lab-guidelines.md

Code of Conduct

From The Carpentries CoC:

• Use welcoming and inclusive language
• Be respectful of different viewpoints and experiences
• Gracefully accept constructive criticism
• Focus on what is best for the community
• Show courtesy and respect towards other community members

Solis-Lemus lab guidelines

Based on (shamelessly copied from) "Guidelines for Research in the Baum lab" by David Baum. This is a dynamic document; feel free to suggest modifications to improve these general guidelines.

What I expect from you:

• You will take ownership of your experience

  • Acknowledge that you have the primary responsibility for the successful completion of your work. You should maintain a high level of professionalism, self-motivation, engagement, scientific curiosity, and ethical standards.
  • Ensure that you meet regularly with me (once per week would be ideal) and provide me with updates on the progress and results of your activities and experiments. At the same time, be aware of my time constraints. I will strive to keep an open door policy, but there will be times when I won't be able to meet, and you will need to figure things out on your own. Acquiring problem-solving skills is part of a good research program.
  • Be knowledgeable of the policies of the institute and university. Comply with all institutional policies, including intellectual property rules, and codes of conduct.
    • For grad students with 33-50% RAships, this means enrolling in full time credits (at least 8 credits for non-disserators and 3 credits for dissertators) every semester.

• You will be a team player

  • Attend and actively participate in all laboratory meetings, as well as relevant seminars. Participation in lab meetings does not mean only presenting your own work, but also providing support to others in the lab through constructive questions and shared insights.
    • Please provide one-week notice if you will miss meetings due to classes or exams
    • Please report any travel one month in advance. Use the google spreadsheet in slack.
  • Strive to be the very best lab citizen. Be respectful, tolerant of, and work collegially with all lab colleagues: respect individual differences in values, personalities, work styles, and theoretical perspectives.
  • Acknowledge the efforts of everyone in the lab.

• You will develop strong research skills

  • Take advantage of your opportunity to work at a world-class university by developing and refining stellar research skills. I expect that you will already know or learn how to plan, design, and conduct high quality empirical, conceptual and/or theoretical research. More importantly, I expect that you are open to improve your skills (research/computational/writing) constantly
  • Be responsive to advice and constructive criticism. Remember that the feedback you get from me, your colleagues, your committee members, and your course instructors is intended to improve your scientific work. Do not take criticism personal and use it as an opportunity to grow as a scientist.
  • Present your work at meetings/seminars and prepare scientific articles. The ‘currency’ in science is published papers, they drive a lot of what we do and, because our lab is supported by taxpayer dollars, we have an obligation to complete and disseminate our findings. I will push you to publish your research. I expect that your manuscripts/presentations will adhere to the Guidelines on manuscripts and code. Please expect that at the beginning, I may heavily rewrite and edit your manuscripts
    • Note that everyone in the lab is expected to do one local presentation per year, and graduate students and postdocs (and optional for undergraduate students) should do one conference presentation per year
  • You will follow the best computing practices in all the code/scripts that you do. There is a big gap between code that runs, and code that is suitable for publication/open-source software (see Guidelines on manuscripts and code).
  • You will be reproducible. Maintain detailed, organized, and accurate records of your research. Be aware that your notes, records and all tangible research data are my property as the lab director. When you leave the lab, I encourage you to take copies of your work with you. But one full set of all files/notes must stay in the lab, with appropriate and accessible documentation.
  • Keep up with the literature so that you can have a hand in guiding your own research. Block at least one hour per week to do lit searches and read articles.

• You will work to meet deadlines

  • Strive to meet deadlines: this is the only way to manage your progress. Deadlines can be managed in a number of ways, but I expect you to work your best to maintain these goals. As long as you are meeting expectations, you can largely set your own schedule.
  • Be mindful of the constraints on my time. Allow a minimum of one week prior to submission deadlines for me to read and respond to short materials such conference abstracts and two weeks for me to work on manuscripts or grant proposals. Please do not assume I can read materials within a day or two, especially when I am traveling.

• You will communicate clearly

  • Let me know the style of communication or schedule of meetings that you prefer. If there is something about my mentoring style that is proving difficult for you, please tell me so that I can have an opportunity to find an approach that works for you.
  • Be prompt. Respond promptly (in most cases, within 48 hours) to emails/slack messages from anyone in the lab group and show up on time and prepared for meetings. If you need time to gather information in response to an email/slack message, please acknowledge receipt of the message and indicate when you will be able to provide the requested information.
  • Discuss policies on work hours, sick leave and vacation with me directly. Consult with me and notify fellow lab members in advance of any planned absences. Post-docs and staff are expected to work at least 40 hours per week. Most lab members will not exceed two weeks per year of fully personal travel. I believe that work-life balance and vacation time are essential for creative thinking and good health and encourage you to take regular vacations. Be aware, however, that there will necessarily be times when it may not be ideal to schedule time away (e.g. first week of the semester for mandatory lab meeting to go over lab guidelines)
    • It is the lab member's responsibility to bring up any personal vacation or travel at least 2 weeks in advance and to reschedule any meetings
  • Discuss policies on authorship and attendance at professional meetings with me before beginning any projects to ensure that we are in agreement. I expect you to submit relevant research results in a timely manner. Barring unusual circumstances, it is my policy that researchers are first-author on all work for which they took the lead on the project and preparation of the initial version of the manuscript (but read the authorship guidelines for more information).
  • Help other students with their projects and provide informal mentorship. This is a valuable experience! If you want to add other individuals as authors to your papers, please discuss this with me early on and before discussing the situation with these potential co-authors.

What you can expect from me:

• I will work tirelessly for the good of the lab group; the success of every member of our group is my top priority. I will be transparent about the lab’s financial situation and honest about the amount of further funding that I can provide.
• I will be available for regular meetings and informal conversations. At our scheduled one-on-one meetings (ideally every week or every two weeks), we will address questions or concerns that you have. If you need to miss a meeting, it is your responsibility to reschedule; I will show you the same courtesy. Slack is the best way to communicate with me. I do not always respond on weekends as I spent this time with my family. If my office door is open, feel free to stop by.
• I will involve you in the process of writing grant proposals, from the original ideas through submission. The goal of this is to help expose you to this important aspect of science and help you contribute to my efforts to fund your work and the lab in general.
• I will discuss authorship policies regarding papers with you. I will acknowledge your scientific contributions to the work in my laboratory, and I will work with you to help you publish your work in a timely manner (read the authorship guidelines for more information).
• You can count on me to do my very best to promote you as a scientist and your work. I will help you in your professional development and in your efforts to communicate your work. I will work very hard to adequately fund our laboratory and to disseminate its results. I will do my best to provide timely review of your research.
• My primary role is to (1) help you think clearly about theoretical issues driving your research and (2) successfully bring in grants and to steward our resources so that we all benefit to the maximum extent from our joint efforts. I will also make every attempt to help you network into the scientific community, including assistance finding post-doctoral and faculty positions.
• I am committed to mentoring you, even after you leave my lab. I am committed to your education and training while you are in my lab, and to advising and guiding your career development – to the degree you wish — long after you leave. I will provide honest letters of evaluation for you when you request them.
• I am committed to your research projects. I will help to plan and direct your projects, set reasonable and attainable goals, and establish a timeline for completion of projects.
• I will not require you to perform tasks that are unrelated to your professional development.
• I will lead by example and facilitate your training in complementary skills needed to be a successful scientist, such as oral and written communication skills, lab management, and scientific professionalism. I will encourage you to seek opportunities in teaching or outreach, provided these remain manageable in scope.
• I will encourage you to attend scientific/professional meetings and will make an effort to fund such activities. I will not be able to cover all of requests but I will try.
• I will provide you a work environment that is intellectually stimulating, emotionally supportive, safe, and free of harassment. I will intervene strenuously to ensure that everybody feels safe and welcome.
• I will strive to be supportive, equitable, accessible, encouraging, and respectful. I will try my best to understand your unique situation. I am mindful that we all come from a different backgrounds and have different circumstance. It will help if you keep me informed about your experiences and remember that academic research is a job with very high expectations. I view my role as fostering your professional confidence and encouraging your critical thinking, skepticism, and creativity. If my attempts to do this are not effective for you, I am open to talking with you about other ways to achieve these goals.

Guidelines for manuscripts, presentations, and code

Best computing practices for code

• I expect that you will
  • read and adhere to the guidelines in here
  • study resources on computing practices, reproducibility, version control, organization of projects, naming files. There are some links in here that I expect that you will study, understand and follow when programming
  • understand that reproducibility is a process. No one is reproducible from one day to the next. It is a constant process, and it will feel unnatural a times
  • assume that everything that you are doing right now will need to be redone at some point in the future: be prepared
  • ask for help if you need it. If you are feeling overwhelmed or stressed or don't know where to start, please reach out and I am happy to talk with you to find solutions
  • note that if you are already reproducible and keep good notes by other means (not highlighted here), do continue that way! In fact, I am always eager to learn different ideas! This document is not meant to force anyone to do one particular style of best computing and reproducibility practices. Just keep in mind that whatever your style, we should discuss it and make sure that we are all on the same boat when it comes to expectations and outcomes

Does my code (simulations/data analysis/software) satisfy the lab computing practices? Checklist

• Is all my code on the github repo, properly documented and commented?
• Does the repo have an explicit readme describing the usage, citation, format of the repo and feedback/issues section?
• Does the repo have a license, contributing guidelines and documentation?
• If it is a new software tool, does it have a wiki or website tutorial?

Clear scientific communication: manuscripts and presentations

It is not enough to do "good science", we need to be good communicators of our science.

• I expect that you will
  • actively search ways to improve your oral and communication skills
  • accept that at the beginning I may heavily edit your manuscripts. Don't feel discouraged! It is part of the learning process that we accept feedback from peers. My manuscripts are still edited by colleagues and co-authors all the time!
  • be genuinely interested in communicating your science to any type of audience in a simple and effective manner
  • use the many university resources (like the Writing Center) to your advantage
  • accept that good skills in academic writing are a key component in a scientist's development
  • practice your presentations with multiple people, and be responsive to constructive criticism
  • make writing clear manuscript and delivering clear presentations a priority for your growth as a scientist
  • work hard on the first complete draft of the manuscript before you share it with me and co-authors. You do not want to share a document that is half-baked or not easy to read. You want to be respectful of your co-authors' time by putting your best work forward
  • check out the resources such as 10 simple rules for concise scientific writing by Scott Hotaling
  • acknowledge that it is our job as communicators to connect with different audiences (statisticians, biologists, general public) and communicating our ideas effectively is not an "extra burden", it is at the core of our work as scientists

Manuscripts

• By the time that you finish your first complete version of the manuscript (to send to co-authors), I expect that your manuscript will

  • be properly structured (e.g. introduction, methods, simulations, data analysis). Look at options in the journal/conference of interest to follow specific guidelines related to manuscript structure
  • be well-written. We are constantly learning writing skills, so your manuscript is not expected to be perfect. But you should strive to make an effort to make it understandable and use all necessary resources at your disposal
  • contain good quality figures to present results, but perhaps not in perfect form yet
  • be in the conference/journal format if we have already decided where to submit. This is important in case there are page limits that we need to consider when revising the manuscript
  • have the proper citations

• By the time the manuscript is ready for submission, I expect that your manuscript will

  • be fully reproducible, everything must be backed up and supported by data, simulations, scripts
  • be accompanied by a github repo with the necessary reproducible scripts, textfiles, notes, ... to reproduce the analysis and simulations
  • be well-written, and that you have incorporated the feedback/suggestions from the co-authors
  • have high-quality figures
  • have a graphical abstract, if suitable

Is my manuscript ready for submission to journal? Checklist

• Does it include an extensive literature search (cite everybody)?
• Does it include a graphical abstract and/or summary box for easy reading?
• Are the figures of high quality (good choice of colors: color-blindness aware)?
• Are simulations and data analysis fully reproducible, easy to follow by others and pushed to a github repo?
• Is it well-written and following the rules of concise scientific writing?
• Is it submitted to arxiv or biorxiv?

My paper is published, now what?

In recent years, it has becoming increasingly important to advertise broadly our work and invest heavily on good science communication strategies. We will

• create a 3-min lighting talk to post on the lab youtube channel
  • this presentation should include: 1) motivation, 2) our solution to the problem, 3) some results, 4) advertisement of the paper and github, 5) acknowledgements. Check out this previous talk as an example
• tweet the paper alongside
  • an image of the graphical abstract or an infographics (see canva) or a word cloud
  • a link to the youtube 3-min presentation
• post in the lab instagram a wordcloud and a 1-min presentation of the paper
• include the paper in the lab website (alongside links to the lightning talk and images of the graphical abstract/infographic/word cloud)
• email the paper to collaborators
• do presentations in conferences and symposia (more info)
• if the published paper is for a software tool, create a video tutorial and a wiki documentation
• add a folder in /mnt/dv/wid/projects4/SolisLemus-shared-data in the lab server with the real data that you used (raw and clean) along with a readme file describing the steps from raw to clean

Talks/posters in conferences and symposia

All abstracts, posters, and talks that you work on in the lab are representations of the lab and must be approved by me before submission.

Is my talk/poster ready for presenting? Checklist

• Have you presented in lab meeting to get feedback from others?
• Have you shared your slides/poster with me or others in the lab to check for errors/typos?
• Have you timed yourself to make sure you adhere to the presentation guidelines?
• Have you included an Acknowledgement slide at the end to acknowledge the lab, other collaborators and sources of funding (you can use the template)?
• Do you include QR codes or links to your paper/software?
• Are you giving proper citation to others' work in your slides/poster?

Travel logistics for conferences

Please discuss with me any plans of conferences to make sure that we have the necessary funding.

Steps for conference attendance:

1. Write the abstract and send to me for approval before submitting it. Please give the abstract to me at least 2 weeks prior to the abstract submission deadline
2. Upon receipt, please forward the acceptance email to the conference to me
3. You can register to the conference on your end and get reimbursed, or if it is too expensive, we can cover the cost directly at WID.
4. Do not book flights or make hotel reservations before reading the travel rules! You should always email Janine Harrison and Becky Streich to help with the travel plans.