Welcome!
My name is Danielle Callan and I consider myself a bit of a polymath and autodidact. I love reading, software engineering, learning new things and solving puzzles. From a very early age I found myself interested in understanding all of the living things around me. I also discovered a passion for computers and programming, probably some time during early high school. For a little while I had no idea that I could combine these passions into one field of study…
The Short Version
I now have a BS in Biotechnology and a Professional Science Master’s (PSM) in Bioinformatics, both from Rutgers University. The PSM is a combined business and science program designed to provide students with the skills and mindset needed to produce innovative scientific products. I have worked at RUCDR Infinite Biologics and VEuPathDB which have earned me a cumulative nine years of experience in the field of bioinformatics. During that time, I have learned good software engineering practices and developed knowledge and expertise in processing, analyzing and visualizing complex scientific data. I’m familiar with R, R package development, Shiny, Rserve, Java, Docker and the REST framework among other things. I’ve recently become involved in nf-core and started learning Airflow as well. I’m very interested in metagenomics and applying my skills to that developing field. Find a visual timeline here and details about my work here.
The Long Version
Education
When I arrived at Rutgers University to begin my college career I started in the School of Arts and Sciences. Before long I learned of a Bioinformatics concentration that was offered as a part of the Biotechnology program through the School of Environmental and Biological Sciences. I was too curious and excited to do anything other than immediately transfer schools. During my final year working toward my Bachelor of Science in Biotechnology I learned about another program.
The Graduate School was offering a Bioinformatics concentration and seniors with sufficient credits and a high enough GPA could apply for early admission. The curriculum was still being developed and students had a lot of opportunity for input and flexibility in their course selection. The concentration was part of a combined business and science program and encouraged students to work full-time while completing the degree.
Early Work
Throughout my undergraduate career I spent a lot of time working at Busch Dining Hall as the Student Unit Manager. I was responsible for hiring, scheduling, training and line managing student employees. It was an experience that taught me a lot. In what now feels a remarkably short time I had completed my degree. Not long after I found myself in a graduate program that was encouraging me to work in my field. It was time for something more. I didn’t expect a role in bioinformatics with a degree in biotechnology and no experience. The positions I started applying to were all more traditional biotech roles.
I applied to Medical Diagnostic Laboratories (MDL) for a position I can no longer remember. It wasn’t the position they offered me. They saw my resume, realized I’d be a reasonable fit for another role they hadn’t yet posted and called me. I was offered part-time work providing some technical expertise to a team that was investigating potential biomarkers with prognostic potential for colorectal cancer. I was still a full-time graduate student and it seemed better than I could have hoped for. I didn’t dare dream for anything more yet.
The next thing I knew only a few months had passed when my father pointed out that Rutgers had a bioinformatics position available at RUCDR Infinite Biologics (RUCDR). The position was full-time at a higher rate of pay and would come with tuition remission toward my graduate degree. I applied because I thought it would be stupid to not at least try. Before I knew it I was writing pipelines to pre-process high-throughput Affymetrix microarrays and generate automated reports for clients.
Current Work
I learned quite a lot from my experiences at MDL and RUCDR. Despite that, I’m not sure anything could have prepared me for what was next. Once I had completed my graduate degree I once again decided it was time for something new. I applied to the Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) and its been wonderful and challenging and exhilarating and frustrating and so much more all at once. The VEuPathDB project’s primary expertise is in managing scientific data and developing and maintaining websites that make that data accessible to the public. I have had access to so many different data types and the opportunity to learn from so many experts in different scientific and technical fields. As a result I have learned a lot and grown a lot, both personally and professionally.
Early on at VEuPathDB it became pretty clear that I was stronger in R than a lot of other people on the project. Developing interactive visualizations in R seemed to quickly become something that I owned. I soon became responsible for creating or maintaining Shiny applications for our sister projects ClinEpiDB and MicrobiomeDB. The data are large and complex and their visual and analytical requirements were difficult or impossible to meet as one person developing a Shiny app. When people started talking about replacing the Shiny apps with something bigger and better I was an eager supporter.
The project started developing the new ‘Exploratory Data Analysis Workspace’ (EDA) in earnest. It was a huge effort that exposed me to a lot of new technologies. I wrote the statistical layer of our data visualization software as an R package and made it available as a containerized service using Rserve. I contributed significantly to a Java REST service that defines which visualizations are available in the EDA.
Unfortunately, shortly after completing EDA development the ClinEpiDB project lost funding. I started to focus more on MicrobiomeDB and found I really enjoyed working with metagenomics data. I authored a suite of user-facing R packages that would allow people to reproduce analyses from the website in their local R. I built a prototype for using Apache Airflow to manage nf-core workflows and became involved in nf-core as a developer of metagenomics pipelines.