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Toolomics - building the bioinformatician's Swiss army knife

  • Thursday Aug 18th 2016
  • BioQuant, Heidelberg, Germany

Ice-breaker (15 min; 19:00-19:20)

BYOP - Bring your own problem

Do you have some pesky tasks to do in your work which are tedious and maybe repetitive and you wish there was a tool to do this for you? In this ice-breaker we'll discuss such everyday problems small groups, sharing our experience (and frustration?), maybe learning how other already tackled similar problems, effectively helping each other solving problems.

Flash Presentations/Demos (20 min; 19:20-19:40)

Some volunteers demo their favorite tool/program/workflow.

Main Activity: "Tool me up, Scotty"

In our everyday work and personal life, we use programs, tools, apps, techniques etc. which help us make our lives easier or just getting the job done faster, better, easier.

In this exercise, we'd like to exchange experiences and ideas around those tools, that you just wouldn’t want to be without anymore! For this, we’ll use an Open Space Technology (OST) approach to forming smaller groups to discuss and compare our experiences of handy tools we use, in a range of different domains. OST is set up to make it easy for you to move from group to group as the discussions and conversations you’re having change, and your interests in them change with it.

While doing that, we’ll try and capture online the ideas and tools that people come up with during the session, so that others who are interested in this, but not participating in the session in person, can also see and hear about the tools we’re finding indispensable! For this, we'll use the following piratepad:

Things needed

  • tables
  • chairs
  • wifi
  • projector
  • pens & sticky notes


Here is the awesome list of tools the participants came up with:

Command Line Tools:

  • bash tools: cat / sed / cut / head / awk / paste ... stream manipulation
  • Snakemake - biological workflow management
  • GNU Screen - "virtual terminal tabs" / Tmux - terminal multiplexer - "virtual terminal tabs"
  • git - version control
  • edit your .bashrc - make bash more useful, more beautiful, add aliases
  • sshkey -> login without password
  • rsync - synchronize directories
  • tig - git browser
  • edit your .bashrc - make bash more useful, more beautiful, add aliases
  • socks proxy (ssh) tunneling your trafic through the ssh connection
  • imagemagick - image manipulation
  • pdftk - pdf manipulation
  • zsh - different shell
  • elinks - browser
  • netcat - powerful networking tools
  • Other collections of tools

Visualization tools

Image Analysis

  • knime, : images + workflows + machine learning + R / weka
  • ilastik, pixel based 3D segmentation
  • ImageJ / FIJI, + plugins / macros: difficult to call it in headless mode -> ImageJ2
  • cellprofiler
  • cellcognition
  • imaris bitplane: powerful for 3d data but not freeware

Protein Tools


  • BioPerl
  • BioJS - e.g. 'Sequence' for tertiary structure viewing




Programming tools


  • atom
  • textwrangler / notepad++
  • gedit
  • sublime
  • emacs
  • vim
  • kite
  • nano
  • bash tool collection
  • less (readonly)
  • cat
  • more..


  • pycharm
  • eclipse
  • RStudio / Rmarkdown
  • Jupyter/Ipython Notebook
  • netbeans
  • Matlab
  • Visual Studio (Code)
  • xcode
  • Spyder

Versioning Control

  • git / github / bitbucket / gitlab
  • mercurial
  • SVN
  • CVS

Database admin tools

  • dbvisualizer
  • pgAdmin3
  • phpMyAdmin
  • mysql workbench


  • google
  • /
  • readthedocs
  • bioconductor
  • py coders weekly

continuous integration

  • jenkins
  • gitlab ci runner