Hello Lab! My name is Daniel Cuevas and I just wanted to give myself an introduction here as I am joining the group this week. Hopefully this gives a quick insight into my background experience.

I join the lab as I begin my studies towards a Masters degree with the BMI program here at SDSU. This is not my first time working with Rob Edwards; I have two years under my belt working in Rob’s lab when I was studying for my undergraduate degree in Computer Science. My knowledge in general Biology truly started when my academic career converged here in the field of bioinformatics. My work in the lab involved much introductory work: Android cellphone software development, web application development with JavaScript, algorithm development in Java, and some exposure to bioinformatics tools, like BLAST and assembly tools.

After graduating, I began my internship at Life Technologies where I had a great deal of training doing wetlab experiments as a molecular biologist. I had a months worth of work with the SOLiD sequencing platform. This included the entire DNA library preparation protocol: library fragmentation and preparation, primer ligation, ePCR emulsions, library enrichments, and finally setting up the sequencing instruments to process my DNA samples. Afterwards, running their genome mapping software was also required to determine various analysis on the samples that were sequenced, such as coverage analysis.

In a month’s time, I was absorbed into the newly-acquired Ion Torrent company and continued my mol-bio internship there. I continued performing benchwork duties and running the PGM sequencers, but began to explore the analysis processes that were ran on the sequence data. I slowly became incorporated with the software and bioinformatics aspect of the pipeline, and worked alongside the developing group there. After my internship was completed, I took the position with the software and data analysis team where I eventually accumulated a total of 1 year with Life Tech/Ion Torrent.

Being in a rapidly moving environment, I was forced to very quickly learn new scripting languages like Perl and Python. I also made the effort to expand my web programming knowledge to develop a variety of web tools for our software and mol-bio teams. My experience in JavaScript and jQuery grew tremendously and I also learned the backend language of PHP along the way. I worked alongside mol-bio scientists on a daily basis and frequently collaborated with our multiple sites across the United States. Data analysis was the second half of my workload at Ion where we focused our efforts in performing analyses to explain how mol-bio groups can improve sequencing quality through biology and chemistry.

While working with Ion Torrent, I quickly saw areas where my bioinformatics and analytical skills fell a bit short; areas where I thought more knowledge and an educational-foundation could improve my worth as a scientist and increase my contributions to the R&D teams. This became one of many reasons why I chose to come back to academia in pursuit of higher knowledge and a higher degree in a biological/computational area. I needed re-inforcement of my analysis skills and training in how to look at data and how to develop the questions to ask that would pinpoint problems which could then move this field forward, whether it be related to sequencing improvement, algorithm optimization, cancer-detection software enhancements, or even novel methods that could change the processes set in place now. This now brings me here, on the path to higher education and increase in personal abilities. I hope to become a strong contributor to this group of upcoming scientists and to become a strong one as well.