Latin American R/BioConductor Developers Workshop 2018

Community of Bioinformatics Software Developers

Requirements

Requirements prior knowledge

  • Participants should have basic knowledge of programming language R: variable assignment, reading files: read.csv, read.delim, read.table; data structures: matrix, dataframe, list; data types: character, numeric, factor, logical, etc; installation and use of packages.
  • R: know how to install packages
  • RStudio: know how to use.

Technical requirements

  • Personal computer
  • Minimum 8GB RAM, a mouse and sufficient disk space for text files and image files. Administrator privileges to install and run utilities such as RStudio.

Introduction

In recent years, biology has seen a rise in the use of technologies that enable high-throughput, quantitative, data-rich profiling of cellular states. As a result, the field now faces computational challenges to analyze such data. The R/Bioconductor project is an open source, open development software platform that provides tools to translate complex data sets into biological knowledge.

This workshop is aimed at students and researchers interested in the analysis of biological data. We encourage applications from experts in diverse disciplines, including but not limited to biologists, bioinformaticians, data scientists, software engineers and programmers and R users at large. The main goals of the workshop are:

  1. Teach participants the principles of reproducible data science through the development of R/Bioconductor packages.

  2. Turn bioinformatics software users into bioinformatics software developers.

  3. Foster the exchange of expertise and establish multidisciplinary collaborations.

  4. Create a community of Latin American scientists committed to the development of software and computational pipelines for biological data analysis.

  5. Help train bioinformatics instructors that can continue to grow in their local communities.

This workshop is part of a long-term project to create a community of developers from Latin America. We hope to hold regular meetings in the future (similar to BioC, EuroBioc and BioCAsia) where attendees present their own software contributions. To provide a welcoming environment please follow our code of conduct.

Program

Materials

Day 1: July 30, 2018
09:00 - 10:00 Inauguration in the main auditorium
10:00 - 10:30 Keynote Lecture I: From learning to using to teaching to developing R Leonardo Collado-Torres
10:30 - 11:00 Talk I: Example of Bioinformatics in Mexico Daniel Piñero
11:00 - 11:20 Coffee break
11:20 - 12:20 Creating a package Alejandro Reyes
12:20 - 12:40 Break
12:40 - 14:00 Version control with git and GitHub Selene L. Fernandez-Valverde
14:00 - 15:30 Lunch break
15:30 - 16:15 Open source software projects and collaborative development Selene L. Fernandez-Valverde
16:45 - 17:30 Package documentation Alejandro Reyes
17:30 - Welcome cocktail
Day 2: July 31, 2018
9:00 - 10:00 Keynote Lecture II Martin Morgan
10:00 - 10:30 Talk II: Example of Bioinformatics in Mexico: Using R-Shiny in Agrobiodiversity Alejandro Ponce-Mendoza
10:30 - 11:00 Coffee break
11:00 - 12:15 Best practices for writing efficient functions Martin Morgan
12:15 - 13:45 Bioconductor: core package, common objects and extending classes Benilton de Sá Carvalho
13:45 - 15:30 Lunch break
15:30 - 17:30 S4 - system for object oriented programming Martin Morgan
17:30 - 18:30 Poster session
Day 3: August 1, 2018
9:00 - 10:00 Collaborative project organization and introduction Daniela Ledezma-Tejeida
10:00 - 10:30 Vignette writing with markdown/BiocStyle Benilton de Sá Carvalho
10:30 - 10:50 Coffee break/Event Photo (to be confirmed)
10:50 - 11:30 Unit testing and R CMD check Martin Morgan
11:30 - 12:10 Rcpp (Adding C/C++ code to R packages) Benilton de Sá Carvalho
12:10 - 12:30 Break
12:30 - 14:00 Debugging and Parallelization Martin Morgan
14:00 - 15:30 Lunch break
15:30 - 17:30 Working on a Collaborative Project
Day 4: August 2, 2018
9:00 - 10:00 Keynote Lecture IV Benilton Carvalho
10:00 - 10:30 Talk III: RLadies Community Experience Teresa Ortíz
10:30 - 11:00 Coffee break
11:00 - 14:00 Working on a Collaborative Project
14:00 - 15:30 Lunch break
15:30 - 17:30 Working on a Collaborative Project
Day 5: August 3, 2018
9:00 - 10:00 Working on a Collaborative Project and recovery from La Palapa
10:00 - 10:30 Working on a Collaborative Project
10:30 - 11:00 Coffee break
11:00 - 11:30 Working on a Collaborative Project
11:30 - 12:30 Presentations of collaborative projects
12:30 - 13:00 Closing remarks and community building

Instructors:

Organizing committee:

Code of Conduct

Sponsors

Become our sponsor

Centro de Ciencias Genómicas UNAM

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CDSB
Community of Bioinformatics Software Developers

We want to help you acquire the skills to contribute open source Bioinformatics software using R

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