Gilbert Lab – Expectations and Principles


We value the participation of every member of our community and want to ensure everyone has an enjoyable and fulfilling experience, both professionally and personally. Accordingly, all members of the Gilbert Lab are expected to show respect and courtesy to others at all times. We create our culture and our culture is inclusive.

Please note that this is not a legal document, supplementing, but not supplanting, Department-, and/or university level policies for your level of employment or study.

Inclusivity and diversity

Enjoyable, high-quality research can only be conducted when you feel safe, secure, and supported. All group members are thus dedicated to a harassment-free experience for everyone, regardless of gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age, and/or religion. We do not tolerate harassment by and/or of members of our group in any form, and we ask all members of the community to conform to the following guidelines:

  • All communication, be it online or in person, should be appropriate for a professional audience, and be considerate of people from different cultural backgrounds. Sexual language and imagery is not appropriate at any time.
  • Be kind to others and do not insult or put down other group members.
  • Behave professionally. Remember that harassment and sexist, racist, or exclusionary jokes are not appropriate.
  • Harassment includes offensive verbal comments related to gender, sexual orientation, disability, physical appearance, body size, race, religion, sexual images in public spaces, deliberate intimidation, stalking, following, harassing photography or recording, sustained disruption of discussions, inappropriate physical contact, and unwelcome sexual attention.
  • Participants asked to stop any harassing behavior are expected to comply immediately.
  • Contribute to discussions in meetings with a constructive, positive approach
  • Be mindful of talking over others when discussing in groups, and be willing to hear out the ideas of others.

In addition to making group members feel safe and secure, diversity and inclusion have numerous benefits to us all. Put simply, the greater the mix of people in our group, the greater the mix of skills, experiences, perspectives, and ideas we can collectively draw on. But the benefits of diversity and equality cannot be fully achieved without actively creating an inclusive environment.

Jack will discuss the Code of Conduct with lab members who violate these rules, no matter how much they contribute to the Gilbert Lab, or how specialized or needed their skill set. If inappropriate behavior persists after this initial discussion, formal processes, in line with UCSD’s work practice policies, will commence (Principles of Community: https://ucsd.edu/about/principles.html; Office of the Ombuds: https://ombuds.ucsd.edu/about-us/index.html). To report an issue, please contact Jack Gilbert; all communication will be treated as confidential except in situations where University policy requires mandatory reporting. In these cases, information will be shared only with those university officials who have a need to know the information to assist in the response to, investigation of and resolution of a complaint. If you do not feel comfortable contacting Jack directly, please feel free to contact Sarah Allard or Mariana Salas Garcia. If you would prefer to talk through issues with someone outside of the Gilbert Lab please talk with a member of the Postgraduate Research Committee (postdoc.ucsd.edu) or Human Resources (hhr.ucsd.edu). If you or someone you know is experiencing sexual assault or harassment, our Title IX coordinator is Lori Chamberlain, (858) 534-8298). More information about reporting sexual assault or harassment can be found at https://ophd.ucsd.edu/.

Mental Health

There is increasing evidence that certain attributes of academic research, including PhD-level studies, may challenge your mental health. Specific factors driving this include:

  • Low pay and quality-of-life issues, particularly as a function of living in an expensive city as San Diego
  • Feelings of isolation in your research; e.g. everyone has their own topic and it can often feel as if you are working on your own
  • Uncertainty in your research, although it should be noted that, in research of all kinds, it is not just the outcomes that are uncertain, but the questions themselves!
  • Uncertainty in your post-PhD career
  • So-called “negative results”; i.e. at some point in your research it is likely that certain questions will be more challenging to answer than anticipated, or that you will feel you have spent days/months/years toiling with little to show
  • Feelings of imposter syndrome or uncertainty in your abilities
  • Burnout; i.e. feeling the need to work endless hours to make up for the above issues, and the subsequent exhaustion

All scientists come across most of these issues at some level. I strongly encourage everyone in the group to take an active and pre-emptive approach towards the maintenance of their mental health. I assure you that you have the time and resources needed for a highly successful PhD or postdoc. If there is anything that is causing undue stress, or preventing you from performing at your potential, please do not hesitate to let me or any of the postgraduate tutors in the department know how we can help. You should also be familiar resources on campus: https://wellness.ucsd.edu/CAPS/resources/Pages/default.aspx. Every effort will be made to help you access the right support networks.

UCSD provides free counseling services for faculty and staff. Information and confidential appointments can be made through the Faculty and Staff Assistance Program (FSAP) at https://blink.ucsd.edu/HR/services/support/counseling/index.html.

Outputs, publication expectations and standards, and open science

Where possible, all research outputs (e.g. papers) will be published ‘Open Access’ (OA) (preferably Gold or Diamond OA; for definitions, please see the Open Research Glossary), with manuscripts also uploaded to a relevant pre-print server (e.g. BioRxiv) prior to journal submission, review, and (hopefully) publication. Where Gold or Diamond OA is not possible, the manuscript should be made publicly available via Green OA within three months of acceptance. Please also note that, we are generally committed to eliminating the use of journal-based metrics, such as Journal Impact Factors, in funding, appointment, and promotion considerations; and assessing research on its own merits, rather than on the basis of the journal in which the research is published. Jack is personally committed to these principles, thus you will be encouraged to think broadly about your choice of publication venue. Jack believes that the key guiding principle for choosing a journal is that it is thematically appropriate for the work you wish to publish.

Authorship on any manuscript or presentation will be openly discussed in group meetings and should, if possible, include everyone who has made a significant contribution to the work. A “significant contribution” can include but is not limited to, interpretations of primary data and development of ideas presented in the work; it need not include data curation or financial contribution to the work undertaken. The order of authors on a manuscript or presentation should be dictated by the relative contribution made by each author (see here for further information); in the case these contributions are equal, authors should be listed alphabetically by surname. Where conflict arises, Jack will facilitate discussion to help resolve this. An open dialogue is encouraged about this matter, ideally via authorship ‘check-ins’ that will likely occur several times over the lifetime of the study, starting early on. To help inform Editors, reviewers, and readers of our papers, we will include an author contribution statement as part of a paper.

Reference managers are extremely helpful for preparing publications and grant proposals. You are welcome to use whichever you like, however Jack and several lab members prefer PaperPile. Contact Sarah Allard to have your account added to the lab license.

Papers must be shown to and receive formal approval from all co-authors prior to submission; this is consistent with guidance provided by the Committee on Publication Ethics (COPE), who state that all authors must approve submission of work bearing their names. Please give co-authors at least two weeks to comment on paper drafts; at busy times of the year, they may need longer. We also strongly suggest that the paper receives reviews from at least two colleagues prior to submission to your supervisors; this will help improve the final product, as well as providing a training opportunity. Also note that many Gilbert Lab members have the potential to use confidential human health data and company-provided datasets; for the latter, our confidentiality agreements clearly state we must obtain permission from these companies to publish their data, and that they must have at least 28 days to provide approval. Explicit permission must be sought for every paper; i.e. images approved for use in one paper may not be approved for a different paper. If you require any guidance regarding paper submission, please speak to Jack, Mary Buschmann or Sarah Allard. Upon acceptance (or rejection) of your paper, you must inform all coauthors of the outcome as soon as possible and ensure all co-authors get a chance to look at and comment on page proofs (N.B. many errors can be introduced into manuscripts by the journal at this stage). Note that after paper acceptance, final text and graphics files must be sent, in raw format (e.g. .docx, .ai.) to all co-authors for their records/use within 14 days, with an accepted version (the so-called ‘Author Accepted Manuscript’ or ‘AAM’) uploaded to the UC Publication Management System and an appropriate online archive (e.g. BioRxiv).

All computers should be backed up, daily, to at least one location external to your main computer (e.g. a USB hard drive or network drive). All raw data should be transferred to the lab storage server immediately upon receipt (for sequencing data, Sarah or Mariana will transfer data received from the sequencing core). All microbiome study data (after host filtering, if required) should be uploaded to Qiita with comprehensive metadata by the bioinformatic study lead. Projects should be regularly updated in Blastrace by the study lead and collaborators.

Upon completion of a project and where data confidentiality allows, all data should be placed on an appropriate repository with a DOI; in the case of publication, these data should be published alongside the manuscript on a repository such as figshare. Sequencing data should be made publicly available at the time of submission or publication via a repository such as EBI. A curated version of all datasets used during a project should be provided to made available on the Gilbert lab storage volume, in addition to being provided to Jack Gilbert or Sarah Allard on a hard drive or file share system; the quality of the curation should be verified with Jack. All group members must also adhere to UCSDs Research Data Management Policy.

The group operates numerous computational resources, including the shared storage volume and the Triton Shared Computing Cluster (TSCC). These shared resources should be respected and not abused, and if you need more computation resources then please discuss your individual requirements with Jack Gilbert or Sarah Allard.

Conference Logistics

You will be supported (financially and otherwise) to attend and participate in conferences related to your PhD or postdoctoral research. You can either pay conference and travel fees and be reimbursed, or direct Jack towards any bookings you need. In either case, you are expected to register for the conference as a student (if relevant, or cheapest category) and in advance to obtain discounted registration fees. When possible, you will fly economy class and book the cheapest accommodation possible. You are expected to share hotel rooms if travelling with colleagues, even if they are from outside of Gilbert Lab. You must book no later than 1 month in advance of the conference, and preferably earlier to obtain the lowest cost travel costs and accommodations. In general, each lab member will be supported to attend 1 conference per year if funding allows, with costs decided upon ahead of time on a case by case basis and ideally reflecting existing funding. You are strongly encouraged to apply for travel awards to cover conference expenses.

Some conferences that we regularly attend are below (this is by no means exhaustive, and other more specifically, ad-hoc meetings will likely arise):

  • American Society for Microbiology
  • International Society for Microbial Ecology Meeting
  • Ocean Sciences
  • Keystone Symposia
  • Gordon Conferences
  • CMI International Microbiome Meeting (CIMM)
  • Human Microbiome Symposium

Note that we will typically aim to attend conferences ‘en masse’, such that accommodation costs can be shared and, based on experience, a more significant group ‘impact’ can be achieved. Exceptions can of course be made for conferences specific to your area of study and/or interest. For any questions or concerns regarding your ability to abide by any part of the travel policy or to request alternate arrangements, contact Jack, Sarah, or Megan P.

Conference expectations and requirements

Conference abstracts must be shown to all co-authors at least one week before the abstract deadline and inclusion of authors should follow authorship guidelines for publications. Upon acceptance (or rejection) of your abstract, you must inform all coauthors of the outcome as soon as possible. You must also send a final draft of your presentation or poster to all co-authors at least one week before the date of presentation. Ideally, a near-final draft should be completed two weeks before the date of presentation, so that it can be presented at a Gilbert Lab weekly lab meeting; in this way, you will be able to receive feedback from your colleagues. Presentation and publishing ethics, both of which are at least partly captured by the Committee on Publication Ethics (COPE), state that all authors must approve submission and presentation of work bearing their names. The same applies to papers (see above). Note that after material has been presented at a conference, this must be sent, in raw format (e.g. .ppt, .ai) to all co-authors and data providers for their records/use within 14 days; if appropriate, this material can be uploaded to an appropriate online archive (e.g. FigShare, BioRxiv) where it will be assigned a DOI, and will be useable and citable by the scientific community.

Working hours

We recognize that many of you have personal responsibilities and obligations in addition to your work/PhD/postdoctoral studies. We appreciate that, at times, it can be difficult to balance those demands, and that a classic ‘9-to-5’ day may not be optimal. Because of this, the exact hours you choose to work are up to you. Being on campus between 1000 and 1600 most days may, however, help facilitate collaborative working and, we hope, lead to a more fulfilling research experience. Where possible, meetings and events will not be arranged outside these hours to allow participation by all Gilbert Lab members, and a zoom option will be provided when possible. Jack prefers not to work on weekends unless absolutely necessary – but your work week may be different, and when traveling for work these guidelines may be eroded. Just be flexible with your time, be respectful of other people’s decisions on how they spend their time, and remember it is NOT how hard you are seen to be working, it is the quality of your work and the quality of your accomplishments and outcomes. Working in person is not the rule. Although we always appreciate interacting with people in person, for some in the lab that may not be preferable, necessary, or sometimes possible. Therefore, remote work options, if appropriate to your research goals will be accommodated.


Group meetings: Group meetings are typically held on Tuesday at 9:15am; all group members are expected to attend if they are not otherwise engaged in other research-related activities (e.g., at conference, attending training or a lecture, etc.) or on vacation. The Gilbert Lab meeting is an excellent forum for updating colleagues on project progress, developing research skills, and widening our collective understanding. Meetings provide a forum for the presentation of results, such as ‘dry-runs’ of conference talks, and more informal discussions around research topics arising. At each lab meeting, we will provide an opportunity to discuss good news and announcements from the previous week and talk about any issues that have arisen in the lab. We typically have 1-2 short presentations from lab members or visitors each week. Please sign up to present regularly on Monday.com. Every ~6 weeks we will go through the list of active projects in the lab and ask project leads to give a brief update, and every ~6 weeks we will hold a group journal club discussion. If you have ideas for additional elements to add to lab meeting, they are welcome – please contact Sarah and Jack to discuss.

Individual meetings: Graduate students have individual standing meetings (30 min) every 1-2 weeks with Jack and Sarah. For all others, meetings occur on an ad-hoc basis as personal situations require. If any lab member(s) want to meet with Jack, just drop Megan Preovolos an email and request a time. These will give you an opportunity to discuss your progress and any administrative issues that you need addressed. You are encouraged to send a short agenda ahead of time and to come fully prepared for individual meetings; in this way, discussions can be focused such that all concerns are addressed. Prepared updates can be short (e.g. 5-10 PowerPoint), but should ideally contain an overview of: (i) what your plans were for the last 1-2 weeks; (ii) work undertaken; (iii) issues arising; and (iv) a forward plan for the next 1-2 weeks. Such reports are an important way to self-monitor your progress, as well as keeping your supervisor(s) informed of both positive and negative developments. They are particularly important for those who have supervisors based in other institutions. The lab has template for these updates, available on the shared OneDrive.

Collaborative work

All lab members will be asked to help with projects outside of their primary research from time to time. Please be prepared to dedicate a few hours each week to helping in the wet lab, running bioinformatic analyses, or assisting with grant writing. Advance notice will be given as much as possible for these requests, so that you can discuss any questions or concerns with Jack and/or Sarah.

The Gilbert Lab often collaborates with other research groups in academia, industry, and government. As representatives of the lab, we expect that members of the lab will act with professionalism and respect, including preparing materials ahead of meetings and responding in a timely manner to communications. It is encouraged to share presentation materials with Jack at least 24hrs before meetings with collaborators.


Where possible, avoid sending work-related email outside of 0800 and 1800. Most email servers provide functionality for saving an email as a draft, such that it can be sent within the hours stated above. Please give consideration to the timing of the email with respect to what the recipient needs to do; for example, try not to send an email at 1759 for something that is required for a 1000 meeting the next day. No lab members are required nor should feel obligated to reply to email outside of their typical work hours. However, prompt replies to emails, within these times, is helpful. If you experience any challenges related to flexible working within the Gilbert Lab, please do not hesitate to contact Jack. All communication will be treated as confidential except in situations where University policy requires mandatory reporting.

Social media

In your work-related life, you may wish to engage with social media (e.g. Facebook, Twitter, and Instagram). Please be considerate of others when using these platforms, and respectful of how others may wish to use them. For instance, Jack uses Twitter and Facebook in a personal and professional nature, and his account has a wide audience (including the Head of Department, prospective students, funders, and other academics); you must therefore bear in mind the very public nature of interactions on social media, and that many people (who may not be on a specific platform) will read and hear of online correspondence. We are not compelled to engage with any social media, use any such media for work-related purposes, and we will never pressure each other to ‘friend’ or ‘follow’ each other.


You should be familiar with recently published material relevant to your PhD project. Below are some academic journals that may be of interest:

  • American Society for Microbiology Journals, including mSystems and mBio
  • Nature journals, including Nature Medicine, Nature Microbiology, etc
  • Science journals, including Science Translational Medicine
  • Cell journals
  • Microbiome
  • PNAS
  • PLOS
  • ISME

Signing-up to ‘mail alerts’ from specific journals and more general publication ‘feeds’ (e.g. Google Scholar) are highly recommended; by doing this, you can be kept informed of newly published literature related to your studies. Our lab encourages publishing in society journals as a first priority.


You are expected to take c. 3 weeks of vacation per year, beyond public holidays and the college closure at Christmas. I strongly encourage you to take this time so you can relax, visit family and friends, and generally unwind from the rigors of work or PhD study. Please inform Jack, Sarah or Megan of holidays or notable absences in advance via email or, preferably, submission on Monday.com. Permission for holiday is very rarely required, but please respect key deadlines within the calendar year and the fact we work in a research group. It is important to take vacations, respect weekends (or time in lieu) and establish a sustainable work-life balance. It is also important to respect the time and efforts of others, and the contribution of funders, and to note that effective working will improve the quality of your research. Where there are key time pressures, it is important to plan ahead to prioritize meeting deadlines. If you struggle with establishing a sustainable work life balance, please discuss this with Jack or Sarah at any stage.

Thanks, and please enjoy your time in the Gilbert Lab!

This document borrows heavily and is modified from six open source Code of Conduct documents: (i) BahlaiLab CoC (Christine Bahlai); (ii) WhitakerLab (Kirstie Whitaker); (iii) Hill Lab (Jon Hill); (iv) Krevorlab (Sam Krevor); (v) MicroMicEng (Ben Britton); (vi) Basins Research Group – Christopher Jackson.