List of Software Tools

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Downloadable Tools


FreeCAD is an open source tool for modeling and creation of "Parts". These can be for engineering, but also rather simple geometrical constructs.

Open Source Structure Design (FreeCAD)


The Slic3r is a program that translates geometrical data of files (usually in .obj or .stl format) into "g-Code" which are instructions for pathplanning and extrusion that can be used for most commercially available 3D-Printers.

Open Source Slicer (Slic3r)


Atom is a hackable Text-Editor with powerful tools and options.

Open Source Hackable Text Editor (Atom)

R and RStudio

R is a statistical computing software that is free, relatively easy to use and features a ton of additional packages and options developed by the community. R-Studio is a graphical user interface that makes handling easier.

R Project


Online Tools


Collaborative writing e.g. for editing Wiki pages together.



Overleaf is an easy to learn and collaborative online writing tool. It is based on Latex which is preferable for scientific protocols/articles/paper. With this tool you circumvent the nasty installation of a working Latex enviroment and invites to work together on scientifc documentations.

Writing (Overleaf)


Sketching via Awwapp is fun, easy to do and helps to visualize your ideas.

Sketching (Awwapp)


Benchling is a tool for organisation in the lab. Besides an inventory system, a calender for planning, a digital notebook and the opportunity to upload your protocols, Benchling also features a rudmentary Genomic Editor for simple Cloning or CRISPR experiments. You can share your data, findings, protocols and list with other users or even working groups!


Scientific Tools


This open source tool allows a scientific analysis of your images. It is based on Javascript and thus includes the gold-standard image analysis program ImageJ. However, Icy enhances the usability by adding in-built plugin download, batch processing of images via scripts and sharable protocols.

Open Source Image Processing (Icy)

Open Science Framework

This online framework enables to organize the scientific experiments and share your scientific data (e.g. images, protocolls, contributors, milestones etc.). Each project has its own 'Repository' which can be shared via link (see below)

Open Science Framework

ScieBo - The Cloud for data storage in Bochum

ScieBo offers 30GB free space in the cloud and allows you to store and share your research data in a decentralized manner. Synchronization with your mobile devices (Smartphone, Tablet) is also included. The servers are stationed in Germany and fall under the legislation here, meaning your data should in principle be safer than on other platforms that reside in i.e. China or the US.

ScieBo Campuscloud - sharing Protocols allows to optimize and share protocols. It features group support as well as discrimination between private and public protocols. However, private protocols are limited to a number of 5.

Current Nydus One Project Repositories

Open Source Bioprinter