My Must-Have Apps for Science, 2013 Edition

December 22, 2013 § 3 Comments

2103 is the year when I finally bought a MacBook Air as my main machine. I have thus been able to shift to a Apple-only software environment, although I still have a Thinkpad in the lab (yeah, don’t ask).

Like any academic, my four main activities are reading, writing, compiling data, and preparing figures.

My main requirement is that I need to keep my machines in sync. This include 2 laptops (Apple and PC) and 1 desktop (Apple). The tricky part is that I cannot go online in the lab with the MBA, for corporate reasons (this is a Windows environment). I rely thus on a few pieces of software able to sync from behind the firewall (and no, I cannot use Dropbox on my PC at work), and exchange a few files, when needed, by bluetooth.

Here are my most-used app for 2013, with no particular order.

Main

  • 1Password. Takes care of all my password needs and more. I have only 50 characters passwords now.
  • Keynote. I gave up with Powerpoint when moving to the MBA, and enjoy using Keynote so far. My needs are very basic, as most of my slides usually have just a title and one figure.
  • Alfred. I use it mostly as a launcher for apps. I use spotlight a lot, but Alfred appears in the center of my screen (yes, it’s silly, I know) and the text is larger.

Writing and code

  • iAwriter. For all my drafts. A perfect distraction free-environment. Love the font.
  • SublimeText. For coding. This is an outstanding piece of software. I don’t even understand how people can code without it. Also great for LaTeX writing, once you’ve set a few snippets.
  • TexPad. I wrote a few long and structures documents this year (such as my habilitation), which was a good excuse to be back to LaTeX. TexPad is real pleasure to use. The interface is uncluttered and does the job perfectly. Mendeley automatically generate a .bib file of my library, which is super convenient.
  • MS Word. alas. I only use it to prepare the final version of manuscripts and exchange with co-authors. One thing I like, though, is the revision mode.
  • F.lux. This little gem automatically adjusts the color of the screen. Warm at night and bright during the day. I cannot use a computer where it’s not installed. This is the first piece of software I actually install on a new machine.

Image Editing

  • Adobe Illustrator. For all my figure needs when preparing manuscripts. Been using it for years. Keeps getting better. Just love it.
  • Picasa. To keep track of all the images on my PC and some shared resources on the internal network, without actually organizing them. A time saver.
  • Fiji and ImageJ. Fulfill all my image analysis needs. Even better since you can use python with it.

References and Science stuff

  • Mendeley. My reference manager of choice. I use it constantly. Tends to be a bit slow when running search (>2k papers). Just perfect for preparing manuscript. I know, I know, Elsevier owns it now, but it’s just too useful for me. The competition is getting fierce, though, which is good, with the release of Paper 3 and Readcube. The automatic bib file saving is a must have for me.
  • Simplenote and Notational Velocity. I’m throwing everything here: notes, to-do list, recipes, drafts. The killer is the shortcut ((Maj+Cmd+E) to open the file in an external editor (iA Writer for me). Using Markdown for the drafts. I’m very keen on keeping everything in text file, to ensures readability on the long-term.
  • Graphclick. This little gem automatically extract the values from plots when you don’t have access to the raw data. Super useful, when compiling data from the literature, for instance. It hasn’t been updated for years, but does the job perfectly. Ridiculously cheap.
  • Gephi. I had fun with networks recently (more info coming soon, hopefully). Beware, this is a mesmerizing piece of software. Be ready to waste a lot of time.
  • Mediawiki. We finally set up a wiki for the lab last year, and have used Mediawiki. Does the job perfectly.

Online tools

  • Doodle. To find a date for meetings. Does the job simply and perfectly.
  • Instapaper. For my casual (i.e, not papers) reading needs. I sometime send full text papers, and it’s actually a pleasure in this context. Using the snippet to save the articles during the day, and read everything on my iPad.
  • Twitter. Been using it more and more, but this might be a story for another post. I tweet here @devillesylvain.

Next for 2014 ?

Who knows what 2014 will be made of ? Pretty much all my needs are fulfilled now, so I am not really looking for anything special. A few apps are under my radar nevertheless, and could be possible new additions to my workflow.

  • Scrivener. For complex documents such as review papers. I downloaded the trial version and started playing with it. Seems to be very powerful. Make sure to check out the tutorials.
  • Mindnode. For mind mapping. I’m a visual type of person.
  • WriterPro. The new version of iA Writer. I don’t care about the workflow thing, but the syntax highlighting could be a game changer for my academic writing, as I am still not a native-english speaker and am still working hard on improving my writing.

Got any advice ? Let me know if I miss anything in the comments.

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§ 3 Responses to My Must-Have Apps for Science, 2013 Edition

  • David says:

    I recently discovered WinPython which is a very useful Python distribution on Windows.
    – It is portable (meaning “no installation”, just copy/paste the files), which is very convenient at work since my corporate rules are the same then yours 🙂
    – It contains Spyder (the matlab-like environment) which now has a IPython version compatible with the notebook (it was not the case before…)

    If you like graphical thinking, I sometimes use concept maps as an alternative to mind maps
    https://www.msu.edu/~luckie/ctools/
    That Cmap software is far from perfect, but I’m not aware any good alternative.
    (actually I tend to draw mindmaps on paper – yes, with pens ! – and draw concept maps on the computer)

    • I’m surprised they don’t let you install Python ! We didn’t have any problems with it here.
      I do my mind mapping… on my windows ! Plenty of space, but then I ends up taking a pic of it with my cellphone to keep track of it. Mindnote might brings some convenience here.

  • […] the right tools to write. Yes, there’s a life beyond Word, but too few people seem to be aware of it. I am now using Writer for all the steps from drafting […]

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