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¡Nuestros estudiantes en internados de verano 2016!

Soy Anibal Tornes Blanco y estoy en el Programa Interdisciplinario en la facultad de Ciencias Naturales en la UPR-Río Piedras. Al concluir mi segundo año en la universidad, se me dio una gran oportunidad para explorar mis horizontes en el campo de la Biología Computacional con los líderes en este campo.

Actualmente formo parte de la iniciativa de Big Data to Knowledge (BD2K), impulsado por el National Institutes of Health (NIH). Gracias la colaboración de la Universidad de Puerto Rico-Rio Piedras (UPRRP) y University of Pittsburgh (UPitt) soy parte del Internship in Biomedical Research, Informatics, and Computer Science (iBRIC). Mi proyecto durante este verano ha sido desarrollar un modelo de clasificación para mejorar la capacidad predictiva de datos de relevancia en los Electronic Medical Records (EMR). La popularidad de los EMR en los últimos años ha crecido exponencialmente, sin embargo, los doctores se encuentran ante el “Information Overload”. Este fenómeno se debe a que como seres humanos, nuestra capacidad de reconocer patrones entre resultados de laboratorios es limitado y podría llevar a diagnósticos erróneos. Por tal razón desarrollamos el Learning EMR (LEMR) con el fin de enseñarle a un sistema como predecir posibles condiciones de importancia y asistir a los doctores en sus diagnósticos.

El verano ha sido muy retante, pero mucho más enriquecedor. Les exhorto a que soliciten a experiencias como estas para crecer como individuos tanto en un aspecto personal como laboral. Somos casi un equipo de fútbol de puertorriqueños y nunca pensé que seria de esta forma. Explora tus horizontes y sal de tu “Comfort Zone”.

Anibal en su escritorio.
Anibal en University of Pittsburgh.

¡Nuestros estudiantes en internados de verano 2016!

Soy María del Carmen Ramos Álamo. Voy para mi cuarto año en la UPR-RP. Estoy haciendo 3 concentraciones: Matemáticas, Ciencias de Cómputos y Física.

Fui aceptada para participar durante este verano en uno de los programas del IDI-BD2K (Increasing Diversity in Interdisciplinary Big Data to Knowledge): iBRIC (internship for Biomedical Research, Informatics and Computer Science) en la Universidad de Pittsburgh. Esta ha sido mi primera experiencia de investigación e internado y confío que será la primera de muchas.

Para este proyecto me asignaron hacer varios algoritmos y programas para automatizar el proceso de analizar los resultados de laboratorios y clasificarlos con el propósito de que sea más fácil y rápido dar un diagnóstico. Para esto he tenido que aprender algunos nuevos lenguajes de programación y repasar otros que no usaba con frecuencia. He tenido que trabajar con R, Python, Java, SQL a la vez.

Estas 7 semanas que llevo por acá han sido de mucho crecimiento. No me arrepiento de haber participado de este internado y le recomiendo a todos los estudiantes que aprovechen estas experiencias.

Maria Ramos Alamo en su escritorio.
Maria del Carmen Ramos Alamo en Pittsburgh.

Pre-registration and mentoring meeting May 11, 2016

Pre-registration for August starts this week, we’d like to make sure all the BD2K students are enrolled in the courses they need to compete for the internship opportunities.

BD2K students please come to the meeting in room C-356, Wednesday May 11, 2016 from 11:30 AM to 12:50 PM.

Bring a list of courses you have completed. The table of suggested courses is available online:

Get ready for IDI-BD2K

NSF REU Program in Medical Informatics (MedIX)

The NSF REU Program in Medical Informatics (MedIX) at DePaul University and University of Chicago enters its twelfth year. We are looking for bright undergraduate students to get involved in research in the area of Medical Informatics for the summer of 2016. Participants will receive a stipend of $5,000, travel support to/from the REU site, and subsistence allowance.

Important Dates:

  • March 4, 2016: Application submission deadline
  • March 30, 2016: Notification of decision
  • April 6, 2016: Confirmation of participation
  • June 13, 2016: MedIX Program Orientation
  • August 19, 2016: MedIX Program last day

Statistics on the previous REU MedIX Program (2005-2013):

  • 84% students had at least one research publication
  • 65 publications (9 journal papers, 46 conference papers, 10 extended abstracts)
  • 25% of students are in, or have finished, PhD programs; all received support
  • 18% of student participants have finished masters programs
  • 21% of student are in, or have finished, medical degrees; of those, six are active in research.

For the application form and additional information, please have your students visit the MedIX website at http://facweb.cdm.depaul.edu/research/vc/medix/index.htm or contact Dr. Daniela Raicu at draicu@cdm.depaul.edu.

Summer School for Computational Genomics, June 13-24, 2016.

The Icahn School of Medicine at Mount Sinai is currently accepting applications for the Summer School for Computational Genomics, June 13-24, 2016. The application deadline is March 1, 2016.

Description: Summer School for Computational Genomics – The Icahn School of Medicine at Mount Sinai (New York, NY). Our big data science summer program from June 13-24, 2016, is designed for graduate students and professionals who have a strong interest in the intersection of computer science, genetics, and medicine. There will be sessions on the human genome, genetic variation, and genome technologies, and there will be introductory sessions on Unix, Python, Galaxy Toolkit, and scripting. There will also be field trips to New York Genome Center, Columbia University, and Weill-Cornell Medical Center. This program is funded through NIH grant Big Data to Knowledge (BD2K) 1R25EB020393. Educational and housing costs are covered through this grant; travel stipends are also available. The selection process for participants is competitive, and those selected will be awarded the opportunity to be in the program. For more information and to apply: http://icahn.mssm.edu/creeds. Applicants must be U.S. citizens or permanent residents. This program strives to enhance the diversity of the biomedical big data workforce through recruitment of individuals from diverse racial, ethnic, cultural, and socioeconomic backgrounds.summerprogcompgenomics

Workshop: Big Data Causal Discovery

The Increasing Diversity in Interdisciplinary Big Data to Knowledge (IDI-BD2K) Program at the University of Puerto Rico is pleased to announce a workshop on Big Data causal discovery.

Wednesday Feb 17, 2016

A.   Introduction. Presentations from the Center for Causal Discovery of the University of Pittsburgh and from the UPR IDI-BD2K participant faculty. Dr. Gregory Cooper and Dr. Richard Scheines from the University of Pittsburgh and several faculty members from UPR (and other participating institutions) will briefly present their ongoing projects.  These presentations are aimed at introducing students and faculty to Big Data Projects in Causal Discovery as applied to biomedical problems and at establishing collaborations between the BD2K participants and U. Pittsburgh

Wed 17 Feb, 2016
8:30 – 11:00 am

NCN A-211
Natural Sciences
Rio Piedras Campus
University of Puerto Rico

B. STUDENT RECRUITMENT for Big Data Summer Research Experiences. Drs Joseph Ayoob and David Boone will be presenting information on opportunities for training of students in Big Data, particularly in summer programs for undergraduate students at the University of Pittsburgh.

Wed Feb 17, 2016
11:30 am – 12:30 pm

NCN-A-211
Natural Sciences
Rio Piedras Campus
University of Puerto Rico

C.  HANDS ON WORKSHOP

Causal Discovery from Biomedical Data
Dr. Richard Scheines
University of Pittsburgh

Limited to 30 participants.  Those interested must register by writing to: jegarcia@hpcf.upr.edu

Wed February 17,  2016
1:00-3:00 pm

Julio Garcia Diaz building, room 123
Rio Piedras Campus
University of Puerto Rico

Seminar: Bugs, Parasites and Cities: the complex ecology of Chagas disease in Southern Peru.

The Increasing Diversity in Interdisciplinary Big Data to Knowledge (IDI-BD2K) Program at the University of Puerto Rico is pleased to announce a seminar:

Bugs, Parasites and Cities: the complex ecology of Chagas disease in Southern Peru

Dr. Michael Levy
Assistant Professor
Biostatistics and Epidemiology
University of Pennsylvania

Tuesday, February 9, 2016

Noon

Julio Garcia Diaz building, room 123
Rio Piedras Campus
University of Puerto Rico

Seminar: Graphlet kernels for vertex classification

Graphlet kernels for vertex classification

Where:   College of Natural Sciences, Department of Computer Science
When:    Monday, November 23, 2015
Hour:      2:30 pm
Room:    C-356

Graph kernels for supervised learning and inference on graphs have been around for more than a decade. However, the problem of designing robust kernel functions that can effectively compare graph neighborhoods in a variety of practical scenarios (e.g. the presence of incomplete and/or noisy data, auxiliary information) remains much less explored. Here, I will present my methods for vertex classification in large, sparse, and labeled graphs. Then, I will present an application of these methods to predicting protein function as well as molecular mechanisms of disease.

José Lugo-Martinez is a PhD candidate in Computer Science at Indiana University. The focus of his doctoral research has been the development of graph-based classification algorithms in the supervised and semi‐supervised scenarios, as well as statistical inference from large, noisy, biased, and high‐dimensional data. In particular, he develops computational approaches towards understanding protein function and how disruption of protein function leads to disease. Mr. Lugo-Martinez received dual B.S. degrees in Computer Science and Mathematics at the University of Puerto Rico-Rio Piedras, and M.S. degree in Computer Science at the University of California-San Diego. His research interest include machine learning, data mining and structural bioinformatics.

Department of Computer Science

graphlet