TUBI Spring 2023
TUBI handbook
Spring 2023 Treehouse Undergraduate Bioinformatics Immersion (TUBI)
Group meetings:
via Zoom (and sometimes hybrid)
April 3-June 9
MW 1:20–2:25 PM
Optional group work session and office hours:
Friday 1:20–1:55
Recommendation requests and advising:
Friday 1:55–2:25; reserve here
Contact info:
Holly Beale, PhD
she/her; Holly (preferred) or Dr. Beale; pronunciation: http://bit.ly/say_holly_beale
anonymous email: send to op493r2@gmail.com via guerrillamail.com[1]
This handbook is a living document. Please make suggestions for clarity or content via Google Docs or email. All materials for the course are referred to in this document and most are in the group's google drive.
TUBI is an undergraduate bioinformatics immersion research group sponsored by Treehouse and the Vaske lab. Undergraduate researchers will work in a supportive environment on bioinformatic projects relating to finding cancer treatment options for individual kids using gene expression analysis.
The Treehouse Childhood Cancer Initiative and the Vaske lab are led by Olena Vaske, a Molecular, Cell and Developmental (MCD) Biology faculty member. Holly Beale, a member of Treehouse and the Vaske lab, is leading TUBI. Yvonne Vasquez, a Treehouse-Vaske lab graduate student, is co-leading TUBI.
During Spring 2023, TUBI researchers will be testing whether specific mutations can be identified in gene expression data. Each researcher will start by selecting a mutation to investigate. Different mutations will be easier or harder to analyze, but not always predictably. Most people will be able to validate or invalidate multiple mutations.
Each researcher will discuss their work with other people, but each researcher will be studying their own selected mutations.
TUBI aims to advance research in pediatric cancer and help undergraduates develop as scientists and gain experience doing research. Research can be unpredictable and frustrating. A task usually only takes 10% of the time spent to figure out how to do it. We want to give people the opportunity to experience what research is like in a supportive environment.
Integrating a diverse set of experiences is important for a more comprehensive understanding of science and for improving scientific discoveries in the future. We are committed to creating a learning environment for TUBI researchers that supports diversity of thoughts, perspectives and experiences, and honors your identities.
Everyone, including mentors, are expected to treat each other with respect and to avoid perpetuating biases regardless of race, ethnicity, level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, age, or religion.
I (like many people) am still in the process of learning about diverse perspectives and identities. If something was said in class (by anyone) that made you feel uncomfortable, please talk to me about it. Alternatively, you can report hate- or bias-motivated incidents or reach out to the hate/bias response team.
If you would like to make suggestions about how we can improve equity and inclusiveness in TUBI, please feel free to email Holly; see the top of this document for instructions on mailing Holly anonymously.
If you are a student with a disability who would benefit from accommodations, please email Holly to plan a discussion of ways we can ensure your full participation in the group.
You'll be learning a protocol, a process, at the same time as you're learning the theory and meaning of the steps you are doing. I think you'll find that it's really rewarding when you have a new insight about how they match up. Think about how you'd like to balance making progress with understanding. If you don't take action until you understand everything, you won't take any action. Your job is to try things, accepting you'll make mistakes. You will make plenty of them, and they will help you make progress. On the other hand, if you do all the steps without understanding any of their biological meaning, you won't be able to meaningfully apply the steps to other situations. It's always a bit frustrating to figure out the right balance at any given time, so give yourself grace when you experience that frustration.
The following are some programs we'll use for TUBI. Some you probably already know; others probably have familiar interfaces. If you have any trouble with them, please let me know.
Google Drive and Google Docs - Specifically, creating a google document within a specified google drive and assigning a header style in a google document
Slack
Zoom
I'd like everyone in the group to submit a voice recording of how you would like others to pronounce your name. Please link to the recording in the TUBI 2023 researchers document. There are multiple ways to do this. The most secure way is to record it yourself and host it with a free account on Dropbox or your own Google drive. For example, I recorded mine using iOS Voice Memos and uploaded the .m4a file to Dropbox. I created a link to the file (https://www.dropbox.com/s/e9x4suyrezcppai/Holly%20Beale.m4a?dl=0) and used a URL shortening service to make it more manageable. Now I add the short link (http://bit.ly/say_holly_beale) to my email signature when relevant. Yvonne Vasquez used Google drive and I shortened it with TinyURL: https://tinyurl.com/wkc4d25u. If you use Google drive, make sure that I (and whoever else you want to access it) has permissions to access the file.
There are also services that enable recording and sharing how your name is pronounced, but it's unclear how they will use your recording. One such service is on LinkedIn, and others can be found by searching the terms "record your name" in google.
Open a new or existing Google document. You should see "Tools" in the menu.
Go to "Tools|Preferences". In the General section, disable the first six checkboxes and the last one (see images below). In the Substitutions section, disable "Automatic substitution" in the section. For this research, I strongly discourage using Microsoft Office (Word, Excel) or any other tool that changes your text.
This is called writing a "bug report", even if you think it's a mistake you made instead of a bug in the software. It's a format for communicating with people who aren't working on the same thing that you are.
This format makes it easier to provide all the necessary context about what you were doing when the error appeared. You want the person helping you to be able to reproduce the error—to be able to experience it themself—as the first step towards understanding it and fixing it.
Here are a few questions to guide your description when you ask for help. You don't have to provide the answers to all of them. Because we are all solving similar problems on the same Linux server environment, everyone already has some of the context. That means you're not starting from scratch; instead, think about, for each question, whether the people helping you already know what you're about to say.
Thinking about each part of a bug report is a good skill to develop, even when you ultimately ask your question in a briefer way.
Additional resources
We will first connect to the servers together during our meeting on Wednesday April 5. Here are the instructions: Connecting to the TUBI March 2023 server
On Windows computers, Ctrl-C is used for copy. On the command line, Ctrl-C stops a command. PuTTY had to come up with a way to support copying to and from your PuTTY window. Here is a concise description and here is the official documentation. Basically, to copy FROM PuTTY, select the text (click the left mouse button in the terminal window, keep the left mouse button down and drag the text you want to copy, then let go of the left button). The text will be automatically copied to the clipboard. To copy TO PuTTY, just click the right mouse button.
If you have an inconsistent internet connection or other difficulties staying consistently connected to a network, you might consider using GNU Screen for your work on a server. It's not very intuitive, so feel free to ask for help with it.
The outcomes of the projects are not yet known, and projects may be easier or harder than expected. The most important contribution is well-documented work. Quality of work is more important than quantity.
Research projects expand to consume all available time. We ask that you spend 10 hours a week on the project; you are not required to spend more. Do the best you can with the time available.
All your work, including raw notes and mistakes, should be recorded in your lab notebook.
Following are the expectations for TUBI researchers.
Please reach out to me if you would benefit from accommodations.
This is described in the variant detection protocol. Here is an example of a Lab Notebook document.
Each week you'll give a brief (~1 minute) check-in on your progress, but I'll ask you to give a more in-depth presentation about your progress during our session as well. You will spend about 5 minutes describing the work you've done for your project since the beginning of the session, with an emphasis on things you learned that might help other people. The easiest way to approach this is to share your screen showing your lab notebook and walk through the process.
We'll spend a couple meetings looking at the bash operators, commands and programs in more detail (I'll call them commands for brevity). Each researcher has been assigned a command in the participant list. I'd like each researcher to prepare at least three slides on their command, one defining it, one giving an example of how it's supposed to work (not an example from the protocol) and another giving an example of mistakes one can make using it. The last two slides should have screenshots from running the command on the server showing the examples. You should be prepared to spend no more than 5 minutes walking people through your command. Please put your slides in the google drive folder called "presentations describing commands". Here is an example set of slides.
The main variant detection protocol describes how to identify single nucleotide polymorphisms (SNPs), which are variants where one nucleotide is changed to another nucleotide. For your first variant, you can pick one at random or based on what genes and cancers you find most interesting. For your second variant, pick a variant another researcher in the group has completed, and check whether you get the same results. For your second and third variants, you'll put your name and a link to the lab notebook in the "Validation researcher" and "Link to validation lab notebook" columns instead of the "Researcher" and "Link to lab notebook" columns. For your third variant, browse through the variant list to find variants with the word "prioritize" in the "prioritize" column. If all those are completed and validated, you can pick a variant at random. When you are confident in calling SNPs, you can try calling variants that are more difficult for variant callers to identify and more difficult for researchers to interpret the results. The protocol for calling these variants is called 2023 hard variant detection protocol.
Details on this presentation are in Instructions for reporting on a variant.
When you have a question, first check this handbook, the linked documents and google. If you're having trouble finding the answer, ask your question on the TUBI Spring 2023 Slack workspace so Holly and the other TUBI researchers can see it (invitation to the TUBI 2023 Slack workspace; you have to click the invitation before you can post). If you're still having trouble finding the answer, email Holly.
I will send emails with announcements and anything that I need everyone to know. I will use Slack to answer questions that come up and make suggestions. You don't need to stay up to date with the Slack channel, but it's the best place to go with questions, because someone else might have asked it already.
TUBI 2023 handbook (this document)
TUBI 2023 Shared google drive
Date | Meeting plan | Milestone due before meeting |
Week 1: 4/3 | Introduction to Treehouse by Olena Vaske | |
Week 1: 4/5 | Introduction to the scientific question we'll investigate; walkthrough of logging in to the server; discussion of genome sequences | Record your name and update the TUBI participant spreadsheet with a link to the recording. Configure your google docs. Look up which subgroup you will be part of. |
Week 2: 4/10 | Continue discussion of Treehouse cases with Olena Vaske | Learn how to open Terminal (Mac) or install and learn how to open PuTTY (Windows) on your computer. Join the Slack channel. Post the link to your pronounced name to the General channel on TUBI Spring 2023 Slack. |
Week 2: 4/12 | Demo of variant calling process | Complete the Treehouse Unix shell tutorial. |
Week 3: 4/17 | Demo of variant calling process | Start protocol. Claim a mutation; create Lab Notebook for first mutation; add URL to mutation spreadsheet; proceed with analysis. You can look at mycancergenome.org or COMSIC to see what cancers are associated with each variant. |
Week 3: 4/19 | Demo of variant calling process | Continue with variant testing and updating your Lab Notebooks |
Week 4: 4/24 | Demo of variant calling process | Continue with variant testing and updating your Lab Notebooks |
Week 4: 4/26 | Discuss validation | Continue with variant testing and updating your Lab Notebooks |
Week 5: 5/1 | Demo hard variant protocol | |
Week 5: 5/3 | Olena leads workshop on variant interpretation | |
Week 6: 5/8 | Yvonne talks about her experiences as a first-gen undergrad researcher and graduate student | |
Week 6: 5/10 | Guests speakers discuss cancer advocacy | In preparation for explaining your variant, please finalize your slides by 5/12 and add them to the google drive per the instructions in the handbook |
Week 7: 5/15 | Geoff discusses Treehouse case analysis Review of hard variant conundrums; Holly talks about her career path | |
Week 7: 5/17 | Researchers explain their assigned bash operator, command or program | |
Week 8: 5/22 | Continue with researchers explaining their assigned bash operator, command or program | |
Week 8: 5/24 | Probably: Undergraduate researcher panel on life after TUBI | |
Week 9: 5/29 | No meeting (Memorial day) | |
Week 9: 5/31 | Variant presentations | |
Week 10: 6/5 | Brennan Decker, MD, PhD talks about about his career path and learning computational biology | |
Week 10: 6/7 | Variant presentations | |
Finals meeting session: Thursday, June 15 8:30–11:00 a.m. | Final session: Student presentations, friends and family welcome |
Description of how variants are described by HGVS the human genome variant society
You need a computer that can run SSH through Terminal or PuTTY during meetings. If you lose access to your computer, please let me know. At UCSC, there is a laptop borrowing program through the library or EOP office (for eligible students).
The goals of TUBI are to advance research in pediatric cancer and help undergraduates and others develop as scientists. The work is not graded. Students may wish to request a recommendation for an application for subsequent work in another lab, for a job, or for a graduate program. We will provide recommendations reflecting students' progress, lab notebook, communication and presentations. The outcomes of the research are not yet known, and some individuals' investigations may be easier or harder than expected, so a good recommendation may be provided even when a project is not completed. Quality of work is more important than quantity.
(For students applying for graduate school, we recommend getting additional recommendations from a mentor who has worked with you more).
For me to be able to write a good recommendation, I need to have a series of evidence-based statements I can make about you. It helps me to remember things you say and do during group meetings if I have talked to you 1:1. as early as possible in the session. For you to be eligible for a recommendation, I need to meet you 1:1 (virtual or in person) before TUBI ends. If you want a recommendation or general mentoring, please sign up for a 1:1 meeting slot. If none of those times work for you, please reach out to me by email. We can use the session to talk about your interests, potential future opportunities, review your CV, or whatever you'd like to talk about.
This is an MIT class designed to improve proficiency with computer tools like using the command line: https://missing.csail.mit.edu/
https://uspa.ucsc.edu/symposium/
Free. My favorite science event at UCSC.
This is a general resource. Many of the paid summer internship programs are called research experiences for undergraduates (REUs). https://www.pathwaystoscience.org/Undergrads.aspx
https://www.nsf.gov/crssprgm/reu/
Mega-thread:
https://twitter.com/robertnulrich/status/1220129404271022080?s=12
Notice for paid summer internship with Anne Carpenter in Boston: https://twitter.com/drannecarpenter/status/1217058986253541379?s=12
Notice for paid summer internship with Sandra Loesgen in Florida:
https://twitter.com/LoesgenLab/status/1216851836944158725
UCSC faculty re-tweet of paid summer internships at UCSF:
https://twitter.com/jordan_d_ward/status/1218182870369333248?s=12
University of Rhode Island Marine biology internship:
https://twitter.com/URIGSO/status/1225466744313131018
Twitter has been a great place to keep up with issues in science, although its future is unclear. Here's a snapshot list of scientists I was following on 11/23/2019: https://twitter.com/hollybeale/lists/following-nov23-2019 (made with R because twitter is missing a lot of tools). I especially recommend Needhi Bhalla, a UCSC faculty member.
How to read a scientific paper
Postbaccalaureate Research Education Programs
https://www.nigms.nih.gov/training/PREP/Pages/default.aspx
Note - these are research programs that pay you, not the kind that are mostly classes and cost a lot. "PREP provides an opportunity for undergraduates who hold a recent bachelor's degree and who have the desire to pursue a research doctorate (PhD or MD-PhD) to have meaningful research experiences to guide them towards careers in the biomedical sciences."
MINT
https://womenscenter.ucsc.edu/get-involved/mint-gallery-page.html
Website: "a mentoring program that centers underrepresented (first-generation, low-income, and/or person of color) undergraduate womxn in the pursuit of graduate degrees".
Is it worth going to graduate school?
Most of the people teaching and mentoring you in college chose graduate school, so it's hard to get an unbiased perspective on the value of graduate school. Here's a twitter thread mostly arguing against going to graduate school: https://twitter.com/vanesaringle/status/1224488613121069058?s=12. Another perspective: https://twitter.com/Sternarchella/status/1224759488571416576
This thread discusses questions you might want to ask potential mentors when you interview for a graduate program. I suggest you discuss these questions with your peers and mentors before you ask; I think some are better geared for rotation interviews (e.g. "will you share all expectations for thesis work with me now, or should I expect them to increase as I work in your lab?") https://twitter.com/amycharkowski/status/1223682402079260672?s=12
Women in Science and Engineering (WiSE)
https://graddiv.ucsc.edu/current-students/underrepresented-students/wise.html
Their newsletter has a lot of great events listed.
SACNAS - Society for Advancement of Chicanos/Hispanics and Native Americans in Science
SACNAS is a national organization based in Santa Cruz. They're awesome and have a great annual conference.
UCSC Research Mentoring Institute (RMI)
Jackie Roger, a Treehouse/RMI alumn, says: Provides a collaborative mentoring structure, professional development workshops and community building events.
Additional student groups: https://undergrad.soe.ucsc.edu/student-organizations
The MARC Program offers research training to participating honors students to help prepare them to compete successfully for entry into graduate programs leading to the Ph.D. in the biomedical sciences
IMSD, also known as the Minority Biomedical Research Support (MBRS) program, provides participating students with the opportunity to receive an in-depth experience in the academic and experimental aspects of biological research. Funded through the National Institutes of Health, the program consists of a laboratory-training program during the summer and laboratory research projects during the academic year.
(All of the above STEM Diversity programs offer stipends.)
Academic Excellence (ACE)
ACE is an academic support program that is dedicated to increasing the diversity of UCSC students earning bachelors' degrees in science, technology, engineering, and mathematics. ACE is a community of scholars who strive for and commit to academic excellence.
Additional academic (and general) support:
https://advising.ucsc.edu/success/support.html
Handling hate- or bias-motivated incidents
You can report hate- or bias-motivated incidents or reach out to the hate/bias response team.
[1] ucsc.edu addresses don't accept email from guerrillamail, so I have it sent to a gmail account instead.
[2] Modified from https://www.brown.edu/sheridan/teaching-learning-resources/inclusive-teaching/statements
