The Incidental Informationist is officially an informationist!

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

Demo-ing Apps in the Classroom

Does anyone have any handy tips they use for demo-ing mobile resources in their workshops and presentations to students, residents, nurses etc? I just happened upon a very neat new (at least to me) feature in Chrome that I had not noticed in the “inspect element” development tool, which I occasionally use to look at source code for troubleshooting purposes. If you’re not confident about, responsible for, or interested in coding intricacies, you may not have ever explored this set of tools, and while there are a number of interesting and useful features for the non-techie person, this trick really jumped out at me as being something that I could immediately incorporate into my everyday work.

Apologies in advance for the many readers who are in institutions that don’t support Chrome. I weep for you daily. For the rest, here are the instructions:

When you right-click on a page in chrome, or CTRL-shift-I, you’ll see an option at the bottom of the list to “inspect element”. There’s an icon in the lower panel of the display, which shows the code, that represents a mobile/tablet device, and which, if clicked, resets the page to display as if it were on such a device. At the top of the page, there is also a drop-down menu with options for specific devices, so you can display a page which emulates the display of different iPhone models, iPads, Android devices- even BlackBerry (in case you are going back in time to do an instruction session.)

While, obviously, the display on-screen in the classroom will be small, if one is discussing mobile resources, there’s something to be said about showing them in their native habitat. Does anyone have a favorite tip or tool that they like to use? I’ve struggled with this in the past and basically given up, because the various emulators that were on-line for this kind of use were not especially reliable and certainly weren’t integrated into the instructional process in the same way. Comment away.

I need a vacation after my co-worker’s vacation…

As I stated in my introductory post, I work in a One Librarian Library. I have a .24 FTE library tech. Time manages us more than we manage it.

I dread the middle of August. That is when my co-worker goes on vacation every year. So, last week I was alone. The time alone caused me to gain a greater appreciation of actual One PERSON Libraries. I don’t know how they manage to get everything done. Everything is important to everybody.

So I sat down each morning and had to decide who I would make happy and who I wouldn’t. Do I do searches or do I process Interlibrary Loans? I think the only thing I new for sure that week was that journal renewals would not be on my radar. Especially after I discovered that EBSCO had migrated us over to their Full Text Finder product.

I finally decided that I should try to make each group at least a little happy. I divided up my day into three parts. I spent the first 3rd of my day doing searches. Spent the next 3rd processing article requests. Spent the last 3rd getting myself up to speed on the new product. Did it work? As best as it could I suppose.

I would love to read in the comments how other OPL’s or OLL’s do it. What are your tips and tricks that keep you sane?

Searching in a Comparative Effectiveness Research Way

I know you have been thinking and searching in an evidence based way, but have you switched to thinking in a broader comparative effectiveness way? The mantra for EBP is “based on the evidence available to me today, I will practice.” The mantra for CER starts there and pays attention to real life settings and can have different sizes to the populations. So, for CER, the mantra chatted is, “what works best for what populations in real world settings.” EPB and CER involve experiences of the health care provider, what the literature shows and the preferences of the patient.

There are 4 main ways to search for CER information, PubMed Health, PubMed Topic Specific Queries-Comparative Effectiveness Research, ANDing effectiveness[sb] to your strategy, or just ANDing the phrase “comparative effectiveness“ to your search strategy.

PubMed Health searches in an clinical effectiveness way. It is geared for the lay public. It has topic reviews, systematic reviews, guidelines and a drug database. When you search PubMed Health, you are searching PubMed at the same time. Be more general in your search topic. It is not a huge database.

Get to PubMed Topic Specific Queries-Comparative Effectiveness Research from the PubMed front page or Put your topic in the search box and click on All for CER results. Notice also you can select a type of study, health disparities, costs and cost analysis or CER as topic.

ANDing effectiveness[sb] to your search strategy is the same as clicking on the Topic Specific Queries-CER page.

Remember you want to search PubMed with words, phrases and MeSH to retrieve all the citations, including inprocess, supplied by publisher or PubMed Central papers. So the phrase “comparative effectiveness” will bring citations for all of PubMed, including the MeSH term, comparative effectiveness research.

Try out any of these methods and send in your comments and questions.

Helen-Ann Brown Epstein

The Incidental Informationist: NCBI Office Hours

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

Value of Libraries: Presentations at IFLA

I went to the session for the Measuring Impact and of course like all conferences there is another session, What is Value, I want to attend is at the same time and on the opposite side of the convention center. I have my walking shoes on today.

Here is the summary of the two sessions I mentioned.

Measuring Impact: This focused on measuring the impact on IFLA’s Lyon Declaration. Interesting to an American because I think we take our access to information so granted.

What is Value: I came late to this program so I only got some of the session. British National Library talked about the value to the cities they serve. They were able to determine that for every pound the government spend on libraries they had a ROI of 4 pounds in business, development and jobs. They had a really good slide on the different values which is on my Facebook page.

Awesome presentation from Elliott Shore, executive director at ARL, Measures of Our Time: The Value of Libraries. Perhaps it is because I’m a big proponent of killing of sacred cows but Elliott’s talk really hit home. The best way for me to describe his talk is to point you to the pictures of his slides on my Facebook page. But here are some memorable quotes.

-The world has changed, have we?

-We need a radical change in how we collect statistics.

-We need predictive analysis rather than descriptive analysis.

He also gave a nice shout out to Becker Medical Library as example of a library that is doing a good job of rethinking and showing their value. Good job Becker!

Live from Cape Town its IFLA

Since most readers will be reading this when I’m asleep, I probably should say this has been previously recorded. I will be posting pictures and thoughts on the fly on my Facebook page so check it out.

So this is my first IFLA conference and so far I’ve attended the U.S. Caucus meeting, Newcomers breakfast, the Opening Ceremony, and the Exhibits Opening.

I will give my quick thoughts on the sessions I have attended.

US Caucus: It is like the business meeting for the Americans.  They summarize IFLA business as a whole. CEO of ALA started everything off and introduced people. The planning committee members for 2016 IFLA (in Columbus, OH) were there as well to try to drum up interest.

Newcomers breakfast: It was very typical of many newbie conference sessions.  They explained the elaborate color coding in the program and encouraged people to talk and meet others. It would have been nice if they explained IFLA structure a bit, but that really did not happen. Perhaps the structure is too complex for a brief newbies breakfast.  There were a lot of people at this session so there was no opportunity to do the speed networking session that we have done at MLA and has been so successful. Instead we were let out “early” to enjoy coffee and “cakes” (muffins) and to get to know each other.

Opening Ceremony: The opening ceremony was huge. There are approximately 3,000 attendees and the reception hall reflected that with three big screens and rows and rows of chairs.  There were beautiful songs and story telling in the custom of Africa to open the proceedings.  The President of IFLA spoke on their Lyon Declaration on Access to Information and Development. The Key Note speaker, Dr. Rob Adam, spoke on the SKA Project and data. He brought up several interesting things about the big data that will come from the SKA project.

– They will need a super computer faster than anything that has been created in 2015.

–  There will be so much data they will need a network so robust that it can handle the entire world’s data worth.

– The data will be open access but embargoed. While they want to make the data available to everyone, they acknowledge that participating in SKA is expensive and they must recognize those who have the foresight to participate have first access.

Opening Exhibits: There are lots of vendors in the exhibit area with lots of variety. I was amazed by the giant photo and preservation machines displayed (and working) at some booths.

BTW very little vendor swag at the opening exhibit. Not even a lot of pens.

The Accidental OPL

My name is Alexia Estabrook and I am honored to be part of the group of fine librarians assisting Michelle Kraft with her blog during her tenure as MLS President. Some of you may remember me as the Medlib Maven from a while back. It’s been quite a while since I’ve blogged and I’m excited to be back.

I am the Librarian at Providence-Providence Park Hospital (PPPH), Southfield Campus, and have been a medical librarian for over 20 years now. When I started at PPPH, the library had a staff of 5 FTE’s and now we are down to 1.5 FTE’s. While I plan to write on a myriad of topics, my mail focus will be on my journey to becoming a one librarian library.

We are also in the process of moving the library and adding a Patient and Family Education Center, so when I’m not talking about being a OPL I’ll be talking about all the fun I’m having planning a new library.

Nice to meet you all!

Another Kraft Worker

It’s an interesting idea to have a communal blog.

My name is Rob Penfold and like one of the other posters (Tobin), I also have a PhD in microbiology and genetics and funnily enough also worked in the malaria area.

I now work in a hospital library setting and hail from Down Under so perhaps can provide a different perspective.

Once, at the forensic library where I worked, we had a Crappy Craft day. My contribution was Krappy Koasters made out of Kraft cheese slices. This rather bemused the lucky recipient. This is my passport for being able to post to the Krafty Librarian blog.


I’m Rebecca Carlson, the Mercy College of Nursing and Health Sciences Library  Director at Southwest Baptist University in Springfield, Missouri. I’ll be one of the guest writers sharing Krafty posts with you this year.

I am the solo librarian on the SBU health sciences campus and I work with faculty and students in our nursing and radiology programs. I wear many hats and have a lot of “other duties as assigned,” but I love the challenges and unique opportunities of medical librarianship. This summer I have been teaching an online class with a nursing instructor on professional writing and APA style for healthcare and have learned a lot from the experience.

I’m looking forward to sharing my thoughts and ideas with y’all and learning from all the fantastic librarians Michelle has assembled here.