I've been doing a lot of emerging infectious disease tracking in the last 18 months. In that time, I've developed a set of tools that make the very time-intensive pursuit go more quickly.
My most important tool is actually Twitter (I'm @cmyeaton), because most news breaks there first these days. I follow other epidemiologists, health organizations like WHO, science journalists, and public health professionals. That's also where I find a lot of the best news stories, blog posts, and information about the diseases I track. I use Vellum to quickly survey the links my Twitter friends are sharing, and usually spend at least half an hour every morning catching up on what's new.
I couldn't live without the Chrome extension Page Monitor, which I rely on to tell me when the WHO, CDC, or Ministry of Health websites are updated. When I learn new data are available, it's often in PDF form (which is a bummer); I use Tabula to extract that data more quickly and with fewer errors than if I did it by hand. I keep all my data on Google Docs so I can access it from any computer, and can share it with my collaborators. I also sometimes keep copies on Figshare or Github so that other people can download it.
When it's time to analyze, I use Python, and (rarely) R. I don't even remember how to code without pandas, so hopefully I'm never stuck on a desert island without it. I also use epipy, but that's probably just because I wrote it. Seaborn is my favorite package for prettifying my plots, although ggplot and mpltools are also nice. All my analyses are usually done in IPython Notebooks, which I share with my collaborators using Google Drive, github, or nbviewer. I recently learned that the notebooks also convert nicely into slides, which is very useful since a lot of presentations are updates of previous work*.
The notebooks capture my results well for preliminary sharing, but when it's time to write manuscripts I like Google Docs or Writelatex, depending on who I'm working with and how much math is involved (LaTeX is better for math). Then it's back to Twitter to share and discuss my results!
*Update: I have since decided that this is a lie. Notebooks convert nicely into slides if you are happy with the default output. Customizing is a huge pain.
"Send me your data - PDF is fine," said no one ever
The public health paradox ("When public health works, it's invisible")
Let's make data a civic right
Scholarly impact of open access journals
Six months later, disease detectives still battling fungal meningitis outbreak