From e06eb02492d36ca4558e8fded80c0148e8d9e013 Mon Sep 17 00:00:00 2001
From: Janani Ravi <janani.ravi@cuanschutz.edu>
Date: Fri, 8 Mar 2024 09:05:46 -0700
Subject: [PATCH] minor edits

- to offboarding --> g drive, mermaid
- how to x (needs more links on Py/alpine)
- culture --> leave policy

Co-Authored-By: Evan Pierce Brenner <108823789+epbrenner@users.noreply.github.com>
---
 culture.qmd       |   9 ++--
 docs/culture.html |   9 ++--
 docs/howto.html   | 116 +++++++++++++++++++++++-----------------------
 docs/search.json  |  38 ++++++++++-----
 howto.qmd         |  66 +++++++++++++-------------
 offboarding.qmd   |  22 ++++-----
 6 files changed, 136 insertions(+), 124 deletions(-)

diff --git a/culture.qmd b/culture.qmd
index f3694f3..e5deef8 100644
--- a/culture.qmd
+++ b/culture.qmd
@@ -2,7 +2,7 @@
 
 ## Mission
 
-We value and believe in investing in and nurturing scientists as much as the science (we primarily love all things related to computational biology/biomedical data science + microbial genotypes, phenotypes, and diseases). We pride ourselves on providing a safe and inclusive space for people across intersectionalities. We are committed to mentoring (postdocs, students, programmers), education and outreach, and personalized professional development. We are passionate about finding new, better ways to increase diversity and retention in STEM and quantitative sciences. If you share our passion, please [reach out to us](//jravilab.github.io/joinus)!
+We love all things related to computational biology, biomedical data science, and microbial genotypes, phenotypes, and diseases, but we value and believe in investing in and nurturing scientists as much as the science. We pride ourselves on providing a safe and inclusive space for people across intersectionalities. We are committed to mentoring (postdocs, students, programmers), education and outreach, and personalized professional development. We are passionate about finding new, better ways to increase diversity and retention in STEM and quantitative sciences. If you share our passion, please [reach out to us](//jravilab.github.io/joinus)!
 
 ### Mentoring Philosophy \| [full_post](https://github.com/JRaviLab/group/blob/main/docs/mentoring_philosophy.md)
 
@@ -23,7 +23,7 @@ I have mentored 30+ diverse undergraduate and graduate students. Several joined
 
 ## Roles and expectations
 
-The following sections were drafted by folks at each of these levels, while edited by rest of the group for maximal cohesion.
+The following sections were drafted by folks at each of these levels, and edited collectively by the entire group for cohesion.
 
 ### PI
 
@@ -231,9 +231,10 @@ Always be a happy researcher! To be a happy researcher means you need a good bal
 
 #### Leave policy
 
--   For staff: The University of Colorado's [leave policies are available here](https://www.cu.edu/employee-services/leave-policies).
--   For graduate students: Details may vary per your specific graduate program's handbook, but [the Graduate School offers basic guidelines here](https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2).
 -   Because our group is tightly collaborative, please plan non-sick leave ahead of time to best fit all schedules when possible.
+-   For graduate students: Details may vary per your specific graduate program's handbook, but [the Graduate School offers basic guidelines here ](https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2)[for vacation and leav](https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2)[e](https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2).
+-   Undergraduate and Masters Students: [Student Employment Handbook](https://www.ucdenver.edu/docs/librariesprovider41/student-employment/student_hourly_employment_handbook.pdf?sfvrsn=8e3963ba_6)
+-   Staff (postdocs, research professionals): The University of Colorado's [leave policies](https://www.cu.edu/employee-services/leave-policies)
 
 ## Publication, Authorship & Research Misconduct
 
diff --git a/docs/culture.html b/docs/culture.html
index 3464dcc..ac25faa 100644
--- a/docs/culture.html
+++ b/docs/culture.html
@@ -247,7 +247,7 @@ <h1 class="title d-none d-lg-block"><span class="chapter-number">2</span>&nbsp;
 
 <section id="mission" class="level2" data-number="2.1">
 <h2 data-number="2.1" class="anchored" data-anchor-id="mission"><span class="header-section-number">2.1</span> Mission</h2>
-<p>We value and believe in investing in and nurturing scientists as much as the science (we primarily love all things related to computational biology/biomedical data science + microbial genotypes, phenotypes, and diseases). We pride ourselves on providing a safe and inclusive space for people across intersectionalities. We are committed to mentoring (postdocs, students, programmers), education and outreach, and personalized professional development. We are passionate about finding new, better ways to increase diversity and retention in STEM and quantitative sciences. If you share our passion, please <a href="//jravilab.github.io/joinus">reach out to us</a>!</p>
+<p>We love all things related to computational biology, biomedical data science, and microbial genotypes, phenotypes, and diseases, but we value and believe in investing in and nurturing scientists as much as the science. We pride ourselves on providing a safe and inclusive space for people across intersectionalities. We are committed to mentoring (postdocs, students, programmers), education and outreach, and personalized professional development. We are passionate about finding new, better ways to increase diversity and retention in STEM and quantitative sciences. If you share our passion, please <a href="//jravilab.github.io/joinus">reach out to us</a>!</p>
 <section id="mentoring-philosophy-full_post" class="level3" data-number="2.1.1">
 <h3 data-number="2.1.1" class="anchored" data-anchor-id="mentoring-philosophy-full_post"><span class="header-section-number">2.1.1</span> Mentoring Philosophy | <a href="https://github.com/JRaviLab/group/blob/main/docs/mentoring_philosophy.md">full_post</a></h3>
 <p>My experiences as a mentee have varied widely: fantastic professors in college inspired me to start a research career; later, a mentor overlooked my whole dissertation work resulting in prolonged authorship discussion. In my postdoctoral lab, I was the sole computational researcher collaborating with a dozen experimental biologists. I seized this invaluable opportunity to restart my academic career from scratch in a different field (i.e., studying microbial diseases), to learn, understand, and speak the language of both experimental and computational biologists, and to bring these worlds together. Collectively, these experiences have shaped my mentoring philosophy.</p>
@@ -270,7 +270,7 @@ <h3 data-number="2.1.2" class="anchored" data-anchor-id="inclusive-lab-climate-f
 </section>
 <section id="roles-and-expectations" class="level2" data-number="2.2">
 <h2 data-number="2.2" class="anchored" data-anchor-id="roles-and-expectations"><span class="header-section-number">2.2</span> Roles and expectations</h2>
-<p>The following sections were drafted by folks at each of these levels, while edited by rest of the group for maximal cohesion.</p>
+<p>The following sections were drafted by folks at each of these levels, and edited collectively by the entire group for cohesion.</p>
 <section id="pi" class="level3" data-number="2.2.1">
 <h3 data-number="2.2.1" class="anchored" data-anchor-id="pi"><span class="header-section-number">2.2.1</span> PI</h3>
 <p>My role as a PI would be to ensure your growth and success as a trainee, and the success of the project. Towards this, I will</p>
@@ -499,9 +499,10 @@ <h4 data-number="2.5.3.2" class="anchored" data-anchor-id="time-off"><span class
 <section id="leave-policy" class="level4" data-number="2.5.3.3">
 <h4 data-number="2.5.3.3" class="anchored" data-anchor-id="leave-policy"><span class="header-section-number">2.5.3.3</span> Leave policy</h4>
 <ul>
-<li>For staff: The University of Colorado’s <a href="https://www.cu.edu/employee-services/leave-policies">leave policies are available here</a>.</li>
-<li>For graduate students: Details may vary per your specific graduate program’s handbook, but <a href="https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2">the Graduate School offers basic guidelines here</a>.</li>
 <li>Because our group is tightly collaborative, please plan non-sick leave ahead of time to best fit all schedules when possible.</li>
+<li>For graduate students: Details may vary per your specific graduate program’s handbook, but <a href="https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2">the Graduate School offers basic guidelines here</a><a href="https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2">for vacation and leav</a><a href="https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2">e</a>.</li>
+<li>Undergraduate and Masters Students: <a href="https://www.ucdenver.edu/docs/librariesprovider41/student-employment/student_hourly_employment_handbook.pdf?sfvrsn=8e3963ba_6">Student Employment Handbook</a></li>
+<li>Staff (postdocs, research professionals): The University of Colorado’s <a href="https://www.cu.edu/employee-services/leave-policies">leave policies</a></li>
 </ul>
 </section>
 </section>
diff --git a/docs/howto.html b/docs/howto.html
index 2838e8b..eea8f98 100644
--- a/docs/howto.html
+++ b/docs/howto.html
@@ -189,19 +189,21 @@ <h2 id="toc-title">Table of contents</h2>
    
   <ul>
   <li><a href="#get-started" id="toc-get-started" class="nav-link active" data-scroll-target="#get-started"><span class="toc-section-number">3.1</span>  Get started</a></li>
-  <li><a href="#learn-r" id="toc-learn-r" class="nav-link" data-scroll-target="#learn-r"><span class="toc-section-number">3.2</span>  Learn R</a></li>
-  <li><a href="#helpful-links-to-learn-more-about-machine-learning" id="toc-helpful-links-to-learn-more-about-machine-learning" class="nav-link" data-scroll-target="#helpful-links-to-learn-more-about-machine-learning"><span class="toc-section-number">3.3</span>  Helpful Links to learn more about Machine Learning</a></li>
-  <li><a href="#use-vpn" id="toc-use-vpn" class="nav-link" data-scroll-target="#use-vpn"><span class="toc-section-number">3.4</span>  Use VPN</a></li>
-  <li><a href="#learn-gitgithub" id="toc-learn-gitgithub" class="nav-link" data-scroll-target="#learn-gitgithub"><span class="toc-section-number">3.5</span>  Learn Git/GitHub</a></li>
-  <li><a href="#readwritepresent" id="toc-readwritepresent" class="nav-link" data-scroll-target="#readwritepresent"><span class="toc-section-number">3.6</span>  Read/write/present</a></li>
-  <li><a href="#code" id="toc-code" class="nav-link" data-scroll-target="#code"><span class="toc-section-number">3.7</span>  Code</a></li>
-  <li><a href="#plan-your-semesteryear" id="toc-plan-your-semesteryear" class="nav-link" data-scroll-target="#plan-your-semesteryear"><span class="toc-section-number">3.8</span>  Plan your semester/year</a></li>
-  <li><a href="#remote-server-work-jravilab-server-alpine-hpc" id="toc-remote-server-work-jravilab-server-alpine-hpc" class="nav-link" data-scroll-target="#remote-server-work-jravilab-server-alpine-hpc"><span class="toc-section-number">3.9</span>  Remote server work (JRaviLab server &amp; Alpine HPC)</a>
+  <li><a href="#code" id="toc-code" class="nav-link" data-scroll-target="#code"><span class="toc-section-number">3.2</span>  Code</a>
   <ul class="collapse">
-  <li><a href="#jravilab-server" id="toc-jravilab-server" class="nav-link" data-scroll-target="#jravilab-server"><span class="toc-section-number">3.9.1</span>  JRaviLab server</a></li>
-  <li><a href="#alpine-hpc" id="toc-alpine-hpc" class="nav-link" data-scroll-target="#alpine-hpc"><span class="toc-section-number">3.9.2</span>  Alpine HPC</a></li>
+  <li><a href="#learn-r" id="toc-learn-r" class="nav-link" data-scroll-target="#learn-r"><span class="toc-section-number">3.2.1</span>  Learn R</a></li>
+  <li><a href="#intro-to-machine-learning" id="toc-intro-to-machine-learning" class="nav-link" data-scroll-target="#intro-to-machine-learning"><span class="toc-section-number">3.2.2</span>  Intro to Machine Learning</a></li>
+  <li><a href="#learn-gitgithub" id="toc-learn-gitgithub" class="nav-link" data-scroll-target="#learn-gitgithub"><span class="toc-section-number">3.2.3</span>  Learn Git/GitHub</a></li>
   </ul></li>
-  <li><a href="#others" id="toc-others" class="nav-link" data-scroll-target="#others"><span class="toc-section-number">3.10</span>  Others</a></li>
+  <li><a href="#access-hpc-servers" id="toc-access-hpc-servers" class="nav-link" data-scroll-target="#access-hpc-servers"><span class="toc-section-number">3.3</span>  Access HPC, servers</a>
+  <ul class="collapse">
+  <li><a href="#jravilab-server" id="toc-jravilab-server" class="nav-link" data-scroll-target="#jravilab-server"><span class="toc-section-number">3.3.1</span>  JRaviLab server</a></li>
+  <li><a href="#alpine-hpc" id="toc-alpine-hpc" class="nav-link" data-scroll-target="#alpine-hpc"><span class="toc-section-number">3.3.2</span>  Alpine HPC</a></li>
+  <li><a href="#use-vpn" id="toc-use-vpn" class="nav-link" data-scroll-target="#use-vpn"><span class="toc-section-number">3.3.3</span>  Use VPN</a></li>
+  </ul></li>
+  <li><a href="#readwritepresent" id="toc-readwritepresent" class="nav-link" data-scroll-target="#readwritepresent"><span class="toc-section-number">3.4</span>  Read/write/present</a></li>
+  <li><a href="#plan-your-semesteryear" id="toc-plan-your-semesteryear" class="nav-link" data-scroll-target="#plan-your-semesteryear"><span class="toc-section-number">3.5</span>  Plan your semester/year</a></li>
+  <li><a href="#others" id="toc-others" class="nav-link" data-scroll-target="#others"><span class="toc-section-number">3.6</span>  Others</a></li>
   </ul>
 <div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/jravilab/lab_docs/edit/main/howto.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/jravilab/lab_docs/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
     </div>
@@ -232,8 +234,17 @@ <h2 data-number="3.1" class="anchored" data-anchor-id="get-started"><span class=
 <p>To re-familiarize yourself with R/Python/Unix, check out these two resources in addition to Slack | <a href="https://github.com/jananiravi/compbio-gists">CompBio gists</a> and <a href="https://github.com/rladies-eastlansing">R-Ladies East Lansing</a>. If you are new to R-Ladies Aurora, R-Ladies East Lansing, and Women+ Data Science, check them out and join <a href="https://meetup.com/rladies-aurora">Meetup-RLA</a>/<a href="https://meetup.com/rladies-eastlansing">Meetup-RLEL</a> and their <a href="https://bit.ly/rladies-aurora-discord">Discord</a>/<a href="https://rladies-eastlansing.slack.com/">Slack</a> to remain apprised of upcoming events and to connect with the local R and data science communities.</p>
 <p>💡<em>If you find other useful resources, please add them to <a href="https://github.com/jananiravi/compbio-gists">this list</a> (or share them with me).</em></p>
 </section>
-<section id="learn-r" class="level2" data-number="3.2">
-<h2 data-number="3.2" class="anchored" data-anchor-id="learn-r"><span class="header-section-number">3.2</span> Learn R</h2>
+<section id="code" class="level2" data-number="3.2">
+<h2 data-number="3.2" class="anchored" data-anchor-id="code"><span class="header-section-number">3.2</span> Code</h2>
+<ul>
+<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_write_source_code.md">Write, work with, and manage source code and data</a></li>
+<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_do_code_review.md">Prepare for and carry out code review</a></li>
+<li><a href="https://github.com/jtleek/datasharing">Share data</a></li>
+<li><a href="https://github.com/jtleek/rpackages">Write an R package</a></li>
+<li><a href="https://cu-dbmi.github.io/set-website/blog">DBMI software engineering team tips &amp; tricks blog posts</a></li>
+</ul>
+<section id="learn-r" class="level3" data-number="3.2.1">
+<h3 data-number="3.2.1" class="anchored" data-anchor-id="learn-r"><span class="header-section-number">3.2.1</span> Learn R</h3>
 <p>To learn R, I would recommend getting started with the pinned posts in <a href="https://jravilab.slack.com/archives/CARJ72W3U">#courses-primers</a>.</p>
 <p>A couple of helpful GitHub repositories - <a href="https://github.com/jananiravi/workshop-tidyverse" class="uri">https://github.com/jananiravi/workshop-tidyverse</a> (Intro to <code>R's tidyverse package</code> — handy to learn right away) - Other R workshop materials from our R-Ladies East Lansing chapter: <a href="https://github.com/rladies-eastlansing" class="uri">https://github.com/rladies-eastlansing</a> - Interactive tutorials with <a href="https://rstudio.github.io/learnr/">learnr</a> &amp; <a href="https://swirlstats.com/">swirl</a>. - <a href="https://datacarpentry.org/R-genomics/index.html">R for Genomics from Data Carpentry</a> - <a href="https://github.com/JRaviLab/group/tree/master/resources-courses/r-on-hpc">R on HPC</a></p>
 <ul>
@@ -245,9 +256,14 @@ <h2 data-number="3.2" class="anchored" data-anchor-id="learn-r"><span class="hea
 <li>… and more | explore by topic, duration, skill-level</li>
 </ul></li>
 </ul>
+<p>📌 Go-to books (also in pinned posts on Slack)</p>
+<ul>
+<li><a href="https://r4ds.had.co.nz/">R for Data Science</a> (for tidyverse and such)</li>
+<li><a href="https://rstudio-education.github.io/hopr/">Hands-On Programming with R</a> (for base R) Intro to Git, GitHub resources</li>
+</ul>
 </section>
-<section id="helpful-links-to-learn-more-about-machine-learning" class="level2" data-number="3.3">
-<h2 data-number="3.3" class="anchored" data-anchor-id="helpful-links-to-learn-more-about-machine-learning"><span class="header-section-number">3.3</span> Helpful Links to learn more about Machine Learning</h2>
+<section id="intro-to-machine-learning" class="level3" data-number="3.2.2">
+<h3 data-number="3.2.2" class="anchored" data-anchor-id="intro-to-machine-learning"><span class="header-section-number">3.2.2</span> Intro to Machine Learning</h3>
 <ul>
 <li>YouTube Videos
 <ul>
@@ -258,7 +274,7 @@ <h2 data-number="3.3" class="anchored" data-anchor-id="helpful-links-to-learn-mo
 <li><a href="https://www.youtube.com/watch?v=aircAruvnKk">Understanding Neural Networks</a></li>
 <li><a href="https://www.youtube.com/watch?v=ExxFxD4OSZ0">Basic Computer Parts Explained</a></li>
 </ul></li>
-<li>Articles:
+<li>Articles
 <ul>
 <li><a href="http://jalammar.github.io/illustrated-transformer/">Transformers</a></li>
 </ul></li>
@@ -267,18 +283,9 @@ <h2 data-number="3.3" class="anchored" data-anchor-id="helpful-links-to-learn-mo
 <li><a href="https://leetcode.com/">LeetCode</a></li>
 </ul></li>
 </ul>
-<p>📌 Go-to books (also in pinned posts on Slack)</p>
-<ul>
-<li><a href="https://r4ds.had.co.nz/">R for Data Science</a> (for tidyverse and such)</li>
-<li><a href="https://rstudio-education.github.io/hopr/">Hands-On Programming with R</a> (for base R) Intro to Git, GitHub resources</li>
-</ul>
-</section>
-<section id="use-vpn" class="level2" data-number="3.4">
-<h2 data-number="3.4" class="anchored" data-anchor-id="use-vpn"><span class="header-section-number">3.4</span> Use VPN</h2>
-<p><a href="https://www.ucdenver.edu/offices/office-of-information-technology/software/how-do-i-use/vpn-and-remote-access" class="uri">https://www.ucdenver.edu/offices/office-of-information-technology/software/how-do-i-use/vpn-and-remote-access</a></p>
 </section>
-<section id="learn-gitgithub" class="level2" data-number="3.5">
-<h2 data-number="3.5" class="anchored" data-anchor-id="learn-gitgithub"><span class="header-section-number">3.5</span> Learn Git/GitHub</h2>
+<section id="learn-gitgithub" class="level3" data-number="3.2.3">
+<h3 data-number="3.2.3" class="anchored" data-anchor-id="learn-gitgithub"><span class="header-section-number">3.2.3</span> Learn Git/GitHub</h3>
 <ul>
 <li><a href="https://happygitwithr.com/" class="uri">https://happygitwithr.com/</a> Happy Git and GitHub for the useR (connecting git/GitHub w/ R)</li>
 <li><a href="https://docs.github.com/en/get-started/quickstart/git-and-github-learning-resources">Git and GitHub learning resources</a> from GitHub</li>
@@ -286,42 +293,20 @@ <h2 data-number="3.5" class="anchored" data-anchor-id="learn-gitgithub"><span cl
 <li><a href="https://www.coursera.org/learn/introduction-git-github">Coursera Intro to Git and GitHub course</a></li>
 </ul>
 </section>
-<section id="readwritepresent" class="level2" data-number="3.6">
-<h2 data-number="3.6" class="anchored" data-anchor-id="readwritepresent"><span class="header-section-number">3.6</span> Read/write/present</h2>
-<ul>
-<li><a href="https://github.com/JRaviLab/readingpapers">Read papers</a></li>
-<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_make_a_poster.md">Make a poster</a></li>
-<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_write_a_paper.md">Write a paper</a></li>
-<li><a href="https://www.coursera.org/learn/sciwrite">Writing in the Sciences on Coursera</a></li>
-</ul>
-</section>
-<section id="code" class="level2" data-number="3.7">
-<h2 data-number="3.7" class="anchored" data-anchor-id="code"><span class="header-section-number">3.7</span> Code</h2>
-<ul>
-<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_write_source_code.md">Write, work with, and manage source code and data</a></li>
-<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_do_code_review.md">Prepare for and carry out code review</a></li>
-<li><a href="https://github.com/jtleek/datasharing">Share data</a></li>
-<li><a href="https://github.com/jtleek/rpackages">Write an R package</a></li>
-<li><a href="https://cu-dbmi.github.io/set-website/blog">DBMI software engineering team tips &amp; tricks blog posts</a></li>
-</ul>
-</section>
-<section id="plan-your-semesteryear" class="level2" data-number="3.8">
-<h2 data-number="3.8" class="anchored" data-anchor-id="plan-your-semesteryear"><span class="header-section-number">3.8</span> Plan your semester/year</h2>
-<p><a href="https://github.com/JRaviLab/group/tree/master/docs/templates">Templates</a> on yearly/<a href="https://github.com/JRaviLab/group/blob/master/docs/Yearly-Planning-Document.pdf">semester planning</a> and professional development are available <a href="https://github.com/JRaviLab/group/tree/master/docs">here</a>.</p>
 </section>
-<section id="remote-server-work-jravilab-server-alpine-hpc" class="level2" data-number="3.9">
-<h2 data-number="3.9" class="anchored" data-anchor-id="remote-server-work-jravilab-server-alpine-hpc"><span class="header-section-number">3.9</span> Remote server work (JRaviLab server &amp; Alpine HPC)</h2>
+<section id="access-hpc-servers" class="level2" data-number="3.3">
+<h2 data-number="3.3" class="anchored" data-anchor-id="access-hpc-servers"><span class="header-section-number">3.3</span> Access HPC, servers</h2>
 <p>For computing that requires high performance hardware and computing clusters, we utilize two different remote servers.</p>
-<section id="jravilab-server" class="level3" data-number="3.9.1">
-<h3 data-number="3.9.1" class="anchored" data-anchor-id="jravilab-server"><span class="header-section-number">3.9.1</span> JRaviLab server</h3>
+<section id="jravilab-server" class="level3" data-number="3.3.1">
+<h3 data-number="3.3.1" class="anchored" data-anchor-id="jravilab-server"><span class="header-section-number">3.3.1</span> JRaviLab server</h3>
 <ul>
 <li>A single high performance machine used only by our group.</li>
 <li>To request access, contact the system administrator <code>shaddai.amolitos@cuanschutz.edu</code> by sending him your CU username (e.g., the CU auto-generated <code>ravijan</code> instead of <code>janani.ravi@cuanschutz.edu</code>) and a brief message that you will need access to the server. CC janani.ravi@cuanschutz.edu, so they can both verify your access.</li>
 <li>If you are new to remote server work, then it maybe helpful to learn about using an <a href="https://linuxize.com/post/using-the-ssh-config-file/">ssh config</a> for managing your remote hosts.</li>
 </ul>
 </section>
-<section id="alpine-hpc" class="level3" data-number="3.9.2">
-<h3 data-number="3.9.2" class="anchored" data-anchor-id="alpine-hpc"><span class="header-section-number">3.9.2</span> Alpine HPC</h3>
+<section id="alpine-hpc" class="level3" data-number="3.3.2">
+<h3 data-number="3.3.2" class="anchored" data-anchor-id="alpine-hpc"><span class="header-section-number">3.3.2</span> Alpine HPC</h3>
 <ul>
 <li>Alpine is the HPC cluster for all the University of Colorado campuses, including Anschutz.</li>
 <li>There is extensive <a href="https://curc.readthedocs.io/en/latest/clusters/alpine/index.html">documentation about getting setup</a></li>
@@ -329,9 +314,26 @@ <h3 data-number="3.9.2" class="anchored" data-anchor-id="alpine-hpc"><span class
 </ul>
 <p>Whenever possible, we highly recommend using the <a href="https://code.visualstudio.com/docs/remote/ssh">VSCode extension</a> which provides an IDE on the remote host without having to worry about server-side installation of other IDEs like RStudio or Jupyter.</p>
 </section>
+<section id="use-vpn" class="level3" data-number="3.3.3">
+<h3 data-number="3.3.3" class="anchored" data-anchor-id="use-vpn"><span class="header-section-number">3.3.3</span> Use VPN</h3>
+<p><a href="https://www.ucdenver.edu/offices/office-of-information-technology/software/how-do-i-use/vpn-and-remote-access" class="uri">https://www.ucdenver.edu/offices/office-of-information-technology/software/how-do-i-use/vpn-and-remote-access</a></p>
+</section>
+</section>
+<section id="readwritepresent" class="level2" data-number="3.4">
+<h2 data-number="3.4" class="anchored" data-anchor-id="readwritepresent"><span class="header-section-number">3.4</span> Read/write/present</h2>
+<ul>
+<li><a href="https://github.com/JRaviLab/readingpapers">Read papers</a></li>
+<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_make_a_poster.md">Make a poster</a></li>
+<li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_write_a_paper.md">Write a paper</a></li>
+<li><a href="https://www.coursera.org/learn/sciwrite">Writing in the Sciences on Coursera</a></li>
+</ul>
+</section>
+<section id="plan-your-semesteryear" class="level2" data-number="3.5">
+<h2 data-number="3.5" class="anchored" data-anchor-id="plan-your-semesteryear"><span class="header-section-number">3.5</span> Plan your semester/year</h2>
+<p><a href="https://github.com/JRaviLab/group/tree/master/docs/templates">Templates</a> on yearly/<a href="https://github.com/JRaviLab/group/blob/master/docs/Yearly-Planning-Document.pdf">semester planning</a> and professional development are available <a href="https://github.com/JRaviLab/group/tree/master/docs">here</a>.</p>
 </section>
-<section id="others" class="level2" data-number="3.10">
-<h2 data-number="3.10" class="anchored" data-anchor-id="others"><span class="header-section-number">3.10</span> Others</h2>
+<section id="others" class="level2" data-number="3.6">
+<h2 data-number="3.6" class="anchored" data-anchor-id="others"><span class="header-section-number">3.6</span> Others</h2>
 <ul>
 <li><a href="https://github.com/JRaviLab/group/blob/master/docs/career_dev_week.md">Career development week</a></li>
 <li><a href="https://github.com/JRaviLab/group/blob/master/docs/howto_work_remotely.md">Remote work</a> | <a href="https://www.ucdenver.edu/docs/librariesprovider284/default-document-library/4000-human-resources/4032---alternative-schedules-and-remote-work-arrangements.pdf?sfvrsn=3ee7f3ba_2">CU remote work policy</a> | <a href="https://app.smartsheet.com/b/form/f5c5dd3f01dc4eefb3711a4fce6955fe">CU DBMI remote work agreement</a></li>
diff --git a/docs/search.json b/docs/search.json
index e6e6a21..08fefc8 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -39,14 +39,14 @@
     "href": "culture.html#mission",
     "title": "2  Lab culture",
     "section": "2.1 Mission",
-    "text": "2.1 Mission\nWe value and believe in investing in and nurturing scientists as much as the science (we primarily love all things related to computational biology/biomedical data science + microbial genotypes, phenotypes, and diseases). We pride ourselves on providing a safe and inclusive space for people across intersectionalities. We are committed to mentoring (postdocs, students, programmers), education and outreach, and personalized professional development. We are passionate about finding new, better ways to increase diversity and retention in STEM and quantitative sciences. If you share our passion, please reach out to us!\n\n2.1.1 Mentoring Philosophy | full_post\nMy experiences as a mentee have varied widely: fantastic professors in college inspired me to start a research career; later, a mentor overlooked my whole dissertation work resulting in prolonged authorship discussion. In my postdoctoral lab, I was the sole computational researcher collaborating with a dozen experimental biologists. I seized this invaluable opportunity to restart my academic career from scratch in a different field (i.e., studying microbial diseases), to learn, understand, and speak the language of both experimental and computational biologists, and to bring these worlds together. Collectively, these experiences have shaped my mentoring philosophy.\n\nOpening doors and leveling the playing field (i.e., not gate-keeping)\nLives bigger than work\nCollaborative mentoring (i.e., not top-down advising)\nMentoring is not imprinting\n\n\n\n2.1.2 Inclusive lab climate | full_post\nI have mentored 30+ diverse undergraduate and graduate students. Several joined my lab as first-time coders and have co-authored computational papers; five have contributed to submitted manuscripts (see Bibliography). All these students have had positive research experiences, presented at (inter-)national conferences, and won awards/support from national programs, including NIH-funded T15 and R25-BRUSH, NSF-funded REU-ACRES, SROP, and NSURP. Several undergraduate trainees have graduated and started advanced studies at prestigious graduate and medical schools or jobs at pharmaceutical/IT companies. Using lessons learned from these experiences, I will focus on the following key areas to ensure an equitable and inclusive lab climate.\n\nRecruiting practices - e.g., working with the Offices of Inclusion/Diversity, R/Py-Ladies, W+DS, and online groups for minorities in STEM (e.g., Black in Computational Biology, LatinR, AfricaR, AsiaR, ArabR, RainbowR).\nSafe space for full participation - for people from all intersectionalities, zero tolerance to discriminatory or exclusionary behavior, appropriate pronoun usage, sustain a culture rooted in mutual respect.\nEmpowering mentees to forge their path - e.g., co-developing semester plans, conducting professional development workshops within the lab, creating networking opportunities through local/national/international meetings, and tailoring mentoring strategies to each mentee’s career aspirations."
+    "text": "2.1 Mission\nWe love all things related to computational biology, biomedical data science, and microbial genotypes, phenotypes, and diseases, but we value and believe in investing in and nurturing scientists as much as the science. We pride ourselves on providing a safe and inclusive space for people across intersectionalities. We are committed to mentoring (postdocs, students, programmers), education and outreach, and personalized professional development. We are passionate about finding new, better ways to increase diversity and retention in STEM and quantitative sciences. If you share our passion, please reach out to us!\n\n2.1.1 Mentoring Philosophy | full_post\nMy experiences as a mentee have varied widely: fantastic professors in college inspired me to start a research career; later, a mentor overlooked my whole dissertation work resulting in prolonged authorship discussion. In my postdoctoral lab, I was the sole computational researcher collaborating with a dozen experimental biologists. I seized this invaluable opportunity to restart my academic career from scratch in a different field (i.e., studying microbial diseases), to learn, understand, and speak the language of both experimental and computational biologists, and to bring these worlds together. Collectively, these experiences have shaped my mentoring philosophy.\n\nOpening doors and leveling the playing field (i.e., not gate-keeping)\nLives bigger than work\nCollaborative mentoring (i.e., not top-down advising)\nMentoring is not imprinting\n\n\n\n2.1.2 Inclusive lab climate | full_post\nI have mentored 30+ diverse undergraduate and graduate students. Several joined my lab as first-time coders and have co-authored computational papers; five have contributed to submitted manuscripts (see Bibliography). All these students have had positive research experiences, presented at (inter-)national conferences, and won awards/support from national programs, including NIH-funded T15 and R25-BRUSH, NSF-funded REU-ACRES, SROP, and NSURP. Several undergraduate trainees have graduated and started advanced studies at prestigious graduate and medical schools or jobs at pharmaceutical/IT companies. Using lessons learned from these experiences, I will focus on the following key areas to ensure an equitable and inclusive lab climate.\n\nRecruiting practices - e.g., working with the Offices of Inclusion/Diversity, R/Py-Ladies, W+DS, and online groups for minorities in STEM (e.g., Black in Computational Biology, LatinR, AfricaR, AsiaR, ArabR, RainbowR).\nSafe space for full participation - for people from all intersectionalities, zero tolerance to discriminatory or exclusionary behavior, appropriate pronoun usage, sustain a culture rooted in mutual respect.\nEmpowering mentees to forge their path - e.g., co-developing semester plans, conducting professional development workshops within the lab, creating networking opportunities through local/national/international meetings, and tailoring mentoring strategies to each mentee’s career aspirations."
   },
   {
     "objectID": "culture.html#roles-and-expectations",
     "href": "culture.html#roles-and-expectations",
     "title": "2  Lab culture",
     "section": "2.2 Roles and expectations",
-    "text": "2.2 Roles and expectations\nThe following sections were drafted by folks at each of these levels, while edited by rest of the group for maximal cohesion.\n\n2.2.1 PI\nMy role as a PI would be to ensure your growth and success as a trainee, and the success of the project. Towards this, I will\n\nPlan and design\n\nSounding board. You will have the freedom to work on your best ideas broadly aligned with the lab’s vision and you will always find in me an audience to discuss and brainstorm.\nI will help outline and plan your project(s) and design appropriate analyses.\nI will check-in with you once a semester as you plan your time, and more regularly to ensure you’re on track – based on the professional, scientific, and personal goals you’ve set for yourself. In addition to the project/group meetings, check-in with me often (bi)weekly (or as needed) to make sure you are staying on track towards your primary research and professional goals, and to help me help you as best as I can.\n\nHoning your skills –> career development. I will provide resources to develop your research program and technical skills as you plan the next stage of your career (e.g., PRA –> grad school, PhD student –> postdoc/industry, postdoc –> PI/research lead).\nScientific communication. I will provide ample opportunities within and outside the group to develop your reading, writing (grants and papers), and presenting skills, including engaging and networking at (inter)national meetings.\nProfessional networking. I will connect you with potential collaborators and mentors for scientific and professional growth and reciprocity. Team science is one of several skills you will learn during your tenure with us – you will learn to communicate effectively not just with other computational colleagues but with the admin, grants, and scientific writing teams, experimental and clinical collaborators.\nSafe space. I will continually work towards creating a diverse and inclusive safe space for all intersectionalities in the lab to ensure everyone thrives and grows scientifically, professionally, and personally while respecting and supporting their colleagues.\nEducation and outreach. I will enable and strongly encourage you to pay forward by creating inclusive communities through scientific and technical education and outreach reach opportunities within and beyond CU (e.g., R-Ladies, AsiaR, WiSTEM, SACNAS).\n\n\n\n2.2.2 Graduate students\n\nLearning to be a well-rounded scientist\n\nStrive to be creative, independent, and collaborative (as a team scientist).\nBe willing to learn new things and be open-minded to new ideas/directions. Be thoughtful and think deep about your rationale and hypothesis. Be critical and rigorous in your methods and evaluation. It is perfectly OK to find your passion and love (and dream about) certain topics/fields, but remain open enough to like/appreciate other topics (and avoid maintaining a curtailing hate/dislike list). This will ensure you read, listen to, and consume ideas constructively, ultimately honing your scientific growth.\n\nReading\n\nHave a clear and deep understanding of concepts (computational and biological) related to your research project.\nKeep up with the literature and have a sound reading system (update your project/group members and PI of your most recent exciting reads via Slack/Journal clubs). Post updates regularly to the #papers-articles channel based on your self-assigned journals here.\n\nCoding\n\nWrite clean and well-documented code, and commit to GitHub regularly.\nDo code reviewor request review(s) from other lab members at a proper frequency e.g., once a month.\nYour work must be reproducible; this applies to the methodology, codebase, software, and data you work on. (e.g., Ten Simple Rules for Reproducible Computational Research)\n\nWriting\n\nKeep applying for internal/external funding opportunities (good practice for scientific writing).\nContribute pro-actively to grant proposal writing with the PI by proposing new ideas and generating preliminary results.\n\nScientific communication\n\nFormal/semi-formal scientific writing, e.g., abstracts, manuscripts, grant/fellowship applications, blog posts.\nGive oral presentations in different settings, e.g., group meetings, posters, talks, research updates, and journal club meetings.\nKeep well-organized meeting notes. In group meetings, take turns as the scribe.\nLook out for opportunities that PI/others often posts in the lab Slack, the DBMI Slack, or email. Opportunities to look out for are but are not limited to funding, poster events, presentations, conferences, seminars, and courses.\n\nMeeting and engagement\n\nAttend all required meetings specific to your project and group meetings. If you would like to gain a general understanding of the other projects, you are welcome to attend other project meetings.\nSchedule regular (weekly/biweekly, as needed) one-on-one meetings here. Maintain a good frequency of one-on-one meetings, especially when you are co-mentored. Do your best to keep both PIs on the same page.\nInteract professionally (and respectfully) with all your peers within and outside the group.\nActively (and voluntarily) engage in lab, department, and program activities.\nIf a personal, scientific, or professional issue/concern is keeping you from engaging actively and fully with the group, let the PI and the group know so we can make reasonable accommodations and allow you to heal/recover and better integrate.\nIf co-mentored, it is expected that the trainee respectfully engages with both group members and attends events/meetings from both (unless exempted due to reasonable requests).\n\nCommunication\n\nCheck and respond appropriately to Slack and Outlook email and calendar regularly during working hours. Set reminders, as needed, for what is relevant/expected of you so your PI/colleagues do not have to remind you.\nRespect everyone’s time by showing up to meetings regularly and on time (and in person if from CU and if that’s how everyone else is attending), and by not expecting prompts for responses and engagement.\nCommunicate regularly and clearly with the PI(s) on research, academic progress, and other professional development goals. Constructive feedback both ways is important for a strong long-term relationship.\nHave good/proper interpersonal communication with everyone, and create an approachable environment.\nCome prepared for all the meetings by noting your open questions, reading relevant material, planning your next steps, or the results you want to present.\n\nPeer-mentoring\n\nMentor junior/newer trainees by giving primers, helping them troubleshoot anything related to their projects, helping them contact the correct individuals when you can’t help them, and answering their questions.\n\nProject/time management\n\nSet aside 3-4 hours of productive slots on days without classes for (i) writing code, (ii) reading/writing papers, and (iii) generating results.\nInculcate good time management skills. Ensure you have an efficient work-life balance to nurture your physical and mental health.\n[Side projects] Learn more about other projects in the lab and make meaningful contributions to them, especially those most relevant to your research program (co-attendees of project meetings).\nDeadlines. Establish clear deadlines/academic plans, e.g., comprehensive exam, defense. Plan to graduate within 5 years; finishing your comprehensive exam by the start of your third year (end-of-second-year would be preferable and ideal to keep you on track).\nAdhere to general work ethics laid out for the lab.\n\nSemester planning. In addition to detailed research goals, set SMART goals for professional and personal development. Below is a general list of what semester planning entails.\n\nAcademic planning: required/elective courses.\nTake on leadership roles through mentoring or presenting.\nAttend seminars (regularly/weekly) and conferences.\nSet clear reading, writing, coding, and presenting goals.\nVolunteer | education, outreach, JEDI.\nSet recurring meetings with the PI(s) and attend project meetings.\n\n\n\n\n2.2.3 Postdocs\nAs a postdoctoral researcher, you wear many hats besides those of more junior scientists in the lab. So, in addition to the expectations from a graduate-level researcher (above), these might be relevant to your senior level and experience.\n\nTraining opportunity. you are here to learn new skills and expand your scientific boundaries. You are not expected to know everything, but you should be comfortable (and preferably excited!) throwing yourself into new problems and solving them.\nPeer mentoring. You are also here to help others learn. Postdocs have considerable experience in many aspects, typically involving academia, research, and more. That experience can be beneficial for scientists who are earlier in their careers. Contribute generously where you can, and make yourself available for others in the group. A rising tide lifts all boats.\nScientific independence. Postdocs are strongly encouraged to pursue their independent research interests aligned with the group’s research interests. For projects that succeed, they should have “future directions” they can take forward into their independent careers in the future.\nCollaboration. In addition, you may work on several existing projects across the lab – either leading them or helping each team navigate research obstacles. Postdocs have already had experience troubleshooting their way through their work in the past, and are expected to be able to leverage that experience by operating more independently. Some projects you work on might be new and higher risk, and some might be stalled and in need of a fresh perspective. Postdocs are also strongly encouraged to engage in a few active collaborations outside the group (from our ongoing list) — to test their methods on interesting biomedical applications, gain diverse perspectives, while balancing basic and translational research. The professional networking aspect is critical, too.\nGrants and fellowships. Grant/fellowship writing is a crucial aspect of a postdoc’s job. It funds your position and research where possible and, most critically, gives you practice and experience seeking and applying for funding opportunities needed for launching into independent faculty positions.\nCommunication. Communicating science is a fundamental and essential part of this role, be it through manuscripts, conference presentations, or workshops. Expect to keep busy presenting your work at regional and (inter)national platforms, and use the experience to get your name out there and network!\nCareer development. Finding your next step is the ultimate goal of your position. For all the roles you have, they should help focus your skillset, CV, and open future opportunities for you to move onwards and upwards towards where you want to end up in life.\n\n\n\n2.2.4 Research professionals (PRAs / postbac, post-MS trainees)\n\nIn addition to most applicable points from the Graduate Student section above (barring rare exceptions like comprehensive exams, etc.), the following are great pointers for research professionals.\nIndividual and team scientist\n\nLead individual projects and contribute new ideas and research directions, while also supporting other lab members’ projects collaboratively.\nAssist with the design and development of major bioinformatics-related programming projects.\nThe supportive role can overlap with the project-related scientific tasks, or other technical and software-development tasks like code review and any assistance with coding/environment/installation issues.\n\nTechnical contribution\n\nPerform scientifically rigorous data management and bioinformatic analyses.\nDevelop and disseminate a variety of tools designed to access relevant experimental and clinical data.\nDevelop and implement complex analysis pipelines, modular functional programming, and data visualization techniques (e.g., for multi-layered -omics datasets)\nCreatively and effectively integrate data from multiple sources to accelerate discoveries; write custom scripts to access databases and analyze data.\nWrite custom web tools and R/Py packages for the group and the larger scientific/technical community.\n\nCommunication\n\n(In addition to the opportunities/modes highlighted above …) Present research/technical updates periodically, host journal clubs, workshops/tutorials, and attend all group and project meetings.\n\nProfessional development and networking\n\nIt is in the best and mutual interest of PRAs and the lab to hone and develop scientific, technical, and personnel/leadership skills that will benefit all involved parties, especially the PRAs’ professional and career development.\nWork with the PI to make short- and long-term research, professional, and career plans to stay on track towards your next steps (e.g., grad school applications).\nWork with the PI, others in the group and department, and collaborators to form a strong professional network that you can later rely on.\n\n\n\n\n2.2.5 Undergraduates (Short-term interns/Visiting scientists)\nThe Graduate Student section above should give you a fair idea about how to be trained as a well-rounded scientist. As a junior researcher, however, the following would be excellent starting points.\n\nBe present. Attend meetings and bring forth your best effort.\nAsk for help. We encourage you to be proactive; ask questions and provide any updates or ideas to our Slack channels.\nStrive for growth. It will be challenging, but we want you to keep trying and persist – learning is the main goal, and being receptive and open to constructive feedback is a great way to improve.\nGive yourself grace. You’ve earned a spot in our community, and you belong here. Failure is inevitable with the work we’re doing; your work doesn’t define you or your abilities. We’re all here for you!\nStay organized. Keeping track of your priorities, tasks, and responsibilities will allow you to monitor your progress and make it easier for others to help you. Time management is essential for pacing yourself to achieve your goals.\nCollaborate. We encourage you to present your work and discuss it with others frequently. Learn about the projects your labmates are working on, communicate any troubles or issues before they boil over (work-related and not), and keep a positive mental attitude!\nOwn your research. This is your research process, so be sure that you’re putting forth your best work and that you continue to practice scientific reading and writing.\nTake advantage of resources. There are many avenues for learning in research. Here are a few to get you started:\n\nJRaviLab: How to X\nSlack channels\nStack Overflow\nNIH NCBI\nGoogle, Google Scholar\nChatGPT"
+    "text": "2.2 Roles and expectations\nThe following sections were drafted by folks at each of these levels, and edited collectively by the entire group for cohesion.\n\n2.2.1 PI\nMy role as a PI would be to ensure your growth and success as a trainee, and the success of the project. Towards this, I will\n\nPlan and design\n\nSounding board. You will have the freedom to work on your best ideas broadly aligned with the lab’s vision and you will always find in me an audience to discuss and brainstorm.\nI will help outline and plan your project(s) and design appropriate analyses.\nI will check-in with you once a semester as you plan your time, and more regularly to ensure you’re on track – based on the professional, scientific, and personal goals you’ve set for yourself. In addition to the project/group meetings, check-in with me often (bi)weekly (or as needed) to make sure you are staying on track towards your primary research and professional goals, and to help me help you as best as I can.\n\nHoning your skills –> career development. I will provide resources to develop your research program and technical skills as you plan the next stage of your career (e.g., PRA –> grad school, PhD student –> postdoc/industry, postdoc –> PI/research lead).\nScientific communication. I will provide ample opportunities within and outside the group to develop your reading, writing (grants and papers), and presenting skills, including engaging and networking at (inter)national meetings.\nProfessional networking. I will connect you with potential collaborators and mentors for scientific and professional growth and reciprocity. Team science is one of several skills you will learn during your tenure with us – you will learn to communicate effectively not just with other computational colleagues but with the admin, grants, and scientific writing teams, experimental and clinical collaborators.\nSafe space. I will continually work towards creating a diverse and inclusive safe space for all intersectionalities in the lab to ensure everyone thrives and grows scientifically, professionally, and personally while respecting and supporting their colleagues.\nEducation and outreach. I will enable and strongly encourage you to pay forward by creating inclusive communities through scientific and technical education and outreach reach opportunities within and beyond CU (e.g., R-Ladies, AsiaR, WiSTEM, SACNAS).\n\n\n\n2.2.2 Graduate students\n\nLearning to be a well-rounded scientist\n\nStrive to be creative, independent, and collaborative (as a team scientist).\nBe willing to learn new things and be open-minded to new ideas/directions. Be thoughtful and think deep about your rationale and hypothesis. Be critical and rigorous in your methods and evaluation. It is perfectly OK to find your passion and love (and dream about) certain topics/fields, but remain open enough to like/appreciate other topics (and avoid maintaining a curtailing hate/dislike list). This will ensure you read, listen to, and consume ideas constructively, ultimately honing your scientific growth.\n\nReading\n\nHave a clear and deep understanding of concepts (computational and biological) related to your research project.\nKeep up with the literature and have a sound reading system (update your project/group members and PI of your most recent exciting reads via Slack/Journal clubs). Post updates regularly to the #papers-articles channel based on your self-assigned journals here.\n\nCoding\n\nWrite clean and well-documented code, and commit to GitHub regularly.\nDo code reviewor request review(s) from other lab members at a proper frequency e.g., once a month.\nYour work must be reproducible; this applies to the methodology, codebase, software, and data you work on. (e.g., Ten Simple Rules for Reproducible Computational Research)\n\nWriting\n\nKeep applying for internal/external funding opportunities (good practice for scientific writing).\nContribute pro-actively to grant proposal writing with the PI by proposing new ideas and generating preliminary results.\n\nScientific communication\n\nFormal/semi-formal scientific writing, e.g., abstracts, manuscripts, grant/fellowship applications, blog posts.\nGive oral presentations in different settings, e.g., group meetings, posters, talks, research updates, and journal club meetings.\nKeep well-organized meeting notes. In group meetings, take turns as the scribe.\nLook out for opportunities that PI/others often posts in the lab Slack, the DBMI Slack, or email. Opportunities to look out for are but are not limited to funding, poster events, presentations, conferences, seminars, and courses.\n\nMeeting and engagement\n\nAttend all required meetings specific to your project and group meetings. If you would like to gain a general understanding of the other projects, you are welcome to attend other project meetings.\nSchedule regular (weekly/biweekly, as needed) one-on-one meetings here. Maintain a good frequency of one-on-one meetings, especially when you are co-mentored. Do your best to keep both PIs on the same page.\nInteract professionally (and respectfully) with all your peers within and outside the group.\nActively (and voluntarily) engage in lab, department, and program activities.\nIf a personal, scientific, or professional issue/concern is keeping you from engaging actively and fully with the group, let the PI and the group know so we can make reasonable accommodations and allow you to heal/recover and better integrate.\nIf co-mentored, it is expected that the trainee respectfully engages with both group members and attends events/meetings from both (unless exempted due to reasonable requests).\n\nCommunication\n\nCheck and respond appropriately to Slack and Outlook email and calendar regularly during working hours. Set reminders, as needed, for what is relevant/expected of you so your PI/colleagues do not have to remind you.\nRespect everyone’s time by showing up to meetings regularly and on time (and in person if from CU and if that’s how everyone else is attending), and by not expecting prompts for responses and engagement.\nCommunicate regularly and clearly with the PI(s) on research, academic progress, and other professional development goals. Constructive feedback both ways is important for a strong long-term relationship.\nHave good/proper interpersonal communication with everyone, and create an approachable environment.\nCome prepared for all the meetings by noting your open questions, reading relevant material, planning your next steps, or the results you want to present.\n\nPeer-mentoring\n\nMentor junior/newer trainees by giving primers, helping them troubleshoot anything related to their projects, helping them contact the correct individuals when you can’t help them, and answering their questions.\n\nProject/time management\n\nSet aside 3-4 hours of productive slots on days without classes for (i) writing code, (ii) reading/writing papers, and (iii) generating results.\nInculcate good time management skills. Ensure you have an efficient work-life balance to nurture your physical and mental health.\n[Side projects] Learn more about other projects in the lab and make meaningful contributions to them, especially those most relevant to your research program (co-attendees of project meetings).\nDeadlines. Establish clear deadlines/academic plans, e.g., comprehensive exam, defense. Plan to graduate within 5 years; finishing your comprehensive exam by the start of your third year (end-of-second-year would be preferable and ideal to keep you on track).\nAdhere to general work ethics laid out for the lab.\n\nSemester planning. In addition to detailed research goals, set SMART goals for professional and personal development. Below is a general list of what semester planning entails.\n\nAcademic planning: required/elective courses.\nTake on leadership roles through mentoring or presenting.\nAttend seminars (regularly/weekly) and conferences.\nSet clear reading, writing, coding, and presenting goals.\nVolunteer | education, outreach, JEDI.\nSet recurring meetings with the PI(s) and attend project meetings.\n\n\n\n\n2.2.3 Postdocs\nAs a postdoctoral researcher, you wear many hats besides those of more junior scientists in the lab. So, in addition to the expectations from a graduate-level researcher (above), these might be relevant to your senior level and experience.\n\nTraining opportunity. you are here to learn new skills and expand your scientific boundaries. You are not expected to know everything, but you should be comfortable (and preferably excited!) throwing yourself into new problems and solving them.\nPeer mentoring. You are also here to help others learn. Postdocs have considerable experience in many aspects, typically involving academia, research, and more. That experience can be beneficial for scientists who are earlier in their careers. Contribute generously where you can, and make yourself available for others in the group. A rising tide lifts all boats.\nScientific independence. Postdocs are strongly encouraged to pursue their independent research interests aligned with the group’s research interests. For projects that succeed, they should have “future directions” they can take forward into their independent careers in the future.\nCollaboration. In addition, you may work on several existing projects across the lab – either leading them or helping each team navigate research obstacles. Postdocs have already had experience troubleshooting their way through their work in the past, and are expected to be able to leverage that experience by operating more independently. Some projects you work on might be new and higher risk, and some might be stalled and in need of a fresh perspective. Postdocs are also strongly encouraged to engage in a few active collaborations outside the group (from our ongoing list) — to test their methods on interesting biomedical applications, gain diverse perspectives, while balancing basic and translational research. The professional networking aspect is critical, too.\nGrants and fellowships. Grant/fellowship writing is a crucial aspect of a postdoc’s job. It funds your position and research where possible and, most critically, gives you practice and experience seeking and applying for funding opportunities needed for launching into independent faculty positions.\nCommunication. Communicating science is a fundamental and essential part of this role, be it through manuscripts, conference presentations, or workshops. Expect to keep busy presenting your work at regional and (inter)national platforms, and use the experience to get your name out there and network!\nCareer development. Finding your next step is the ultimate goal of your position. For all the roles you have, they should help focus your skillset, CV, and open future opportunities for you to move onwards and upwards towards where you want to end up in life.\n\n\n\n2.2.4 Research professionals (PRAs / postbac, post-MS trainees)\n\nIn addition to most applicable points from the Graduate Student section above (barring rare exceptions like comprehensive exams, etc.), the following are great pointers for research professionals.\nIndividual and team scientist\n\nLead individual projects and contribute new ideas and research directions, while also supporting other lab members’ projects collaboratively.\nAssist with the design and development of major bioinformatics-related programming projects.\nThe supportive role can overlap with the project-related scientific tasks, or other technical and software-development tasks like code review and any assistance with coding/environment/installation issues.\n\nTechnical contribution\n\nPerform scientifically rigorous data management and bioinformatic analyses.\nDevelop and disseminate a variety of tools designed to access relevant experimental and clinical data.\nDevelop and implement complex analysis pipelines, modular functional programming, and data visualization techniques (e.g., for multi-layered -omics datasets)\nCreatively and effectively integrate data from multiple sources to accelerate discoveries; write custom scripts to access databases and analyze data.\nWrite custom web tools and R/Py packages for the group and the larger scientific/technical community.\n\nCommunication\n\n(In addition to the opportunities/modes highlighted above …) Present research/technical updates periodically, host journal clubs, workshops/tutorials, and attend all group and project meetings.\n\nProfessional development and networking\n\nIt is in the best and mutual interest of PRAs and the lab to hone and develop scientific, technical, and personnel/leadership skills that will benefit all involved parties, especially the PRAs’ professional and career development.\nWork with the PI to make short- and long-term research, professional, and career plans to stay on track towards your next steps (e.g., grad school applications).\nWork with the PI, others in the group and department, and collaborators to form a strong professional network that you can later rely on.\n\n\n\n\n2.2.5 Undergraduates (Short-term interns/Visiting scientists)\nThe Graduate Student section above should give you a fair idea about how to be trained as a well-rounded scientist. As a junior researcher, however, the following would be excellent starting points.\n\nBe present. Attend meetings and bring forth your best effort.\nAsk for help. We encourage you to be proactive; ask questions and provide any updates or ideas to our Slack channels.\nStrive for growth. It will be challenging, but we want you to keep trying and persist – learning is the main goal, and being receptive and open to constructive feedback is a great way to improve.\nGive yourself grace. You’ve earned a spot in our community, and you belong here. Failure is inevitable with the work we’re doing; your work doesn’t define you or your abilities. We’re all here for you!\nStay organized. Keeping track of your priorities, tasks, and responsibilities will allow you to monitor your progress and make it easier for others to help you. Time management is essential for pacing yourself to achieve your goals.\nCollaborate. We encourage you to present your work and discuss it with others frequently. Learn about the projects your labmates are working on, communicate any troubles or issues before they boil over (work-related and not), and keep a positive mental attitude!\nOwn your research. This is your research process, so be sure that you’re putting forth your best work and that you continue to practice scientific reading and writing.\nTake advantage of resources. There are many avenues for learning in research. Here are a few to get you started:\n\nJRaviLab: How to X\nSlack channels\nStack Overflow\nNIH NCBI\nGoogle, Google Scholar\nChatGPT"
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-    "text": "2.5 Lab Proceedings\n\n2.5.1 Communication\n\nCommunication within the group | Slack | In-person/Zoom co-work\n\nIn all meetings and interactions, it is imperative that lab members are constructive in feedback and respectful of each other. Critiques are always welcome and encouraged, but they should be supportive and aimed at building others up and improving our science, not tearing others down. At the same time, we shouldn’t shy away from providing critical feedback! As scientists, we all need regular practice critically analyzing and interpreting what we read and hear, and a friendly environment like our lab group is the best place to work on these skills together.\n\n\n2.5.2 Meetings and formats\nSince communication is key to good science, we meet regularly as a lab in a variety of formats. The details about these meetings can be found here.\n\n\n2.5.3 Remote work & working hours\nAt a very broad level, the more time you put into your work, the more you’ll get accomplished. However, this is also an obvious oversimplification. Some people prefer a typical 9-5, others thrive with a 10 hour/4 day workweek, and others still find their productivity falls off after 6 hours of work. Adding to this, our work can often be asynchronous, and working remotely can be integrated into a routine as well.\nRegardless of your working style, taking breaks is important! Stretch, take a brisk walk, hydrate, enjoy some caffeine (in moderation).\nIf you are working remotely for extended periods, communicate regularly on Slack, and schedule a few co-work times where you and others can log on together and work in a shared virtual space that makes spontaneous interactions possible. Remote work has advantages, but a major drawback is the lack of this spontaneity. Being able to walk to a neighboring desk and ask a quick question, take a shared tea break, and see the faces of the people you work with are real advantages to collaborative science. Some of these aspects can still be done remotely, but they require active effort. Please stay involved like this even if you aren’t on campus!\nGenerally speaking, if you are meeting milestones, participating in project and group discussions, and comfortable with your work-life balance in our lab, the details of your work schedule are flexible. For a diverse group, a schedule that accommodates everyone necessarily requires compromise. Your exact schedule will come down to your role in the lab, your preferences, and the group’s availability. There are some basic rules and tenants to be aware of.\n\n2.5.3.1 Work hours\nFor full-time members (e.g., PRAs, postdocs, grads), expect to put in 40 hours of work per week on average. For part-time members (e.g., undergraduates during the semester, interns, and other volunteers), you might be in the range of 10-30 hours a week typically.\nThese ranges are estimates, and will vary across people and over time. We never want to find ourselves in a crunch, but deadlines sometimes do pile up, and some weeks may require more hours. At the same time, some weeks will be lighter, breaks are encouraged, and working to the clock, or overtime should not be glorified either. Most importantly, maintain a comfortable work-life balance that leaves you wanting to come back for more, and keeps you far from the burnout line! If you ever feel stressed about your schedule/workload, talk to your PI & group to see how we can change things.\nPresenteeism isn’t a healthy mindset, and health and productivity rank ahead (in that order!) of simply being present.\n\nWorking remotely | CU Remote Work Agreement\n\nFor any student-employee-related questions, please refer to the University of Colorado Denver student hourly employment handbook or the student employment website. Both handbooks define the student employment rules for the Denver and Anschutz Medical Campus.\n\n\n2.5.3.2 Time Off\nAlways be a happy researcher! To be a happy researcher means you need a good balance between work and time off. We encourage you to take time off when needed, but there are a few things to remember. If there are meetings/deadlines involved, please let me (PI) and team members know ahead of time if you can’t make it during crunch time.\n\nIt’s understandable that things occasionally come up – so, it’s for a few hours/1 day, feel free to drop me (PI) a quick note and take off, as needed.\nIf it’s more than 1-3 days (or recurring few hours/single days), let me (PI) know in advance so we can plan ahead.\nIf it’s >3 days, please include me (PI) in the conversation during the planning phase (before booking your tickets/planning your travel). It’s better for all parties involved if this is a conversation rather than an FYI. *Similar for >few days remote work, unless previously requested.\nMark your time off on the lab calendar (in a non-disruptive way – darkest color background and NO notifications per event for everyone in the group) and notify your PI and co-workers in advance.\nLet others know if you miss any meetings during your time off. Please do your best to plan your work accordingly when known vacation times (no meeting weeks) are approaching. Don’t leave too much undone before going on vacation because you may have too much to do when you return, which can cause stress.\nAlso, leave good notes on what you were working on and what you must do when you return. Sometimes, when you are gone for too long, remembering where you left off can be hard, so having these notes can help you get back on track.\nStudies have shown not having a sustainable work-life balance can lead to difficulties in maintaining an efficient, productive, and healthy research experience. Therefore, it is essential to maintain a healthy work-life balance to ensure the best and most productive research experience.(Bartlett et al., 2021)\nBe respectful of your labmates and avoid sending them messages when they are on vacation. If you are working closely with them on a project or need their help, notify them of any deadlines that may overlap with their vacation. This way meetings can be determined before your labmate leaves for vacation.\nIf you receive work-related messages during vacation/holidays (incl. weekends), you are not obligated to answer them unless they are critical. If the message is urgent (esp. something you’ve committed to prior to your vacation and have missed checking during working days), please do your best to answer them as soon as possible. This is more so important when there are deadlines approaching. It is OK if there are occasional instances when you can’t make it to a deadline – but this can’t be a norm and you *must* let me (PI) know in advance so we plan ahead.\n\n\n\n2.5.3.3 Leave policy\n\nFor staff: The University of Colorado’s leave policies are available here.\nFor graduate students: Details may vary per your specific graduate program’s handbook, but the Graduate School offers basic guidelines here.\nBecause our group is tightly collaborative, please plan non-sick leave ahead of time to best fit all schedules when possible."
+    "text": "2.5 Lab Proceedings\n\n2.5.1 Communication\n\nCommunication within the group | Slack | In-person/Zoom co-work\n\nIn all meetings and interactions, it is imperative that lab members are constructive in feedback and respectful of each other. Critiques are always welcome and encouraged, but they should be supportive and aimed at building others up and improving our science, not tearing others down. At the same time, we shouldn’t shy away from providing critical feedback! As scientists, we all need regular practice critically analyzing and interpreting what we read and hear, and a friendly environment like our lab group is the best place to work on these skills together.\n\n\n2.5.2 Meetings and formats\nSince communication is key to good science, we meet regularly as a lab in a variety of formats. The details about these meetings can be found here.\n\n\n2.5.3 Remote work & working hours\nAt a very broad level, the more time you put into your work, the more you’ll get accomplished. However, this is also an obvious oversimplification. Some people prefer a typical 9-5, others thrive with a 10 hour/4 day workweek, and others still find their productivity falls off after 6 hours of work. Adding to this, our work can often be asynchronous, and working remotely can be integrated into a routine as well.\nRegardless of your working style, taking breaks is important! Stretch, take a brisk walk, hydrate, enjoy some caffeine (in moderation).\nIf you are working remotely for extended periods, communicate regularly on Slack, and schedule a few co-work times where you and others can log on together and work in a shared virtual space that makes spontaneous interactions possible. Remote work has advantages, but a major drawback is the lack of this spontaneity. Being able to walk to a neighboring desk and ask a quick question, take a shared tea break, and see the faces of the people you work with are real advantages to collaborative science. Some of these aspects can still be done remotely, but they require active effort. Please stay involved like this even if you aren’t on campus!\nGenerally speaking, if you are meeting milestones, participating in project and group discussions, and comfortable with your work-life balance in our lab, the details of your work schedule are flexible. For a diverse group, a schedule that accommodates everyone necessarily requires compromise. Your exact schedule will come down to your role in the lab, your preferences, and the group’s availability. There are some basic rules and tenants to be aware of.\n\n2.5.3.1 Work hours\nFor full-time members (e.g., PRAs, postdocs, grads), expect to put in 40 hours of work per week on average. For part-time members (e.g., undergraduates during the semester, interns, and other volunteers), you might be in the range of 10-30 hours a week typically.\nThese ranges are estimates, and will vary across people and over time. We never want to find ourselves in a crunch, but deadlines sometimes do pile up, and some weeks may require more hours. At the same time, some weeks will be lighter, breaks are encouraged, and working to the clock, or overtime should not be glorified either. Most importantly, maintain a comfortable work-life balance that leaves you wanting to come back for more, and keeps you far from the burnout line! If you ever feel stressed about your schedule/workload, talk to your PI & group to see how we can change things.\nPresenteeism isn’t a healthy mindset, and health and productivity rank ahead (in that order!) of simply being present.\n\nWorking remotely | CU Remote Work Agreement\n\nFor any student-employee-related questions, please refer to the University of Colorado Denver student hourly employment handbook or the student employment website. Both handbooks define the student employment rules for the Denver and Anschutz Medical Campus.\n\n\n2.5.3.2 Time Off\nAlways be a happy researcher! To be a happy researcher means you need a good balance between work and time off. We encourage you to take time off when needed, but there are a few things to remember. If there are meetings/deadlines involved, please let me (PI) and team members know ahead of time if you can’t make it during crunch time.\n\nIt’s understandable that things occasionally come up – so, it’s for a few hours/1 day, feel free to drop me (PI) a quick note and take off, as needed.\nIf it’s more than 1-3 days (or recurring few hours/single days), let me (PI) know in advance so we can plan ahead.\nIf it’s >3 days, please include me (PI) in the conversation during the planning phase (before booking your tickets/planning your travel). It’s better for all parties involved if this is a conversation rather than an FYI. *Similar for >few days remote work, unless previously requested.\nMark your time off on the lab calendar (in a non-disruptive way – darkest color background and NO notifications per event for everyone in the group) and notify your PI and co-workers in advance.\nLet others know if you miss any meetings during your time off. Please do your best to plan your work accordingly when known vacation times (no meeting weeks) are approaching. Don’t leave too much undone before going on vacation because you may have too much to do when you return, which can cause stress.\nAlso, leave good notes on what you were working on and what you must do when you return. Sometimes, when you are gone for too long, remembering where you left off can be hard, so having these notes can help you get back on track.\nStudies have shown not having a sustainable work-life balance can lead to difficulties in maintaining an efficient, productive, and healthy research experience. Therefore, it is essential to maintain a healthy work-life balance to ensure the best and most productive research experience.(Bartlett et al., 2021)\nBe respectful of your labmates and avoid sending them messages when they are on vacation. If you are working closely with them on a project or need their help, notify them of any deadlines that may overlap with their vacation. This way meetings can be determined before your labmate leaves for vacation.\nIf you receive work-related messages during vacation/holidays (incl. weekends), you are not obligated to answer them unless they are critical. If the message is urgent (esp. something you’ve committed to prior to your vacation and have missed checking during working days), please do your best to answer them as soon as possible. This is more so important when there are deadlines approaching. It is OK if there are occasional instances when you can’t make it to a deadline – but this can’t be a norm and you *must* let me (PI) know in advance so we plan ahead.\n\n\n\n2.5.3.3 Leave policy\n\nBecause our group is tightly collaborative, please plan non-sick leave ahead of time to best fit all schedules when possible.\nFor graduate students: Details may vary per your specific graduate program’s handbook, but the Graduate School offers basic guidelines herefor vacation and leave.\nUndergraduate and Masters Students: Student Employment Handbook\nStaff (postdocs, research professionals): The University of Colorado’s leave policies"
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     "title": "3  How to X",
     "section": "3.3 Helpful Links to learn more about Machine Learning",
-    "text": "3.3 Helpful Links to learn more about Machine Learning\n\nYouTube Videos\n\nMachine Learning from Scratch by AssemblyAI\nMIT Deep Learning Course\nDeep Learning by Assembly AI\nUnderstanding Tensors by Dan Fleisch\nUnderstanding Neural Networks\nBasic Computer Parts Explained\n\nArticles:\n\nTransformers\n\nCoding Practice Sites\n\nLeetCode\n\n\n📌 Go-to books (also in pinned posts on Slack)\n\nR for Data Science (for tidyverse and such)\nHands-On Programming with R (for base R) Intro to Git, GitHub resources"
+    "text": "3.3 Helpful Links to learn more about Machine Learning\n\nYouTube Videos\n\nMachine Learning from Scratch by AssemblyAI\nMIT Deep Learning Course\nDeep Learning by Assembly AI\nUnderstanding Tensors by Dan Fleisch\nUnderstanding Neural Networks\nBasic Computer Parts Explained\n\nArticles\n\nTransformers\n\nCoding Practice Sites\n\nLeetCode\n\n\n📌 Go-to books (also in pinned posts on Slack)\n\nR for Data Science (for tidyverse and such)\nHands-On Programming with R (for base R) Intro to Git, GitHub resources"
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-    "section": "3.6 Read/write/present",
-    "text": "3.6 Read/write/present\n\nRead papers\nMake a poster\nWrite a paper\nWriting in the Sciences on Coursera"
+    "section": "3.4 Read/write/present",
+    "text": "3.4 Read/write/present\n\nRead papers\nMake a poster\nWrite a paper\nWriting in the Sciences on Coursera"
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-    "section": "3.7 Code",
-    "text": "3.7 Code\n\nWrite, work with, and manage source code and data\nPrepare for and carry out code review\nShare data\nWrite an R package\nDBMI software engineering team tips & tricks blog posts"
+    "section": "3.2 Code",
+    "text": "3.2 Code\n\nWrite, work with, and manage source code and data\nPrepare for and carry out code review\nShare data\nWrite an R package\nDBMI software engineering team tips & tricks blog posts\n\n\n3.2.1 Learn R\nTo learn R, I would recommend getting started with the pinned posts in #courses-primers.\nA couple of helpful GitHub repositories - https://github.com/jananiravi/workshop-tidyverse (Intro to R's tidyverse package — handy to learn right away) - Other R workshop materials from our R-Ladies East Lansing chapter: https://github.com/rladies-eastlansing - Interactive tutorials with learnr & swirl. - R for Genomics from Data Carpentry - R on HPC\n\nCoursera\n\nIntro to R programming and tidyverse\nData visualization and Dashboarding with R specialization\nGetting Started with Data Visualization in R\n… and more | explore by topic, duration, skill-level\n\n\n📌 Go-to books (also in pinned posts on Slack)\n\nR for Data Science (for tidyverse and such)\nHands-On Programming with R (for base R) Intro to Git, GitHub resources\n\n\n\n3.2.2 Intro to Machine Learning\n\nYouTube Videos\n\nMachine Learning from Scratch by AssemblyAI\nMIT Deep Learning Course\nDeep Learning by Assembly AI\nUnderstanding Tensors by Dan Fleisch\nUnderstanding Neural Networks\nBasic Computer Parts Explained\n\nArticles\n\nTransformers\n\nCoding Practice Sites\n\nLeetCode\n\n\n\n\n3.2.3 Learn Git/GitHub\n\nhttps://happygitwithr.com/ Happy Git and GitHub for the useR (connecting git/GitHub w/ R)\nGit and GitHub learning resources from GitHub\nGit 101\nCoursera Intro to Git and GitHub course"
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-    "section": "3.8 Plan your semester/year",
-    "text": "3.8 Plan your semester/year\nTemplates on yearly/semester planning and professional development are available here."
+    "section": "3.5 Plan your semester/year",
+    "text": "3.5 Plan your semester/year\nTemplates on yearly/semester planning and professional development are available here."
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-    "section": "3.10 Others",
-    "text": "3.10 Others\n\nCareer development week\nRemote work | CU remote work policy | CU DBMI remote work agreement"
+    "section": "3.6 Others",
+    "text": "3.6 Others\n\nCareer development week\nRemote work | CU remote work policy | CU DBMI remote work agreement"
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     "title": "Appendix F — Writing papers",
     "section": "F.1 How to write a scientific paper once we decide that you have one or more interesting results",
     "text": "F.1 How to write a scientific paper once we decide that you have one or more interesting results\nStart by discussing with me what the paper is about!\n\nF.1.1 Figures and Tables\n\nCreate a draft of your ideal set of Figures & Tables (in addition to supplements) that can tell an interesting, coherent story.\n\nWrite detailed figure/table legends to help understand what piece of the story each figure/table will convey.\nGet feedback on the entire story draft from colleagues / collaborators / committee.\nBased on these interactions, keep revisiting & revising this draft.\n\n\n\n\nF.1.2 Introduction & Discussion\n\nRead widely and deeply. Read often.\n\nRemember that this exercise is going to entirely feed your Introduction and Discussion sections.\nRecord all the papers in a Zotero library, starting with Slack shares and periodic PubMed searches.\nCreate a single Google Doc and make notes about each paper along with its title & link. The purpose of the notes is to make the points you will write in your manuscript to cite each paper.\nBased on these readings and discussions during project meetings, pick a target journal.\n\n\n\n\nF.1.3 Supplementary data\n\nMake all main and supplemental Figures and Tables along with declarative titles & detailed legends.\n\nRun many controls and sanity checks.\nRapidly iterate with me & colleagues and do additional analyses needed to fill gaps & round-out the story.\nPrepare for & do code review.\n\n\n\n\nF.1.4 Methods & Code+Data\n\nWrite a very detailed Methods section and prepare Code & Data to be released.\n\nDecide (w/ me) what Code & Data need to be released with this manuscript.\nAs you write each sub-section of Methods, organize and document the pertinent code, data, and results.\n\n\n\n\nF.1.5 Results\n\nWrite the Results section and rapidly iterate with me & colleagues to make changes/improvements.\n\n\n\nF.1.6 Tying them together\n\nStart with the story line.\nMake the Figures/Tables (you will keep iterating over these until submission).\nWrite the Methods since that’s the easiest one to tackle.\nThen, write the Results describing your Figs/Tables.\nFinally, write the Introduction and Discussion sections, and add References (e.g., Zotero + Google Docs integration).\n\nThe Introduction section should lead up to the main questions and results of the manuscript.\nThe Discussion should put the new results in the context of existing work, describe novelty & potential impact, and conclude with opportunities for future work.\nPerform any additional analyses/comparisons needed to make these sections airtight.\n\n\n\n\nF.1.7 Title & Abstract\n\nWrite Title and Abstract, and get feedback from me/colleagues/collaborators on this full document.\n\n\n\nF.1.8 Last Steps\n\nWhile others are critically reviewing the manuscript:\n\nCreate a well-organized & documented companion GitHub repo for the manuscript.\n\nThis should contain all the Code & Data (from Step 4) that will be publicly released.\n\nWrite the Cover Letter.\n\nSubmit on bioRxiv, share on social media, and submit to journal! 🎉"
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+    "section": "3.9 HPC, servers",
+    "text": "3.9 HPC, servers\nFor computing that requires high performance hardware and computing clusters, we utilize two different remote servers.\n\n3.9.1 JRaviLab server\n\nA single high performance machine used only by our group.\nTo request access, contact the system administrator shaddai.amolitos@cuanschutz.edu by sending him your CU username (e.g., the CU auto-generated ravijan instead of janani.ravi@cuanschutz.edu) and a brief message that you will need access to the server. CC janani.ravi@cuanschutz.edu, so they can both verify your access.\nIf you are new to remote server work, then it maybe helpful to learn about using an ssh config for managing your remote hosts.\n\n\n\n3.9.2 Alpine HPC\n\nAlpine is the HPC cluster for all the University of Colorado campuses, including Anschutz.\nThere is extensive documentation about getting setup\nAt the moment, a web shell is the only access option for Anschutz members. This is different from a typical SSH login, and it is best to follow the official, latest Alpine documentation.\n\nWhenever possible, we highly recommend using the VSCode extension which provides an IDE on the remote host without having to worry about server-side installation of other IDEs like RStudio or Jupyter."
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+    "title": "3  How to X",
+    "section": "3.3 Access HPC, servers",
+    "text": "3.3 Access HPC, servers\nFor computing that requires high performance hardware and computing clusters, we utilize two different remote servers.\n\n3.3.1 JRaviLab server\n\nA single high performance machine used only by our group.\nTo request access, contact the system administrator shaddai.amolitos@cuanschutz.edu by sending him your CU username (e.g., the CU auto-generated ravijan instead of janani.ravi@cuanschutz.edu) and a brief message that you will need access to the server. CC janani.ravi@cuanschutz.edu, so they can both verify your access.\nIf you are new to remote server work, then it maybe helpful to learn about using an ssh config for managing your remote hosts.\n\n\n\n3.3.2 Alpine HPC\n\nAlpine is the HPC cluster for all the University of Colorado campuses, including Anschutz.\nThere is extensive documentation about getting setup\nAt the moment, a web shell is the only access option for Anschutz members. This is different from a typical SSH login, and it is best to follow the official, latest Alpine documentation.\n\nWhenever possible, we highly recommend using the VSCode extension which provides an IDE on the remote host without having to worry about server-side installation of other IDEs like RStudio or Jupyter.\n\n\n3.3.3 Use VPN\nhttps://www.ucdenver.edu/offices/office-of-information-technology/software/how-do-i-use/vpn-and-remote-access"
   }
 ]
\ No newline at end of file
diff --git a/howto.qmd b/howto.qmd
index 291d776..358f7da 100644
--- a/howto.qmd
+++ b/howto.qmd
@@ -10,7 +10,15 @@ To re-familiarize yourself with R/Python/Unix, check out these two resources in
 
 💡*If you find other useful resources, please add them to [this list](https://github.com/jananiravi/compbio-gists) (or share them with me).*
 
-## Learn R
+## Code
+
+-   [Write, work with, and manage source code and data](https://github.com/JRaviLab/group/blob/master/docs/howto_write_source_code.md)
+-   [Prepare for and carry out code review](https://github.com/JRaviLab/group/blob/master/docs/howto_do_code_review.md)
+-   [Share data](https://github.com/jtleek/datasharing)
+-   [Write an R package](https://github.com/jtleek/rpackages)
+-   [DBMI software engineering team tips & tricks blog posts](https://cu-dbmi.github.io/set-website/blog)
+
+### Learn R
 
 To learn R, I would recommend getting started with the pinned posts in [#courses-primers](https://jravilab.slack.com/archives/CARJ72W3U).
 
@@ -22,7 +30,12 @@ A couple of helpful GitHub repositories - <https://github.com/jananiravi/worksho
     -   [Getting Started with Data Visualization in R](https://www.coursera.org/learn/jhu-getting-started-data-viz-r)
     -   ... and more \| explore by topic, duration, skill-level
 
-## Helpful Links to learn more about Machine Learning
+📌 Go-to books (also in pinned posts on Slack)
+
+-   [R for Data Science](https://r4ds.had.co.nz/) (for tidyverse and such)
+-   [Hands-On Programming with R](https://rstudio-education.github.io/hopr/) (for base R) Intro to Git, GitHub resources
+
+### Intro to Machine Learning
 
 -   YouTube Videos
     -   [Machine Learning from Scratch by AssemblyAI](https://www.youtube.com/watch?v=p1hGz0w_OCo&list=PLcWfeUsAys2k_xub3mHks85sBHZvg24Jd)
@@ -31,47 +44,19 @@ A couple of helpful GitHub repositories - <https://github.com/jananiravi/worksho
     -   [Understanding Tensors by Dan Fleisch](https://www.youtube.com/watch?v=f5liqUk0ZTw)
     -   [Understanding Neural Networks](https://www.youtube.com/watch?v=aircAruvnKk)
     -   [Basic Computer Parts Explained](https://www.youtube.com/watch?v=ExxFxD4OSZ0)
--   Articles:
+-   Articles
     -   [Transformers](http://jalammar.github.io/illustrated-transformer/)
 -   Coding Practice Sites
     -   [LeetCode](https://leetcode.com/)
 
-📌 Go-to books (also in pinned posts on Slack)
-
--   [R for Data Science](https://r4ds.had.co.nz/) (for tidyverse and such)
--   [Hands-On Programming with R](https://rstudio-education.github.io/hopr/) (for base R) Intro to Git, GitHub resources
-
-## Use VPN
-
-<https://www.ucdenver.edu/offices/office-of-information-technology/software/how-do-i-use/vpn-and-remote-access>
-
-## Learn Git/GitHub
+### Learn Git/GitHub
 
 -   <https://happygitwithr.com/> Happy Git and GitHub for the useR (connecting git/GitHub w/ R)
 -   [Git and GitHub learning resources](https://docs.github.com/en/get-started/quickstart/git-and-github-learning-resources) from GitHub
 -   [Git 101](https://product.hubspot.com/blog/git-and-github-tutorial-for-beginners)
 -   [Coursera Intro to Git and GitHub course](https://www.coursera.org/learn/introduction-git-github)
 
-## Read/write/present
-
--   [Read papers](https://github.com/JRaviLab/readingpapers)
--   [Make a poster](https://github.com/JRaviLab/group/blob/master/docs/howto_make_a_poster.md)
--   [Write a paper](https://github.com/JRaviLab/group/blob/master/docs/howto_write_a_paper.md)
--   [Writing in the Sciences on Coursera](https://www.coursera.org/learn/sciwrite)
-
-## Code
-
--   [Write, work with, and manage source code and data](https://github.com/JRaviLab/group/blob/master/docs/howto_write_source_code.md)
--   [Prepare for and carry out code review](https://github.com/JRaviLab/group/blob/master/docs/howto_do_code_review.md)
--   [Share data](https://github.com/jtleek/datasharing)
--   [Write an R package](https://github.com/jtleek/rpackages)
--   [DBMI software engineering team tips & tricks blog posts](https://cu-dbmi.github.io/set-website/blog)
-
-## Plan your semester/year
-
-[Templates](https://github.com/JRaviLab/group/tree/master/docs/templates) on yearly/[semester planning](https://github.com/JRaviLab/group/blob/master/docs/Yearly-Planning-Document.pdf) and professional development are available [here](https://github.com/JRaviLab/group/tree/master/docs).
-
-## Remote server work (JRaviLab server & Alpine HPC)
+## Access HPC, servers
 
 For computing that requires high performance hardware and computing clusters, we utilize two different remote servers.
 
@@ -89,6 +74,21 @@ For computing that requires high performance hardware and computing clusters, we
 
 Whenever possible, we highly recommend using the [VSCode extension](https://code.visualstudio.com/docs/remote/ssh) which provides an IDE on the remote host without having to worry about server-side installation of other IDEs like RStudio or Jupyter.
 
+### Use VPN
+
+<https://www.ucdenver.edu/offices/office-of-information-technology/software/how-do-i-use/vpn-and-remote-access>
+
+## Read/write/present
+
+-   [Read papers](https://github.com/JRaviLab/readingpapers)
+-   [Make a poster](https://github.com/JRaviLab/group/blob/master/docs/howto_make_a_poster.md)
+-   [Write a paper](https://github.com/JRaviLab/group/blob/master/docs/howto_write_a_paper.md)
+-   [Writing in the Sciences on Coursera](https://www.coursera.org/learn/sciwrite)
+
+## Plan your semester/year
+
+[Templates](https://github.com/JRaviLab/group/tree/master/docs/templates) on yearly/[semester planning](https://github.com/JRaviLab/group/blob/master/docs/Yearly-Planning-Document.pdf) and professional development are available [here](https://github.com/JRaviLab/group/tree/master/docs).
+
 ## Others
 
 -   [Career development week](https://github.com/JRaviLab/group/blob/master/docs/career_dev_week.md)
diff --git a/offboarding.qmd b/offboarding.qmd
index cc4f4a7..66a775b 100644
--- a/offboarding.qmd
+++ b/offboarding.qmd
@@ -8,17 +8,17 @@ We are delighted to have been a part of your research life. We wish you great la
 
 Please make sure you have checked these boxes before leaving our group.
 
--   [ ] Please return any devices, cords, or computers that belong to the lab.
+-   [ ] Please return any computers, devices, cords, or accessories that belong to the lab.
 
--   [ ] All your code is on GitHub
+-   [ ] All your code is on GitHub, and all your other non-GH docs are on our shared Google Drive folder.
 
--   [ ] All your processed data files/figures/reports (\<100MB) are on GitHub
+-   [ ] All your processed data files/figures/reports (\<100MB) are on GitHub.
 
--   [ ] Large data files (raw/processed) are on the server (and backed up)
+-   [ ] Large data files (raw/processed) are on the server (and backed up).
 
--   [ ] All your scripts and data files are well-annotated with appropriate `README` files
+-   [ ] All your scripts and data files are well-annotated with appropriate `README` files and `Mermaid` workflows, when relevant.
 
--   [ ] Added detailed status report of where things -- what was tried, what worked/didn't work, where the scripts/data files are, what remains to be done (within the scope of the project, and clear next steps)
+-   [ ] Added a detailed status report of where things -- what was tried, what worked/didn't work, where the scripts/data files are, what remains to be done (within the scope of the project, and clear next steps)
 
 -   [ ] You have reoriented me and at least 1-2 other project members with the precise status (and next steps) of the project and the location of files
 
@@ -28,15 +28,9 @@ Please make sure you have checked these boxes before leaving our group.
 
 -   [ ] If you have worked with us for a considerable period of time, you will remain a part of `#the-continuum` channel on our Slack.
 
--   [ ] Leave and update us of any changes in contact information for authorship purposes in case we need to reach you and add you to the list of authors for all the work you contributed to the published project.
+-   [ ] Leave and update us of any changes in contact information for authorship purposes (in case we need to reach you and add you to the list of authors for all the work you contributed to the published project) and for us to know where you are now thriving.
 
-#### If you need more information on the leave policy, please refer to the appropriate link at the bottom.
-
-Undergraduate and Masters Students: [Student Employment Handbook](https://www.ucdenver.edu/docs/librariesprovider41/student-employment/student_hourly_employment_handbook.pdf?sfvrsn=8e3963ba_6)
-
-Ph.D. Students: [Graduate School Policy for Vacation and Leave](https://www.ucdenver.edu/docs/librariesprovider138/denver-anschutz-graduate-school/resources/gs-student-leavevacpolicy.pdf?sfvrsn=661c22b9_2)
-
-Good luck!
+Good luck with your career next steps!
 
 ## Stay in touch