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− | {{Concordia-Montreal}}
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− | <div class="column full_size judges-will-not-evaluate">
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− | <h3>★ ALERT! </h3>
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− | <p>This page is used by the judges to evaluate your team for the <a href="https://2021.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2021.igem.org/Judging/Awards"> award listed below</a>. </p>
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− | <p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2021.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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− | <h1>Software</h1>
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− | <p>For Software Track teams, while you are not eligible for the Software Tool Special Prize, you can use this page to document your work.</p>
| + | }</style><link href="https://2021.igem.org/Template:Concordia-Montreal/css/contentCSS?action=raw&ctype=text/css" rel="stylesheet"/><meta charset="utf-8"/><meta content="width=device-width,initial-scale=1" name="viewport"/><title>Software | iGEM Concordia-Montreal</title></head><body><!-- # TODO: #6 Fix table caption font--><!-- # TODO: #7 Fix citations links font size--><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:Concordia-Montreal"><span>iGEM Concordia</span></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 aria-labelledby="navbarTeamDropdown" class="dropdown-menu"><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Team">Team</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Attributions">Attributions</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Collaborations">Collaborations</a></div></li><li class="nav-item dropdown"><a aria-expanded="false" aria-haspopup="true" class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" id="navbarProjectDropdown" role="button">Project</a><div aria-labelledby="navbarProjectDropdown" class="dropdown-menu"><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Description">Description</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Contribution">Contribution</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Implementation">Implementation</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Genetics">Genetics</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Model">Model</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Hardware">Hardware</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Software">Software</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Engineering">Engineering Success</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Notebook">Notebook</a></div></li><li class="nav-item dropdown"><a aria-expanded="false" aria-haspopup="true" class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" id="navbarHuman PracticesDropdown" role="button">Human Practices</a><div aria-labelledby="navbarHuman PracticesDropdown" class="dropdown-menu"><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Human_Practices">Integrated Human Practices</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Sustainable">Sustainable Development</a></div></li><li class="nav-item dropdown"><a aria-expanded="false" aria-haspopup="true" class="nav-link dropdown-toggle" data-toggle="dropdown" href="#" id="navbarEducationDropdown" role="button">Education</a><div aria-labelledby="navbarEducationDropdown" class="dropdown-menu"><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Communication">Science Communication</a><a class="dropdown-item" href="https://2021.igem.org/Team:Concordia-Montreal/Inclusivity">Inclusivity</a></div></li><li class="nav-item"><a class="nav-link" href="https://2021.igem.org/Team:Concordia-Montreal/Entrepreneurship">Entrepreneurship</a></li><li class="nav-item"><a class="nav-link" href="https://2021.igem.org/Team:Concordia-Montreal/Safety">Safety</a></li><li class="nav-item"><a class="nav-link" href="https://2021.igem.org/Team:Concordia-Montreal/Judging">Judging</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"><div class="jumbotron"><br/><br/><h1>Software</h1><p class="lead pl-1"></p><hr class="my-4"/></div></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><div id="soft_head"><h4>Visit</h4><a href="http://ec2-3-144-178-67.us-east-2.compute.amazonaws.com:3000/"><img src="https://static.igem.org/mediawiki/2021/1/15/T--Concordia-Montreal--img--astrobio.png"/></a><h4>and the</h4><a href="https://igem-concordia.shinyapps.io/astrobio_explorer/" id="a_soft"><h4><i class="fas fa-globe-americas"></i> AstroBio Explorer!</h4></a></div><h1>AstroBio Overview</h1><p>AstroBio is a two year iGEM project. The first year, 2020, consisted of <a href="https://2020.igem.org/Team:Concordia-Montreal">building a gene expression database</a> for organisms experiencing microgravity. The second year consisted of populating the database and building a small web-application to generate interactive visuals and automated gene set expression analysis. The <a href="http://ec2-3-144-178-67.us-east-2.compute.amazonaws.com:3000/">database</a> will soon host fifteen studies, twelve of which are compatible with the web-application.</p><h4>AstroBio Explorer</h4><p>The AstroBio Explorer is a small web-application designed to analyze a curated list of differential gene expression experiments for organisms treated with both spaceflight and simulated microgravity. Using various R packages and the Shiny web development framework, users can both examine results using a variety of interactive plots and download them in a excel spreadsheet format. Using the <a href="https://biit.cs.ut.ee/gprofiler/">g:Profiler</a> API, users can also perform automated gene set enrichment analysis to find differentially regulated functional groups from a large subset of the most popular gene annotation databases (Raudvere et al., 2019). The results are displayed in several interactive plots and tables and are available to download.</p><p>The github release can be found <a href="https://github.com/Clarkvale/astrobio-explorer">here.</a></p><h1>Guide</h1><p>Users can select up to three studies to view simultaneously from the table and perform gene set enrichment (GSE) analysis provided on g:Profiler supported the organism (the GSE_Analysis_Compatible column should list yes). While hovering over the desired row, a summary of the experiment and a contrast table will be shown below. The contrast table shows the linear model used to generate the differential gene expression values with the R package limma (Smyth, 2005). After selecting the studies and checking off the perform Gene Enrichment Analysis option, users can then edit the filter options for both the p values (adjusted, false discovery rate) and the log2 fold change (at above or equal to the absolute value). Excluding IEA GO annotations removes gene ontology annotations which are added via comparative analysis and keeps only manually curated ones. Selecting this option can help remove background annotations from cluttering the analysis. After pressing Import and waiting a few moments the data is ready to view.</p><h3>Gene expression plot</h3><p>The volcano plot shows the log¬2 fold change on the x axis and the -log10 p-value on the y. By clicking on the options in the header, users can subset the genes by their membership in an enriched group category. Users can further subset genes by a particular enriched group by selecting a row in the Enriched Gene Functional Group table and clicking on Reset\Show Genes on Plot with the volcano plot open.</p><div class="image"><img alt="Volcano Plot and Gene Selection" src="https://static.igem.org/mediawiki/2021/d/d2/T--Concordia-Montreal--img--vol_sel_600.gif"/><p>Figure 1: Volcano Plot and Gene Selection</p></div><h3>Manhattan Plot</h3><p>Enriched gene functional groups are displayed in a Manhattan plot provided by g:Profiler where the functional groups are arranged on the x-axis by semantic similarity and the y-axis is the -log10 adjusted p-value for the particular group. Circle size is the term size for the organism in question.</p><div class="image"><img alt="Manhattan Plot" src="https://static.igem.org/mediawiki/2021/4/47/T--Concordia-Montreal--img--manhat_600.gif"/><p>Figure 2: Manhattan Plot</p></div><h3>Biofabric Plot</h3><p>The Biofabric Plot is a network plot that is able to show gene memberships in any combination of enriched groups or subset categories (Longabaugh, 2012). Biofabric plots are useful because they can be arbitrarily large without being too computationally expensive and can still reveal interesting connections at smaller localities. In a Biofabric plot, nodes are depicted as horizontal lines and their edges are propagated vertically and terminated by a small square point. The plot can be subset by functional groups categories and fold change direction in the same way the volcano plot can. Furthermore, users can generate unique biofabric plots by selecting rows in the Enriched Gene Functional Group table and clicking on Reset\Show Genes on Plot to show the genes associated with the selected groups. Be sure to have the correct group category and fold change direction in order to show positive results. Display shadow links in the options forces all edges to be shown in a duplicate manner. This is helpful when highly connected nodes are obscured by being sorted into a wedge and printed in a small font (Longabaugh, 2012).</p><div class="image"><img alt="Biofabric Plot and Gene Selection" src="https://static.igem.org/mediawiki/2021/b/be/T--Concordia-Montreal--img--biofab_sel_600.gif"/><p>Figure 3: Biofabric Plot and Gene Selection</p></div><h1>Sources</h1><p>Longabaugh, W. J. (2012). Combing the hairball with BioFabric: A new approach for visualization of large networks. BMC Bioinformatics, 13(1), 275. https://doi.org/10.1186/1471-2105-13-275</p><p>Raudvere, U., Kolberg, L., Kuzmin, I., Arak, T., Adler, P., Peterson, H., & Vilo, J. (2019). g:Profiler: A web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Research, 47(W1), W191-W198. https://doi.org/10.1093/nar/gkz369</p><p>Smyth, G. K. (2005). limma: Linear Models for Microarray Data. In R. Gentleman, V. J. Carey, W. Huber, R. A. Irizarry, & S. Dudoit (Eds.), Bioinformatics and Computational Biology Solutions Using R and Bioconductor (pp. 397-420). Springer. https://doi.org/10.1007/0-387-29362-0_23</p></article></div></div></div></main><footer><img src="https://static.igem.org/mediawiki/2021/0/0b/T--Concordia-Montreal--img--Footer--sponsors.png" width="100%"/><br/><div class="container text-align-center"><div class="row"><div class="col-lg-6"><h2 class="fadjust">__________</h2><h2 class="fadjust">Discover SynBio Apps</h2><p>We are affiliated with Concordia's <a href="https://www.concordia.ca/research/casb.html">Centre for Applied Synthetic Biology (CASB)</a>, <a href="https://www.concordia.ca/sgs/programs/interdisciplinary/synthetic-biology-applications.html">SynBio Apps NSERC-CREATE</a>, and Canada's only academic <a href="https://www.concordia.ca/research/genome-foundry.html">Genome Foundry.</a></p><br/></div><div class="col-lg-1"></div><div class="col-lg-5"><h2 class="fadjust">__________</h2><h2 class="fadjust">Support Us</h2><p>To support the development and improvement of our project, we launched our own fundraising campaign available via Concordia's FundOne platform.<br/><a class="btn btn-primary btn-lg" href="https://www.concordia.ca/alumni-friends/giving-to-concordia/fundone/igem-concordia.html" role="button">Donate Now</a></p></div></div><br/><h2 class="mr-2 text-left"><a class="fadajust" href="https://www.facebook.com/iGEMConcordia"><i aria-hidden="true" class="fab fa-facebook-square"></i></a> <a class="fadajust" href="https://www.instagram.com/igem_concordia"><i aria-hidden="true" class="fab fa-instagram"></i></a> <a class="fadajust" href="https://twitter.com/iGEMConcordia"><i aria-hidden="true" class="fab fa-twitter-square"></i></a> <a class="fadajust" href="https://www.linkedin.com/company/concordia-igem"><i aria-hidden="true" class="fab fa-linkedin"></i></a></h2><p class="mr-2 text-right">© iGEM Concordia 2021</p></div></footer><script src="https://2021.igem.org/Template:Concordia-Montreal/content-bundleJS?action=raw&ctype=text/javascript"></script></body></html> |
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− | <h3>Best Software Tool Special Prize</h3>
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− | <p>Regardless what's the topic, iGEM projects often create or adapt computational tools to move the bigger project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can even prove surprisingly useful for others. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.
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− | To compete for the <a href="https://2021.igem.org/Judging/Awards">Best Software Tool prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2021.igem.org/Judging/Judging_Form">judging form</a>.
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− | To be eligible, your software has to be documented and made available under an OSI approved open source license.
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− | For software resources, please visit the <a href="https://2021.igem.org/Resources">Resources Hub</a>.
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− | <h3> Inspiration </h3>
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− | <p>You can look at what other teams did to get some inspiration! <br />
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− | Here are a few examples:</p>
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− | <ul>
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− | <li><a href="https://2019.igem.org/Team:Sydney_Australia/Software">2019 Sydney Australia</a></li>
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− | <li><a href="https://2019.igem.org/Team:SMMU-China/Software">2019 SMMU China</a></li>
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− | <li><a href="https://2019.igem.org/Team:Grenoble-Alpes/Software">2019 Grenoble Alpes</a></li>
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− | <li><a href="https://2020.igem.org/Team:DTU-Denmark/Software">2020 DTU Denmark</a></li>
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− | <li><a href="https://2020.igem.org/Team:GunnVistaPingry_US/Software">2020 GunnVistaPingry US</a></li>
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− | <li><a href="https://2020.igem.org/Team:Rochester/Software">2020 Rochester</a></li>
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