Author: humberto

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.

Seminar: “This is how it sounds like when doves cry … and coquies sing and monkeys howl and warblers tweet and …”

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

“This is how it sounds like when doves cry … and coquies sing and monkeys howl and warblers tweet and …”

by

Carlos Corrada, PhD
Professor
Department of Computer Science
Rio Piedras Campus
University of Puerto Rico

Wednesday, August 29
11:30 AM – 12:50 PM

NCL A-229
New Natural Sciences Building
Rio Piedras

Flyer for seminar.

Workshop: Design Thinking. August 13-16, 2018.

INCREASING DIVERSITY IN INTERDISCIPLINARY BIG DATA TO KNOWLEDGE PROGRAM PRESENTS:

THINKING LIKE A DESIGNER

4-DAY WORKSHOP

AUGUST 13TH-16TH, 2018

8:30AM-4:00PM

UPR RÍO PIEDRAS
DEPARTMENT OF COMPUTER SCIENCE ROOM A 143

This 4-day workshop will introduce students to the design thinking process through a series of hands-on collaborative activities combined with theoretical and practical lectures. Students will focus on a design challenge of their choosing and ground their process in a human need. By utilizing creative problem solving techniques, students will seek to understand the problem from the user’s perspective, generate ideas, make their ideas tangible, and gather actionable feedback. Collaboration as well as communicating their ideas and crafting a compelling narrative will be a consistent thread throughout the workshop.

FOR MORE INFORMATION:
(787) 764-0000; EXT. 88179 OR MARIMAR.VELAZQUEZ1@UPR.EDU REGISTER AT https://tinyurl.com/idi-bd2k2018

Data Carpentry Genomics workshop August 17-18, 2018

South Big Data Hub/DataUP/Georgia Tech are sponsoring a Data Carpentry Genomics workshop with IDI-BD2K in Rio Piedras August 17-18, 2018.

Genomics Project Organization

  • Data tidiness
  • Planning NGS Projects
  • Examining Data on NCBI SRA database

The Unix Shell

  • Files and directories
  • Pipes and redirection
  • Creating and running shell scripts
  • Organizing bioinformatics projects

Wrangling Genomics Data

  • Assessing Read Quality
  • Trimming and Filtering Reads
  • Variant Calling
  • Automation

Cloud computing

  • What is the cloud
  • Logging into the cloud
  • Setting up your environment
  • Moving data and results to and from the cloud

See the course page for details and registration:

https://idi-bd2k.github.io/2018-08-17-puertorico-genomics/

Anuncio de Curso de “Big Data” (MATE 4995, Sección 012)

Universidad de Puerto Rico

Recinto de Rio Piedras

Semestre: primer semestre 2018-2019

Codificación: MATE 4995 Sección 012

Título del curso- Análisis de datos masivos en aplicaciones biomédicas I (BBD1)

Profesora-  Dra.  Maria E. Perez

Requisitos-  MATE 3026 o equivalente y CCOM 3030 o permiso de la profesora.

Este curso busca preparar al estudiante para dos objetivos fundamentales:

  1. Poder trabajar con grandes cantidades de datos.  Algo esencial en futuros aspectos de todo tipo de investigación.
  2. Poder participar en el proyecto de IDI-BD2K el próximo verano con experiencias de investigación en los Centro de Excelencia de BD2K en las universidades de Harvard, Pittsburgh y la Univ. de California, Santa Cruz.

Estudiantes de cualquier bachillerato de Ciencias Naturales pueden matricularse.

Mas información sobre el proyecto IDI-BD2K

Hoy como nunca antes la investigación  biomédica está generando cantidades masivas de datos, cuyo análisis e interpretación tiene el potencial de producir dramáticos avances en nuestro conocimiento sobre la salud humana y sobre nuestra calidad de vida. El análisis de estos conjuntos masivos de datos (“Big Data”) requiere técnicas que combinan conocimientos en Biología, Química, Estadística, Ciencias  de Cómputo y otras áreas.

El proyecto IDI-BD2K estará ofreciendo el curso MATE 4995 Sección 23 – Análisis de datos masivos en aplicaciones biomédicas I (BBD1) en otoño 2017. En este curso podrás aprender cómo encontrar grupos de genes sobreexpresados en una condición, como el cáncer. Puedes aprender a crear e interpretar modelos lineales que describen la respuesta a un tratamiento. Verán cómo manejar conjuntos masivos de datos genómicos y analizarlos.

Estudiantes que completen este curso y su continuación BBD2 calificarán para ir a un internado en alguno de los Centros de Excelencia de BD2K como Harvard, University of California Santa Cruz, y Pittsburgh.

Para información adicional puedes comunicarte con la Dra. Perez:  maria.perez34@upr.edu

Si aun no estas preparado para tomar BBD1 y 2, asegurate que estas tomando los cursos sugeridos por los Centros de Excelencia BD2K para tu concentración consultando la tabla a continuación: