Open Source software and tools for better research

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The first webinar of the Open Science MOOC focused on Module 5: Open Research Software and Open Source and was pesented by our team colleague André Maia Chagas.

 

View the slides of this presentation at zenodo.org/record/3242340

Cite as: Maia Chagas, Andre. (2019, June). Bringing science to the 21st Century: Open Source tools for better research. Zenodo. http://doi.org/10.5281/zenodo.3242340

Online Course

Take the free Open Science MOOC online course: Module 5: Open Research Software and Open Source.

Resources and key takeaways

Why we need Open Source in Science

– REF: Ziemann,  M., Eren Y., El-Osta A. (2016). Gene name errors are widespread in the scientific literature.Genome Biology201617:177. doi.org/10.1186/s13059-016-1044-7
Abstract: The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.

– REF: Collins, K. (2015). Why researchers keep citing retracted papers. qz.com/583497/…/
Retraction Watch released a list of the retracted research papers with the most citations, and many of the citations came after those papers were pulled.
– Also see retractionwatch.com

30 seconds to master Open Source

  • Everything (code, hardware design, protocols, cake recipes) created is shared freely via licenses (GNU, Creative Commons, OSHWA, and many other), using any means at hand (Internet, usb sticks, recipe notebook)
  • We’ve always done it. Now we just have a fancy name for it and metrics so that all projects follow a certain standard.
  • Powers your smartphones, data centers, computers in airplanes, supercomputers

– REF: Vaughan-Nichols, S.J. (2015). It’s an open-source world: 78 percent of companies run open-source software. zdnet.com/article/…/

Open Science software

Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. // The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more.

Binder – Turn a Git repo into a collection of interactive notebooks

Search for Open Source Software in your discipline
– Many tutorials online
– Reach out to developers – they will be super happy to answer your questions
– Open Science MOOC Module 5 resources
– Openscapes – mentorship program to empower scientists with open data science tools

 

GOSH

Join the forum:  https://forum.openhardware.science/

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