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<!DOCTYPE html>
<html lang="en">
<head>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-TDC01ELJLN"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-TDC01ELJLN');
</script>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="css/bootstrap.min.css">
<script src="js/jquery.min.js"></script>
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<link type="text/css" rel="stylesheet" href="css/custom.css" />
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<title>VRL Lab Publications</title>
<style type="text/css">
h2{
color: #344bf7;
}
</style>
<script type="text/javascript">
$(document).ready(function () {
$('#header-container').load('template_header.html');
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</head>
<body data-spy="scroll" data-target="#toc">
<div id="header-container"></div>
<div class="jumbotron" style="background-image: url(img/bg-kilroy.jpg);"></div>
<div class="container">
<div class="row">
<div class="alert alert-success" role="alert">
You find this page because you are either a curious soul or got the link directly from me <i class="far fa-smile-wink"></i>. In any case, welcome to the Viral Lab resources.
</div>
</div>
<div class="row">
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<nav id="toc" data-toggle="toc" class="sticky-top">
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<div class="col-sm-9">
<h2>Welcome!</h2>
<p>
Welcome to the VRL Lab manual! I am trying to keep this document up-to-date for sharing useful information on how our group operates. Please share your suggestions and experiences to make this document useful as possible.
</p>
<h2>Onboarding</h2>
<p>
There are couple of things that we request from all our members. You can find information and the instructions below.
</p>
<h4>Website</h4>
<p>
Students <a href="https://www.natureindex.com/news-blog/build-your-own-academic-website-for-scientists-researchers-phd" target="_blank">must have</a> a website. I recommend using your institutional webspace as well with a simple redirection to point your own domain name.
</p>
<p>
There are several free options for hosting your own page. I prefer <a href="https://pages.github.com/" target="_blank">Github Pages</a>. You can also look for academic website templates like <a href="https://academicpages.github.io/" target="_blank">this</a> or <a href="https://themes.gohugo.io/academic/" target="_blank">this</a> one. Google also has a platform (<a href="https://sites.google.com/" target="_blank">Google Sites</a>) to build website with an simple draw and drop interface. You can also assign your own domain name easily on this platform.
</p>
<h4>Calendar</h4>
<p>
Our lab has a private event calendar where we schedule group meetings, seminars, social activities, etc. Please ask for access.
</p>
<h4>Update group website</h4>
<p>
This website contains information about our members, publications, resources etc. We share these content on a Github <a target="_blank" href="https://github.com/ViralLab/virallab.github.io">project</a>. You can send me your information or make a <a href="https://docs.github.com/en/free-pro-team@latest/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request" target="_blank">pull-request</a> for the changes. You should update the file for members and upload a picture of yours to include your profile on the website.
</p>
<h4>Join Github Organization</h4>
<p>
We are organizing the private and public repositories for our lab's projects on <a href="https://github.com/ViralLab" target="_blank">VRLLab github organization</a>. Make sure to become a member of the team and create your repositories under this orgnization and invite me as a collaborator.
</p>
<h2>Meetings</h2>
<h4>Group meetings</h4>
<p>
We condict regular group meeting where everyone will have an opportunity to present their work and get feedback from their labmates. Please be active, share your opinions and give constructive feedback.
<img src="img/lab-meeting-phd-comics.jpg" width="50%"/>
</p>
<h4>One on one meeting</h4>
<p>
If you would like to meet one-on-one to discuss about research, courses or career advice, we can schedule a time for this. Please don't hesitate sending an email.
</p>
<h2>Resources</h2>
<h4>Learning by doing</h4>
I prepared a small document that share my suggestions about the tools, books, softwares etc. You can follow this document to get a practical knowledge. <u>However, the best way to learn is by doing.</u>
<br>
<i class="far fa-question-circle"></i> Follow <a href="https://www.notion.so/Data-Science-resources-d81f19291c5b4b19b2b01dad7c6774a9">this link</a> for the document.
<!--
Server, Github
https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1009330
-->
<br><br>
<h4>Writing (paper, thesis, SOP, etc.)</h4>
There are several great resources on writing. I am listing couple of those below
<br>
<ul>
<li><a href="https://users.aalto.fi/~jsaramak/HowToWriteMastersThesis.pdf">HowToWriteMastersThesis</a> by Jari Saramaki</li>
</ul>
<h2>Tips & Tricks</h2>
<h4>Creating accounts and collecting credentials for APIs</h4>
<p>
Most of our projects rely on public APIs for data collection. Some of these platforms unfortunutaly became more strict about providing access to their data. Make sure to apply early and be a good citizen when using those API keys.
<ul>
<li><a href="https://developer.twitter.com/en/docs/getting-started" target="_blank">Twitter API</a></li>
<li><a href="https://developers.google.com/" target="_blank">Google Dev</a></li>
</ul>
It's always a good practice to keep credentials, email addresses associated with those credentials in a JSON file for easy access and <u>never publish these on a public repository</u>.
</p>
</div>
</div>
</div>
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