Open Source Open Science Workshop - Fall 2014

Course Details

Link to a directory of all files for the course

The focus of the OSOS workshop will be using open source methodologies like R in phylogenetics and molecular evolution. The workshop will be *all day* and will include these great module leaders and modules:

  1. Rebecca Clark: Introduction to OSOS, and R basics: the interface, loading data, basic statistics and graphs
  2. Therese Catanach: Using R in Phylogenetics
  3. Luciano Cosme: Next Generation Sequencing - Data processing and gene expression
  4. Therese Catanach: Phylogenetic and Biogeographic assessments in R

The OSOS workshop will conclude with a super-awesome dinner/evening social hosted by EEBISO and EEB. Check your email soon for announcements and updates about the social.


No previous knowledge of R is required. The course is FREE and open to all students, postdocs, and faculty. A laptop is required.

Prior to the start of the workshop, you need to install R and R Studio, as appropriate for your operating system, as well as the additional packages and collection of packages described in this document (pdf). The software packages that make up the software program R are hosted at a set of mirrored sites around the world, which together make up the Comprehensive R Archive Network (CRAN). For the fastest download speeds, select a CRAN location close to you, such as Revolution Analytics in Dallas, TX. For R STudio, select the open-source desktop version of R Studio.


Memorial Student Center (MSC) 2400 (Ballroom). There will be powerstrips available to keep your laptop charged.


Doors will open at 8AM with modules starting at 8:30. Snacks and coffee will be provided during morning and afternoon breaks and participants will have 1.5 hours for lunch (on their own).

Session 1: 8:30 - 10:00 am

Introduction to OSOS and R basics: the interface, loading data, basic statistics and graphs (Rebecca Clark)

Session 2: 10:15 - 11:45 am

Using R in Phylogenetics (Therese Catanach)

Lunch: 11:45 - 1:30 pm

Session 3: 1:30 - 3:30 pm

Next generation sequencing: data processing and gene expression (Luciano Cosme)

Session 4: 3:45 - 5:00

Phylogenetic and biogeographic assessments in R (Therese Catanach)

Additional Websites