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)
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 (Einnahmenüberschussrechnung) 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.
