Contents
There are many skills that scientists need to learn that are not taught in lectures, but only come from experience.
General advice
First, read this paper. I would recommend reading this paper more than once - once now and periodically as you progress through your studies. The paper is geared towards computer scientists, but is almost all generally relevant.
Differences between this paper and computational biology in Canada (and at UofT) are:
In Canada, the main government funding agencies for science are CIHR, NSERC and NCIC. Genome Canada, CFI and others also exist. Scholarships come from agencies like CIHR, NSERC and OGS. See scholarship information
- Computer science students take 2 years of courses before picking a thesis topic, while biology students start research immediately and only need to take a few courses. It is typical to aim for 2.5 years for a Master's and 4-5 years for a Ph.D.
- In computational biology, you will need to take undergraduate computer science courses if you have none or only informal computer training.
- Maintain a file of ideas that you have. If you plan to continue in research, this can form the basis for projects and grants that you will have to do or write.
Biologists use Microsoft Word and EndNote for writing papers. You must become proficient in the use of these software programs.
- Section 3.3.1 is not as relevant to biologists. For instance, there is no 'outside' thesis option.
- Section 3.3.2 contains some sections that are not relevant to biologists - specifically the 3rd paragraph.
You must learn all departmental regulations. E.g. these are listed for medical genetics
- Section 4.1 - allocating 1 minute per slide is a more realistic guideline.
Sections that make especially good points:
- The motivation section - 3.2
- Section 3.4 - especially the part about having summaries of your work ready to explain.
PLoS Computational Biology (open access journal) has a succinct but practical (frank) advice for graduate students in "Ten Simple Rules for Graduate Students"
Communication
One of the most important things is practice for writing papers, making posters and giving presentations.
Presentation tips
- Always prepare a thorough introduction, stating the goals, motivation and the big picture up front. If the audience already knows it, you can go over it quickly, but don't skip it. Many presentations you see are missing an intro and the audience often gets lost.
- State your question first, then how you answer it. Avoid the temptation to list things in the order you did them, since this usually focuses on technical aspects of the problem and leaves the question answered last.
- Reduce use of technical terms as much as possible. Each technical term you use that someone in the audience doesn't already know hurts the clarity of your presentation.
- Always acknowledge the work of others, but make it clear which work you did.
Papers
See the article by Phil Bourne Ten Simple Rules for Getting Published - Published: October 28, 2005 PDF version
Posters
- Avoid too much text and focus on graphics. Remember, your poster will be in a sea of hundreds of other posters and needs to catch people's attention.
- Instead of listing the abstract, just list the main points of the poster in a large font where the abstract would go. People usually already have the abstract in their book and a point form list is easier to read.
An excellent site with advice on creating effective Scientific posters
Books that include advice about publishing and presentations
Winning the Games Scientists Play
Med Gen specific tips
- Your reclassification meeting will require a lot of background knowledge. You are expected to study 4 full weeks for this and can be asked anything. If you regularly read Science or Nature, this will be much easier.
- Schedule a mock-reclass to practice.
Keeping up with science
You are expected to keep up with your field by reading papers. Learn to read selectively to avoid overload. It is a very good idea to read Science or Nature on a regular basis to stay up to date with biology.
- Sign up for Table of Contents (TOC) e-mail alerts from journals
- Nature
- Science
- Cell
- Bioinformatics
- Genome Biology
- Genome Research
- Nature Biotechnology
- BMC Bioinformatics
- Nature Molecular Systems Biology
- Molecular and Cellular Proteomics
- Proceedings of the National Academy of Sciences (PNAS)
- PLoS Computational Biology
Go to seminars on campus - see Community
RSS feeds from PubMed for favorite queries
Some journals provide RSS feeds also. Check out BaRf for third-party RSS feeds if they are not provided by your journals of interest.
Visit ISI Web of Science regularly and check for new papers that cite favorite papers
News e-mail updates from GenomeWeb
Ryan Lilien maintains a Computational Biology mailing list at UofT called compbio@cs.toronto.edu E-mail him at lilien@cs.toronto.edu if you want to sign up.
Tips on paper reviewing
Follow this format when writing a paper review
- Summary of the paper at the top of the review
- General evaluation of the significance of the paper and summary of the review. Try to include some positive points e.g. the area of study is important, the problem is important to address
- Specific points separated into sections 'major points' and 'minor points'
- Always be concise, positive and constructive
- Include the page number and optionally the section heading for all specific points. If needed, include a quote of the text - use the format P4 – Introduction – “...large changes in our data...” to reference specific words
- Include references whenever discussing previous work (with a PMID)
- Don’t use any rich text formatting, since reviews are sent in plain text.
Courses
"Social knowledge" of Science
What is impact factor? This article tell you what impact factor is and what it is not.