Software Carpentry Workshops (Python and R)

The IDI-BD2K project and the AECC is organizing two workshops January 11-12, 2019 in UPR Rio Piedras, Department of Computer Science. We will be running Software Carpentry workshops in Python and R.

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshops will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Python is a general purpose scripting language popular in scientific computing.

R is a statistical computing language with extensive applications in bio-statistics and ecology.

Please register only for the version you will attend. The workshops will be held at the same time.

Registration for the R version

Registration for the Python version

Seminar: Causal network discovery from biomedical data

The IDI-BD2K program is pleased to present a seminar entitled

Causal network discovery from biomedical data


Gregory Cooper, M.D., Ph.D.
University of Pittsburgh

Date: November 14, 2018
Time: 5:00 PM
Room: CNL A-211
Ciencias Naturales Fase II
UPR Río Piedras

Causal modeling is an up and coming field at the intersection of statistics and machine learning which seeks to discover which features are most responsible for the decisions of ML algorithms. This talk will provide an introduction to concepts and methods for learning causal relationships in the form of causal networks from biomedical and clinical data, including solely observational data. Examples will be given of applying these methods to biomedical data. The talk will also provide pointers to software for learning causal networks from data, including data containing thousands of variables.

IDI-BD2K Poster Session – Wednesday November 7, 2018

Want to know what IDI-BD2K students did last summer? To kick off BD2K week, we will have a poster session Wednesday November 7 from 11:30AM-12:50PM in the lobby of the New Natural Sciences Building in UPR Rio Piedras.

Come see the student’s work and find out how you can participate in a summer internship at one of the National Institutes of Health funded Centers of Excellence in Biomedical Big Data to Knowledge.

Seminar: Exploring Data Science: Application to Biotech Manufacturing

NOTE: Room Change!

The IDI-BD2K program is pleased to present a seminar:

“Exploring Data Science: Application to Biotech Manufacturing”


Pablo J. Rosado, PhD
Senior Engineer, Amgen
Digital Integration and Predictive Technologies

Wednesday, October 3, 2018
New Natural Sciences
NCL A-231
Rio Piedras Campus
University of Puerto Rico
Flyer for seminar

New estimate of deaths from Hurricane Maria

Our friend and colleague, Rafa Irizarry, released a new analysis of death records recently released by the Institute of Statistics.

He has released a preprint on bioarxiv, and most of the data and all the code on github.

Report from the August 2018 Data Carpentry Workshop in Puerto Rico

The IDI-BD2K project organized a Data Carpentry Genomics workshop at the University of Puerto Rico Rio Piedras Campus, sponsored by the South Big Data Hub.

The workshop was a resounding success with 35 learners registered, and 13 more on a waiting list. Attendees ranged from undergraduate and graduate students to faculty and staff. We need to do more Carpentries workshops!

Photo of workshop venue showing Participants in the Data Carpentry Genomics workshop
Participants in the Data Carpentry Genomics workshop

Instructors were Nelly Selem from Mexico and Humberto Ortiz-Zuazaga from Rio Piedras, and a group of volunteer helpers: Eveliz Peguero, Sebastian Cruz, Israel Dilán, Abraham Avelar, and Kevin Legarreta Gonzalez.

Carpentry workshops teach foundational coding and data science skills to researchers, so they are a great match for IDI-BD2K’s goal of creating diverse teams of scientists looking at turning biological data into biomedical knowledge.

Participants learned how to manipulate next generation sequencing data to see variants in a population of E. coli. To do this, they used cloud computing resources, logged in remotely, processed files on the command line, and wrote scripts to automate parts of the analysis.

Example responses from learners on something they learned at the workshop.
What I learned at the workshop.

The Carpentries also disseminate best practices on teaching in STEM, as informed by research and the instructor’s experience. The green and red papers on learners desks or laptops are one example. Learners are asked to place the green paper on their laptop if they complete an exercise, and a red one if they get stuck. This feedback helps maintain an appropriate pace for the workshop. I forgot to use the stickies the first day of the workshop, and at times we went too fast.

Square notes with learner feedback.
One thing I didn’t like about the first day of the workshop.