Lab Contract

The purpose of this contract is to establish policies and guidelines between P.I., Staff, and Students within the B.I.O.N.I.C. Lab (01/2024 to 5/2024) as follows:


1. LAB RULES AND EXPECTATIONS (Grad Student/Postdoc)

a. A Graduate Student Researcher (GSR) is a researcher, distinct from a student, compensated for 20hr/wk dedicated to labor encompassing data collection, surgery, and data analysis. In return, the GSR receives a stipend, financial support for benefits, and tuition coverage for 20hr/wk of learning. Learning involves classes during the semester, and in periods without classes, self-directed learning through literature review, seminar attendance, and workshop participation. Non-FTDH students commit 20 hr/wk to lab activities, guided by the Lab P.I. and funding grants. FTDH/postdoc/full-time staff (excluding summer non-FTDH) are obligated to contribute 37.5 hr/wk (with a 0.5 hr break) to lab work, as stipulated by the Lab P.I. and mandated by funded grants. GSR recess schedules align with "Faculty, Staff, & Designated Offices" rather than the student schedule.

 

b. During periods of vacation or absence from the lab while the University is operational (excluding holidays or recess), it is mandatory for Students, Staff, and Researchers to promptly inform the Lab P.I., ideally at least two weeks before the planned leave date. Students are further obligated to organize and train individuals to sustain 'chronic data collecting' or 'colony management' in their absence. Students are generally expected to take a "recharge" of 10 workdays in the summer, 5 in the fall, and 5 in the spring, alongside appropriate sick days. Additionally, there are extra winter days (+10) allocated for those engaged in chronic data collection. Researchers receiving paid stipends/salaries are aligned with the University schedule rather than the class schedule. Notably, if data collection is necessary when the University is closed, the data collection must proceed (your responsibility).

 

c. Students are instructed to prioritize physical and mental health as their foremost concern within the Lab, encompassing but not confined to adequate sleep (8 hr), nutrition (particularly B-12, recommended at 500 pg/ml), and regular cardiovascular exercise, adhering to AHA guidelines (150 min/wk moderate-intensity or 75 min/wk vigorous aerobic activity). Work hours (9 am-5 pm) may be utilized to foster physical and mental well-being, provided that weekly commitments, including deadlines and meetings, are fulfilled. It is acknowledged that such prioritization may result in missing spontaneous opportunities within the lab. Importantly, this time dedicated to health is distinct and not included in the 20 hr/wk or 40 hr/wk of sponsor-funded work.


d. First semester of first year students. New students are anticipated to allocate approximately half of their lab time, around 10 hr/wk, outside the lab, focusing on building a social network with peers, including classmates from the same year. Establishing connections and cultivating a social and mental health support system is deemed vital for professional development, especially for those transitioning away from their "home" environment. The ability to share challenges and accomplishments with peers outside the lab is considered integral. The remaining half of their lab time, another 10 hr/wk, should be dedicated to shadowing procedures and assisting in data analysis on existing projects, aiming to secure a middle-authorship paper before the commencement of their second year


e. Within the Department of Bioengineering, students are obligated to sustain a minimum "B" average in all courses for their performance to be deemed satisfactory within the program. 


f. Students are expected to know and follow EH&S, OSHA, IACUC (DLAR) guidelines and have read relevant animal protocols.


g. English is the designated language of science. Consequently, it is an expectation that all verbal communication within the lab or any research-related environment where one represents the lab (such as seminars, conferences, etc.) is conducted in English.

 

h. Students delivering a poster or talk at internal or external conferences are required to adhere to submission deadlines specified by the Lab P.I. (Refer to Section 8). The same abstract is not permitted for presentation at different external conferences, although it may be allowed for internal conferences. Abstracts must be approved by the PI a minimum of 10 days in advance and distributed to all co-authors 7 days prior. Poster/Slides need to be approved by the PI 7 days in advance and circulated to co-authors 5 days in advance. Failure to comply may lead to withdrawal from the conference.


i. Staff members are obligated to work in person 8 hours per weekday, inclusive of a 0.5-hour lunch break. Any requests for early dismissal require confirmation from the PI and permission from the Department Chair. Timecards must be promptly submitted either on Friday afternoon or by Monday at 9 am. In the case of salary staff, timecards need to be submitted for sick or vacation time.


j. In the case of remote work (eg. quarantine), trainees and staff should submit accomplishments and quantitative progress update every 1-2 hrs with documented evidence of progress. 


K. If you are not in person, you are expected to respond to emails and Teams chat promptly (acknowledge receipt of message within 15 min) during normal working hours (otherwise, this will be recognized sick time). 


2. FILE STORAGE


i. Google Drive: Ordering, animal inventory, antibody inventory


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 PULSE 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  



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 biweekly basis in “Workshop Facilitators” document on the Google Drive. Facilitator from week before is responsible for ensuring current facilitator completed the back ups. Facilitator responsibilities will be marked off in a section on the white board specifying 1. inventory check, 2. physical/server backup (2p,MVX,ephys). The facilitator is responsible for checking off that they completed the back up, changing their name to “Previous”, and add the next facilitator responsible for a back up on “up next”.



iii. Two photon:

E-phys: backup to external drive and analyzer computer



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.


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 2P - Two-photon microscope

BIONIC 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 Fumehood

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 potlucks after workshop (Workshop facilitator will discuss at workshop theme, who will bring what) (1/26, 2/16 (TBD), 3/29, 4/26, 5/31).


g. In Person: Trainees should make a best effort (Sick, experiments, seminars, classes)  to be present in the Lab on MWF 9:00am-5:00pm plus either Tuesday 9-5 or Thursday 9-5, to facilitate spontaneous group discussions, peer mentoring, and problem solving sessions. Staff are expected to be in person 5 days a week. We will have informal lab lunches/group work on Wednesday. 

lunch


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. Trello will be used to keep track of individual and group to-do lists. (https://trello.com/invite/bioniclab1/4914ae14baa74ed54372e70aea294241 invite link) 


j. Whiteboard/Corkboard: Keep the large whiteboard open for drawings and planning, save the task corner. Use the corkboards by cubicles to communicate to-dos. Labeled index cards will be used to track daily tasks for each person (histology, surgery, imaging, etc.). Updated times should be completed before journal club ends on Monday 2pm.


k. Small Group Meetings. Small groups will be composed of 3-4 randomly selected trainees. Groups will meet weekly in person for at least 1 hour to discuss proposed experiments, provide feedback on outlines and manuscripts, and engage in collaborative communication. These meetings are expected to take place sometime during MWF 9-5. Groups will be changed each month and assigned by the Workshop Facilitator at the beginning of the semester. 

Jan: Group 1 - Teresa, Chris, Khari, (Xiangting?); Group 2 - Fan, Kevin, Collin, Jazlyn; Group 3 - Camila, Adam, Naofumi, Vanshika

Feb: Group 1 - Khari, Kevin, Chris, Fan; Group 2 - Teresa, Collin, Adam, Naofumi; Group 3 - Camila, Jazlyn, Vanshika, (Xiangting?)

Mar: Group 1 - Teresa, Camila, Chris, Naofumi; Group 2 - Collin, Vanshika, Kevin, Fan; Group 3 - Jazlyn, Adam, Khari, (Xiangting?)

Apr: Group 1 - Fan, Kevin, Camila; Group 2 - Khari, Chris, Adam, Collin; Group 3 - Teresa, Jazlyn, Vanshika, (Xiangting?)

May: Group 1 - Collin, Camila, Kevin, Khari; Group 2 - Teresa, Adam, Fan, (Xiangting?); Group 3 - Jazlyn, Vanshika, Chris


4. LAB    WORKSHOP

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 order Kevin, Fan, Jazlyn, Chris, Naofumi, Adam, Camila, Teresa, Collin,  repeat. Schedule 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. 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.

 

d. Time at the beginning of Journal Club will be allotted for a brief (2 min each via oral or 1-2 PWT 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) main topic 4) planned work for the week

 

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. Trello will be used as an optional task tracker for individual/ group projects.


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:




5. 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 routinely 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. Report completion on Teams.


d. Each Student is responsible for making and updating protocols of important lab equipment operations, and the latest physical copy of protocols should be physically available somewhere near the designated lab equipment. (Currently on OneDrive; work on transition to GitWiki)


e. Make use of the 3D printer whenever possible.


f. 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

iv. When in doubt, ask for help.


6. Pandemic Shutdown: Remote work (no longer relevant)

a.   In the event of a quarantine, some of the listed commitments may not be feasible. The following adjustments will be made in order to maintain productivity and ensure everyone is accountable. 


b.  Students are expected to be present on zoom during regular lab meeting times for both journal club and workshop. 


c.  Students are expected to send an email outlining weekly goals and prior week updates to the PI by Monday at noon. These goals and tasks should be broken down into 0.5, 1, 2, 4, 6, 8 hour increments to help students organize their tasks. Including blocking off time for classes. (8 hr increment should only be for experiments, break other tasks into smaller manageable pieces). 


d. Students are expected to send an update by Monday noon detailing the progress made on the tasks outlined by the student on Monday and estimated hours (including classes/learning) and research (labor). These can be sent by email. The student should list crossed out tasks as well as tasks carried over to the next week or that are still in progress. It is expected that the total hours spent on class and research average 20hr/wk each, or 40hr/wk for FTD students.


e. Students are expected to be present in the lab or on zoom for a 1 hour meeting with the PI. Times are scheduled but in the case of time conflict, a 24 h notice should be made to info both parties.      


f.  Class schedules will be assumed to remain in place and students will be assumed to be unavailable during these times.


g. Available by email during work hours keeping in mind that students may still use daytime to promote positive mental health through exercise, meditation, siesta, etc. https://www.hr.pitt.edu/current-employees/work-life-balance/mental-health-wellness


h. Temporary increase in frequency of use for following communication tools:

Zoom: Use for meetings as well as discussing project questions and progress. 

Also, a time may be set up for non work related “social” interaction.

Teams: General messages between members of the lab and not urgent messages. Make sure to check slack at least once a day.

Email:messages 8-6 will be read timely. after 6pm, it will be read in the morning.

Text Message: urgent tasks/messages. Messages sent between 8am and 6 pm are assumed to get a timely response, but messages sent outside this time may not get a response until the next day.

In Person: Everyone should make a best effort to be present in the Lab to facilitate spontaneous group discussions and problem solving sessions (between the hours of X and Y).


i. When using the analyzer or other key equipment, students are expected to be diligent about signing up for time on the Google calendar. Out of respect for other students, anyone who signs up for time is expected to stick to that time and notify others  (eg via email) that are signed up if any change occurs.

I. Reference section 3d for the specific calendars.


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 Google Drive for each project.


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


8. Conferences


For Internal (Pitt/CMU) conferences, you can present a poster at multiple conferences per year.

For an external conference, you cannot present the same poster at the same conference in subsequent years.

For external conferences, you cannot present the same poster at different conferences within a 12 mo period.


Abstract (external team members): Need to be approved by the PI 10 days in advance. 

Note: this is APPROVED BY, not submitted to the PI for the first time. 

Abstracts need to be sent to all co-authors 7 days in advance.


Abstract (internal team members): Need to be approved by the PI 5 days in advance, and sent to co-authors 3 days in advance.


Reimbursement: You can get reimbursed for the gov per diem rate for hotels and meals (but not alcohol) up to the daily limit. 

https://www.gsa.gov/travel/plan-book/per-diem-rates/per-diem-rates-lookup 

This may mean that you have to split a room in order to meet the daily lodging limit. Receipts need to be turned in for all food items.


Reimbursement Travel: The dept will not reimburse upgrades (first class, economy plus) or warranty/travel protection. Flights need to be reasonable with respect to the going economical price 21 days prior to travel, or you risk not being reimbursed for the full amount. To be reimbursed for conferences, you need to “represent” the lab by presenting a poster or talk. Attending a conference without presenting will require you to pay for the conference, travel, lodging, registration, etc from your own fellowship, award, or stipend.


Societal Membership: is considered career development and cannot be reimbursed.


Registration and abstract submission fee will be reimbursed.


Apply to get travel funds to conferences from BioE department (https://www.engineering.pitt.edu/Departments/Bioengineering/_Content/Resources/Graduate-Travel-Grant/), EGSO, or CNBC. It is always encouraged to apply for travel funds for travel, but otherwise travel to one conference of relevance to the specific project is funded by the grant.


Final Poster needs to be approved by the PI 7 days in advance and circulated to co-authors 5 days in advance. The cost of poster printing will not be reimbursed, but BioE offers a free print service for 42in x 42in posters. Oral presentations must receive approval seven days in advance, and slides must be sent to co-authors five days in advance. Failure to obtain timely approval will result in the withdrawal of the poster or oral presentation. Note that these deadlines pertain to approval, not the initial review deadlines. If presentations need to be withdrawn due to missed deadlines or are otherwise unable to be presented at the conference, no reimbursements will be provided.


Note: the poster needs to be submitted 24 hours in advance, and you need to go to the FedEX on Forbes twice (once to approve the proof, and once to pick up the poster). If you miss the window, you will have to print at the conference out of pocket. Note that most places also charge a premium for printing at the conference.


All abstracts require preliminary data and analysis, you cannot submit an abstract on work you “will do” between the abstract submission date and the conference. You can ADD more data and analysis between the abstract submission and conference. However, you need to have some quantified metrics ##+/-## reported within the abstract.


If presentations need to be withdrawn (because deadlines were not met) or are otherwise unable to present at the conference, nothing can be Reimbursed.


Following the conference, present to the rest of the lab presentations and posters of interest.


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.