Category: Internships

Hi! I am Andres Lopez Rivas, a Biology undergraduate student at the University of Puerto Rico, Río Piedras campus. Thanks to the IDI-BD2K program, I am currently on an Internship in Biomedical Research, Informatics and Computer Science (iBRIC) at the University of Pittsburgh. Working with professor Takis Benos, I collaborated with graduate students on a groundbreaking research, examining gene expression and pathway analysis involved in resistance to PD-1/PD-L1 immunotherapy on melanoma patients. We are trying to identify biomarkers that can predict the outcome of the patient’s cancer when the immunotherapy is delivered. Understanding the mechanism involved in this immunotherapy is not only important in melanoma patients but also in numerous cancer types like kidney, bladder, non-small cell lung and others since the pathway that this therapy triggers governs in a multitude of cancer types. Nowadays the researchers of medicine, as well as researchers in other branches of investigation, must assume a more interdisciplinary role to encompass the challenges and find a solution. This program not only deepened my knowledge in biology, mathematics and computer science but also gave me the tools to apply it to problems that every researcher in my field faces. At the end of the week all of the interns will be presenting a poster at Duquesne University along with other interns from different programs. Although it has been a challenging 10 week internship, my colleagues and I have been enjoying every minute of it by going to baseball games, festivals, museums, theaters, concerts and many other things the city of Pittsburgh has to offer.

Hi, my name is Louis Gil. I’m a senior from the University of Puerto Rico Rio Piedras Campus, Department of Computer Science. This summer thanks to the IBD2k program, I worked in a computational genomics
research project in UPMC Shadyside Hospital as part of the University of Pittsburgh and DBMI program iBRIC with my mentor William LaFramboise. Here I worked in my first sequencing lab, having the first-hand experience of having your data created right next to you is an amazing feeling, it’s like getting bread right out the oven.

I’m working with papillary renal cell carcinomas which are rare form of kidney cancer that have been sub-classified into type 1 (PP1) and Type 2 (PP2) based on phenotypic differences. Here we were tasked to find molecular difference between these two classes. By then comparing these data sets we could later infer a pathway for each type, such that we can then distinguish main drivers and differences of both subclasses. We worked with expression data, CNV’s, SNP’s and indels, and used tools that were all new to me such as Galaxy (VarScan), Nexus, NIH David, Genome Oncology Browser and IPA (Ingenuity). This hands-on approach to all these tools was a great experience and facing hurdles along the way just motivates you to keep going and not make mistakes.

Pittsburgh is a great city filled with amazing and lovely people and every corner seemed to be an adventure. I also attended many conferences and talks where I learned of new technologies like Tetrad, learned about graduate school and how to improve my skills in presenting and overall skills associated to my field. I made great friends and contacts that will help me in the future to become a better person and professional.

Hi! My name is Iván Jiménez and I am a senior Computer Science undergrad at the University of Puerto Rico, Rio Piedras Campus (UPRRP). Through the UPRRP’s Increasing Diversity in Interdisciplinary Big Data to Knowledge (IDI-BD2K) program, I was able to participate in the Internship in Biomedical Research, Informatics and Computer Science (iBRIC) during this summer. I worked with Alexander Ropelewski at the Pittsburgh Supercomputing Center (PSC) in Pittsburgh, Pennsylvania. We worked in collaboration with the Department of Biomedical Informatics (DBMI) of the University of Pittsburgh on our project titled “Optimizing High Performance Big Data Cancer Workflows”. The project consisted of running cancer workflows on different file systems of PSC’s new supercomputer: Bridges. We optimized these workflows in terms of execution timings and memory usage and then produced recommendations for future use of programs on each file system.

I also had the chance to develop a project poster and present it at the annual Duquesne Summer Undergraduate Research Symposium at Duquesne University. Our work has been recently accepted for publishing as a student paper for the Practice and Experience in Advanced Research Computing (PEARC-2017) conference.

Apart from work, one of the best highlights of my summer was touring the PSC, UPitt and Carnegie Mellon campuses and buildings with my fellow interns. The list of awesome activities we did as a group is too long to mention in this summary so I’ll just include the schedule we tried to follow throughout the internship.

Thanks to the IDI-BD2K program, I will never forget fun I had while meeting new people, eating lots of pizza and learning about Bioinformatics and High Performance Computing.

Mi nombre es Tatiana P. Ortiz Serrano y actualmente curso mi cuarto año de estudios subgraduados en la Facultad de Ciencias Naturales de la UPR-RP. El verano pasado tuve la oportunidad de completar un internado en la Universidad de Pittsburgh. Puede parecer inusual, pero la realidad es que fui parte de dos programas simultáneamente: Internship in Biomedical Research, Informatics, and Computer Science (iBRIC​) y Training and Experimentation in Computational Biology (TECBio​). Durante 10 semanas trabajé con el Dr. Miller T. Lee en su investigación sobre la embriogénesis en los peces cebra.

Esta representó mi primera experiencia de investigación, por lo que no faltaron las dificultades y tropiezos en el proceso. No obstante, la misma fue sumamente enriquecedora tanto en el ámbito académico como profesional. Puedo decir que amplié mis conocimientos en la disciplina que estudio, que es la Biología, y en el área de la Bioinformática. Incluso, tuve la oportunidad de presentar mi afiche en un simposio en la Universidad de Duquesne. Además, comprobé, de primera mano, la importancia del manejo de los grandes conjuntos de datos que produce la investigación científica diariamente y el rol tan importante que juega la colaboración interdisciplinaria en ello. Por otro lado, establecí lazos interpersonales, que todavía se mantienen, con compatriotas y estudiantes de otras universidades. Conocí buenos mentores quienes me ofrecieron su apoyo y consejería, y con los cuales sé que puedo contar.

Quiero instar a otros estudiantes de ciencias a participar de experiencias de internados como estos porque considero que son oportunidades excelentes para adquirir y aplicar herramientas necesarias para llevar a cabo proyectos de investigación exitosos. Como científicos debemos saber que una parte esencial del proceso de investigación es la interpretación de los resultados que se obtienen. Internados como iBRIC y TECBio brindan la plataforma para aprender más sobre cómo hacerlo y poder aplicarlo a futuros proyectos.