You've recently joined the Ishihara lab in the University of Pittsburgh’s Department of Computational and Systems Biology. We're excited to have you as part of the team! We hope that you'll learn a lot about stem cells, tissue engineering, biological physics, microscopy, and computational biology, develop new skills (wet lab, data analysis, writing, presenting), make new colleagues and friends, and enjoy the whole process.
This handbook was inspired by many others including Aly, Lowe-Power labs. It is meant to be continuously updated with input from lab members and others. If you have ideas on contents to add, items to clarify, please talk to me (Keisuke, PI).
This lab handbook is licensed under CC BY-NC 4.0 Deed. If you’re a PI or a trainee in a different lab and want to write your own lab handbook, feel free to take inspiration from this one (and cite us!).
The Ishihara lab envisions to engineer multicellular tissues as living, programmable materials. Engineered tissues with physiological and synthetic functions will act as new platforms that advance human health.
Our group takes a synthetic approach to multicellular tissue biology. “Synthetic” embodies the experimental creation of states of physical organization and gene expression that push a multicellular system to all possible extremes. The synthetic approach allows us to discover novel regulatory molecules, dormant genetic programs, and general physical principles, which we will critically evaluate as next generation strategies for organ engineering. We will quantitatively capture tissue morphogenesis through imaging, computation, and molecular profiling. Using this knowledge, we will develop genetic, chemical, and physical tools to engineer form and function of in vitro tissues such as human brain and cardiac organoids.
Our core values are curiosity, teamwork, respect, and innovation. We are committed to creating a diverse team that is inclusive to all cultural and racial backgrounds.
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Get building access to BST3 and Murdoch by filling out the CSB Access Request Form. Wait 2-3 days for access. If the form or your card does not work, please contact Jennifer Watt.
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Join departmental mailing list via CSB Email List Subscription Form.
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Join Slack groups (Ask Keisuke or others for invite.)
- IshiharaLab
- Compbiopitt
- Pittsburgh Assembloids (website)
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Join Ishihara lab mailing list (ask Keisuke).
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Add Ishihara lab shared folder to OneDrive. (Site > Documents > Add shortcut to your OneDrive > ReadMe)
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Complete LabMembersInfo including the schedule tab.
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Install printers in BST3 (instructions).
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Join Pitt-IshiharaLab Github group. (Ask Keisuke for CDS membership).
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Add your name to this repository's LabMembers.md following the Ishihara Lab Git Tutorial.
Open communication is the key for every aspect of lab activities!
We thrive on transparently sharing ideas, findings, and concerns among lab members, fostering an environment where everyone feels comfortable expressing their thoughts and collaborating effectively to achieve common research goals.
Our main mode of digital communication is Slack and email. Slack is good for speed, while email is preferred for longer text and archiving purposes. Only members can post to the group's mailing list.
Our Lab Manager is the go-to person if you have any questions about day-to-day wet lab operations and experiments. The Lab Manager places orders for purchasing, ensures that the lab runs smoothly, train new members, and distributes lab duties.
Please read Lab Manager Responsbilities. The guidelines for "Lab Duties" and "Ordering and Purchasing" are found on the shared OneDrive.
To access the lab's workstation, please follow Fuji Workstation Usage Guidelines.
We expect you to spend a minimum of 50% of your non-class time physically in the lab. We need spontaneous, in-person communication.
We will not impose core time. If you'd like to designate a certain day of the week for home office, please share this in the schedule tab in LabMembersInfo. Update your class schedule every semester.
Mark your vacation/absence days on the lab calendar. If you plan to be be away for more than a week, let Keisuke know by email.
- 1-1 meeting summaries (All members): After each 1-1 meeting with Keisuke, please email a brief summary of the discussion and any action items by the end of the next business day. This helps Keisuke and the lab member to follow up on any items and prepare for the next meeting.
- Documentation and record keeping (All members): You are required to document all your research activities. Good documentation will allow others and your future self to follow your work. If you do not have a strong preference, Keisuke recommends Lab Archives Electronic Lab Notebook (Ishihara Lab Common for wet lab work and Ishihara Lab Github for code. Please ask Keisuke for access and an introduction. If you prefer physical lab notebooks, you must periodically scan and upload your entries to Lab Archives or the group's OneDrive folder.
- CSB seminar attendance (PhD students 2nd year and above): You are expected to attend all CSB departmental seminars as part of your training. If you do not attend regularly, the lab will not fund your attendance to external conferences.
We understand that unexpected emergencies arise and you cannot work as you had planned. In such cases, please let Keisuke know (no need to share the details, if you feel uncomfortable). If necessary, reach out for help to your fellow lab members to cover during your absence, but take into account that each person has their own work and family duties.
- Experimental samples
- Check what you have in the 4C, -20C, -80C, and also room temperature. Organize and prune as necessary. If unsure to discard a sample, keep but label it clearly.
- For -20C and -80C, you must create a list of items and add this file to your folder in the Ishihara lab NAS.
- Digital Data
- All digital data must be copied to your folder in the Ishihara lab NAS. This includes the files in the Ishihara lab shared OneDrive.
- (Interim policy) All microscopy data must be copied to the FujiData drive of the Fuji workstation.
- Lab Notebooks
- LabArchives ELN: List Keisuke as Administrator for your notebook(s). Give access to your personal email for continued access after your Pitt account expires.
- Other digital notebooks: Export all entries as Word or PDF documents to your folder in the Ishihara lab NAS.
- Physical notebooks: Physical notebooks stay in the lab. Make a personal copy by scanning relevant pages.
- Move your name to the almuni section in LabMembers.md. Include the period that you were part of the group. This will be your last pull request to this repository!
- Check all of the above with Keisuke.
- Undergraduate fellowships offered by David C. Frederick Honors College
- Summer Undergraduate Research Awards offered by Office of Undergraduate Research
- Departmental computing cluster, HPC
- Travel awards available to School of Medicine graduate students