Objectives
Provide students with basic workflows, platforms and tools to increase reproducibility at all scientific levels
Topics:
- Why reproducibility in science is important.
- Working with Github.
- Data processing workflows to maximize reproducibility.
- Notebooks (R and Jupyter).
- Manuscript and data repositories.
This course can have a recognition of 3 ECTs for FCUL PhD students enrolling in it as part of their first doctoral year.
Minimum formation: Bachelor’s degree in biology or related areas. No previous knowledge is necessary.
Directed to: PhD or MSc students in Biology or related areas, and postdocs and other professionals working in related areas
General Plan
- Why reproducibility is important: we will go through the reason why is it important to keep our research reproducible for others and for ourselves
- Working with Github: students will become familiar with the use of Github as a tool to detail steps of data analysis and data processing and even manuscript writing
- Data processing workflows to maximize reproducibility: students will become familiar with different workflows that allow to create reproducible steps in data processing using open source tools
- Notebooks (R and Jupyter): using two of the most common scripting languages in biology, students will see how notebooks can be used to create fully automated and reproducible analyses
- Manuscript and data repositories: we will go through the different data and manuscript repositories and the advantages of sharing documents in these types of platforms.
Funding
Students fees
Partners
n.a.
Fee
Free for 1st year PhD students in Doctoral programmes at FCUL (e.g. Biologia), Biodiversity, Genetics and Evolution (BIODIV UL; UP) and Biology and Ecology of Global Changes (BEAG UL, UA) when the course counts credits for their formation, in which case the delivery of a final report done after the course is mandatory; the course is also free for more advanced PhD students of the BIODIV programme (ULisboa or UPorto); 15 € for other PhD students from cE3c, 30 € for PhD students from institutions of the PEERS network (CFE); 60 € for FCUL Master students, more advanced PhD FCUL students and unemployed (not from cE3c); 80 € for BTI, BI and other PhD students; 115 € for Professional and postdocs.
Priority is given to non-paying 1st year PhD students mentioned above, being, by order of preference: 1) cE3c students; 2) BIODIV students (not from cE3c); 3) FCUL students (not from cE3c); 4) BEAG students (not from FCUL).
Candidates should send a short CV and a motivation letter to Inês Fragata (irfragata@gmail.com). The cv and letter should be named as 1st-lastNAME-CV.pdf and 1st-lastNAME-ML.pdf (that is personalize the name of each file with your first and last name).
In the email please add the following information:
Full Name:
E-mail:
Phone:
Professional activity: Professional/Postdoc, BTI, BI (or other non-post-doc research grant), PhD student (with/ without scholarship), Lic. (Bachelor)/Master student
PhD student of the 1st year of a Doctoral programme at FCUL, BIODIV (FCUL/FCUP), or BEAG (FCUL or UA)?
If yes to the above question, PhD student doing the Course to count credits for 1st year?:
PhD student of cE3c or CEF (Centro de Ecologia Funcional)?:
Name of the PhD programme:
irfragata@fc.ul.pt
