Open Science, Hardware and Software

Open Science

Starting a new laboratory from scratch comes with challenges, but also with opportunities. One of the opportunities we are trying to implement from the start is building our laboratory around the concepts of "Open Science", "Open Source Hardware" and Free and Open Source Software. This page will step by step being filled with our projects, links to source code, CAD files etc. and other helpful information. Some of these links will point to our own developments, others to already available solutions that we use and adapted. If you are interested in how (and why) we are doing this, please drop us an email. Similar, let us know if you think we missed something useful.

Used Open Source Software:

Most of our computers run Linux as operating system in the one or the other flavour. Ubuntu is the departmental choice and the most common one, but Arch Linux and special adaptations e.g. for the Raspberry pi are in use as well. Below you find a list of software we find useful. Many of the software packages have active repositories on GitHub or SourceForge and often a ppa is available for easy installation in Ubuntu.

  • Libre Office: a full office suite (text, spreadsheet, presentation, etc.) and one of the main driving forces behind the Open Document Format (ODF), an international ISO/IEC standard for storing documents (note: Microsoft's own format isn't). The UK government is recommending ODF (and PDFs) for sharing or collaborating with government documents.
  • FreeCAD: powerful 3D CAD program. Unfortunately, it sometimes struggles with files from proprietary software like AutoDesk Inventor.
  • LibreCAD: a simple 2D CAD modeller, usually works quite good, but needs dxf files.
  • Python: much of our analysis scripts and control of measurement hardware is controlled by Python, a high-level, general-purpose, interpreted, dynamic programming language. If you want to know what it can do, have a look at this.
  • GNU Octave: if you can't do it with python and/or prefer an environment that looks like Matlab, then Octave is a good option. It's a high-level interpreted language, primarily intended for numerical computations.
  • Inkscape: need some vector graphics for your thesis? Try Inkscape.
  • GIMP: a powerful graphics program
  • pyvisa: the Python wrapper for the Virtual Instrument Software Architecture (VISA) library, which is used to control our instruments. Given it's continuing development, it is recommended to use the latest version from the pyvisa homepage or its Github site.
  • gwyddion: a nifty program for SPM (scanning probe microscopy) data visualization and analysis, e.g. for AFM images.
  • DAWN Science: DAWN, the Data Analysis WorkbeNch, is an Eclipse based application for scientific data analysis, which we use mainly for the analysis of our X-ray data. The DAWN source code can be found on Github.
  • One of the many open source web browsers, e.g. Firefox or Chromium.
  • Similarly, there are various open source email clients, e.g. Thunderbird and its calender add-on Lightning. One can even get it to talk to MS Exchange Servers, if needed, using the Exchange EWS Provider add-on by the guys at Ericsson (thanks!).

AFMD Group on GitHub:

We've got our own AFMD Github site which we use for our code as well as the hardware design for our experimental setups. If you find a strange reference with an alpha-numeric code in the experimental parts of our publications, then our GitHub page is where to find further information.

Other useful Code:

  • OSOLSim: A drift-diffusion simulation code for simulating organic solar cells, developed by Wolfgang Tress, a former PhD student at the IAPP of the TU Dresden, Germany. Wolfgang's thesis can be found here.

Data Exchange Formats:

  • FMF File Format: an annotated tabular data format, ideal for adding metadata in a structured and machine readable format for tabular data. We use it for everything from IV curves to EQE and transient measurement data.
  • SDDS Format: a "Self Describing Data Set" file format developed at Argonne National Laboratory. It has some similarities to FMF.
  • HDF5: Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large and complex data collections. We use it for our beamtime data.

Used Hardware:

  • Raspberry pi: a tiny and affordable computer that you can use lots of things, including practical projects.
  • Arduino: Arduino is an open-source electronics platform based on easy-to-use hardware and software. It's intended for anyone making interactive projects.
  • Reprap: an open source rapid prototyping system. Can be convinced to become a spray coater;-).

Further Information:

Below are some more links that contain information about open science, hardware and software: