LAB working agreement

(updated: 5/4/2026-9/1/2026)

This is Section 1 of the B.I.O.N.I.C. Lab working agreement, authored by the Principal Investigator. Sections 2 through 11 are authored by lab members and address day-to-day lab operations (authorship norms, computing, equipment, lab citizenship, social conventions, conflict resolution within the trainee group). The two parts are independent: this section establishes the appointment framework, expectations, and PI responsibilities; the lab-member-authored sections establish the working culture among trainees.

Governing authorities. Where any provision conflicts with the Regulations Governing Graduate Study at the University of Pittsburgh, the Graduate Student Researcher (GSR) Academic Regulations, BioE department policy, the graduate student collective bargaining agreement once finalized, the NIH Grants Policy Statement, NRSA Policy Guidelines, NSF GRFP Administrative Guide, or other sponsor-specific terms, the governing authority controls. This document will be revised when the CBA is finalized.

1. Mission, expectations, and PI commitments

1.1 Mission framing and time accounting

The lab is funded primarily by federal taxpayer dollars (NIH, NSF, DARPA, ARPA-H), with University and foundation support. Graduate Student Researchers are researchers who are also students, not students who happen to do research; the appointment provides stipend, tuition scholarship, and benefits in exchange for approximately 20 hr/wk of research labor that creates knowledge for the public, with coursework as a separate degree obligation the University supports through tuition coverage. The 20 hr/wk GSR appointment, the 40 hr/wk NRSA training program, and the 37.5 hr/wk staff appointment are structured apprenticeship: the apprenticeship produces papers and trained researchers that justify the public investment.

Time beyond the appointment as compound interest. Time invested beyond the appointment hour ceiling is bonus time the trainee owns: extra reading, additional drafts of a fellowship application, side analyses that become second-author papers. These hours pay back over decades. They are voluntary and not obligations to the PI or funding agency.

Class credit calibration. Each credit of a class is anticipated to require about 3 hours per week (1 hour in class, 2 hours outside). Students are advised to enroll in 6 to 7 credits per semester, which translates to roughly 18 to 21 hours of weekly coursework load alongside the 20 hr/wk research appointment. Heavier course loads compress time available for research and self-directed learning.

1.2 Funding mechanisms and time expectations

Trainees in the lab hold appointments under multiple funding mechanisms. The following expectations apply uniformly across all of them:

•        The appointment is the trainee's primary scholarly activity. Per the Pitt GSR Academic Regulations, NIH NRSA Policy, NSF GRFP terms, and grant-defined effort, the appointment encompasses research training, dissertation or postdoctoral research, and the activities required to complete and disseminate that work.

•        Mandatory lab activities count within the appointment. Lab workshop, journal club, 1-on-1 meetings with the PI, and lab safety meetings are part of the training program.

•        Required training counts within the appointment. Onboarding, EH&S, OSHA, IACUC/DLAR, RCR, Title IX, equipment and software training, surgical training, and any other University- or sponsor-mandated training is part of the appointment.

•        Research dissemination counts within the appointment. Manuscript preparation, abstract submission, poster preparation, and presentations on the trainee's project are part of the appointment.

•        Lab citizenship tasks tied to the trainee's project count within the appointment. Genotyping, perfusions, animal husbandry, and equipment maintenance directly tied to the trainee's experiments are part of the appointment.

•        Coursework is a degree obligation, not part of the appointment. Time spent on courses and homework satisfies degree requirements separately from appointment hours.

•        Time beyond the appointment is the trainee's own. The PI does not require, expect, or schedule work beyond the appointment hour ceiling defined by the trainee's funding mechanism (see table below). Trainees may invest additional time in their own professional development (literature reading, fellowship grant writing, scientific writing); this remains voluntary.

The mechanism-specific terms (hour ceiling, employment status, concurrent activity rules, payback obligations, governing authority) are summarized in the table below:

How to read the hour column. The hour ceiling describes research and research-related effort under the appointment, not a budget of time that can be filled by any activity. Coursework, homework, exam preparation, fellowship application writing for one's own benefit, outreach, volunteering, and conference organizing are valuable but separate from appointment hours. A trainee who has spent 20 hours on coursework in a given week has not satisfied the appointment expectation; they have satisfied a separate degree obligation. Coursework load shifts research timing within a semester (more coursework time during exam weeks, more research time during reading weeks), but does not substitute for research over the term as a whole.

Fellowship application writing. Writing one's own fellowship application (NSF GRFP, NIH F30, F31, F32, NDSEG, Hertz, foundation fellowships) is one of the highest-leverage activities a trainee can do for their career. The PI actively supports it: time during 1-on-1 meetings is allocated to discussing strategy, draft review, and revision, and the PI provides extensive feedback across multiple draft cycles, often including mock-review feedback before submission. The trainee, however, owns the writing. The hours the trainee spends writing, revising, and assembling the application are voluntary professional development time, not part of the 20 hr/wk research appointment. This framing matters because it preserves the integrity of the 20 hr/wk research effort that the GSR appointment supports. A trainee on a productive research trajectory who is also writing a fellowship application is doing two things, both valuable, both supported, but only one of them is appointment work.

Trainees are responsible for understanding the terms of their own funding mechanism. The PI provides a copy of the relevant governing policy at the start of each appointment.

Self-funded PhD students. Students enrolled in the BioE doctoral program who are not supported by a GSR appointment, fellowship, or other funded mechanism (i.e., students who pay their own tuition and do not receive a stipend) have no work obligation to the lab. They are subject to BioE program degree requirements and to University policies, and if they participate in lab research as part of their dissertation work they follow the same safety, animal protocol, RCR, authorship, and lab citizenship norms as funded trainees, but the appointment-hour expectations in this section do not apply to them. The PI does not direct their time. Self-funded students who wish to participate in lab research projects discuss scope, timing, and authorship expectations with the PI at the start, on the same authorship norms that apply to all lab members. PI supervisory authority over laboratory safety, EH&S compliance, IACUC and DLAR animal protocol compliance, RCR, biohazard handling, and equipment use applies to every person working in the lab regardless of funding status. A self-funded student who participates in lab research is bound by the same protocol and safety oversight as a funded trainee.

Undergraduate researchers. Unfunded undergraduates are encouraged to commit roughly 10 hr/wk to make a meaningful contribution. Funded undergraduates (e.g., SSOE or A&S fellowships) commit 20 hr/wk during the semester and 40 hr/wk during summer.

1.3 Risk taking and the structure of research time

Research effort divides into low-risk work (known protocols, predictable output: chronic data collection on an established prep, image analysis on a defined dataset, manuscript revision) and high-risk work (uncertain timelines and output: a new technique, a new prep, an unproven hypothesis). Both are essential. During coursework periods, research time emphasizes low-risk steady progress because adding high-risk work to coursework load tends to produce neither completed coursework nor completed research. After coursework, most appointment hours continue on steady research output that produces papers; some allocation to high-risk experiments is encouraged. High-risk experiments transition into appointment time once preliminary work has reduced uncertainty enough that the experiment has a defined hypothesis, methods, and success criterion. Risks that don't pan out are part of learning, not evidence of failure; the lab supports thoughtful risk-taking with clear hypotheses and writes up negative results when they are informative.

1.4 Lab meetings, 1-on-1s, communication, and absences

Lab workshop, journal club, scheduled 1-on-1 meetings, and any other lab events are mandatory and counted within the appointment. Anticipated absences (conference travel, family events, illness, academic obligations) are communicated to the PI in advance.

1-on-1 meetings are coaching time covering research progress, technical troubleshooting, career planning, work-life balance, fellowship strategy, and any other topic the trainee wants to discuss. Trainees come prepared with specific questions or topics. If the standard meeting time conflicts in a given week, alternatives include Sunday morning or weekday evenings at 8:30 PM. Unless circumstances are unusual, 1-on-1s are scheduled Monday through Wednesday to leave the rest of the week for execution. If the PI or trainee is running late within 12 hours of a scheduled meeting, the other party is notified by Teams; otherwise the meeting is rescheduled on the calendar with notification to lab admin.

Communication response times

Trainees who are not in person from 9 AM to 5 PM (because they are working remotely on an approved day, attending a conference, on a recess day, or otherwise away from the lab) are still expected to respond to emails and Teams messages promptly during normal working hours. The lab's communication standard does not change because the trainee is not physically in lab; what changes is the trainee's location, not their availability.

During working hours (Monday–Friday, 9:00 AM–5:00 PM), trainees acknowledge action-related messages within the following windows:

•        DLAR-related: as soon as possible during working hours

•        Teams messages: within 3 hours

•        Email: within 24 hours

•        Text from the PI: within 30 minutes

•        Phone or Teams calls: as soon as possible

A brief acknowledgment counts. The format is direct: "Got it, will respond by 3 PM today" or similar, with a calendar reminder set so the trainee actually follows through. Outside working hours, on weekends, holidays, and recess days, no response is expected. The PI does not expect after-hours responsiveness.

Escalation when responsiveness is a problem. If lack of response or delayed response becomes apparent and is mentioned, the issue is discussed in the next 1-on-1 meeting. If the pattern continues after that conversation, the unresponsive time is reclassified as sick time, on the principle that a trainee who is unreachable during working hours was not engaged in research effort during those hours. This is not a punitive sanction; it is the same accounting that would apply if the trainee had been ill or on personal time.

In-person versus remote work

The lab's research (animal experiments, surgery, two-photon imaging, electrophysiology, chronic data collection, equipment maintenance) is fundamentally in-person work. Standard hours are 9:00 AM to 5:00 PM in lab. Remote work is appropriate for specific tasks (manuscript writing, data analysis on cloud-accessible datasets, reading, fellowship applications) and is approved on a case-by-case basis.

Staff and postdoc scheduling. Full-time research staff (lab managers, research associates, technicians) work in-person 7.5 hours per weekday with a 0.5-hour unpaid lunch (8 hours total per workday). Postdocs on non-NRSA mechanisms work 7.5 hours with a 1-hour unpaid lunch (8.5 hours total per workday). Specific clock hours are set in the appointment letter (typical staff window 8:30 AM–4:30 PM; typical postdoc window 9 AM–5:30 PM). Requests for early dismissal require PI confirmation and, where required by department policy, Chair permission. Timecards are submitted Friday afternoon or Monday by 9:00 AM. Salary staff submit timecards specifically for sick or vacation time.

Remote work requires advance approval, not retroactive notification. A trainee who plans to work from home on a given day notifies the PI the prior day or earlier and confirms approval. Repeated unannounced "remote days" without prior approval are not remote work; they are absence. The lab is in person by default; remote work is the exception, not the standard.

On approved remote days, the trainee submits a daily plan at the start of the day (an 8-hour version of the weekly plan with task-level detail) and a daily update at the end of the day with quantitative progress and documented evidence (OneDrive uploads, code commits, draft sections). If a trainee is too unwell to be productive on a remote day, they take a sick day instead.

Absences and travel notification

Anticipated absences (vacation, family events, conference attendance, weddings, medical procedures requiring recovery time) are communicated to the PI at least two weeks in advance, scheduled on the lab calendar, and accompanied by a coverage plan for any active animal cohorts or chronic experiments. International travel during the appointment requires advance notification because some appointments (especially F-mechanism and visa-dependent appointments) have specific requirements about international time, and because the lab needs to plan around the trainee's absence.

Notifying the PI that you have left the country after you have already left is not advance notification; it is a fait accompli. The lab does not retroactively approve travel that was not communicated in advance, and time spent on unannounced international travel is reclassified as recess or unpaid absence, with appointment and visa implications addressed as appropriate. Genuine emergencies (family medical crisis, immigration emergency, bereavement) are an obvious exception and are accommodated; the trainee notifies the PI as soon as feasible.

1.5 Working calendar

Graduate students and postdoctoral fellows follow the University Faculty, Staff, and Designated Offices calendar, not the undergraduate or graduate class calendar. Per the GSR Academic Regulations, the relevant standard is whether the University itself is open or closed, not whether classes are in session.

University closure days (Memorial Day, Independence Day, Labor Day, Thanksgiving and the day after, the winter recess between Christmas and New Year's, and other designated University holidays) are non-working days. No research, meetings, or weekly plans are expected on these days, except where time-sensitive experiments or animal care are explicitly required by the appointment letter and offset by alternative breaks.

Days when the University is open but classes are not in session are workdays for GSRs and postdocs. This includes:

•        Spring Break (typically the first full week of March): University open, classes paused, lab operates normally

•        Fall Reading Days and any Self-Care Days: University open, lab operates normally

•        Days between the end of fall classes and the start of the winter recess

•        Days between the end of spring classes and the start of summer term

•        Finals week, grading days, and any other class-calendar pauses that do not correspond to University closure

Trainees who wish to use these days for travel, family time, or other personal purposes do so by scheduling them as recess days (Section 1.6) with at least two weeks of notice to the PI. They do not default to non-working status because classes happen not to be meeting.

1.6 Recess days, leave, and after-hours work

Recess days. Per the GSR Academic Regulations, 12-month GSR appointments include a minimum of 10 additional break days per calendar year beyond University holidays. The lab provides recess days at this minimum: 5 summer + 2 fall + 3 spring workdays. Trainees on fractional appointments receive proportional recess days.

Compensatory days for chronic data coverage. Trainees who cover chronic data collection or animal cohort coverage during the University winter closure (between Christmas and New Year's, when the University is closed but cohorts require continued attention) receive up to 5 additional workdays as compensatory time, taken at a mutually agreed alternative date. These compensatory days are tied to documented winter coverage and are separate from the standard 10-day recess allotment.

Sick leave is separate from recess days and is taken as needed without negotiation. NRSA fellows (F30, F31, F32, T32) receive vacation, holidays, sick leave, and parental leave per NIH NRSA Policy (up to 15 calendar days of paid sick leave per year, up to 30 calendar days of parental leave per year). Recess days are scheduled by the trainee with at least two weeks of notice when the University is in session.

Continuity during absences. Trainees with active chronic experiments or animal cohorts coordinate coverage during planned absences (training a labmate, arranging DLAR support, or pausing the cohort where biologically acceptable). The plan is communicated to the PI before the absence is confirmed. DLAR weekend animal care can be arranged at posted rates ($10 Saturday, $270–300 Sunday as of 2026); use of DLAR support is encouraged when feasible.

Additional recess days through performance. Recess days beyond the 10-day floor can be negotiated with the PI on the basis of consistently above-and-beyond performance, leveraged through documented productivity (manuscripts submitted ahead of timeline, fellowships secured, conferences won, technical contributions that benefit other lab projects). The default is 10 days; performance-based extension is a recognition of substantive contribution rather than an entitlement.

Weekend and after-hours research. Some experiments (chronic recordings, imaging windows, time-sensitive animal care) require off-hours work. When this occurs, the time is part of the appointment and is offset by reduced hours during the standard week. Required after-hours work is specified in the appointment letter. While off-hours work is sometimes necessary, regular-hours attendance is encouraged because it supports team communication, problem-solving, and the apprenticeship aspect of the training. Off-hours schedules are communicated in weekly updates and Teams messages at the earliest opportunity.

Academic standing. Per BioE departmental policy, graduate students maintain a minimum B average in coursework for satisfactory program standing. Students whose GPA falls below 3.0 are placed on probation per the GSR Academic Regulations and are not eligible to take preliminary or comprehensive examinations or to graduate while on probation. The PI supports academic standing through 1-on-1 discussion of course load and study strategy when concerns arise.

1.7 Weekly planning, milestone-based feedback, and effort calibration

The weekly plan and update is the lab's primary mechanism for joint visibility into research progress and for calibrating task estimates against actual time. It is also the lab's diagnostic tool for distinguishing three different reasons that a trainee might fall behind:

•        Calibration. Were the milestones realistic given technical and biological constraints?

•        Capability. Is there a skill or training gap to address?

•        Fit. Is the project, lab, or research area a good match for the trainee's interests and strengths?

Each diagnosis requires a different response, which is the purpose of the structured plan over hour-counting.

Why hour tracking matters: effort calibration as a core training outcome

The hour-tracking exercise is not surveillance. It is calibration practice. The skill the trainee builds is honest estimation of how long research tasks actually take, and the related skill of recognizing when a deadline is unrealistic before agreeing to it. Both are essential professional skills and neither is innate; they are learned through deliberate practice.

A concrete example. A trainee discusses an F31 application with the PI for several months in 1-on-1 meetings (aims, hypotheses, preliminary data, training plan), then begins writing 48 hours before the submission deadline, expecting that months of conversation will translate to a polished application in 24 hours of writing. It does not. The Specific Aims page alone takes 30 to 60 hours across multiple drafts; the full application is 80 to 120 hours of focused writing for a first-time applicant. The failure is uncalibrated effort estimation, not laziness. The trainee genuinely believed conversational understanding was 90 percent of the application; in fact it is closer to 10 percent. The weekly plan and update exercise builds this calibration over time.

Honest capacity and deadline-meeting as professional standards

Industry employers value honest capacity assessment and deadline-meeting more highly than nearly any other professional skill. The reason is structural: a researcher who agrees to deliver and then cannot deliver is the highest-risk profile from a manager's perspective. The manager cannot redirect resources, cannot reassign personnel to higher-priority work, and cannot communicate accurate timelines to their own management. By the time the missed deadline is apparent, it is too late to recover. In layoff cycles and performance reviews, the colleague who consistently meets deadlines (including by saying "no" when asked to commit to something they cannot deliver) is the colleague who keeps the position, regardless of technical brilliance.

The lab teaches this skill explicitly: estimate honestly, commit only to what you can deliver, deliver what you commit to, and when an estimate proves wrong, surface it to the PI early enough to renegotiate the timeline rather than miss the deadline. "I'm running 20 percent behind on the analysis and need another week" is a professional communication. Silent missed deadlines are not.

Mechanics of weekly planning

Weekly plan. By Monday at 10:00 AM, each trainee emails the PI a weekly plan structured as specific, measurable tasks with time estimates in 0.25 to 8 hour increments. Tasks should be concrete deliverables that can be checked off as complete or not complete.

Vague and unactionable

Review literature (3 hr)

Ephys analysis (4 hrs)

Microglia stim analysis (3 hr)
Specific and measurable

Annotate 15 paragraphs of microglia review (3 hr)

SNFRR analysis and figure for N animals, n days (4 hr)

Process 10 microglia motility recordings (3 hr)

Eight-hour increments are reserved for experiments. Other tasks are broken into smaller segments. Course time, fellowship deadlines, and required training are blocked on the calendar but listed separately from appointment-hour tasks.

Weekly update. By Monday at 10:00 AM (covering the prior week), each trainee emails the PI a brief update listing accomplishments with quantitative deliverables and the time each task actually took. Comparing planned versus actual time across many weeks is what builds estimation skill. The trainee will, over time, develop a personal calibration table: this kind of analysis takes me X hours, this kind of figure takes me Y hours, this kind of writing takes me Z hours per page. That table is portable to every future role.

Late or missing plans. If a weekly plan or update is missed, the PI follows up by email or Teams the same day. Repeated missed plans (three or more in a four-week period) trigger a 1-on-1 meeting to identify the cause (calibration, capability, fit, or external circumstances such as illness, family obligations, or mental health). The response is matched to the cause. Persistent issues that are not resolved through 1-on-1 discussion may be addressed through the formal annual written feedback process described in Section 1.11.

1.8 Training-to-productive-research transition

Training time is allocated for acquiring specific skills (surgery, two-photon imaging, electrophysiology, image analysis pipelines, statistical methods, or other competencies required by the trainee's project). Training is not an open-ended status. Each major training block is paired with:

•        Defined competencies. The specific skill or method, framed as something the trainee can demonstrate (perform N successful surgeries, complete an analysis pipeline on a defined dataset, pass a quantified proficiency check by a senior trainee or the PI).

•        Expected duration. The estimated time to competency, set at the start of the training block, calibrated against historical lab data and the trainee's prior experience.

•        Transition milestone. The point at which the trainee assumes independent productive contribution using the skill, agreed at the start.

Once a trainee has demonstrated competency, that activity is no longer training; it is productive research. Repeating training on the same skill across multiple appointment terms requires explicit justification (a substantively new technique, an extended absence, or documented technical drift requiring recertification). The annual written feedback (Section 1.11) reviews progress against transition milestones agreed at the previous review.

This subsection is not intended to penalize trainees who genuinely need additional training time. The diagnostic frame (calibration, capability, fit) applies: if a trainee is not transitioning to productive contribution on the expected timeline, the PI and trainee identify whether the original timeline was unrealistic, whether additional structured training would close the gap, or whether the project or research area is not the right match. The response is matched to the cause.

1.9 First-year graduate students: shadowing, peer support, and the shift to research thinking

First-semester PhD students enter the lab during a high-load transition period: new city, new cohort, new coursework, new lab culture, often new country. The first semester prioritizes coursework, building peer support with cohort classmates, and beginning lab integration through low-stakes activities. Independent experimental projects are not expected of first-semester students.

The cognitive-mode shift from K-undergraduate to research. K-12 and undergraduate education trains a specific cognitive mode: there is one correct answer, the path to it is followable, and grades reward students who follow the path. Research is structurally different. The answer is not known, the path is not mapped, and progress involves substantial time feeling around in the dark before reaching anything publishable. The trainee must discover the answer and then build the path so others can replicate, validate, and extend the work. Trainees who continue to expect the K-undergrad pattern ("tell me exactly what to do, I'll execute it, give me the next instruction") tend to get frustrated when the lab does not provide that structure, because the lab cannot provide that structure for work that is by definition novel. The frustration is real and is a normal part of the transition; it is not a signal that the trainee is failing. The mentorship response is to coach the trainee through the cognitive shift over the first 6 to 18 months, with explicit conversation about the mode change, not to dismiss the frustration as immaturity.

Building peer support. The first-semester transition is frequently when trainees experience the most isolation, particularly trainees who have moved away from their home environment. Connections with cohort peers, both inside and outside the lab, are vital for professional and mental health development. The PI actively supports trainees making time for cohort social events, study groups, and informal peer mentorship.

Lab integration tasks. Lab time during the first semester is dedicated to shadowing established lab members during procedures (surgery, two-photon imaging, electrophysiology, perfusions), assisting with data analysis on existing datasets, and learning lab-standard analysis pipelines. Specific entry-level tasks include perfusions, genotyping, image annotation on already-collected datasets, ROI segmentation on existing imaging data, and code review of established analysis pipelines. The goal is to contribute in a way that produces real research products without requiring the first-year student to lead an independent experimental program.

Middle-authorship trajectory. The lab's developmental target for first-year PhD students is to contribute to a middle-authorship paper before the start of the second year. This is achievable through analysis contributions to in-progress manuscripts, supporting figure preparation, contributing to literature review for review papers, or providing technical or computational contributions to a senior trainee's project. The PI matches first-year students to active projects based on technical fit and project timeline, and revisits the assignment in the annual review.

1.10 Professional self-management: sleep, metabolism, and the neurovascular coupling research domain

This section addresses self-management of sleep, exercise, and nutrition as professional standards. Trainees with diagnosed sleep disorders, mental health conditions (depression, anxiety, ADHD, bipolar disorder), autoimmune or metabolic conditions, eating disorders, neurological conditions, or any other clinical issue affecting energy or focus coordinate accommodations through Disability Resources and Services (DRS, 140 William Pitt Union, (412) 648-7890), through their healthcare provider, and through 1-on-1 conversation with the PI. Clinical conditions are accommodated, not framed as self-management failures. The remainder of this section addresses choices within the trainee's control.

The B.I.O.N.I.C. Lab studies neurovascular coupling, glial-vascular metabolic interactions, and the energetic demands of cortical computation. The trainees in this lab are reading, writing, and presenting on the metabolic substrate of cognition. This makes basic self-management (sleep, cardiovascular fitness, metabolic and nutritional adequacy) a professional standard rather than a personal preference. A trainee whose dissertation argues that hemodynamic coupling supports sustained cognitive computation, but who routinely shows up sleep-deprived and sedentary, has an internal consistency issue with the science alongside a productivity issue. "I'm not productive today because I stayed up late" is a self-management issue, not a circumstance the lab accommodates by lowering expectations. How the trainee achieves a state to do good science is their choice; that they achieve it is part of the professional expectation.

Time during the standard workday may be used for medical and mental health appointments, exercise, and other wellness activities, on the same terms as any other professional self-management activity, provided that scheduled meetings, deadlines, and time-sensitive experimental commitments are met.

The following are observational patterns from lab history, shared because they connect directly to the research domain. They are guidance, not medical advice or conditions of appointment.

•        Sleep. Lab members consistently getting less than 6 hours over multiple weeks underperform on tasks requiring sustained focus (image annotation, surgical precision, statistical analysis, scientific writing). Roughly 8 hours appears to be the threshold above which most function well. Being professional includes getting enough sleep to be functional the next day, the same standard a surgical resident, pilot, or trial attorney is held to.

•        Cardiovascular exercise and metabolic health. The lab studies the mechanism by which local metabolic demand drives local hemodynamic response. The same coupling we measure in mice operates in the trainee's own cortex. Sustained cardiovascular fitness improves cerebral perfusion, sustains mitochondrial function, and supports cognitive work. AHA suggests roughly 150 min/wk moderate-intensity or 75 min/wk vigorous activity; consistency matters more than the specific number. "I'm too busy to work out" in a neurovascular coupling lab is self-defeating.

•        B-12 and metabolic adequacy on plant-based diets. Several lab members on vegetarian or vegan diets have presented with cognitive symptoms (brain fog, fatigue, difficulty concentrating during long experiments) that resolved with B-12 supplementation or dietary change. B-12 deficiency is straightforwardly diagnosed with a blood test (serum B-12 above 500 pg/mL is commonly cited as adequate, though clinical thresholds vary). The lab does not advocate any specific diet; it does observe that metabolic adequacy is a precondition for the cognitive work the trainee is here to do.

On the framing. These observations are shared because the lab has watched bright trainees struggle with productivity for reasons that turned out to be addressable (sleep debt, B-12 deficiency, sedentary patterns) and only got identified through 1-on-1 conversations. The PI does not require any specific health behavior or condition appointment status on wellness practice. What the PI expects is that the trainee shows up able to do good science.

1.11 Performance feedback, the calibration-capability-fit frame, and addressing problem patterns

Annual written feedback. Per the GSR Academic Regulations, the PI provides each GSR with written feedback on the quality of their work at least once per year, with a copy retained by the trainee and the lab. NRSA postdocs receive comparable annual written feedback. Feedback addresses research progress against agreed milestones, technical skill development, scientific writing and communication, career trajectory, areas of strength, and areas requiring improvement with specific actionable goals. Mid-cycle feedback is provided through 1-on-1 meetings, manuscript and abstract review, and weekly plan calibration. Concerns about progress, calibration, capability, or fit are raised in 1-on-1 meetings before they appear in a written annual review.

Addressing problem patterns. Some patterns of behavior, while individually defensible, become problematic when used systematically to avoid productive contribution. Naming them protects both the lab from drift and the trainee from a slow accumulation of habits harder to address later. The PI's response is dialogue and mutual problem-solving first, formal performance management second. Most trainees never encounter these structures as friction; they exist for the small subset of cases where they are needed.

•        Indefinite training status. Repeated re-training on the same skill across appointment terms without demonstrated competency, used to avoid productive research contribution. Response: Section 1.8 transition milestones, with the annual review tracking whether transitions are happening.

•        Volunteering counted as research. Counting outreach, volunteering, conference organizing, or service toward appointment hours. Service is valuable and supported, but it is personal time, not appointment hours.

•        Coursework substituting for research. Treating coursework hours as if they counted toward the research appointment. Occasional load shifting (a final exam week with reduced research time) is normal; sustained substitution requires advance discussion with the PI to plan makeup time or schedule adjustment.

•        Class-calendar interpretation. Treating University-open-but-class-paused days (Spring Break, Reading Days, finals breaks) as default vacation. Section 1.5 disambiguates: these are workdays, with personal time taken via the recess day allocation.

•        Selective communication. Going dark on email or Teams during the workweek without acknowledgment. Response: Section 1.4 response time expectations, with reclassification of unresponsive time as sick time if the pattern continues after 1-on-1 discussion.

•        Unannounced remote work, or remote work as cover for personal time. Two related patterns: (a) repeatedly taking "remote days" without prior PI approval, and (b) claiming a remote workday but actually being at a movie, with friends, playing video games, or running personal errands. The daily plan and end-of-day update with documented evidence (Section 1.4) makes remote-as-personal-time visible. Repeated unannounced remote days, or remote days where deliverables are inconsistent with claimed work hours, are reclassified as recess or sick time.

•        Hidden travel and post-hoc notification. Notifying the PI of travel after departure, especially when the absence affects experiments, animal cohorts, or lab meetings. For some appointments, advance notification is a regulatory and visa requirement. Time on unannounced travel is reclassified as recess or unpaid absence; genuine emergencies are an exception.

•        Deadline acceptance without honest capacity assessment. Agreeing to deliver on a timeline the trainee has not estimated honestly (the F31 example in Section 1.7), then missing it. The lab supports "I cannot deliver that in that timeframe" as a professional communication; it does not support silent missed deadlines.

•        Manuscript and grant review delay. Sitting on a co-author's draft or feedback request for weeks, slowing the project for everyone else. Review windows are agreed at the time of request; persistent slow-walking is a lab citizenship issue.

•        Last-minute conference submissions or skipped approval. Submitting an abstract, poster, or oral presentation slides without PI approval, or requesting approval the day before submission so there is no time for review. Conference deliverables represent the lab and co-authors. Section 1.14 timelines apply, with withdrawal and loss of reimbursement for missed approval.

•        Conference travel extended into personal vacation. A 2-day conference becoming a 7-day trip with the additional days framed as conference time. Conference reimbursement covers conference days plus reasonable travel; days extended for personal travel are scheduled as recess days, not appointment time.

•        Padded or recycled weekly plans. The same task appearing week after week without completing; deliverables recycled from prior weeks. A task in four consecutive weekly plans without completion triggers 1-on-1 discussion to identify whether scoping is wrong, the trainee is blocked, or the task is being padded.

•        Indefinite literature review. "Still reading background" at month 6 of a project where reading should have been done in month 1 to 2. Response: 1-on-1 discussion of specific reading list with bounded milestones and a transition date to the next project phase.

•        Delegation as accomplishment. Handing experiments, analyses, or writing to undergraduates or labmates and counting that delegated time as the trainee's own appointment hours. Mentoring is a real activity but is not the same as performing the work. Weekly plans distinguish trainee-performed tasks from supervised tasks.

•        Protocol drift without IACUC amendment. Modifying surgical, experimental, or analytical procedures beyond what the IACUC protocol or agreed methods authorize. The DLAR animal protocol is binding; modifications require amendment before implementation. Unauthorized drift is reported through normal compliance channels.

•        Cherry-picking data with vague biological excuse. Excluding animals or sessions retroactively with vague reasoning ("that animal seemed sick") in ways that conveniently leave the cleanest data. Legitimate exclusion criteria are pre-specified, applied consistently, and logged at the time of exclusion (not after seeing the result). The PI reviews exclusions when reviewing analysis.

•        Lab reagent or supply diversion. Using lab reagents, animals, or equipment for personal projects, side projects in another lab, or work outside the active grant portfolio without authorization. Any use of lab resources for work outside the trainee's primary project requires advance discussion.

•        Selective citation in proposals or reviews. Citing only papers that support the lab's hypothesis or methods while ignoring contradictory literature. PI review of proposals and reviews includes literature balance as a substantive criterion.

•        Selective memory of feedback. Receiving specific feedback in 1-on-1, then later claiming "you never told me that" when the instruction was not followed. Significant 1-on-1 feedback is summarized in a follow-up email or Teams message so there is a written record.

•        Self-management as accommodation request. Treating recurring self-inflicted productivity loss (chronic sleep deprivation by choice, sedentary patterns, dietary inadequacy left unaddressed) as a circumstance the lab should accommodate by lowering expectations. Genuine illness, mental health crises, family emergencies, and disability needs are accommodated through DRS and sick leave; chronic self-management failures are addressed through 1-on-1 discussion of the standards in Section 1.10.

•        Avoidance through reframing. Re-categorizing experiments as "still preliminary" indefinitely to avoid the writing and publication phase. Section 1.8 transition milestones extend to the experiment-to-manuscript transition; the annual review tracks paper progress.

1.12 PI commitments to trainees

The PI commits to the following responsibilities, mirroring the trainee expectations above:

•        Provide a written appointment letter at the start of each appointment specifying duration, expectations, and any required after-hours commitments

•        Provide annual written feedback per Section 1.10 with specific actionable goals

•        Provide training and mentorship for technical skills, scientific writing, grant writing, and career development

•        Respond to trainee emails and Teams messages within the same windows expected of trainees during working hours

•        Hold scheduled 1-on-1 meetings as agreed; reschedule rather than cancel without rescheduling

•        Approve abstracts, posters, and manuscripts within agreed timelines, or communicate revised timelines in advance

•        Maintain confidentiality of trainee personal information disclosed in 1-on-1 meetings

•        Not retaliate against trainees who raise concerns through the grievance pathways listed in Section 1.13

•        Not require work beyond the appointment hours specified by the trainee's funding mechanism

•        Comply with all University, federal, sponsor, and CBA requirements that apply to each trainee's appointment

1.13 Trainee rights, accommodations, and grievance pathways

Trainees seeking disability-related accommodations contact DRS (140 William Pitt Union, (412) 648-7890, drsrecep@pitt.edu, (412) 228-5347 for P3 ASL users). The PI implements approved accommodations promptly and without retaliation. New parents follow the GSR Academic Regulations and Graduate Student Parental Accommodation Guidelines.

Trainees who believe they have been treated unfairly are encouraged but not required to raise concerns first with the PI in a 1-on-1 meeting or by email. Trainees may at any time, and without first raising concerns with the PI, contact:

•        The BioE Graduate Program Coordinator (currently Dr. Kurt Beschorner)

•        The BioE Department Chair (currently Dr. Sanjeev Shroff)

•        The Office of the Vice Provost for Graduate Studies

•        The Pitt Concern Connection (https://www.compliance.pitt.edu/pitt-concern-connection)

•        The Office of Institutional Engagement and Wellbeing

Per the GSR Academic Regulations, GSRs may also seek review under the University's Guidelines on Academic Integrity. Termination or suspension of a GSR appointment requires written notice from the department chair stating the reasons, and may be appealed in writing to the dean within 10 business days. The PI does not retaliate against trainees who raise concerns through any of these channels.

1.14 Conferences, abstracts, and posters

Conference presentations are a primary mechanism by which trainees develop scientific communication skills, build professional networks, and disseminate the lab's research. The lab actively supports conference attendance for trainees who present (poster or talk). Attending without presenting is a personal choice that the lab does not fund.

Submission rules

For internal conferences (Pitt, CMU), the same poster may be presented at multiple conferences in a year. For external conferences, the same poster may not be presented at the same conference in subsequent years, and the same poster may not be presented at different external conferences within a 12-month period. Internal posters can be expanded or modified for external presentation; the standard is whether the scientific content is materially the same.

Approval timelines

Conference deliverables (abstracts, posters, oral presentation slides) require PI approval and co-author circulation on a fixed timeline. The deadlines below refer to approval, not to first submission to the PI. Drafts should be circulated to the PI well before the approval deadline so there is time for substantive feedback and revision.

•        Abstract with external co-authors. PI approval at least 10 days before the abstract submission deadline. Circulation to all co-authors at least 7 days before submission.

•        Abstract with internal-only co-authors (lab members and PI). PI approval at least 5 days before submission. Circulation to co-authors at least 3 days before submission.

•        Final poster. PI approval at least 7 days before the presentation date. Circulation to co-authors at least 5 days before presentation.

•        Oral presentation slides. Same timeline as posters: PI approval 7 days before presentation, co-author circulation 5 days before.

Failure to obtain timely PI approval results in withdrawal of the abstract or presentation and loss of any associated travel reimbursement. This is not a punitive policy; it reflects that an abstract or presentation that has not been reviewed represents the lab and its co-authors without their consent. If the deadline is unworkable for a specific case (e.g., a late-breaking abstract opportunity), discuss with the PI as soon as the opportunity arises rather than after the standard window has passed.

Abstract content requirements

All abstracts require completed preliminary data and analysis at the time of submission. Submitting an abstract on work the trainee "will do" between submission and the conference is not permitted. Additional data and analysis can be added between abstract submission and the presentation, but the abstract must include quantified metrics (mean ± SEM with sample size, or other appropriate quantitative summary) at the time of submission.

Reimbursement

Reimbursement follows GSA per diem rates (https://www.gsa.gov/travel/plan-book/per-diem-rates/per-diem-rates-lookup) and Pitt BioE departmental policy. Per diem covers meals and lodging up to the daily limit; trainees may need to share hotel rooms with another conference attendee to stay within the lodging cap, and the first and last days of travel are typically reimbursed at a reduced per diem rate. Confirm specific reimbursement details with the BioE business office before booking.

Receipts are required for all food items for graduate students; faculty and staff may take per diem; postdocs confirm category with the BioE business office. The Department does not reimburse first-class or economy-plus upgrades, travel insurance, or society memberships (society membership is career development, not conference attendance). Alcohol is not reimbursable. Flights must be booked at reasonable economy rates with reasonable advance booking (~21 days). Trainees without P-Cards book through Concur using Anthony Travel.

State tax exemption. The University is tax-exempt; trainees can use the State Tax Exemption and W-9 forms (available through Pitt Purchase, Pay & Travel) to remove sales tax on lodging and other reimbursable purchases. Filing the tax exemption forms before arrival saves processing time on the reimbursement back-end.

Reimbursement requires the trainee to represent the lab through a poster or talk. Attending without presenting is funded by the trainee's own fellowship, award, or stipend. Reimbursement requests must be submitted within 90 days of the trip or the reimbursement is processed as taxable income. Trainees are encouraged to apply for BioE departmental travel grants (https://www.engineering.pitt.edu/Departments/Bioengineering/_Content/Resources/Graduate-Travel-Grant/), EGSO, CNBC, or society travel awards to supplement lab grant funds; this is part of professional development. Lab grant funds typically support travel to one conference of relevance to the specific project per year per trainee.

Registration and abstract submission fees are reimbursable. If a presentation is withdrawn because PI approval deadlines were not met, no reimbursement is provided for any portion of the trip, including registration. The trainee is responsible for confirming abstract acceptance, presentation logistics, and the approval timeline before booking travel.

Poster printing

BioE offers a free print service for 42 in × 42 in posters. Trainees should submit the final poster file to the BioE print service or to FedEx (or equivalent commercial printer) at least 24 hours before departure, with a printing proof requested before final printing to confirm accuracy. The lab maintains poster printing instructions and FAQs in the Teams Workshop channel for reference. If the trainee misses the printing window and prints on-site at the conference, the cost is not reimbursed (and conference printing typically charges a premium).

Post-conference debrief

Following each conference, trainees present highlights to the rest of the lab during workshop or journal club. This includes the trainee's own poster or talk and any other posters or talks of relevance to lab research directions. The intent is to share information broadly so that lab members who did not attend benefit from the trainee's experience.

1.15 Research integrity standards

Research integrity is the load-bearing standard for everything the lab does. Several of the patterns in Section 1.11 (cherry-picking data, selective citation, protocol drift) connect directly to research integrity, but the standard is broader than the enumerated patterns. The lab follows the University of Pittsburgh Research Integrity Policy (RI-07), the NIH Grants Policy Statement requirements on data, the ICMJE authorship criteria, and the journal-specific reporting standards for the venues the lab publishes in.

Operational expectations:

•        Data preservation. Raw data, analysis code, and intermediate analysis outputs are preserved on lab-managed storage (OneDrive, lab servers, version-controlled repositories) for at least the period required by the funding agency (typically 3 years post-award close, but longer for some sponsors). Trainees do not delete or take exclusive control of project data when leaving the lab.

•        Pre-specified analysis. Hypotheses, primary outcome measures, exclusion criteria, and statistical analysis plans are specified before data are collected (or before unblinding for pre-existing datasets). Post-hoc changes to the analysis plan are documented as exploratory, not reported as primary findings. The lab does not engage in p-hacking, garden-of-forking-paths analysis, or selective reporting.

•        Negative results. Experiments that produce negative or inconclusive results are reported in lab updates and considered for publication when the negative result is informative. The lab does not silently abandon negative results or pretend experiments did not happen.

•        Image and figure integrity. Image processing follows the agreed pipeline (e.g., contrast adjustments applied uniformly across the image, no selective brightness changes, no removal of artifacts that change scientific interpretation). Figures show the actual data; representative images are labeled as such and chosen by criteria documented at the time, not after seeing reviewer feedback.

•        Authorship per ICMJE criteria. Authorship reflects substantial contribution to conception or design, data acquisition or analysis, manuscript drafting or critical revision, and final approval. Order of authorship is discussed openly at project initiation and revisited as scope changes. The lab does not engage in honorary authorship, ghostwriting, or authorship as personnel management.

•        Honest representation in proposals and reviews. Fellowship applications, grant proposals, and peer reviews represent the science honestly, including contradictory literature, methodological limitations, and prior negative results. The lab's reputation depends on this and accumulates over decades.

Trainees who become aware of possible research integrity issues, in their own work or in others', are encouraged to raise them with the PI directly, with the BioE Department Chair, with the University Research Integrity Officer, or through the Pitt Concern Connection. The PI does not retaliate against trainees who raise integrity concerns in good faith.

1.16 Regulatory framework and degree milestones

This subsection consolidates the University and program-level requirements that govern the trainee's appointment and degree progress. The lab document does not duplicate the full regulatory text; it points to the binding sources and notes the milestones most likely to require lab-side coordination.

•        Continuous registration. GSRs are expected to maintain at least 9 credits per term during fall and spring (or the Full-Time Dissertation Study option for post-coursework PhD students). Trainees who do not register for at least 1 credit during a 12-month period are transferred to inactive status per the Regulations Governing Graduate Study and must apply for readmission before resuming.

•        Conditional appointment. Per the GSR Academic Regulations, appointments are conditioned on satisfactory progress toward the degree as defined by the BioE program. Examples of unsatisfactory progress include GPA below 3.0, completing fewer than 6 credits per term, or failing preliminary or comprehensive examinations.

•        PhD statute of limitations. Per the Regulations Governing Graduate Study, PhD requirements must be completed within 10 years of initial registration (8 years if the student received credit for a master's degree appropriate to the field). Extensions require dean approval. Long-running PhDs should track this milestone and surface it in 1-on-1 discussion well before the limit.

•        Annual doctoral committee meetings. After admission to candidacy, the doctoral committee must meet with the candidate at least once per year per the Regulations Governing Graduate Study. The trainee organizes the annual meeting in coordination with the PI and the committee, prepares a progress summary, and circulates it to committee members in advance.

•        International student visa constraints. Per the GSR Academic Regulations, graduate students on J-1 or F-1 visas may not engage in research that is not directly integrated with the student's thesis or dissertation for more than 20 hours per week on campus during fall and spring terms. Students on these visas confirm any additional appointment opportunities with the Office of International Services (OIS) before accepting.

•        Required first-semester training. Per the Regulations Governing Graduate Study, graduate students enrolled in programs requiring more than 10 credits of in-person instruction complete Title IX training in their first semester at the University. The lab provides additional onboarding training (EH&S, OSHA, IACUC/DLAR, RCR) within the first month of the appointment.

•        Editorial assistance disclosure. Per the Regulations Governing Graduate Study, trainees using professional editorial assistance for dissertations or other written work disclose this assistance and confirm with the PI that the editorial scope is limited to language rather than content. The lab supports peer review and PI feedback as the primary editorial mechanisms.

•        Authorship and intellectual property. IP arising from work conducted in the lab is governed by University Policy RI-10 and the terms of relevant grants. The PI explains the IP framework at the start of each appointment. Authorship follows ICMJE criteria as specified in Section 1.15.

1.17 NIH and NSF grant compliance

Trainees and staff supported by federal grants have specific compliance obligations beyond the University-level requirements in Section 1.16. The PI ensures the requirements are operationalized; trainees ensure their own work meets them.

•        RCR training. NIH requires Responsible Conduct of Research training for all trainees on T32, F-mechanism, and K-mechanism awards, with a face-to-face component and a minimum of 8 contact hours per training cycle, repeated approximately every 4 years. NSF requires Responsible and Ethical Conduct of Research (RECR) training for all undergraduates, graduate students, and postdocs supported by NSF awards. The lab uses CITI online modules plus in-person lab discussion sessions to satisfy both standards. RCR/RECR training counts within the appointment.

•        Public access (manuscripts). Manuscripts arising from NIH-funded research are deposited in PubMed Central within 12 months of publication per the NIH Public Access Policy; the lab uses PMCID assignment via NIHMS. Manuscripts arising from NSF-funded research are deposited in NSF-PAR within 12 months of publication per the NSF Public Access Plan. Trainees confirm with the PI which deposits apply at the time of acceptance.

•        Data Management and Sharing (DMS). Per the NIH DMS Policy (effective January 2023), all NIH-funded projects have a Data Management and Sharing Plan that the trainee follows for data preservation, sharing schedule, and metadata standards. NSF projects similarly require a Data Management Plan. The PI provides the relevant DMS/DMP at the start of each project; trainees follow the schedule for shared deposition (e.g., DANDI for electrophysiology, FigShare for tabular data, GitHub for analysis code).

•        Effort certification and Other Support reporting. Federal grants require time and effort certification for personnel charged to the grant. Pitt SPA manages the institutional process; trainees confirm effort allocations annually. Other Support (NIH) and Current and Pending Support (NSF) reports list all federal and non-federal support a trainee or PI has, including pending fellowships. Trainees notify the PI of any new fellowship application or award promptly so the PI can update Other Support records.

•        Rigor and reproducibility. NIH requires rigor and transparency in research design, biological variables (sex as a biological variable), authentication of key biological and chemical resources, and statistical methods justification. NSF requires similar standards through the rigor element of merit review. The lab's Section 1.15 standards (pre-specified analysis, documented exclusion criteria, image and figure integrity, negative results) operationalize these requirements at the project level.

•        Safe and inclusive research environments. NSF requires a Safe and Inclusive Research Environments plan for off-campus or off-site research; NIH similarly requires safe-environment certifications for some mechanisms. Field work, animal facility work, and shared core facility work follow Pitt's environmental health and safety, IACUC, and Title IX policies regardless of funder. Trainees who experience harassment or unsafe conditions raise it through the channels in Section 1.13.

Section 1 is the PI-authored portion of the working agreement. The appointment letter takes precedence on terms specific to the appointment, and that University, federal, sponsor, and CBA policies take precedence on any matter where they conflict with this document. Sections 2 through 7 are lab-member-authored portion.

Lab Contract: Operational agreement written and agreed by all members

2. FILE STORAGE

1. There are 4 main services used for the storage of files pertaining to lab organization, inventory, and research in the lab. The services are 1) Google Drive, 2) One Drive, 3) the Lab’s server, and 4) Github. The lists below detail what types of files can be found at each of these file storage services.

i. Google Drive: Ordering, animal inventory, antibody inventory, round table slides

ii. One Drive: Files pertaining to individual research projects (shared with people working on the project), data sharing, processed data (might benefit other’s analysis)

iii. Lab server (SSOE-BIOE online storage drive; requires Global Protect to login from non-lab computers): All raw data, individual data backup

See Teams channel ‘server’ for detailed instructions on the two servers

iv. Github: programming stuff, tutorial, processing scripts, processing pipeline, data structures  

2. Guidelines for backing up the raw/analyzed data from temporary storage to backup hubs are detailed in the list below. Use the Workshop_Facilitators.xlsx in the Google Drive as a record.

i. Biweekly backups of raw data are made from sources (2-p computer, MVX, Ephys computer, Confocal) in which data was added during the time period to the respective folder on the server. Assignments are scheduled on the Workshop Facilitator Sheet. For example, imaging data will be saved into folders on the “data” folder on the MVX or “temporary storage” drive on the 2p computer. Everyone should save their data to a folder with their name. Depending on the schedule. 

ii. Facilitators assigned to backing up the data on a biweekly basis in “Workshop Facilitators” document on the Google Drive. Facilitator from week before is responsible for ensuring current facilitator completed the back ups. 

iii. Backups are made on 2 physical harddrives at a time that are named like “Imaging Backup Year A/B”. This means that drives Year A and Year B are identical. Then when those drives do not have any more space to backup the recent 2 week time period the facilitator is responsible for initializing the next two harddrives for that year (i.e. Year C/D etc). Both hard drive backups should be transferred from the source, not from one hard drive to the other.

Iv. File sizes and number of files should be checked on the source and on the hard drives to ensure all files were transferred. Do not check file sizes on a Mac computer as this will create an invisible file that messes up the file size of the folders. Do not delete any files from the “temp” folder on the 2p to ensure file sizes match.

I. Note that The Facilitator should update the Facilitator list to indicate which drive the data was backed up to. This will allow the next facilitator to know which harddrives to use and will maintain accountability of the facilitator to follow through with the backups.

iv. Two photon and MVX

• There should be 3 folders backed up on the hard drive and server: 2P_244, 2P_242, MVX

• Backups of the ‘Temp’ drive will occur every 2 weeks on the Friday of that week.

• RAW drives will not be backed up

• Once the temp drive is full, old folders in ‘Temp’ drive will be wiped. Hard drive and server backups should be double checked before deleting from “temp”.

• Do not attempt to convert raw image formats if the RAW drive is entirely full. This may create issues in the conversion.

E-phys: 

• Starting 2026, folders will be grouped by project

• It is the project’s members responsibility to backup the ephys to 2 external hard drives and the server.

Confocal:

• Starting 2026, folders will be grouped by project

• It is the project’s members responsibility to backup the confocal images to 2 external hard drives and the server.

3. LAB COMMUNICATIONS

a. All administrative lab business, workshop/journal club items, important information/opportunities, and useful documents will be shared via the Lab listserv (bioniclab@googlegroups.com) and via Microsoft Teams (ask to be added) with an announcement message in the appropriate channel.

b. Ordering within the lab is organized via a Google sheet on the Lab Google Drive folder. It is each Student’s responsibility to follow the “second-to-last” rule when ordering items (i.e. place order when second-to-last box/package is opened). Animal orders must be placed by end-of-day on Tuesday of each week in order to be processed by DLAR for that week. Failure to do so will extend the length of time by a week before an animal order is processed. Any questions about orders should be directed to the Lab manager.

1. Orders over $5,000 require a requisition and department approval through Alexis Delgrosso

2. Orders over $10,000 require Sole source justification (signed by TK and Department Head) as well as export control form (signed by vendor, regardless if it is international or not)

3. If there is an item to be ordered from an external vendor (vendor that Pitt doesn’t have agreement with) you must fill out a purchase form and send to Kim Trost. If ordering from Amazon, you must provide proof that the item is cheaper than if purchased with a Pitt associated Vendor (PantherExpress and Suppliers List).

4. Deliveries 

   1. Everyone should take care of their own deliveries.

   2. Guangfeng will notify the upcoming deliveries

   3. Whoever ordered the package should determine if he/she comes to get it by themselves or have someone else to help get it.

   4. When delivered, mark ordering sheet with the delivery date. 

5. For the weekly inventory check performed by facilitators, or when doing an ETO or Autoclave, facilitator will place any items on the order sheet according to the “second-to-last” rule and fill out the printed inventory list.

c. The mouse inventory is organized via a Google sheet on the Lab Google Drive folder. It is each Student’s responsibility to update the mouse inventory to accurately reflect the number of animals that have been purchased or are available for surgery (https://docs.google.com/spreadsheets/d/1-yDIVo9eeqS3nPkpIoX5qoa49qQfHk3mf13yjQjNaS8/edit#gid=0). It is required that each student keep an inventory of their own to reflect which cages they are responsible for in order to accurately reflect the total number of cages being used and for what project/purpose.

d. Students are responsible for reserving time for equipment or lab space on the Lab Google calendar. If a reservation needs to be canceled the Student must do so with at least a 48 hour advance notice (message lab on Teams). In the case of emergency or sudden change in schedule, as soon as possible followed by notification of the Lab via e-mail/TEAMS correspondence.

BIONIC 242 2P

BIONIC 242 Surgery

BIONIC 242 MVX

BIONIC 242 Stimulator

BIONIC 244 2P - Two-photon microscope

BIONIC 244 2P/MVX - Surgery table in 2P room in front of MVX 

(e.g. Label 2P and 2P/MVX calendars if you need to perform surgeries while imaging in 2P room)

BIONIC Stimulator - TDT stimulator for ICMS

BIONIC Analyzer - Processing of data sets

BIONIC Autolab - Impedance recording, IROx activation

BIONIC Confocal - Confocal microscope (4th floor)

BIONIC Cryostat - Cryostat (room 243)

BIONIC 243 Fumehood (book perfusions + ETOs)

BIONIC Staining and Histology Bay

BIONIC Surgery Room - Surgery room connecting 2P room and Utility room

BIONIC Utility Room - Ephys recording

bioniclaboratory@gmail.com - General lab events, 1-on-1 meetings, JC/Workshop,

 student/staff time off

e.    A secondary form of lab communication designed for instant/real-time interaction (i.e. Team) will be established to facilitate separate Lab functions (general lab business, ordering, workshop, journal club papers, accomplishments, miscellaneous, etc.) amongst lab members.

f. Social, communication, and collaboration.

i. Regular Social:  Once a semester (plan a month in advance) (https://docs.google.com/document/d/16Z4R4AxeeLrD42Wfj6o0ZBzwzNS-4RIXb7TMX_95PIU/edit ) Scheduling can be done the week before using a polling software (doodle, when2meet, slack)  to  determine when everyone would be available. It is understood that sometimes/activities will not work for all lab members. Will add events to the general calendar (and post in “social” Teams channel). 

ii. Last Friday of every month social after working hours (Options: Pins, coffee shop, picnic, etc.).

g. In Person: Trainees should make a best effort (Sick, experiments, seminars, classes, etc.)  to be present in the Lab on M-F 9:00am-5:00pm to facilitate spontaneous group discussions, peer mentoring, and problem solving sessions. Staff are expected to be in person 5 days a week. 

1. If you are sick, but able to attend meetings virtually, everyone should be on zoom with cameras on, and use Push to talk.

h.  When a lab member is notified of a seminar of interest, it is that lab member’s responsibility to add that seminar date and location to the “Research Seminars” Google calendar as soon as possible or within that day. Add the speaker, location, title, and abstract of the talk or other relevant information available within the description box of the event. 

i. Whiteboard: The large white board should be used for drawing out figures/analyses and collaborative thoughts. If the board is filled and you would like to use it, take a picture and send the image to Teams before erasing.

j. Small Group Meetings (Fall Only). Small groups will be composed of 3 randomly selected trainees. Groups will meet weekly on Wednesdays after Journal Club in person for 30 minutes to discuss proposed experiments, provide feedback on outlines and manuscripts, and engage in collaborative communication. Groups will be changed each month and assigned by the Workshop Facilitator at the beginning of the semester. May be adjusted for new trainees to meet with more of the senior trainees to discuss ongoing work in the lab.

May:

G1: Yalikun, Camila, Anna, Adam

G2: Heejin, Vanshika, Karlie, Teresa

June:

G1: Karlie, Anna, Teresa, Yalikun

G2: Heejin, Camila, Adam, Vanshika

July:

G1: Karlie, Yalikun, Vanshika, Teresa

G2: Heejin, Camila, Anna, Adam

August:

G1: Adam, Yalikun, Vanshika, Karlie

G2: Heejin, Camila, Anna, Teresa

k. New member orientation. When new members join the lab, current members will take turns presenting ongoing projects in the lab and opportunities for learning so that they can choose what skills to learn and which projects to get involved in. 

4. LAB    WORKSHOP:

 Each lab member is expected to participate in the 2-hour Team Workshop (~1% of total time). This is a dedicated space to support one another in identifying, analyzing, and resolving scientific or technical challenges, and to share knowledge, tools, and experiences that strengthen the group as a whole. Active engagement is expected, this is not time for individual work such as checking email, doing homework, or completing personal tasks. These sessions are designed to foster collaborative thinking, improve communication, and team problem-solving skills, and ensure collective success by leveraging the diverse expertise of the lab. If something is unclear, it is not only acceptable but expected to ask for clarification. It is each member’s responsibility to help the presenter improve how they communicate their science, through thoughtful questions, constructive feedback, and requests for clarification that reveal gaps in understanding or presentation. This mutual accountability ensures scientific rigor and strengthens the team’s collective ability to think critically and communicate effectively

a. Each week, a Facilitator will be chosen to lead the focus/discussion of the upcoming workshop and weekly journal club. Facilitators will be chosen ahead of time and, in the event that no Facilitator has been assigned, the Student who has not been selected to lead workshop longest will be automatically chosen. The schedule of facilitation will be decided within the first month of each semester. 

(If necessary, Facilitator will follow the schedule, which can be found on the workshop worksheet: Workshop Facilitators.xlsx)

i. In the event that the scheduled facilitator does not have an outline/data to discuss, then it is their responsibility to discuss with the lab to find another topic to discuss. This can include but is not limited to:

Lab wiki pages (lab protocols for various experimental procedures)

Methods papers/pseudo journal club

Group project updates

Data processing tips

Organizing data for open access

b. Students must submit any action items or desired discussion topics to the Facilitator by end of day (5 pm) on the day prior to Workshop (Friday, when workshop is on Monday). The Facilitator will send out agenda items to the Lab (via bioniclab@googlegroups.com) prior to Workshop by the morning of. 

c. In the event that another Student wishes to facilitate workshop discussion they must notify the current Facilitator ahead of time, in which case the current Facilitator will be assigned to lead the subsequent Workshop and the schedule will be adjusted accordingly.

e. Time at the end of Workshop (5-10 mins) will be allotted for wrap-up, workshop summary, and discussion of any administrative items for the following week. Any updates or business items should be summarized and posted by the Facilitator to the Workshop channel in Teams during the meeting - recommended to open up the workshop channel and type in updates as the meeting starts.

f. In cases of extreme bad weather (Delays and Closures / Inclement Weather FAQ (pghschools.org)), workshops will be conducted on zoom via the link on google calendar. (Snow days or 2 hour delays) Alert via the Microsoft Teams channel. 

g.      Workshop Facilitator Weekly responsibilities besides leading workshop:

1. Physical and server 2P backup and it is to be done by the end of the week (schedule can be seen in workshop facilitator excel spreadsheet). If not scheduled for backup, facilitator is responsible for checking that all files were backed up.

2. Checking inventory and making sure items noted in the Teams channel “ordering” have been ordered by the end of the week. 

   1. A print out of the inventory list will be provided to each week’s facilitator for them to fill out over the course of the week. The facilitator will also be responsible for filling any necessary orders from the inventory list. Facilitators should update the digital (and/or physical) inventory sheet before the end of the week.  https://docs.google.com/spreadsheets/d/13CKOJSVozA_cpsWirwEs5MwtFifdnCrdsr0C6fflUcE/edit#gid=0 

3. Choose Journal club paper

   1. Place journal club paper on Google Drive and send reminder via email and/or Teams by Monday morning prior to Workshop (for Journal Club on Wednesday).

5. Journal Club

1. Time at the beginning of Journal Club will be allotted for a brief (2 min each 1-2 PPT slides via Google Drive folder) roundtable presentation of each Student’s summary of the week’s work/accomplishments and plans for the coming week (required). Agenda: 1) Business Items, 2) Round Table 3) Journal Club.

2. It is suggested that the facilitator will prepare a ~5 min slide presentation to motivate the background of the paper and summarize the story of the paper. Notably it can be helpful to explain why it is relevant to the lab. What is motivating the facilitator’s interest in the paper for the lab. See BIONIC_LAB/StandardProtocols/Journal Reading Checklist.docx for general guidelines.

3. Introduction slides should be made in that week’s roundtable slides.

4. Especially, when new students enter the lab, pre-paper discussion presentations can be framed to discuss the background of the paper on a deeper level (i.e. background on the cell, receptor, method being used) and then dive into the motivation behind the questions answered in the paper.

5. Journal club agenda can be flexible (ex. Additional time for extra workshop time, presentations, etc.)

6. LAB SPACE

a. Each Student is responsible for the cleanliness and preservation of lab equipment or lab space in which they are working. After a procedure is completed, the Student must return the equipment or space back to its original state in which it was prior to use. The last person in the lab will check that the lights are off and doors are locked for both rooms. 

b. Each Student is responsible for backing-up recorded data to 3 different locations: 1) the Lab’s SSOE-BIOE online storage drive in individual Student folders, 2) at least two back-up hard drives for storage, 3) a personal hard drive. It is the Student’s responsibility to keep their data backed up for routine clearance of space on imaging and recording computers.

i. Data will be backed up to harddrives every two weeks and to the server once a month. The current week's facilitator will be responsible for this. 

ii. The raw storage drive on the two-photon computer will be purged within a week of the drive reaching 75% capacity, or as needed. An email will be sent via the lab listserv to notify the Lab members that have data stored on the drive. 

c. Cleaning two-photon filter (front and back) and filling coolant, etc. Person will be assigned during Workshop the week that the filter needs to be cleaned for both 2P microscopes. Report completion on Teams. There is a sheet to track the cleaning on the cabinet beneath the sink where the coolant is stored.

d. Keys to the drug box should never be left in the box. They should always be returned to their designated locations after use.

e. Biohazard waste should be taken out biweekly by the assigned staff members. All biohazard bins should be collected and the box taken to the loading dock. The schedule is found here: biological waste

i. Whoever is responsible for the biohazard waste is also responsible for a walkthrough of the lab and notifying any students who are responsible for the space to clean the area.

f. Each Student is responsible for making and updating protocols of important lab equipment operations available on OneDrive.

g. Make use of the 3D printer whenever possible. Replace the tray once a year. 

h. Lab training:

i. Learn surgical, imaging, and recording from older students

ii. Learn sectioning (cryostat) from Guangfeng (email her in advance to find a day/time to meet)

iii. \BIONIC_LAB\StandardProtocols (on OneDrive)

iv. When in doubt, ask for help.

i. If there is any equipment repair or adjustment that takes more than 15 minutes, contact the staff members to assist. If a longer repair/adjustment is required, they will take care of it. It is not the trainees’ responsibility to fix issues in the lab.

7. Authorship guidelines: 

https://hms.harvard.edu/sites/default/files/assets/Sites/Ombuds/files/AUTHORSHIP%20GUIDELINES.pdf

https://www.elsevier.com/researcher/author/policies-and-guidelines/credit-author-statement

i. It is encouraged to send out drafts of your manuscript to the entire lab in order to get feedback from others.

ii.  At the minimum, one week before submission (ideally two weeks), the first-author must send out the final manuscript to the entire lab over the bionic lab email so that all lab members can assess potential authorship.

iii. Draft Credit list: A document/contract should be agreed upon by all contributors during the outline process. The document should be a live document with constant revisions/ edits as the project develops and/or new people are involved. The agreement will be saved in One Drive for each project.

Authorship agreement from Pitt: https://teamsciencetools.icre.pitt.edu/login?redirectTo=%2Fforms%2Fauthorship-agreement

iv. Figure widths must be 58, 88, 180, or 185 mm and height no more than 225 mm. Images need to be 300 dpi or for a combination image + line art 1200 dpi. Line art needs to be saved at eps where each element is separately preserved (don’t convert a .jpg to an .eps). Font sizes should be Arial, with a max of 11 and min of 5. Color scheme, subpanel label, and axes label should be consistent size and format for all figures. 

• Make sure to follow submission journal requirements. These are just a starting point.

v. Raw figure files, such as powerpoint, illustrator, prism, .eps, .ai, .fig files need to be saved in a separate folder in the submission folder.

vi. Data points used need to be saved in an xls file with separate sheets for each subpanel (inclusive of N and n) and stored in the submission folder. 

vii. Consult with authorship guidelines for the target journal. All necessary forms and files should be in the submission folder. 

viii. Use Endnote for references, (free copy software.pitt.edu )

ix. Consult BIONICLab/How to write a paper/0_PresubmissionChecklist for all necessary files in the submission folder.

By signing below, the P.I./Staff/Student agrees to the above policies and guidelines to be upheld and maintained during employment at the B.I.O.N.I.C. Lab.