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 (09/2022 to 12/2022) as follows:
1. LAB RULES AND EXPECTATIONS (Grad Student/Postdoc)
a. A GSR is a Researcher who is paid for 20hr/wk of labor (data collection, surgery, data analysis) in exchange for 1) a stipend AND 2) receives financial support for Benefits AND 3) receives tuition for 20hr/wk of learning (Workshop and Journal club are group learning, literature search is individual learning). During the semester, learning generally takes the form of classes. During periods without class, GSRs are expected to learn on their own via reading literature, attending seminars, participating in workshops, etc. Each non-FTDH Student is required to put in 20 hr/wk of lab time or as outlined by the Lab P.I. and funding grants. Students who are FTDH (and non-FTDH during the summer) are required to put in 37.5 hr/wk (excludes break; eg. lunch) of lab time or as outlined by the Lab P.I. and mandated by funded grants.
Each credit of class is expected to occupy 3 hours (1hr in class, 2 hrs out of class). Therefore, students are expected to take 6-7 credits of class per semester to maintain a balanced class:lab balance
Any additional time put in beyond the sponsor funding institution expectations of 20 hr/wk (37.5 hr/wk FTDH, Postdocs, or class is not in session) (NIH/NSF/DARPA/etc), is bonus time invested in yourself, it is not for me or the funding agency. Non-FTDH graduate students are also expected to spend 20 hr/wk on coursework and learning.
Weekly plans (a list of tasks and estimated amount of time in increments of 0.25-8 hrs/day) should be emailed to the PI between Friday 4pm and Monday noon. (8 hr increment should only be for experiments, break other tasks into smaller manageable pieces).
A list of weekly accomplishments with revised amounts of time tasks consumed should be emailed to the PI between Monday by noon. This should include classes/classwork/literature-search/seminars (avg 20hr/wk), and research/labor (avg 20hr/wk), but not social activities.
These two reports can be combined.
For Undergraduates, on average 10 hr/wk should be planned to make significant contribution to a project (at a co-author level). Acknowledge that this might shift week to week based on course schedule and exams. This goes up to 20 hrs/wk during the semester or 40 hrs/wk during the summer if the position is funded (ie. by a SSOE or A&S fellowship).
See Section 6
All Students are expected to be present for the lab workshop, journal club, 1-on-1 meeting times, and any other scheduled lab events. Any anticipated absences or emergencies need to be communicated with the Lab P.I. This time is included in the 20 hrs/wk of learning (37.5 hr/wk FTDH, postdoc)
1-on-1 meetings are coaching time for research, career, learning, work-life balance, retirement, etc. Come prepared with questions.
b. In the event of vacation or absence from the lab while the University is open (i.e. not University holiday or recess), Students are required to notify the Lab P.I. as soon as possible or at least two weeks in advance of the anticipated leave date. Students are expected to arrange/train individuals to continue ‘chronic data collecting’/’colony management’ during their absence. In general, students are expected to “recharge” 10 summer, 5 fall, and 5 spring workdays, as well as appropriate amounts of sick days. (+10 winter for anyone who stays to collect chronic data) Researchers with paid stipends/salaries should follow the University schedule (rather than the class schedule). Note: If you need to collect data when the University is closed, the data still needs to be collected.
c. Students are expected to prioritize physical/mental health above all other priorities within the Lab. This generally includes, but is not limited to, adequate sleep (8 hr), nutrition (especially B-12: recommend 500 pg/ml), and regular cardiovascular exercise (AHA guidelines 150 min/wk moderate-intensity or 75 min/wk vigorous aerobic activity). Work hours (9am-5pm) may be used to promote physical/mental health as long as weekly commitments are met (deadlines/meetings), with the understanding that this may result in the student missing out on spontaneous opportunities that may come about in the lab. This time is not included in the 20hr/wk or 40hr/wk of sponsor funded work.
d. First semester of first year students. New students are expected to invest approximately half of their lab time (~10 hr/wk) outside of the lab building a social network among peers (eg. classmates of the same year). Networking and building a social and mental health safety net is an important part of a professional career, especially for many of you who may be leaving “home” for the first time. It is important to be able to share struggles and achievements with your peers outside of the lab.
e. Students within the Department of Bioengineering are required to maintain at least a “B” average in all courses in order to be considered passing 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 language of science. Therefore it is expected that while you're in the lab or a research environment representing the lab (seminars, conferences, etc). It is expected that all verbal communication be done in English.
h. Students presenting a poster/talk at internal/external conferences are expected to abide by submission deadlines set by the Lab P.I. (See Section 8) The same abstract cannot be presented at a different external conference, but the same abstract could be allowed to be presented at an internal conference. Abstracts need to be approved by the PI 10 days in advance and sent to all co-authors 7 days in advance. Failure to do so may result in withdrawal from the conference.
2. FILE STORAGE
There are 5 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) Box, 3) Dropbox, and 4) the Lab’s server. 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
ii. One Drive: Files pertaining to individual research projects (shared with people working on the project)
iii. Dropbox: (Files uploaded here are open to ALL individuals with access to the BIONICLabPaper folder): Grant information, manuscript drafts, project outlines (and drafts)
To be migrated to One Drive (fall 2022)
iv. Lab server (SSOE-BIOE online storage drive; requires PULSE to login from non-lab computers): All raw data, individual data backup
See slack channel ‘server’ for detailed instructions on the two servers
V. Github: programming stuff
Guidelines for backing up the raw/analyzed data from temporary storage to backup hubs are detailed in the list below. Upon completion of a backup, a label with the date of when the backup occurred should be placed on the hub for reference. When data is added to one of the sources , a note will be made on the white board to specify that the source needs
i. Biweekly backups of raw data are made from sources (2-p computer, Ephys computer, MVX, 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.
ii. Monthly backups of raw data will be made from sources (2-p computer, Ephys computer, MVX, Confocal) in which data was added during the time period to the respective folder on two external physical drives specific to each source. Note: raw data is any unprocessed data and not solely from the ‘RAW” drives on the 2p. Assignments are scheduled on the Google calendar.
iv. Two photon:
Backups of the ‘Temp’ drive will occur every 2 months
RAW drives will not be backed up
Following backup the ‘Temp’ drive will be wiped
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 (firstname.lastname@example.org) and via Microgsoft Teams (ask to be added) with a backup individual messages on Slack (bioniclab.slack.com via mobile app) 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.
Orders over $5000 require a requisition and department approval through Alexis Delgrosso
Orders over $10000 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)
If the order requires someone to come to campus for training or installation needs to fill out a Provider Covenant to Comply with COVID Protocol form that needs to be sent out.
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).
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 advised 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 or, in the case of emergency or sudden change in schedule, as soon as possible followed by notification of the Lab via e-mail correspondence.
BIONIC 2P - Two-photon microscope
BIONIC 2P/MVX - Surgery table in 2P room in front of MVX
BIONIC Analyzer - Processing of data sets
BIONIC Autolab - Impedance recording, IROx activation
BIONIC Confocal - Confocal microscope (4th floor)
BIONIC Cryostat - Cryostat (room 243)
BIONIC Stimulator - TDT stimulator for ICMS
BIONIC Surgery Room - Surgery room connecting 2P room and Utility room
BIONIC Utility Room - Ephys recording
email@example.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. Slack) will be established to facilitate separate Lab functions (general lab business, ordering, workshop, journal club papers, accomplishments, miscellaneous, etc.) amongst lab members.
f. In Person Only: Each Student is responsible for updating the Lab whiteboard with tasks they expect to perform/focus on for the current week. Once a task is completed the Student will cross out that task and/or notify the other lab members. The whiteboard will be wiped every Friday at the end of the day (as defined by the person in charge of board wipe/archiving). Each individual will then be responsible for updating their tasks for the upcoming week by the end of Monday. Before the white board is wiped clean, a photo of the board will be uploaded to Slack in the whiteboard channel. Each month a person will be assigned the task of wiping the board weekly and uploading an image of the board onto Slack.
i. If 2(+) lab members are performing similar tasks, consider the option of working together to improve efficiency and productivity.
ii. If students are working together on a specific day, make notes on the Lab calendar/whiteboard, so that other Students are aware and can join in if they wish to do so.
iii. It is advised that Students keep a digital or written record of these accomplishments and the time to completion. This can help other students make accurate estimates for time commitments on certain projects/analyses.
g. Supplementing communication during remote work.
i. Separately, Teams channels can be created to reach out to other students to help with communication. If you would like to discuss a topic with another student or students reach out on slack channel ‘social’ or other private messages or make a new channel.
ii. Regular Social: first week of the month (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. Longer activities such as hiking at a park >20 min away would be better to plan in advance. 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). Determine in the workshop the week before (facilitator in charge).
iii. CNBioMIRM Social: once a month (summer 2022), plan with other labs
iv. In Person: Everyone should make a best effort to be present in the Lab on Monday and Friday to facilitate spontaneous group discussions and problem solving sessions. We will have lab lunches/group work after the workshop on Monday.
allocate 30 minutes after finishing discussing Journal club paper to be social and lunch
If journal club paper takes up entire 2 hours, then journal club can be extended for social component
Will make list of topics as backup to kick-start conversations
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 which can also be viewed in-person on the whiteboard in the office space. (https://trello.com/invite/bioniclab1/4914ae14baa74ed54372e70aea294241 invite link)
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 Steven, Jazlyn, Chris, Keying, Olivia, Naofumi, Kevin, Fan 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 firstname.lastname@example.org) 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 Workshop will be allotted for a brief (2 min each via oral or 1-2 PWT slides via OneDrive 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.
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. Add summary and to-dos to the notion or trello workspace.
f. In cases of extreme bad weather, workshops will be conducted on zoom via the link on google calendar. (Snow days or 2 hour delays) Alert via the slack channel.
g. Workshop Faciliator is also in charge of physical or server 2P backup and it is to be done by the end of the week (schedule can be seen in workshop facilitator excel spreadsheet).
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.
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 weeks facilitator will be responsible for this.
ii. A routine purge of solid-state (raw) drives will occur every 2 months, at which point an e-mail announcing a data purge will be sent via the Lab listserv warning Lab members to consolidate their stored data. Data will be cleared following confirmation from all members of the Lab.
iii. The temporary 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. Each equipment or space will be assigned to a Student who will be responsible for routine maintenance if/when necessary.
i. The task of maintaining certain lab equipment will rotate between Students and will be assigned routinely (beginning of each semester). These tasks include but not limited to 1) item inventory and ordering items which are low in quantity, 2) cleaning recording cages, imaging space, cryostat, 3) calibrating two-photon laser, 4) cleaning two-photon filter (front and back) and filling coolant, etc.
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)
f. Make use of the 3D printer whenever possible.
6. Remote work/quarantine
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 (Fridays, 2:00pm-4:00pm) and workshop (Mondays, 10:00am-12:00pm).
c. Students are expected to send an email lining out 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 (<10 MB), on dropbox (<100MB), or Box (>100 MB). 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 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.
Slack: 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 on Monday and Friday to facilitate spontaneous group discussions and problem solving sessions. We will have lab lunches/group work after the workshop on Tuesdays.
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
Abstract (external): 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): 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.
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.
Societal Membership: is considered career development and cannot be
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/) or EGSO.
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
Poster needs to be approved by the PI 7 days in advance and circulated
to co-authors 5 days in advance. Poster print cost will not be
reimbursed, but BioE has a free print service for 42in x 42in posters.
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.
Oral Presentations need to be approved 7 days in advance, and slides
need to be sent to co-authors 5 days in advance.
For Internal 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.
If presentations need to be withdrawn (because deadlines were not met)
or are otherwise unable to present at the conference, nothing can be
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.