Life as a Bioinformatics Freelancer: The tools

This post is part of a series of short articles about bioinformatics freelancing.

In this part of the story I’ll share what technology I found useful for doing my work for different projects as a consulting bioinformatics scientist. This is the current state as of the end of 2018. It might change, but it might be useful for people in similar situations.

Computer set-up:

I do most of the work remotely, i.e. from my office at home with some visits to clients where possible. There I’m using:

  • An Apple MacBook Pro running the latest OSX.
  • on a Griffin Elevator stand – When you’re sitting many hours you need to keep a good posture!
  • A number of external USB hard disks like this one with 2 TB – Don’t fill up your machine and make sure you do backups!
  • Either a TrackMan Marble (to avoid bending your wrist) or a Logitech M330 Silent Plus mouse – I don’t know why not everybody is using the silent mouse! The constant clicking and scrolling get too annoying!
  • An Apple wired aluminum keyboard (with numeric keypad)
  • Connected to an HP 27es  HDMI monitor
  • The internet comes through a TP-Link power line connection
  • with a Thunderbolt Gigabit Ethernet Adapter 

Software set-up:

Part A: Programming, etc.

  • The key is the Unix-based OS, I wouldn’t want to work without access to the powerful command-line tools, etc.
  • For small or visual Python projects the iPython Jupyter Notebooks are great
  • For larger Python (or other) projects I like PyCharm CE
  • To do any more data- or processing-intensive tasks I use machines of suitable size in the Amazon cloud.
    I keep an image (AMI) there which has the software installed that I usually need, so starting work there is quick and much cheaper than buying your own server. These cloud machines are also better secured than most on-site servers!
  • I also share data and results with my clients through S3 on the Amazon cloud. Alternatively I set up a Nextcloud storage on my web-hosting server.
  • For most code-reading and -writing as well as for note-taking I love the TextMate editor.

Part B: Project management, marketing, etc.

  • I maintain a WordPress-based website hosted at all-inkl, with some companion pages (1, 2) to drive traffic.
  • The profiles at LinkedIn and XING are of key importance  in order to be found when people search for your bioinformatics service.
  • Tracking the time I spend on different projects is done with a slightly customized version of Anuko that I installed on my server.
  • Expenses and other money-related tracking for net income determination (Einnahmen├╝berschussrechnung) is done with MS Excel or LibreOffice first. It is then entered in the (cloud-based) tax software LexOffice for the regular VAT submissions (Umsatzsteuer-Zahlungen an das Finanzamt via ELSTER). This software is not perfect, but you can do a 30-day test (or a 1-year test if there are promotions) to try if it is for you.

As you can see many of the tools are open-source or at least free software solutions.

Feature Image by Victoria_Regen from Pixabay