ground- water, geo- statistics, environmental- engineering, earth- science

Software tools of the trade (PhD student)

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A joiner likes to talk about his saws. Similarly, Phd students need to use some “tools of the trade”. Recently, some improvements on old tools emerged, and some new guys showed up on the scene. I thought these are worth pointing out. Mostly, these tools don’t offer incredible novel features. Rather, they offer slight improvements which on a daily basis offer nice benefits

Scrivener 2.0

As I see it, the new scrivener is a great tool to – organize thoughts; – collect data / “research” — it even has some features I wish DEVONthink Pro would have; – Write — I am writing this post in scrivener. However, I still haven’t found an ideal solution, hence I still write most of what I write in latex or markdown using TextMate. So far, I have even written all blog posts using TextMate (I am aware of MarsEdit, but I haven’t tried it yet). The thing is, for scientific writing, I don’t see an option to latex. And TextMate is probably as good as a latex editor in the foreseeable future will get.

I see scrivener’s strong points especially for writing combined with organization. It has some really nice features like split panes, internal links, or how it handles comments. But it does not cover my most important needs for scientific writing (even though there are some workarounds (here and here) via markdown, but they remain workarounds. Also for organization, DEVONthink Pro is still superior in my opinion. I haven’t tried the new Yojimbo. Also, there is the classic outliner OmniOutliner which together with OO3eq offers basic latex capabilities.

To conclude, I use a combination of DevonThink, Scrivener, and Textmate for blogging, OmniOutliner for writing notes in courses and meetings, and TextMate for scientific writing. It sure would be nice to have one for all. But isn’t that always the problem?


A common complaint is that Yahoo never gave much love. is an online bookmark storage/sharing tool. Recently, pinboard showed up. It’s fast, it can be nicely integrated into Safari, and it has some nice features like “read later”.


As a PhD student, I need to read scientific papers. And since there are many, I need a way to store and find them. Also, I need to reference them when writing a scientific article. So far, I’ve been fairly happy with BibDesk‘s capabilities, especially, it’s easy link to writing latex documents in TextMate and its ability to automatically store pdfs. A factor that counts pro BibDesk is that BibDesk is open source software.

I’m aware that the functionality for reading and commenting in Papers is supposed to be improved compared to BibDesk. Recently Mendeley showed up on the scene. It’s an approach to social-web-style-reference management funded by Skype,, and Warner Music. You have to sign up, and the basic version is free and comes with 500MB personal space and 500MB shared space.

Mendeley is still pre v.1.0, and I had and still have issues importing my bibtex library into Mendeley. The interesting part is that you can look for people with similar research interests, say statistics in earth sciences, and see what those people are reading. Also, Mendeley has a public API, so programmers can access research paper statistics, for example. It will be interesting to see what will be created with these options.

MS Office 2011 for Mac

Since MS Word 6.0 is gone, my positive feelings for Word and its office suite have disappeared. However, sometimes it’s not possible to avoid it, especially since at work we’re using Excel to teach students. And granted, excel is pretty intuitive. Recently, a new version for the Mac came out, and some of those long-lost positive feelings have re-surfaced.

  • the biggest plus: it finally is fully integrated into OSX 64bit. Hence, general performance is improved.
  • Excel: the formula bar is back to a fixed location! Yay!
  • Word has a distractive-free writing mode, similar to writeroom, think!, or the even more general solution – because it provides a distraction-free environment for any application isolator
  • VBA is back – not that this is huge, but it sometimes helps in labs that I teach
  • Excel: some improvements to charting, but I bet it’s still the same old charting engine from the last millenium
  • The solver is again VBA-based and hence better “includeable” into excel

Written by Claus

December 2nd, 2010 at 5:00 pm

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