bertha: Project skeleton for scientific software

Science depends heavily on reliable and easy-to-use software packages, such as mathematical libraries or data analysis tools. Developing such packages requires a lot of effort, which is too often avoided due to the lack of funding or recognition. In order to reduce the efforts required to create sustainable software packages, we present a project skeleton that ensures the best software engineering practices from the start of a project, or serves as reference for existing projects.

[1]  Matjaz Perc,et al.  Modeling the Seasonal Adaptation of Circadian Clocks by Changes in the Network Structure of the Suprachiasmatic Nucleus , 2012, PLoS Comput. Biol..

[2]  Sarah R. Smith,et al.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing , 2014, PLoS biology.

[3]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[4]  Christian Jirauschek,et al.  Modeling and analysis of polarization effects in Fourier domain mode-locked lasers. , 2015, Optics letters.

[5]  Anna Nowogrodzki,et al.  How to support open-source software and stay sane , 2019, Nature.

[6]  Lex Nederbragt,et al.  Good enough practices in scientific computing , 2016, PLoS Comput. Biol..

[7]  Wolfgang Bangerth,et al.  What makes computational open source software libraries successful , 2013 .

[8]  David Thomas,et al.  The Pragmatic Programmer: From Journeyman to Master , 1999 .

[9]  Andreas Prlic,et al.  Ten Simple Rules for the Open Development of Scientific Software , 2012, PLoS Comput. Biol..

[10]  C. Jirauschek,et al.  mbsolve: An open-source solver tool for the Maxwell-Bloch equations , 2020, Comput. Phys. Commun..

[11]  Alfonso Valencia,et al.  Towards FAIR principles for research software , 2020, Data Sci..

[12]  Christian Jirauschek,et al.  Efficient simulation of the swept-waveform polarization dynamics in fiber spools and Fourier domain mode-locked (FDML) lasers , 2017, 1810.04858.

[13]  Ian M. Mitchell,et al.  Best Practices for Scientific Computing , 2012, PLoS biology.

[14]  W. R. Howard Agile Project Management: Creating Innovative Products , 2010 .

[15]  C. Jirauschek,et al.  Optoelectronic Device Simulations Based on Macroscopic Maxwell–Bloch Equations , 2019, Advanced Theory and Simulations.

[16]  Solon Barocas,et al.  Ten simple rules for responsible big data research , 2017, PLoS Comput. Biol..

[17]  Hans-Joachim Bungartz,et al.  Performance evaluation of numerical methods for the Maxwell–Liouville–von Neumann equations , 2018 .

[18]  Carina Haupt,et al.  DLR Software Engineering Guidelines , 2018 .