h5><ul><li>Wetlab: Troubleshooting restriction digest, sequenced extracted DNA</li><li>Drylab: Continued sequence gathering for model training, and set up Docker for pipeline testing. Emailed iGEM Toronto for questions and possible</li></ul><h5><a href="https://docs.google.com/presentation/d/1e_fsa3oVsSB6Vjj1LR-ediGt81HpuG82O8tiv4Ml5Ys/edit#slide=id.p">Week 2</a></h5><ul><li>Wetlab: Performed SDS-PAGE and troubleshooting</li><li>Drylab: Continuation of Week 1, UniRep tutorial started</li></ul><h5><a href="https://docs.google.com/presentation/d/1732h4edFuFtsL7opWxOv2zII7vPEOd4SOkVL6_YdC_E/edit#slide=id.p">Week 3</a></h5><ul><li>Wetlab: Ran more SDS-PAGEs, began preparation for protein purification</li><li>Drylab: Began pipeline work, continued literature review for enzyme characteristics like thermostability and catalytic activity</li></ul><h5><a href="https://docs.google.com/presentation/d/1W9yBFgRXfXQg_uo0MR4lhWxRc_zov9LZnZNO2CN_kr0/edit#slide=id.p">Week 4</a></h5><ul><li>Wetlab: Additional troubleshooting for previous protocols, began collaboration with UT Austin’s wetlab group for protein purification troubleshooting</li><li>Drylab: Tested iGEM Toronto 2019’s initial pipeline for any output, continue studying code architecture for incorporation of our training set</li><li>Attended JulyGEM meetup with other iGEM teams to receive feedback on our progress so far</li></ul><h1>August</h1><h5><a href="https://docs.google.com/presentation/d/17_5iAI87U401O_xrUQ04Xyg3rb6hqcKarI4hcfO6AdU/edit#slide=id.p">Week 1</a></h5><ul><li>Wetlab: Literature review for protocols, especially alternative lysis</li><li>Drylab: Pipeline tested, several technical issues and platform issues with Docker and Colab debugged. Working to create CRUD table for a PETase web database</li></ul><h5><a href="https://docs.google.com/presentation/d/1C-FhNVVKdUvdJexONQ4QcEqYbhHCq2UOJdfQp825t_A/edit#slide=id.p">Week 2</a></h5><ul><li>Wetlab: Worked on protocols for coming weeks (competent cells)</li><li>Drylab: Completed basic pipeline debugs, able to generate sequence output. Began preparation of training set for the pipeline</li></ul><h5><a href="https://docs.google.com/presentation/d/1LLjLETke3wk_n3dQZuqzZxWiW8mHVzdNdIu2xISO3ic/edit#slide=id.p">Week 3</a></h5><ul><li>Wetlab: No updates, continued work from Week 2</li><li>Drylab: Completed further modifications to pipeline and ran model with our training data, output sequences generated flawlessly. Continued work on web PETase database in collaboration with iGEM Toronto</li></ul><h5><a href="https://docs.google.com/presentation/d/1TggnsJ_xugIN7gk8kPTjVbrc9-qeXwC2fiJHrbi5uxg/edit#slide=id.p">Week 4</a></h5><ul><li>Wetlab: Began plasmid purification and protein purification prep, update protocols</li><li>Drylab: No updates, aside from further pipeline testing and database work</li><li>Interviewed Dr. Ting Lu in Bioengineering</li></ul><h1>September</h1><h5><a href="https://docs.google.com/presentation/d/1GkzuJP3rYdNdVgg0MVCc-qhCz09jTsw2LfuX5AzwOhA/edit#slide=id.p">Week 1</a></h5><ul><li>Wetlab: Protein and plasmid purification, ordered mutants</li><li>Drylab: Sent three mutant candidates to wetlab for validation. Began package development</li></ul><h5><a href="https://docs.google.com/presentation/d/15HUNq47EgKIL7vwKNleM1yt11M4WhEJ320mbNDacIJs/edit#slide=id.gf07a4d5387_0_0">Week 2</a></h5><ul><li>Wetlab: Continuation of Week 1, continued contact with UT Austin for troubleshooting</li><li>Drylab: Drafting master document for wiki and compiling all information. Continued collaboration with iGEM Toronto for PETase sequence database. Package development in progress.</li></ul><h5><a href="https://docs.google.com/presentation/d/15HUNq47EgKIL7vwKNleM1yt11M4WhEJ320mbNDacIJs/edit#slide=id.gf07a4d5387_0_0">Week 3</a></h5><ul><li>Wetlab: Obtained PET band on SDS-PAGE gel, began prep for FPLC</li><li>Drylab: Continued work on master wiki document</li></ul><h5>Week 4</h5><ul><li>Off-week for midterms and other commitments</li></ul><h1>October</h1><h5><a href="https://docs.google.com/presentation/d/1j1odutGd0F6B3LYI3fbc72fkV40GRizPUPmH3CzStjw/edit#slide=id.gef963dee75_0_27">Week 1</a></h5><ul><li>Wetlab: FPLC preparation and training</li><li>Drylab: Drafting for wiki complete, started illustrations and design work. Initial version of package published on test index</li></ul><h5><a href="https://docs.google.com/presentation/d/1bmM6EnKCqU50CG7Y4gG0vCpFoXZDeVKAUl2GpxDPTeo/edit#slide=id.p">Week 2</a></h5><ul><li>Wetlab: Finalized additional protocols for wiki, continued FPLC prep</li><li>Drylab: Package made available on GitHub. Met with iGEM Toronto for mutant analysis and thermostability predictions. Troubleshooted the wiki pipeline and began incorporating content to the main wiki page</li></ul><h5><a href="https://docs.google.com/presentation/u/2/d/1BlX2LE6Emv2fiA03aXMV2PaMOVdpxqPK5JgzOYjIqrc/edit">Week 3</a></h5><ul><li>Wetlab: Performed FPLC and began work with mutants</li><li>Drylab: Continued incorporation of content into the wiki before deadline</li><li>Wiki freeze on Oct 21</li></ul><h5>Week 4</h5><ul><li>Worked on the final presentation video</li></ul></article></div></div></div></main><footer><div class="container"><div class="row justify-content-center"><div id="footerTeamLogo"></div><div id="UIUCLogo"></div><div id="CABBILogo"></div><div id="IGBLogo"></div></div><p>iGEM UIUC_Illinois</p><p>Email: <a href="mailto:igembitsgoa@gmail.com">illinoisigem@gmail.com</a></p><p>Headquarter: <a href="https://www.igb.illinois.edu/">Carl R. Woese Institute for Genomic Biology</a></p><p>1206 W Gregory Dr. Urbana IL 61801</p><br/><p>Sample template built using the iGEM Wiki Starter Pack by BITS Goa.</p><p>2021 UIUC_Illinois[Judging Form](https://igem.org/2021_Judging_Form?id=3713)</p></div></footer><script src="https://2021.igem.org/Template:UIUC_Illinois/content-bundleJS?action=raw&ctype=text/javascript"></script></body></html> |
