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Lab Manual

Mission

Our lab's mission is to solve problems of biomedical relevance while training world-class scientists at the interface of experimental and computational biology. Our core research focus is on mechanisms of mRNA translation, but we also study immunity and cancer through collaborations.

Roles & Expectations

Everyone

  • is motivated to learn new ideas and techniques. Projects in our lab are rarely repetitive. You should be willing to get outside your comfort zone on a regular basis and embrace a steep learning curve. It is normal to struggle and be frustrated when you are learning something new, so you should not feel discouraged. Most ideas and experiments are not correct the first time, and need to be iteratively refined. Your project's success depends on how well you are able to learn from failures.

  • develops the ability to formulate and solve problems on their own. Irrespective of your career stage and career goals, we aim to train independently thinking scientific leaders, and not merely skilled research technicians. In practice, this means you should spend your first year in the lab learning skills and concepts from others. After that, your focus should shift towards learning to solve problems on your own. After a few years in the lab, you should be able to formulate questions, design strategies to answer them, and mentor junior lab members.

  • is organized in performing experiments, analyzing data, and recording work. Results of our work are often unpredictable, so it is important to follow a systematic approach for performing and recording our work so that you can rigorously interpret your results. Following lab-wide conventions will help others and the future-you to think critically about your results without struggling to understand your old workflows.

  • is collaborative and collegial. All new projects in the lab build off the discoveries and expertise of previous lab members. When you join our lab, you will work closely and learn from others in the lab. When you have spent a few years in the lab, you will help others get started with new techniques even if you do not directly benefit from them.

  • is respectful. All of us share a common passion for scientific research, but we often come from different cultural backgrounds, have distinct strengths and weaknesses, personalities, and working styles. Be respectful of your fellow labmates even if you do not see eye-to-eye with them on some professional or personal matter.

PhD and Postdoc Trainees

  • Keep track of all academic requirements in a timely manner (for PhD students). This includes setting up thesis committee meetings, finishing course work, and teaching requirements.

  • Work closely with Rasi to craft and revise research proposals and presentations.

  • Be prompt and diligent in your lab duties.

  • Apply for all available sources of stipend and fellowships.

Long-term Research Staff

  • Help move others' projects forward by contributing unique skills.

  • Establish new techniques in the lab and take on risky projects.

  • Manage day-to-day operations such as equipment maintenance and lab duties.

  • Ensure that the lab space is well organized with all equipment and supplies in their assigned location.

PI

  • Provide feedback on research design, execution, and results.

  • Provide feedback on manuscripts, presentations, and fellowship applications.

  • Help lab members meet their training and career development goals.

  • Ensure a vibrant and safe lab atmosphere conducive to learning and research for all lab members.

  • Acquire funding through writing grants.

  • Highlight lab's research and trainees through conferences and outside seminars.

  • Set long-term vision and trajectory for the lab.

  • Manage the portfolio of projects in the lab to balance productivity and impact.

Logistics

Communication

We use Slack for informal non-scientific communication.

We use GitHub Issues for recording and organizing all our scientific communication. All GitHub repositories are set up to automatically ping to Slack upon updates. For more information on how to use GitHub Issues, see How to use GitHub issues and branches..

Lab Notebooks

We use GitHub Repositories to record all our scientific work. GitHub repositories are essentially cloud-synced folders which enable collaborative work, version control, discussion, and project management, all in one place. In our lab, GitHub repositories are divided by projects, and not by individual lab members. Record your day-to-day scientific work as well as fellowship and manuscript drafts in the appropriate project repository. For more information on how to record your work on GitHub repositories, see our paper on using GitHub for scientific research.

Weekly Updates

We use GitHub Project Boards for tracking progress on individual Issues. Before the end of every work week, lab members update their project board to indicate what Issues they worked on the past week and plan to do so in the next week. Then post a new detailed comment in each Issue with the title Update indicating what you did or plan to do along with links to notebooks, figures, code as appropriate.

Lab Meetings

We have weekly lab meetings on Wednesdays at 2pm and 3:30pm, and they typically last for 1-1.5 hours. We cycle between short updates by everyone, longer updates by one lab member, journal club, and a no-meeting week every month. See current lab meeting calendar here.

Work Hours and Vacation

Everyone will typically be in the lab between 10am and 5p on weekdays. Outside this window, each lab member sets their own schedule based on their research activity and personal constraints.

If you are taking time off during regular hours, put it on the lab calendar.

If you are planning to take more than a few days off, plan in advance so that your research is at a good stopping point. Additionally, let Rasi know and add it to the lab calendar as early as possible.

Contact Info

If you need to urgently contact lab members when they are not in the lab, see here.

External Logins

We create a single common login for ordering using all external vendors. See this page for login information. We have standing POs for a few vendors that we use frequently. Make sure to use the most recent standing PO numbers.

Grant Numbers

See here for information on grant numbers to use for ordering and shared resources use.

Technical How-Tos

We have detailed how-to pages with sub sections for experiments, data analysis, software, and writing.

Onboarding

  1. Join Github and share username with Rasi.
  2. Join Slack and share username with Rasi.
  3. Get access to our lab Github repository for your project.
  4. Give yourself access to the lab Google calendar using the info here.
  5. Get access to rhino computing cluster by contacting scicomp@fredhutch.org. We use this for all computational work.
  6. Get access to lab AWS S3 storage by contacting helpdesk@fredhutch.org. We use this for storing all experimental data and large files.
  7. Learn lab organizational structure for experiments and data analyses.
  8. Learn git.
  9. Learn VSCode and Markdown for writing and version control.
  10. Learn to use Jupyter Notebooks within VSCode and the tidyverse R package for routine data analysis tasks.
  11. Open a GitHub Issue to discuss an idea, collate literature, plan your first experiment, or start a data analysis task.
  12. Get access to lab database for ordering, plasmids, cell lines, oligos.
  13. Add yourself to our lab website (not necessary for rotation students).

Offboarding

Data and Analysis

  1. Create a summary post of key to-do items for your projects in the respective GitHub repository at notes/USER/offboarding_summary.md.
  2. In the summary post, include all boxes that you are leaving for future use.
  3. Move plasmid maps you entered into our plasmid / cell line database into the lab_database folder in Snapgene.
  4. All your raw data should be in AWS S3 under fh-pi-subramaniam-a-eco/data/USER/.
  5. Commit all your presentations to rasilab/PROJECT/presentations/USER.
  6. Put all your fellowship applications reports in rasilab/PROJECT/grants/USER repo.
  7. Commit any code that you wrote from /fh/scratch/delete90/subramaniam_a/user/git/PROJECT to http://github.com/rasilab/PROJECT.

Lab Bench

  1. Give enzyme or expensive reagent aliquots to suitable lab member. If in doubt, ask Rasi.
  2. Put all lab ware (unopened pipettes, tube racks, cardboard boxes) in their common places or give to another lab member.
  3. Throw away all tubes and intermediate samples in the freezer and on your bench.
  4. Throw away any agar plates with bacteria / yeast or tissue culture plates.
  5. Get rid of inexpensive buffer aliquots.
  6. Clean out your drawers.
  7. Put pipettors in drawer 73.

Organization

  1. Go through your oligo, plasmid, and cell line boxes with Rasi to decide what to keep and what to throw out.
  2. Put all your published cell lines and plasmids in a separate box, and change their location in the lab database at http://rasilab.org/db.
  3. Put your oligo and plasmid boxes in the bottom rack of our lab's common –20 ℃ freezer.
  4. Organize your –80 ℃ boxes into the common lab rack.
  5. Give lab key to our lab's current Research Administrator.