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Open Science in Bioinformatics

OpenScienceKE

#OpenScienceKE @Calkibet

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What to expect...

  • What is Open Science
  • Why Open Science
  • Open Science Taxonomy
  • Open Science Tools
  • Open Science in Bioinformatics
  • KBN

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We are Scientists, Lecturers, Students, and Researchers who Love Open Science.

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What is Open Science ?

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Open Science is the practice of science in such a way that others can collaborate and contribute, where research data, lab notes and other research processes are freely available, under terms that enable reuse, redistribution and reproduction of the research and its underlying data and methods.

(https://www.fosteropenscience.eu/foster-taxonomy/open-science-definition )

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Why Open Science ?

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"When all researchers are aware of Open Science, and are trained, supported and guided at all career stages to practice Open Science, the potential is there to fundamentally change the way research is performed and disseminated, fostering a scientific ecosystem in which research gains increased visibility, is shared more efficiently, and is performed with enhanced research integrity."

Open Science Skills Working Group Report (2017)

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Open Science is good for the researcher...

  1. Increased quality of research from reduced errors and fraud due to wider scrutiny and evaluation brought about by transparency
  2. Increased opportunities for both local and global participation in research
  3. Faster transfer of knowledge required to solve problems
  4. Fosters innovation which produces new products and services
  5. Improves productivity and research output due to reduced duplication
  6. Promote awareness among citizens which improves willingness in participation in experiments and data collection.

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Open Science Taxonomy

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Your Open Data should adhere to...

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The monster of Paywalls and Impact Factors...

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“When a measure becomes the target, it ceases to be a good measure”

--Goodhart's Law

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The Irony...

“Open Science is transparent and accessible knowledge that is shared and developed through collaborative networks”

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The Paper is the advertisement...

But...

by Patrick Hochstenbach

CC-BY

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“An article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code and data, that produced the result.”

Buckheit and Donoho (1995)

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What are your options?

So, even with closed Journals, you can still be Open:

  • Preprint
  • Postprint

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Some Great Options...

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Journals with open access and open review:

  • F1000Research
  • The AAS Open Access Journal
  • Wellcome Open Research
  • eLife

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But avoid Predatory Journals...

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Code is the Scholarship...

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Open Science Tools

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Git and GitHub

Git is a Version Control System.

  • Helps to keep track of the entire history of things that you are working on.
  • Facilitates collaboration on projects

GitHub is a hosting service for Git Repositories

  • Web-based service for version control and online collaboration
  • The social networking site for developers
  • Used to build a portfolio and get noticed by potential recruiters

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RMarkdown

  • Provides an authoring framework for data science
  • It can be used to save and execute code
  • As well as generate high quality and reproducible reports or presentations that can be shared with an audience
  • It has built-in support for HTML, PDF, MS_Word, RTF, Github, ODT etc

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Literate Programming: Jupyter Notebooks...

  • Open web application for creation and sharing of documents with live code, equations, visualization
  • Notebook documents are human-readable and can contain analysis description, results as well executable code that can be run to perform data analysis.

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Zenodo

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Data repositories

  • Zenodo - is an open access research data repository that provides a place for researchers in any field to deposit datasets up to 50 GB. It has an integration with GitHub to make code hosted on GitHub citable.
  • Figshare - is an online digital repository where researchers can preserve and share their research output i.e. figures, datasets, images and videos.
  • Dryad - is a curated a general-purpose repository that makes the data undisclosed in scientific publications discoverable, freely reusable and citable
  • Dataverse - is an open source web application to share, preserve, cite, explore and analyze research data. Dataverse repository hosts multiple dataverses

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How I’ve practiced Open Science...

F1000: https://f1000research.com/articles/4-1429/v2

Jupyter: https://github.com/kipkurui/MARS_Evaluation/blob/master/MARS_Evaluation/Complete_Analysis-MARS_Evaluation.ipynb

BioRxiv: https://www.biorxiv.org/content/early/2016/11/14/065615

Zenodo: https://zenodo.org/record/46440#.WweEXe6FOM8

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Open Science in Bioinformatics

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Bioinformatics is becoming a Data Science, therefore, Open Science Tools should be adopted.

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But some specific ones exist...

Singularity

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Leading Players Adopting Open Source

www.theinquirer.net/

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But I’m Only a Biologists...

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We got you...

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To learn more about Open Science...

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Kenya Bioinformatics Network (KBN)

  • Who are we: A network of Bioinformaticians working in Kenya
  • What do we do: Collaborate in research projects, conduct training and seminars on Bioinformatics, promote open science, and organize meetups.
  • How can you join: If you are trained or has an interest in Bioinformatics, send us an email to: kenyabioinformaticsnetwork@gmail.com
  • Where can you find us: https://kipkurui.github.io/studyGroup/

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Our hope is that...

“Future generations [will] look on the term “open science” as a tautology – a throwback from an era before science woke up.

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“Open science” will simply become known as science,

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and the closed, secretive practices that define our current culture will seem as primitive to them as alchemy is to us.”

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-- Brian Nosek and Chris Chambers

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Acknowledgements

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Contact Us

Caleb Kibet Rosaline Macharia Kelvin Muteru Pauline Karega

@Calkibet @luckrosa1 @Kmut2030b @KaregaP

Tweet with #OpenScienceKE

Email: kenyabioinformaticsnetwork@gmail.com

Watch: https://github.com/kipkurui/OpenScienceInBioinformatics-Kenya

Site: https://kipkurui.github.io/studyGroup/

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Possible additions

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