Author: Tobin Magle

I recently attended the NLM Georgia Biomedical Informatics Course at the lovely Brasstown Valley Resort in Young Harris, GA. This week-long semiannual course is hosted by the Robert B. Greenblatt, M.D. Library, Georgia Regents University and funded by the National Library of Medicine. If you’ve ever heard library colleagues talk about the Woodshole course, this is the current version of that course. The content changes every session, which is necessary in such a fast moving field.

Attendees were a nice mix of librarians, clinicians, researchers and others involved in medical information technology. Instructors who are in the forefront of their field came from around the country to teach in this prestigious course. I found it to be a great overview of current important topics in informatics, and I learned so much about the breadth of this essential field from both the instructors and the other attendees. We also did some networking and shooting pool at the local watering hole, Brassies.

Read more to see what was covered (and some cool pictures from a field trip we took)

Continue reading NLM Georgia Biomedical Informatics Course

I recently found out that the NLM Administrative Supplement for Informationist Services that I am included on received funding! This opportunity is very exciting to me because I will be working on an interesting project with a great group of people.

I will be providing data curation services for an R01 project by Dr. Katerina Kechris that generated a Next Generation Sequencing (NGS) dataset from an inbred mouse panel. The mice are closely related, but have known genetic differences. They also exhibit an array of behavioral traits that relate to alcohol use disorders, such as ethanol sensitivity, tolerance and consumption. The NGS dataset is limited to a small RNA molecules known as micro RNAs (miRNAs). These molecules typically regulate gene expression rather than getting read by ribosomes to make protein, as the central dogma dictates. The goal of this project is to discern whether expression any of these miRNAs correlates with the alcohol use phenotypes mentioned above. Additionally, these miRNAs are closely related to those in humans, which could give clues to the mechanisms of alcohol use disorders in humans.

The mouse panel that the NGS samples came from can be used for much more than this alcohol use disorder study, and Dr. Kechris had already written in her R01 proposal that she wanted to share this resource with the research community in the PhenoGen database. Thus, we proposed the following Aims to increase the usability of this dataset by other research groups:

Aim 1 Make the NGS data, appropriate metadata, and code publicly available.

I will deposit the raw data in the NCBI databases along with appropriate metadata, or data that describes their data, to give it context and reusability. I will also deposit the code that they have used to clean and analyze their data to GitHub, so other people can repeat their analyses. This aim also supports a web programmer who will add functionality to the PhenoGen database to support this new dataset. We are also creating an entry for our institutional repository to link all this information together and to our campus.

Aim 2 Create tutorials to show other researchers how to use these data.

All the information is on the web, so it should be usable, right? Well we’re going to make it even easier to use these data by making tutorials in a variety of formats: video, text/static images, and Guide on the Side. These resources will also be referenced on the repository entry.

Aim 3 Evaluate the efficacy of Aims 1 and 2.

Finally, we will evaluate whether the first 2 aims are effective. I will do this by tracking data download and citation statistics, and by including assessments within the tutorials to evaluate their efficacy.

I’m so excited about this project! I can’t wait to get started. Now I just need to figure out how grant funding works here.

Questions and feedback are, of course, welcome.

– Tobin

I attended a web meeting last week hosted by NCBI staff member Peter Cooper. These meetings are open to anyone who has participated in the course A Librarian’s Guide to NCBI. This course is composed of an asynchronous web class (Fundamentals of Bioinformatics and Searching) and a week long training at NCBI. The course itself is free, but you have to provide your own lodging and travel expenses.

I attended this course last spring, and it was great. Because of my background, I already knew a lot of the molecular biology background information, but attending the course allowed me to observe and example of how to teach this material to novices.  As far as the content about the databases, the amount of information we received was mind-blowing! I can say with certainty that most of the researchers where you work are not proficient at using these tools (even if they think they are) and that you will be able to use them more effectively than they can if you take this course.

Once completing the course, you will have access to a web forum and monthly web meetings to discuss topics covered in the course and implementing NCBI database services at your library. it’s a great, responsive community that has been invaluable to my work.

Follow the link above if you’re interested in applying. I can’t say enough about how great this course was for me.

In addition to a plug for the Librarian’s Guide, we talked about PubMed Labs: a forum for NCBI to test out new functionality of their databases earlier in the development process. New features are being announced via a new category on the NCBI insights blog. Currently, they have two new features: PubMed Also Viewed and SmartBLAST. Let them know about what you think of the new features by commenting on their respective blog posts.

– Tobin

I’m Tobin Magle, the Biomedical Sciences Research Support Specialist at the Health Sciences Library on the University of Colorado Anschutz Medical Campus. I’m so excited to be a guest writer for the Krafty Librarian as she takes on her responsibilities as MLA president.

My dirty little secret is that I don’t have a library degree: my background is in research science. I have a PhD in microbiology, and my research focused on parasites like Toxoplasma gondii and Plasmodium falciparum, the causative agent of malaria.

While working on studying these pathogens is a very worthwhile and necessary pursuit, it just wasn’t for me. I began investigating careers outside the research laboratory and came across the listing for my position at CU Anschutz, somewhat incidentally you might say.

To make a long story short, it ended up being a perfect fit. I can focus on helping others do all the very important aspects of research science that often get short changed. I honestly feel like I won the lottery. I can’t believe I’ve been working at the CU Anschutz HSL for almost a year now! Time flies when you’re having fun I guess.

I primarily focus on bioinformatics, data management and sharing, and scholarly communication (if you can call that focus). These all fall under the theme of providing research support on our campus. I aim to bring a research/informatics perspective to the blog. I hope you enjoy it!