Starting a new laboratory from scratch comes with challenges, but also with opportunities. One of the opportunities we seized is setting up our laboratory around the concepts of "Open Science", "Open Source Hardware" and Free and Open Source Software right from the start. The Open Science Training Handbook is a good starting point if you are interested in learning more.
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.
Our 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.
Used Open Source Software:
Most of our computers run Linux as operating system in the one or the other flavour. Ubuntu and Debian are 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, Gitlab 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. How much people adhere to this recommendation is a different question...
- Python: much of the control software for our measurement hardware and our data analysis (incl. plotting) is done with python, a high-level, general-purpose, interpreted, dynamic programming language. If you want to know what it can do, have a look at this.
- Inkscape: need some vector graphics for your thesis? Try Inkscape!
- GIMP: a powerful graphics program for dealing with pictures of all kinds.
- GNU Octave: if you cannot do it with python and/or prefer an environment that looks like Matlab, then Octave is a good option. It is a high-level interpreted language, primarily intended for numerical computations.
- Alphaplot: software for interactive scientific graphing and data analysis, similar to Origin, i.e. for those who prefer point & click rather than scripting for generating graphs, but open source!
- LibreCAD: a simple 2D CAD modeller, usually works quite good, but needs dxf files.
- FreeCAD: a powerful 3D CAD program. Unfortunately, it sometimes struggles with files from proprietary software like AutoDesk Inventor.
- OpenSCAD: good for generating models for 3D printing. It is also very mature and widely used, though the scripting language needs some time to getting used to.
- CadQuery: it can import, modify and export industry standard .step files, making it suitable for anything from CNC to 3D printing. It also uses python as scripting language, which makes it very powerful. The challenge is that CadQuery is work in progress, but seems to have very active maintainers and a growing community.
- 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.
- 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.
- 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 365 Servers, if needed, using the tbsync addon .
Other useful Open Source 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.
- GPVDM is a very powerful and well maintained tool to simulate organic/perovskite solar cells, organic field effect transistors (OFETs), and organic light emitting diodes (OLEDs). Developed by Roderick MacKenzie at the University of Nottingham.
Open 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. SDDS and FMF share some similarities.
- HDF5: Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large and complex data collections. It's used for example for our beamtime data at Diamond Light Source.
Used Open 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;-), see here.
Further Information on Open Science:
Below are some more links that contain information about open science, hardware and software:
- TWAS has a list of sites where open info for science can be found. See here.
- Open Source Scientific Tools
- Science for All: How to Make Free, Open Source Laboratory Hardware
- List of resources and references of free and open software for libraries and scholarly use
- “Global Access to Research Software: The Forgotten Pillar of Open Science Implementation", a report of the Global Young Academy.
- FOSTER Plus (Fostering the practical implementation of Open Science in Horizon 2020 and beyond)
- European Commission Study about the impact of open source software and hardware on technological independence, competitiveness and innovation in the EU economy