News – IDI-BD2K https://idi-bd2k.hpcf.upr.edu Increasing Diversity in Interdisciplinary Big Data to Knowledge Mon, 07 Mar 2022 13:36:01 +0000 en-US hourly 1 https://wordpress.org/?v=6.2.2 CONVOCATORIA ABIERTA | PROGRAMA IDI-BD2K | VERANO 2022 | FECHA LÍMITE EXTENDIDA 31 DE MARZO https://idi-bd2k.hpcf.upr.edu/2022/03/07/convocatoria-abierta-programa-idi-bd2k-verano-2022-fecha-limite-extendida-31-de-marzo/ Mon, 07 Mar 2022 13:35:59 +0000 https://idi-bd2k.hpcf.upr.edu/?p=549 Continue reading "CONVOCATORIA ABIERTA | PROGRAMA IDI-BD2K | VERANO 2022 | FECHA LÍMITE EXTENDIDA 31 DE MARZO"]]> C O N V O C A T O R I A A B I E R T A 📢

El programa Increasing Diversity in Interdisciplinary Big Data to Knowlege (IDI-BD2K) desea anunciar que ha abierto la convocatoria para participar en un internado de verano en una de las instituciones adscritas: University of California, Santa Cruz (UCSC), University of Pittsburgh (UPitt) y Harvard University

Requisitos:

Estudiante subgraduado/a a tiempo completo en la UPR-Río Piedras.
Interés en trabajar en ciencia de datos y/o realizar investigación biomédica.
Cursos aprobados en Ciencia de Cómputos y Estadísticas.
Completar la solicitud en línea en todas sus partes.
Proveer dos (2) cartas de recomendación y transcripción de crédito no oficial.

Para solicitar, favor de completar la solicitud en línea: https://tinyurl.com/applybd2k2022
Fecha límite: 28 de febrero de 2022

]]> Applications open https://idi-bd2k.hpcf.upr.edu/2021/03/08/applications-open/ Mon, 08 Mar 2021 18:04:41 +0000 http://idi-bd2k.hpcf.upr.edu/?p=533 Applications are open for Summer 2021.
https://www.tinyurl.com/bd2k2021

]]> Applications open for Summer 2020 internships https://idi-bd2k.hpcf.upr.edu/2020/01/21/applications-open-for-summer-2020-internships/ Tue, 21 Jan 2020 12:18:58 +0000 http://idi-bd2k.hpcf.upr.edu/?p=510 The IDI-BD2K Summer 2020 Internship applications are open. If you would like to work on Data Science this summer at one of our partner institutions (Harvard University, University of Pittsburgh, and University of California Santa Cruz), apply now:

https://tinyurl.com/idibd2k2020

]]> CyVerse Seminar and Workshops https://idi-bd2k.hpcf.upr.edu/2019/12/03/cyverse-seminar-and-workshops/ Tue, 03 Dec 2019 14:15:48 +0000 http://idi-bd2k.hpcf.upr.edu/?p=501 Continue reading "CyVerse Seminar and Workshops"]]> The IDI-BD2K project presents a seminar and workshop on CyVerse

Seminar:

“Computational Learning, Thinking, and Doing in 21st Century Biology”

Jason Williams
Assistant Director
External Collaborations Lead, CyVerse EOT
Cold Spring Harbor Laboratory

Day: Dec. 3, 2019
Time: 12:00 -1:00pm
Place: Amphitheater JGD-123
Julio Garcia Diaz Building
Rio Piedras Campus
University of Puerto Rico

Workshop

DAY 1: General Introduction to CyVerse- Transforming Science through Data-Driven Discovery

Date: Dec. 4, 2019
Time: 9:30am – 4:30pm
Place: Multipurpose Room
Natural Sciences Library
UPR-RP

DAY 2: Using and Customizing Reproducible Workflows in CyVerse
CyVerse Workshop :

Date: Dec. 5, 2019
Time: 9:30am – 4:30pm
Place: Multipurpose Room
Natural Sciences Library
UPR-RP

]]> Big Data Week https://idi-bd2k.hpcf.upr.edu/2018/11/03/big-data-week/ Sat, 03 Nov 2018 23:17:38 +0000 https://idi-bd2k.hpcf.upr.edu/?p=431 The IDI-BD2K program is kicking off more than a week of events next Wednesday November 7, 2018. Come join us for Big Data Week 2018!

]]> IDI-BD2K Poster Session – Wednesday November 7, 2018 https://idi-bd2k.hpcf.upr.edu/2018/10/26/idi-bd2k-poster-session-wednesday-november-7-2018/ Fri, 26 Oct 2018 12:29:33 +0000 https://idi-bd2k.hpcf.upr.edu/?p=426 Continue reading "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 https://idi-bd2k.hpcf.upr.edu/2018/09/28/seminar-exploring-data-science-application-to-biotech-manufacturing/ Fri, 28 Sep 2018 16:45:32 +0000 https://idi-bd2k.hpcf.upr.edu/?p=416 NOTE: Room Change!

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

“Exploring Data Science: Application to Biotech Manufacturing”

by

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

Wednesday, October 3, 2018
11:30AM-12:50PM
New Natural Sciences
NCL A-231
Rio Piedras Campus
University of Puerto Rico
Flyer for seminar

]]> New estimate of deaths from Hurricane Maria https://idi-bd2k.hpcf.upr.edu/2018/09/06/new-estimate-of-deaths-from-hurricane-maria/ Thu, 06 Sep 2018 22:58:31 +0000 https://idi-bd2k.hpcf.upr.edu/?p=407 Continue reading "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.

]]> Workshop – How to Fund Your Education: Writing Award Winning Applications https://idi-bd2k.hpcf.upr.edu/2018/09/03/workshop-how-to-fund-your-education-writing-award-winning-applications/ Mon, 03 Sep 2018 14:34:45 +0000 https://idi-bd2k.hpcf.upr.edu/?p=404 Programas MARC, RISE y IDI-BD2K te invitan
Seminario y Taller
How to Fund Your Education: Writing Award Winning Applications
Sábado, 8 de septiembre de 2018
10am-3pm
NCL A-229
Recinto de Río Piedras
Universidad de Puerto Rico
Flyer for graduate fellowship applications workshop.

]]> Report from the August 2018 Data Carpentry Workshop in Puerto Rico https://idi-bd2k.hpcf.upr.edu/2018/08/29/report-from-the-august-2018-data-carpentry-workshop-in-puerto-rico/ Wed, 29 Aug 2018 21:11:19 +0000 https://idi-bd2k.hpcf.upr.edu/?p=394 Continue reading "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.

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