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.

1.1.4 Coursework load and 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.

1.1.5 Undergraduate researchers and self-funded students

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

Self-funded PhD students have no work obligation to the lab. 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. 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.

1.2 Working calendar

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

Non-working days

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, with the exception of time-sensitive experiments or animal care explicitly required by the appointment letter and offset by alternative breaks.

Workdays when classes are not in session

Days when the University is open but classes are not in session are workdays for GSRs and postdocs. These include the following.

• Spring Break, typically the first full week of March.

• Fall Reading Days and Self-Care Days.

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

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

• Finals week and grading days.

Trainees who wish to use these days for travel or personal purposes do so by scheduling them as recess days with at least two weeks of notice to the PI.

1.3 Recess days, leave, and after-hours work

Recess day allotment

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, structured as 5 summer + 2 fall + 3 spring workdays. Trainees on fractional appointments receive proportional recess days. Recess days are scheduled by the trainee with at least two weeks of notice when the University is in session.

Compensatory days for chronic data coverage

Trainees who cover chronic data collection or animal cohort coverage during the University winter closure 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

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).

Continuity during absences

Trainees with active chronic experiments or animal cohorts coordinate coverage during planned absences, through 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 to $300 Sunday as of 2026).

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. Documented productivity (manuscripts submitted ahead of timeline, fellowships secured, conferences won, technical contributions that benefit other lab projects) supports the case. The default is 10 days.

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. Off-hours schedules are communicated in weekly updates and Teams messages at the earliest opportunity.

1.4 Communication response times

During working hours (Monday through Friday, 9:00 AM to 5:00 PM), trainees acknowledge action-related messages within the following windows. A brief acknowledgment counts ("Got it, will respond by 3 PM today" with a calendar reminder set to follow through):

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

•        Teams messages: within 3 hours

•        Email: within 24 hours

•        Text from the PI (for emergencies only): within 30 minutes

•        Phone or Teams calls (for emergencies only): as soon as possible

Outside working hours, on weekends, holidays, vacation days, and recess days, no response is expected. DLAR emergencies are the exception. After-hours responsiveness is not expected of trainees.

1.5 In-person and remote work

Lab 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 to 4:30 PM, typical postdoc window 9 AM to 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 approval

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.

Daily plan and update on remote days

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). At the end of the day the trainee submits a daily update 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.

1.6 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, both verbally and in writing (email, Teams, note in the weekly plan). The absence is scheduled on the lab calendar and accompanied by a coverage plan for any active animal cohorts or chronic experiments. Document absences through weekly emails or Teams messages to keep a record.

International travel during the appointment requires advance notification. Some appointments (especially F-mechanism and visa-dependent appointments) have specific requirements about international time, and the lab needs to plan around the trainee's absence. Genuine emergencies (family medical crisis, immigration emergency, bereavement) are an exception and are accommodated, with the trainee notifying the PI as soon as feasible.

1.7 Lab meetings, 1-on-1s, and mandatory activities

Lab workshop, journal club, scheduled 1-on-1 meetings, and 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

1-on-1 meetings are coaching time covering research, 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. Standard scheduling falls Monday through Wednesday, leaving the rest of the week for execution. If the standard time conflicts in a given week, alternatives include Sunday morning or weekday evenings at 8:30 PM. If either party runs late within 12 hours of the meeting, the other is notified by Teams, with the meeting rescheduled on the calendar if needed and notification sent to lab admin.

1.8 Weekly planning and updates

 What a researcher actually did in a given week is hard to reconstruct after the fact. Experiments run for weeks before producing a readable result, code accumulates in branches nobody else opens, and the gap between starting a project and showing what it produced often runs many months. The weekly plan and update produces the trainee's own running record of research activity, used in real time and referenced years later.

 The record serves three functions. First, it documents what was planned and what actually happened, supporting annual reviews, fellowship and grant progress reports, dissertation milestones, and any case where the trainee needs to recount or defend their actual work. Second, comparison between planned and actual time builds awareness of how research effort behaves under uncertainty, a reflection skill. Third, the PI gains visibility into where the trainee is and what help they might need, without real-time check-ins or status meetings.

 Honest estimation of research effort under uncertainty is the portable skill being built, and the stakes attached to that skill rise at every career stage after graduation. Postdoc fellowships and K99/R00 transition awards depend on feasible 5-year plans that withstand reviewer scrutiny. Faculty positions extend that horizon, requiring research aims and tenure-track timelines defensible across multiple grant cycles. Industry roles operate on faster cycles, with sprint commits, OKR check-ins, and roadmaps reviewed monthly or quarterly by peers, executives, and investors. The trainee who learns calibration when a missed estimate costs a lab meeting carries the skill into stages where a missed estimate costs a fellowship, a faculty offer, or a promotion to leadership track.

 The plan-and-update format is one substrate for building this skill. Agile sprint planning, project management software (Jira, Asana, Linear), and quarterly OKR check-ins are industry equivalents.

1.8.1 Mechanics

• Weekly plan, due by Monday at 10:00 AM. Structure 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.

• Weekly update, due by Monday at 10:00 AM covering the prior week. List accomplishments with quantitative deliverables and the time each task actually took.

• 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.

1.8.2 Specific versus vague task framing

Specific tasks can be estimated, executed, and verified. Vague tasks resist all three, so the calibration loop cannot grip them. The table contrasts the two framings:

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)

1.8.3 Where weekly planning sits in the timeline

The weekly plan sits at the bottom of a four-level decomposition tree, with the following levels.

1. Dissertation, 4 to 6 years.

2. Aims, 3 to 4 aims at 12 to 18 months each.

3. Monthly milestones, 4 to 6 weeks each.

4. Weekly tasks, 5 working days.

Each weekly plan opens with two anchor lines naming the monthly milestone the week feeds into and the aim that milestone serves. Monthly milestones are set in the 1-on-1, with aim-level milestones set in the annual review.

Anchoring each week to a milestone and aim prevents the failure mode of busy weeks that do not add up to dissertation progress.

1.8.4 Time investment

Weekly planning takes about 30 minutes per week initially, dropping to 10 to 15 minutes after 6 months of practice as task decomposition becomes faster with repetition. Across a 4-year training arc the total investment lands between 80 and 100 hours, roughly 1% to 2.5% of total research time over the same period. The return is calibration accuracy that converges by year 2, a defensible week-by-week record of research effort, and a portable practice that transfers to every post-graduation role described above.

1.8.5 When plans are missed

If a weekly plan or update is missed, the PI follows up by email or Teams the same day to ask whether something is in the way. Repeated misses (three or more in a four-week period) open a 1-on-1 conversation about what is interfering, using the calibration-capability-fit framework described in the Performance Management Process document. Catching the pattern at three-in-four-weeks keeps the conversation about a current obstacle rather than months of accumulated drift.

1.9 Training-to-productive-research transitions

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). Each training block is bounded, not open-ended, and paired with three elements set at the start.

·       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 reviews progress against transition milestones agreed at the previous review.

1.10 First-year integration and middle-authorship trajectory

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.

Lab integration tasks

First-semester lab time 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. 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.

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. First-year students are matched to active projects based on technical fit and project timeline, with the assignment revisited in the annual review.

1.11 Conferences, abstracts, posters, and travel reimbursement

Conference presentations 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.

1.11.1 Submission rules

Internal conferences (Pitt, CMU) allow the same poster at multiple events in a year. External conferences do not allow the same poster at the same conference in subsequent years, or at different external conferences within 12 months. Posters from internal events can be expanded or modified for external presentation, with the standard being whether the scientific content is materially the same.

1.11.2 Approval timelines

Conference deliverables (abstracts, posters, oral presentation slides) require PI approval and co-author circulation on a fixed timeline. Deadlines below refer to approval, not first submission to the PI. Circulate drafts to the PI well before the approval deadline 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 punitive, it reflects that an unreviewed abstract or presentation represents the lab and its co-authors without their consent. If the deadline is unworkable for a specific case (late-breaking abstract opportunity), discuss with the PI as soon as the opportunity arises rather than after the standard window has passed.

1.11.3 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 presentation, but the abstract must include quantified metrics (mean ± SEM with sample size, or other appropriate quantitative summary) at the time of submission.

1.11.4 Reimbursement

Reimbursement follows GSA per diem rates and Pitt BioE departmental policy. Per diem covers meals and lodging up to the daily limit, with reduced rates on first and last travel days. Trainees may share hotel rooms to stay within the lodging cap. Confirm specifics with the BioE business office before booking.

• Receipts for food are required for graduate students. Faculty and staff may take per diem. Postdocs confirm category with BioE business office.

• Items not reimbursed include first-class or economy-plus upgrades, travel insurance, society memberships, and alcohol.

• Book flights at reasonable economy rates with ~21 days advance booking. Trainees without P-Cards book through Concur using Anthony Travel.

• State tax exemption forms (Pitt Purchase, Pay & Travel) remove sales tax on lodging. File before arrival.

• Reimbursement requires presenting a poster or talk, and attendance without presenting is funded by the trainee's own award.

• Submit reimbursement requests within 90 days, otherwise processed as taxable income.

• Lab grant funds typically support one conference per year per trainee. Apply for BioE travel grants, EGSO, CNBC, or society awards to supplement.

1.11.5 Poster printing

BioE offers a free print service for 42 in × 42 in posters. Submit the final poster file to the BioE print service or to FedEx (or equivalent commercial printer) at least 24 hours before departure. Request a printing proof before final printing to confirm accuracy. If the trainee misses the printing window and prints on-site at the conference, the cost is not reimbursed.

1.11.6 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.

1.12 Research integrity standards

Research integrity is the load-bearing standard for everything the lab does. 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 journal-specific reporting standards for the venues the lab publishes in. Diagnostic procedures for integrity concerns are covered in the Performance Management Process document.

• 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, 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 are documented as exploratory, not reported as primary findings.

• Negative results. Experiments producing negative or inconclusive results are reported in lab updates and considered for publication when informative.

• Image and figure integrity. Image processing follows the agreed pipeline (uniform contrast adjustments, no selective brightness changes, no removal of artifacts that change interpretation). Representative images are labeled as such and chosen by criteria documented at the time.

• Authorship per ICMJE criteria. Authorship reflects substantial contribution to conception or design, data acquisition or analysis, manuscript drafting or critical revision, and final approval.

• Honest representation. Fellowship applications, grant proposals, and peer reviews represent the science honestly, including contradictory literature, methodological limitations, and prior negative results.

Trainees who become aware of possible research integrity issues 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.

1.13 Regulatory framework and degree milestones

This section points to the binding University and program-level requirements that govern the trainee's appointment and degree progress, with focus on milestones that require lab-side coordination.

• Continuous registration. GSRs maintain at least 9 credits per term during fall and spring, or Full-Time Dissertation Study 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.

• Conditional appointment. Appointments are conditioned on satisfactory progress (GPA above 3.0, at least 6 credits per term, passing preliminary and comprehensive examinations).

• PhD statute of limitations. 10 years from initial registration (8 years with master's credit). Extensions require dean approval.

• Annual doctoral committee meetings. After admission to candidacy, the doctoral committee meets with the candidate at least once per year. The trainee organizes the meeting and circulates a progress summary in advance.

• International student visa constraints. J-1 and F-1 visa students confirm appointment opportunities with the Office of International Services (OIS) before accepting, since some research activities are constrained.

• First-semester training. Title IX training in the first semester. Onboarding (EH&S, OSHA, IACUC and DLAR, RCR) within the first month of the appointment.

• Editorial assistance disclosure. Trainees using professional editorial assistance for dissertations disclose this assistance and confirm the editorial scope is limited to language rather than content.

• Intellectual property. IP arising from lab work is governed by University Policy RI-10 and grant terms.

1.14 NIH and NSF grant compliance

Trainees and staff supported by federal grants have specific compliance obligations beyond the University-level requirements in Section 1.13.

• RCR training. NIH requires Responsible Conduct of Research training for trainees on T32, F, and K mechanisms (face-to-face component, minimum 8 contact hours per cycle, repeated approximately every 4 years). NSF requires comparable RECR training for all funded trainees. The lab uses CITI modules plus in-person sessions, counted within the appointment.

• Public access. NIH-funded manuscripts are deposited in PubMed Central (PMCID via NIHMS) and NSF-funded manuscripts in NSF-PAR, each within 12 months of publication.

• Data Management and Sharing (DMS). Every NIH-funded project has a DMS Plan and every NSF project a DMP, provided at project start. Trainees follow the schedule for shared deposition (DANDI for electrophysiology, FigShare for tabular data, GitHub for analysis code).

• Effort and Other Support reporting. Pitt SPA manages effort certification, and trainees confirm allocations annually. Trainees notify the PI of any new fellowship application or award so Other Support records stay current.

• Rigor and reproducibility. NIH and NSF require rigor in design, biological variables (sex as a biological variable), authentication of key resources, and statistical justification. Section 1.12 standards apply these requirements at the project level.

• Safe and inclusive research environments. NSF requires a SIRE plan for off-campus or off-site research. Field, animal, and shared core facility work follows Pitt EH&S, IACUC, and Title IX policies regardless of funder.

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.