About Beverley M. Dancy

Ph.D. Candidate Labs of Philip A. Cole and Jef D. Boeke Department of Pharmacology and Molecular Sciences The Johns Hopkins University School of Medicine Baltimore, Maryland, USA

Thesis-writing tips

It’s that time of year again – the thesis-writing deadline for the May graduation ceremony is approaching (29 March 2013). Like me, many of you will be writing your thesis. I’d like to take a moment from my writing to share with you some things that helped me.

1. Where to work

Apart from accessing data on lab computers and looking up methods in your lab notebooks (which are not allowed to leave the lab), thesis writing can take place in many locations: desk in lab, communal area in lab, Welch library or computer center, cafe… Sometimes it can help the creative process to to switch location. A few things about where you work are important, regardless of location:

  • Make lots of backups via internet and/or with external hard drives or USB thumb drives.
  • Sit comfortably and stretch your hands between long stretches of typing.
My desk in the Cole lab, where I do most of my thesis writing.

My desk in the Cole lab, where I do most of my thesis writing.

2. Making figures

Here are some applications and tools that I used to make some of my figures.

  • When writing out mathematical equationsLaTeX online editor allows you to export .gif files with nicely drawn equations.
Some equations I wrote describing my RT-PCR calculations

Some equations I wrote in LaTeX describing my RT-PCR calculations.

 

  • When making figures of protein structurePyMol wiki has instructions for how to replicate certain effects.
A figure I made in Pymol highlighting different aspects of a p300 crystal structure

A figure I made in Pymol highlighting different aspects of a p300 crystal structure.

  • When drawing the exon-intron structure of a gene, the Exon-Intron Graphic Maker lets you make and export nice simple diagrams.
One of several gene structures I made for a figure.

One of several gene structures I made for a figure.

  • When making graphs, I highly recommend Graphpad Prism, which has a free demo. When the demo expires, you may need to clean it off your computer (for example, by using CleanApp) before you can download the demo again.

3. Vocabulary

  • When providing recombinant DNA to cells, say “transformed” if it is bacteria, “transfected” if it is mammalian cells and you used lipids or electroporation, and “transduced” if it is mammalian cells and you used viruses. Note that “transformed” for mammalian cells means the conversion of normal cells to a cancerous state.
  • When using C. elegans, phenotypes are non-italicized 3-letter abbreviations with the first letter capitalized (e.g. Glo), genes are 3 italicized letters – hyphen – number (e.g. glo-1), and proteins are 3 non-italicized capital letters – hyphen – number (e.g. GLO-1). There are even more rules, available here.

4. Microsoft Word tricks

  • When you get revisions from more than one person on one Word document (with or without “track changes”) you can consolidate them by clicking Tools -> Merge Documents, and this preserves all the comments and edits and style changes. It does NOT work if you click Tools -> Track Changes -> Compare Documents.
  • If you embed a bunch of pictures in your Word document, they may stop printing when you go File -> Print. If that happens, try going File -> Print Preview and then print from there. Worked for me!
  • For figure legends and table titles, use Insert -> Caption. That way, you can make an automated “list of figures” and “list of tables” (by going Insert -> Index and Tables -> Table of Figures) and automated references to figures within your text (by going Insert -> Cross-reference). These automated features update the figure numbers as you add more, update the page numbers in the list, and embed hyperlinks that make it east to scroll back to the figure.
  • Making backups is key. Hopefully it goes without saying, but still worth mentioning! I use Google Drive (easy drag and drop, access anywhere online), external hard-drive Time Machine, and USB thumb drives religiously. I also print each chapter when it’s done so that I have a physical copy in case I ever need to re-write the text. Without these measures, I don’t think I could sleep at night!

Good luck to you when you write your thesis! I hope something in this article helps you.

Peter Devreotes’ BCMB Friday Seminar

Our latest BCMB Friday Seminar, held on 9 November 2012, was by Peter Devreotes , a BCMB faculty member. He spoke about his lab’s contribution to the field of cell migration. After a wonderful introduction by BCMB student Chris Mitchell, the seminar began with a historical overview of chemotaxis, which is an essential part of human development.

Devreotes

Dr. Devreotes speaking about cell migration.

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