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Corners, Edges, and the Boundary

I’ve recently gotten more interested in software engineering, despite having taken a course on it previously. As an aspiring computational biologist, I find myself writing more code. So naturally, software engineering concepts pop up.

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366 Papers for 2016

I stumbled upon a Twitter hashtag #366papers. The text usually associated with this is a summary or the title of an article they read. Presumably, they have read the paper and will read an article every day of this year (which happens to be a leap year!).

As a graduate student, I find this challenge great. It’ll help me make a habit of reading journal articles. Additionally, I hope to keep a log of the papers I read with this post. So I will regularly update this post with new papers I read and links to them. Enjoy and wish me luck!

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Translational Medicine Talk Summary

I recently attended the joint conference between International Conference on Intelligent Systems for Molecule Biology and European Conference on Computational Biology in Dublin, Ireland. One talk I went to was Winston Hide’s talk “Translational Medicine: The Current Landscape and Future Directions.” The following is my summary of that talk, along with some personal commentary from me.

On a quick side note, Hide mentions that Russ Altman’s annual Translational Bioinformatics Year in Review talk has influenced his talk. Here is an awesome list of links from Altman’s talk.

Brief Intro to Translational Medicine

One definition of “translational medicine” is the combination of scientific discovery and health improvement. Another succinct way to put it is a “bench-to-bedside” approach, taking research findings at the “bench” and applying it to the “bedside” where it affects patients, public health, and others fields such as policy. This is a very powerful approach and as Winston Hide puts it, “we’re dealing with people, bringing quantitative information to people.”

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Introduction to OpenMP and Open MPI

Computers today are getting faster and more powerful everyday. In the past, the answer to faster computers was to increase the clock speed (e.g. 2.0 GHz to 2.5 GHz) of the computer. This, however, also increases the power consumption of the computer. This increasing power consumption is not sustainable because with more power, the most heat that is generated and even more power is needed to cool down the processors. Thus, faster hardware is not the answer.

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Telling a Story

Reading Time: 5 minutes

Today, I thought about some advice professors have given me in the past while doing course work. Several have told me when giving a presentation or doing research that you should tell a story. But yet, they never go into detail about what that actually means. This can be very frustrating for a learning student! Every time I have heard that, I always think, “Yeah, I get that. I can make a story no problem.” It turned out to be more difficult the more I thought about it.

What does telling a story mean?

Over time, I’ve gotten a sense of what telling a story means when doing research. Several years ago, I had a class project for my introduction to bioinformatics course. Our professor assigned each of us a gene to study and to “tell a story about it” using the tools we’ve learned. We learned about analyses such as: using BLAST to perform sequence alignment; performing multiple sequence alignments using MUSCLE to find homology; and a network analysis of our assigned gene and it’s expressed protein interactions with other genes products.

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