Welcome to the lab!
This page is created for new comers to the lab.
For a quick overview of what we are up to, please check out a list of papers, projects, software and data-sets we work on in the lab.
You should have received onboarding instructions from the HR office prior to your start day. Please follow those to complete all the paperwork. If you are new to Columbia and NYC, you might find some helpful information on this page.
When you get a chance, please email me (email@example.com) your account information for slack and github. We use slack for daily communications and quick exchange of information, and github to keep track of our research work. I will add you to relevant slack channels and github repositories.
Since we work in a highly collaborative environment, it is important that lab members are aware of and respect each other’s work style. To establish a common ground of collaboration and communication, it is highly recommended that lab members follow these 3 lab rules:
- Reproducible Research on github – see this page for details and examples of this requirement.
- Communication through github issues and daily pull request(s) (PR) – as detailed in the “Github issues” and “Daily pull request(s)” sections of the reproducible research document above.
- Weekly in person meetings. Lab members are expected to meet with me (roughly) weekly to review projects, or to educate me on topics that you have become a better expert on due to your hard work. The meeting should not be status check or progress report, because these should have been achieved already via daily github PR. The meeting should be used to discuss questions already raised on github that we have not yet sorted out during the week, or to discuss next steps, or any other difficulties (professional or personal) that you think I could help with. Please take an initiative on your end to book me every week on my calendar. Please take good notes during the meeting. After the meeting please post (on slack DM or github issues) the action items for the next steps.
Additionally, it is highly recommended that you install computer app for slack for instant communications on projects. I apologize in advance that I might slack you after hours and over the weekends but you are not obliged to get back to me until normal hours — I do so only in case I forget to send them later if I hold on to my messages until normal hours …
For master student research assistants:
- In order to make any non-trivial progress on projects, we expect a minimum of 10 hours per week effort during the semester (ideally 15 hours and more for senior Master students) and 40 hours per week in summer (except during your days of vacation), for a total of at least 6 months.
- Most projects can take one year or more to complete to the point of publishing the results in peer reviewed journals. We therefore expect long term contribution from student researchers.
- All students will be offered a non-paid position for starters. The first month in the lab will be considered rotation period. At the end of the rotation we will discuss the possibility of continuing the research at the lab.
- Students may be offered a stipend after 3 months of excellent work in the lab; student may be considered having left the lab after 1 month of absence of research activities (exceptions can be made if communicated in advance).
- For those intended to use our work for the Biostatistics Practicum project, you must send me the write-up for comments before submitting it to the Department of Biostatistics.
Explore lab wiki
In addition to some links you have previously checked out, you are encouraged to explore the lab wiki checking out material on other pages. On this wiki you should find answers to the most frequently asked questions as a new comer. In particular,
- A list of learning material on various topics in computational biology, if you wonder where to get more background knowledge for the research we conduct.
- A list of “must know” shell commands.
- High Performance Computing cluster usage and computational resource sharing guideline.
- Install JupyterLab, SoS and Docker to your computer.
- Some random FAQ.
- This and that, tips about life on campus, the city and places to visit & eat.