Capra Lab Philosophy

Our fundamental goal is to advance understanding of how the world works. In particular, we study how genomes evolve and function. We believe that the best way to pursue this goal is through open and welcoming scientific practices that engage with diverse perspectives. Thus, mentoring and training one another is an essential component of our mission, along with the communication of our results to broad audiences beyond specialists. Our main goal is NOT to publish a paper in Science, obtain a faculty job, or make millions of dollars. While we hope all of these happen if you want them, they are side effects of and secondary to our fundamental goal. When we lose sight of this, bad things are likely to happen.

Science is hard. But it should also be enjoyable. To that end, we strive to maintain a positive, engaging, hostility-free, and rewarding lab environment. To maintain that environment, we all have responsibilities: Respect your lab mates. Respect their culture, sexual orientation, religion, and beliefs. If you cannot honestly and wholeheartedly commit to this, you should not join our lab. Work on projects you are passionate about, work hard, and be proud of your work. There are highs and lows on all projects, but if you find that you have gone months without feeling passion and pride, something is wrong. You should talk with Tony and your labmates about it. Be careful. Don’t rush your work. Think before analyzing. Double and triple check your inputs and results. Incorporate sanity checks and unit tests. Ask others to look at your code or data. We have so many rubber ducks in the lab for a reason. We all make mistakes; plan for them. When you do make a mistake, do not hide it. We admit our mistakes; we correct them; and we move on. Be honest. We all want to accomplish great things, but we must do them honestly. Incorrect results are a major barrier to progress. It is never ok to plagiarize, tamper with, make up, or omit data, or fudge results in any way. Support your lab mates. Help them out when you can, whether it is by running an analysis or just lending a sympathetic ear. Healthy science is collaborative, not competitive. If you are having trouble, tell someone. While our work is important, your health and happiness are more important. This lab looks out for the well-being of all its members. If you do not feel comfortable talking with Tony or others in the lab, UCSF has confidential support services. Do not tolerate tension or hostility in the lab. We believe that good work requires a safe and supportive environment. Disrespectful behavior and rudeness are not acceptable in the lab. Tell Tony immediately if you or others in the lab do not feel comfortable for any reason. Tell Tony if you have problems with him. I (Tony) may not always tell you what you want to hear, but I strive to always act respectfully, give reasons for my actions, and do what I believe to be in your best interest. However, I want to know if something I am doing is causing problems. If you are not comfortable discussing the issue with me, then talk with other mentors or administrators (e.g., DGS or committee chair for graduate students).

Essential Policies The lab, and the university, is an environment that must be free of harassment and discrimination. All lab members are expected to abide by the UCSF policies on discrimination and harassment, which you can (and must) read about here. The lab is committed to ensuring a safe, friendly, and accepting environment for all. We will not tolerate any verbal or physical harassment or discrimination on the basis of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, or religion. We will not tolerate intimidation, stalking, following, unwanted photography or video recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention. Finally, it should go without saying that lewd language, behavior, and dress have no place in the lab, including any lab outings. If you see someone being harassed, or are harassed yourself, tell Tony immediately. If Tony is the cause of your concern, then reach out to another trusted faculty member in the University. UCSF also has resources for reporting harassment. If you are concerned for your or anyone else’s safety, call Campus Security immediately at XXX. Scientific Integrity Research (Mis)conduct The lab and UCSF are committed to ensuring research integrity. Research misconduct is unacceptable and grounds for immediate termination. We do not tolerate fabrication, falsification, or plagiarism. Read UCSF policies on the conduct of research carefully (). We strive to create an environment in which many of the factors that lead to misconduct are not present. Tony’s goal is honest, transparent, and reproducible research. However, if you ever feel pressures that make you consider misconduct or you feel that someone else (e.g., a collaborator) is pressuring you, let Tony know. We will often discuss the best ways to present our results to maximize clarity and impact, but these discussions should never lead to misleading claims about results. Publishing misleading or falsified results does an incredible disservice to the field and wastes massive amounts of other researchers’ time. And it also risks your entire career and the career of those around you. It is never right and never worth it. Don’t do it. Reproducible Research We are committed to publishing reproducible research. All manuscripts will be made available as preprints on biorXiv at the time of submission and all code and data (respecting IRB/legal limitations) will be made public on github (or other appropriate websites) upon publication. Reproducible research is an essential part of science, and requirement for all projects in the lab. For results to be reproducible, the data and analyses must be organized and well documented in Notion and/or Jupyter notebooks. To meet these goals, you should take notes on each step of your analysis pipeline. This means writing down how you did things every step of the way (and the order that you did things), from any pre-processing of the data, to running models, to statistical tests. Additionally, your code should also be commented and commented clearly. Comment your code so that every step is understandable by someone else. Often this outsider will be you in 6 months or a year, when I or a collaborator ask you to rerun an analysis. There are many resources to support this, including jupyter lab notebooks and R options. Finally, use version control (e.g., git) to manage code. Link to lab github. Authorship Authorship on manuscripts is the main currency in science. In our field the order of authors implies information about different author’s roles in the projects. It is generally assumed that the first listed author completed most of the analyses and the last listed author supervised the work. As science becomes more and more collaborative, it is common for papers to list multiple “first” and “last” authors. We will follow the APA guidelines with respect to authorship: “Authorship credit should reflect the individual’s contribution to the study. An author is considered anyone involved with initial research design, data collection and analysis, manuscript drafting, and final approval. However, the following do not necessarily qualify for authorship: providing funding or resources, mentorship, or contributing research but not helping with the publication itself. The primary author assumes responsibility for the publication, making sure that the data are accurate, that all deserving authors have been credited, that all authors have given their approval to the final draft; and handles responses to inquiries after the manuscript is published.” At the start of a new project, we will have a conversation with all involved about authorship expectations. The trainee taking on the lead can expect to be first author, and Tony will typically be the last author, unless the project is primarily under the guidance of another PI. Trainees who help over the course of the project may be added to the author list depending on their contribution, and their placement will be discussed with all parties involved in the paper. If a trainee starts a project, but subsequently drops it or hands it off to another student or post-doc, they will most likely lose first-authorship to that student or post-doc, unless co-first-authorship is appropriate. All of these issues will be discussed openly, and you should feel free to bring them up if you are not sure of your authorship status or want to challenge it. Since the first and last author system is not very specific about contributions, we are committed to providing a detailed accounting of the contributions of all authors following the X guidelines at the end of each manuscript. Human Subjects Research Adherence to approved IRB protocols is essential, and non-adherence can lead to severe consequences for the entire lab (e.g., losing access to any human/patient data and/or loss of grant funding). All lab members must read and comply with IRB consent forms and research summary for any project that they work on. If you are not on the appropriate IRB, you cannot analyze data or be in any way involved with the project. Lab members must complete CITI Training and save their certificate. To be added to an existing IRB, talk to the lab manager and present them with your CITI certificate.