Chapter 5 Research
5.1 General Graduate School Advice
- Tips for PhD Students by Claes Backman
- How to Be a Successful PhD Student (in Computer Science in NLP/ML) (PDF)
- Tips for PhD students and early-career researchers by Mick Watson
- Advice for early-stage Ph.D. students by Philip Guo
- Surviving a PhD - 10 Top Tips by Alex Hope
- Completing Your Dissertation: Strategies for Success by S.A. Koblinsky, J. Leichty, and C. Schull (PDF)
5.1.1 Work-life balance
I've spent a lot of time this week thinking about the transient nature of social support that really is a hallmark of #phdlife as an early career academic. As a graduate student, the friends you make are virtually guaranteed to leave at regular intervals. 1/n
— Katie Grogan 👩🔬🧬 (@Dr_KatieG1) September 28, 2019
5.1.2 Dealing with failure/rejections
I had a major rejection this week, was plagiarized earlier this month, and still feel like I’ve had a happy and productive month. I’d like to share my rejection rituals with y’all, since this is common. 1/7
— Dr. Calla Hummel (@CallaHummel) September 26, 2019
5.2 Reading Journal Articles
- Ten simple rules for developing good reading habits during graduate school and beyond (2018)
- How to Read a Paper - Suggests a three-pass method to reading research papers, each pass increasing the depth of details you read into
5.3 Performing dissertation literature review
Consider using the matrix method to organize your reviewed sources.
To begin, start with three columns:
| Authors, title, journal | Year Pub | Purpose |
|---|---|---|
| Martin, JE et al. “A DNA vaccina for Ebola virus is safe…” | 2006 | Determine safety and immunogenicity of Ebola vaccine in… |
Here are some templates.
5.4 Keeping Up with Literature
- PubChase
- Google Scholar Alerts
- Follow academic leaders in your field on Twitter
- Staying Current in Bioinformatics & Genomics: 2017 Edition
It is not recommended to use Sci-Hub to quickly and easily access almost all of science.
5.5 Writing
General tips:
If you use Emacs, you can use the Academic-phrases package to help write phrases typical of academic papers. A list of these phrases can be found at the bottom of this page in a link titled, “Free Download: Useful Phrases”.
5.7 Conferences
If running on a budget, look for opportunities to volunteer at conferences. It is a good way to mean other graduate students or other early career researchers and learn how conferences are hosted.
Also look for student discounts if possible. If there are none listed, don’t be afraid to email the conference organizers to see if there is a student discount.
Locally, you can also apply for travel awards through the Graduate Student Organization (GSO). The deadline to apply is the term before your anticipated travel.
Some nearby and prominent conferences to consider:
- Institute of Systems Biology (ISB) Symposium (Seattle, WA) - Around April, two days, around $50 for students and postdocs.
- Pacific Symposium on Biocomputing (PSB) (Hawaii) - Around January, submit proceedings to be publication.
- rstudio::conf - Around January, the 2020 conference is in San Francisco, CA.
- American Medical Informatics Association (AMIA)
- Health Information and Management Systems Society (HIMSS)
5.8 Conference Posters
Some tips from Hello PhD on making poster presentations:
- In preparation
- Know your audience
- Start early
- Practice
- Find your story
- Presenting
- Timing is everything
- Act like an actor and show enthusiasm
- Personalize your pitch based on your audience’s background
Feel free to also skim through https://betterposters.blogspot.com/, a blog for advice and critiques on making better scientific posters.
5.8.1 Poster Templates
Better Scientific Poster
A novel poster format, dubbed the “better scientific poster”, has been created and a template of it can be found here.
posterdown
Use RMarkdown to generate PDF Conference Posters via HTML or LaTeX xhttps://github.com/brentthorne/posterdown
5.9 Applications
Here is a repository of successful job and grant applications that may be helpful https://github.com/RILAB/statements.
5.10 Modern Scientist
“How to be a modern scientist” is an affordable book by Jeff Leek on how to navigate the academic world (e.g., publishing, data sharing, blogging, etc.).
https://leanpub.com/modernscientist
Description:
The face of academia is changing. It is no longer sufficient to just publish or perish. We are now in an era where Twitter, Github, Figshare, and Alt Metrics are regular parts of the scientific workflow. Here I give high level advice about which tools to use, how to use them, and what to look out for. This book is appropriate for scientists at all levels who want to stay on top of the current technological developments affecting modern scientific careers.
5.11 NLM and NIH Fellows
This doesn’t directly apply to trainees, but this site is a nice reference to have when reviewing the terms of the fellowship https://www.nlm.nih.gov/ep/trainingdirectors.html.
5.12 Miscellaneous Research
Curated list of tools to help with research https://github.com/emptymalei/awesome-research.
Excellent blog dedicated to the topic of doing a PhD and completing a dissertation https://thesiswhisperer.com/. Extensive catelog of blog posts with valuable advice and links to useful resources, ranging from writing advice and presentation advice to dealing with academia and post-graduate school career hunting. Advice is directed towards PhD students, but it is helpful for all students.