What is Bioinformatics Librarianship?

Welcome to Bioinformatics Librarianship. With Katie and with me
today are Molly Knapp from the NNLM Training Center and Bonnie Maidak from
the NCBI, as well as eight librarians who support molecular biology and genetics
databases and tools. Before we begin I like to define bioinformatics
and touch briefly on the central role that NCBI plays in this
field. According to Dorland’s Medical
Dictionary bioinformatics is the organization and analysis of biological
and related information usually involving use of computers to develop
Databases, retrieval mechanisms, and data analysis tools especially in the fields
of molecular biology structural biology and genetics. You probably know that
bioinformatics often has a broader definition that includes medical
Informatics. For the purposes of today’s
webinar we’re using bioinformatics in this narrower sense focusing on
biomolecular data. Who we are. So the National Center for
Biotechnology Information is really at the core of bioinformatics as we just
defined it. Our overarching goal is to
develop new information technologies, that means computers, to help and
understanding molecular and genetic processes that affect health and disease. NCBI has developed some of the best
known and most heavily used bioinformatics databases in the world,
including public sequence of genomics databases and curated gene information. So I had some medical librarians around
the world who are now working with and assisting patrons with these types of
biological data, including the data management and stored and curated at
NCBI. During the webinar today eight
librarians will briefly describe their roles in bioinformatics and how they have
integrated these services in the programs of their institutions. I want to mention before we start that
all of our speakers are also graduates of an introductory bioinformatics
training program that comprised the online introductory fundamentals of
bioinformatics and searching. It was
created by the National Network of Libraries of Medicine Diane Rein from
the University of Buffalo. We also had a
more advanced in-person NCBI-specific training called the Librarian’s Guide to
NCBI. These courses were offered from
2013 to 2016 online and here at the NIH. We’re currently in the process of
refactoring and updating this training based on the needs of the community. Therefore, another purpose of today’s
webinar is to gather input from you on the development of new bioinformatics
training materials for librarians. As
Kate mentioned during the webinar, we’ll ask you to participate in several polls
about your experience and interest surrounding molecular biology, genetics
tools, and databases. We’re also going to
invite you to join us for a focus group session at a later date were you can
provide further input on what bioinformatics topics are important to
You, through what medium or methods you would like to receive training. So now that we’ve covered this background,
let’s turn to our speakers today. We’re
going to hear from librarians that are listed on the screen
Julie Arendt and Karen Gau from Virginia Commonwealth University,
Marci Brandenburg from the University of Michigan, Rolando Garcia Milian from
Yale, Tobin Magle from Colorado State, Robin Reed from Penn State at Hershey,
Elliott Smith from the University of California at Berkeley, and Rob Wright
from Johns Hopkins School of Medicine. So I’m now going to turn it over to our
speakers beginning with Karen and Julie. Karen and Julie will present together
since they are from two parts if the same institution Virginia Commonwealth
University. As promised after each
speaker we will conduct a brief poll to get input from you and then move on to our
next speaker. Thanks, Peter. So I thought I’d start with
some bioinformatics related background on Virginia Commonwealth University. My
name is Karen Gau, and I’m a librarian on our Health Sciences Campus where we have
various department centers and institutes with biomedical interests. In
bioinformatics I work with the basic sciences departments on this campus. Julie Arendt is our science and
engineering librarian and she works on our general academic campus. This campus
includes our bioinformatics degree Programs, as well as other departments
that have an interest in bioinformatics. Neither Julia nor I are bioinformatics
librarians, but we knew that given these demographics we needed to be able to
support this area. We both have a limited
educational background in molecular Biology, so we decided a couple years ago
to enroll in a Librarian’s Guide to NCBI, which is the free training program that
Peter just mentioned. And after
completing this course, Julie and I held a series of three lunchtime webinars
last summer where we provided a very high-level overview of NCBI resources
just to let people know what’s out there. This was really a pilot project for us,
so we didn’t advertise it heavily. We
weren’t comfortable with getting in too deep yet, but we wanted to give it a shot
based on the limited feedback we Received. However, it seemed that even
something this high-level was useful to our attendees. A couple months later I saw
that our Wright Center for Clinical and Translational Research was launching a
new Bioinformatics 101 certificate Series. I decided to complete this
program and found that it didn’t really overlap with what Julie and I had been
Doing. So I spoke with the series
Coordinator, Amy, and learned that she had gotten a number of requests for guidance
with bioinformatics databases. She was
interested to learn about the webinar series that Julie and I had conducted, so
she invited Julie and me to work with her and another bioinformatics specialist to
develop a second certificate series that would focus on bioinformatics databases. For the Bioinformatics 102 series
that we developed through this partnership, we co-taught one and a half
hour morning sessions to small groups for one week. The first half of each session
started with brief presentations and walkthroughs and then attendees were
given time to complete database assignments. Julie and I conducted
the first three sessions on Gene, Blast and Variation databases, and the
bioinformatics specialist taught sessions on Geo and the Cancer Genome Atlas. Assignments were submitted via online
forms and certificates were awarded to participants who completed four out of
five assignments. And you can see here an
example of the first part of one of our assignments. Registration for the
Bioinformatics 102 series was full in a week, and the series was fairly
well received. You can see here that the
27 attendees who responded to our survey felt that the overall quality of
Bioinformatics 102 was good or excellent. Everyone surveyed also indicated that
they would recommend this workshop to their colleagues or students. And I’m
going to pass things on to Julie now who will talk about what’s happened since
Bioinformatics 102. So after the workshop
one of the attendees asked if we could have some more training that were very
similar to that for his lab group. I
agreed to do it, and over that same summer Amy Olex from the Wright CCR and I
retaught sessions from the workshop and I taught ReactDOM a pathways database
that the professor had requested. I learned
ReactDOM just to be able to teach it to this group. Also, because Peter
Cooper at NCBI knew that we had been doing things with bioinformatics, he
contacted us and Karen and I, as well staff from the Wright CCR, worked
with him on a workshop on EDirect a tool for accessing NCBI databases via UNIX
and pre-written scripts. And we conducted
a webinar with in-person exercises. Another invitation came indirectly from
the Bioinformatics 102 workshop. A faculty member from the Bioinformatics
Department contacted Karen about teaching a session on NCBI resources
for her class, so Karen and I co-taught a class session. Neither Karen nor I had met
that faculty member before and what we discovered was that that faculty member’s
spouse had been one of the other presenters at the Bioinformatics 102
Workshops. And then finally for a
class that I’ve worked with for a long time the professor out of the blue asked
if I could include some information on resources regarding
genetic variation. Because I had watched
Karen’s presentation on variation resources during the Bioinformatics 102
workshops my preparation for this class was much easier. So that’s what we
did. As you can see it isn’t a huge
program, but we don’t have bioinformatics as our primary jobs. It’s a lot more than
we would have done if we hadn’t gotten started by doing something, and one of
the biggest hurdles has been instilled somewhat to some extent is the intimidation
that we felt that we didn’t know enough. But that hurdle has gotten smaller
with practice from presenting more and just learning more. We’re lucky that we’re
able to partner with the Wright CCR because their contact list connects us
with a lot more people, and we’re all benefiting from team teaching. Some of
our success has come from saying yes to things that we weren’t 100% sure
we were ready to do, and then asking for help from other librarians who do
bioinformatics work, and from the NCI when we need it. Going forward the challenge for us in
the future is similar to what we had when we started which is figuring out
what we can do next and taking steps to make that happen. So with that I’m going
to pass things back to Peter and for the poll. Okay, thank you. The first poll is showing. This is basically asking you about how
you feel about bioinformatics education, so please fill out the poll on the
right-hand panel of your screen. We’ll pause here for a moment while we
collect data from the poll. Okay, great. The poll is ended. Thanks for
answering and we’re going to move on to our next speaker
who is Marci Brandenburg who is a bioinformatics informationist with the
Taubman Health Sciences Library at the University of Michigan. So let me pass
this back to Marci. Thank you, Peter. So hi, I’m Marcy
Brandenburg, Bioinformationist at the University of Michigan Taubman Health
Sciences Library. I have a master’s
degree in biology and a master’s degree in information services, although my
appointment is with the library by funding a split between the library, our
medical schools Department of Computational Medicine and
Bioinformatics, and our medical school by Bioinformatics core all to do information
related Activities. If you are not familiar with
the concept of a core facility, it is a for-fee service unit as opposed to
the department which is a degree bearing Unit. Sorry, I forgot to forward my slides. All right. I do a lot of instruction
related activities. I do open training
sessions, especially on the Cytoscape software which is an open source network
visualization tool. These are training
sessions that are open for anyone to attend. I also do some curriculum-based
instruction. For example, for the last six
years I’ve taught a single lab session for bioinformatics foundation class
covering Cytoscape and a couple of other bioinformatics tools. I also teach
workshops. For example, our metabolomic
groups on campus hold an annual summer meeting and for the last three years I
have been involved in providing hands-on instruction for MetScape which is a
locally developed bioinformatics tool that works with the Cytoscape software. MetScape is used to visualize and
interpret metabolomic and gene expression data in the context of human
metabolism. I’ve also provides c courses
and other seminars specifically on Cytoscape and general data visualization
concepts. One thing that I have done is
develop partnerships and collaborations with a couple of our bioinformatics
faculty around documentation for their locally developed by informatics tools. When I started my job they were about to
release a new version of the MetScape software and the existing user
manual needed an overhaul. The PI asked
if I would update the user manual which led to an ongoing long-term
collaboration. I now update the user
manual for each new major release. Librarians are used to providing
step-by-step instructions on how to find information which translates well to
creating user manual. I’ve also created
the user manual for MetDisease another locally developed tool that works with
the Cytoscape software and ConceptMetab a locally developed web-based
bioinformatics too. When the ConceptMetab
manuscript was submitted a reviewer noted
lack of documentation at which time the PI reached out to me for help. This
shows the importance of tool documentation and the value of my health
and expertise. I found that creating documentation is a
great way to learn a tool. These
partnerships have led to my providing hands-on instruction, writing letters of
support for grants, and even being written into grants. I should also mention
that many of these locally developed tools incorporate NCBI data and
resources as source data, link outs and more. So having knowledge of the NCBI
resources is extremely helpful. In
addition to user manual, I’ve also created video tutorials, and given
webinars on bioinformatics tools. I
created two video tutorials on how to use MetScape software, and one video
tutorial on how to use LRpath, a locally developed web-based tool for gene set
enrichment testing. In addition, I have
mentored students through the creation of video tutorials for other locally
developed bioinformatics tools. I’ve
given Cytoscape webinars, both open webinars and ones that are targeted to
specific institutions. I’m always happy to
talk about offering Cytoscape webinars to other institutions or organizations. This slide covers some of the work that
I do specifically for the Bioinformatics Core. I’m currently the bioinformatics course
project manager, so I meet weekly with each analyst to ensure that projects are
moving forward. I help determine the cost
for each project, ensure consistency between projects and customers, resolve
conflicts when needed, and explore ways to further streamline the workflow. This
requires good organization and communication skills, and has taught me a
tremendous amount about bioinformatics analysis and the workings of the Bioinformatics
Core. I do outreach for the Core by
staffing a table at several showcases and events throughout the year, and I
manage the Core software licenses by being the primary contact to the
software vendors. We make some of these
license tools accessible to others on Campus as recharge,
so I handle the recharge and make sure the appropriate individuals are getting
access. When needed, I’ve also helped with
RNA-Seq analysis. The last thing I will
mention is something that I do specifically for our Department of
Computational Medicine and Bioinformatics. I
do all the programming for weekly tools and technology seminar series, which is
attended by a mix of faculty students and staff. It is a venue to discuss biomedical
informatics tools technologies and our methodologies that are recently
developed, currently in development, or simply being used by researchers at the
time. I find speakers that I think will
be of interest to the audience, contact and schedule them, promote and attend the
seminars, and introduce the speakers. There have been occasional presentations
on NCBI resources such as PubChem, and in the past I’ve even been a presenter
myself. This has been a great way to
increase my visibility on campus. So at
this time I believe we are going to have another poll. Thank you, Marci. You should be seeing the
second poll which asks about the nature of your patrons. Please respond as before
in the right-hand panel of your screen. We’ll leave this open for just a bit and
then we’ll proceed. Okay. I think the poll has ended, so we’re
going to go ahead and move on to our next speaker who’s Rolando from Yale
University. I’ll go ahead and advance the
slide with his name, and I’ll pass the presentation on to him. Thank you. Thank you, so much Peter. So
this is Rolando Garcia-Milian, and I’m a biomedical research support librarian
here at the Yale Medical Library. And for
about more than two years and two and a half years we have been running
this end-user bioinformatics support. What I mean by end-users of bioinformatics
is those users who interact with the software and data through a graphical
user interface in contrast to those who are more a bioinformatics or command
line savvy users who interact with a with the data to a command-line
interface. They both have three main
components, one is the resources and tools, trainings and presentations, and
consultations. I like to show this a graphic to
show the research data lifecycle of the omics data and where we provide the support. At the bottom of the of the graphic you
can see the tertiary stage of the data analysis and we provide
knowledge bases mainly to tune of the main knowledge bases meta quality,
department policies, as well as other tools
to annotate and do some data analysis. And now we have moved to support
the primary and secondary data analysis providing
support with software such as Qlucore and Partek Flow for a
next-generation sequencing data analysis. Knowledge bases are a great tool for
data analysis. In the tertiary take
of the data and the way this works is a team of nvm PhD they curate, they read
the articles, they map the concepts and the relationship between these concepts,
and then they create a huge relationships of
core network of this a concept where they map pathway networks, etc. With these knowledge bases, you can you
can do a, you can search the knowledge bases and answer complex
biomedical questions, and also you can bring your datasets and ask those
complex questions to your data sets. And
these students also have a tools for enriching data analysis where you can find
what are the pathway networks, some diseases that are important in your data. As I said, we also provide support for
the secondary stages of the data analysis. This is one of the latest software that we
just licensed. It’s Qlucore. They present
themselves as a do-it-yourself bioinformatics, and it combines utilization
with the statistical methods with a very user-friendly software, and allows you to
do gene expression analysis, protein arrays, DNA methylation, etc. And also you
can have access to a public databases. For example, this is an illustration
of the analysis done with the gene expression-only use data set. You can
easily download this dataset, re-analyze the dataset, create or generate
hypotheses, or narrow those hypotheses. And without much knowledge in bioinformatics
or statistical analysis you can do heat maps or crosstab maps
very easily as people are fascinated with that. The only component of the of
the brain booster program is trainings. I teach a most of the in
house developed trainings from genome browsers, to enrichment analysis, variation
analysis. But I also invite presenters
from campus and also from outside. As
you can see Peter presenting from the NCBI regional workshop that was last
year here, and also we have also bioinformatics, commercial bioinformatics
companies, training our users. Something that we are just beginning to
try is this a peer teaching or instruction. It’s a where we have
tutors on the scene right now. They are
more savvy in bioinformatics and they are training the rest of the
community, the biomedical community. These are some of the stats of the training
as you can see, registration and attendance
have been growing when you compare from the previous years. The other component of
the use of the program is consultations. We provide the
consultation from simple questions to complex data analysis. Either we say
our times or were patrons to do the analysis or with analysis for them
sometimes they don’t have time, or want to learned, and if that’s the
case we do the necessary work for them then we
get credit as co-authors in the publications. As you can see in the
statistics they say the number of a participants, a total number of
consultations, and also the average duration have been increasing when you
compare with pages here. Finally I’d like
to acknowledge my colleagues for support with this program, and if
you want to learn more about this program you can follow
the link and they say last year’s annual report with many, many details,
including a survey on where the challenges are and behaviors information
seeking behavior of our biomedical researchers. So now I’m passing the
control back to Peter for the poll. Thank You, Rolando. The third poll should
be appearing now and go ahead and answer that question. It’s another question
about the patrons that you serve at your institution. Please respond in the right
hand panel of your WebEx window. Okay, so we have ended the poll. Thanks
for answering. I will now pass our
presentation on to Tobin Magle who is currently at Colorado State University,
but she was formerly at University of Colorado and she’s going to talk about
the bioinformatics support she did at the University of Colorado. Thanks for the introduction, Peter. As Peter said, I am not currently at
the University of Colorado Anschutz Medical Campus but I was employed there
Health Sciences Library for two years previously. And since I don’t really do a
whole lot with bioinformatics, I do more data management now at Colorado State,
I’m going to talk about my work at the University of Colorado Anschutz
Medical Campus. So this is just a
slide to indicate that my background isn’t actually in librarianship, it’s in
molecular biology so when I entered the NCBI training course I had a pretty good
background in the biology, but not so much with the searching databases and
things like that so that’s how the training was helpful to me. When I
started at the Health Sciences Library I realized that the patrons to go there
are very diverse. You have the University
of Colorado Anschutz Medical Campus with the School of Medicine, Dentistry, Graduate
School, Nursing, Pharmacy and Public Health, but we also have partner
hospitals like the University of Colorado Health, Children’s Hospital,
University Physicians and we serve a lot of the medical faculty there and we also
have other affiliate institutions. So
what I realized pretty quickly is that I was going to have to focus my efforts on
places that I thought would need this help more than others. So I focused
largely on units that had graduate programs in relevant disciplines and the
School of Medicine and also with postdoctoral researchers on campus that
often didn’t get a lot of extra training outside of the research training in the
lab. So the areas of interest I had a
while I was at Anschutz was of course bioinformatics, but I was also doing data management and
scholarly communication so I was spread in three different areas, but centrally
what I focused on in all three of these areas is compliance. So because I
didn’t want to already reinvent the wheel I found out who on campus
already provided services in the research areas and I came up with a
lot of stuff but most of these were compliant centered or fee-for-service. So we decided to focus on making free
services to researchers and the three areas that I mentioned. Because when I was a graduate student, I was
pretty convinced that if it wasn’t online it didn’t exist, I decided to
establish a web presence for my work there and we couched it under the
library’s website. We had a special
section for research support under the bioinformatics pages. We outlined
databases and tools primarily the NCBI databases that are useful for different
subject areas so we separated by subject because if there’s somebody else doing
cancer research and they came in we wanted them to easily be able to find out what
resources would be relevant to them. I
also started doing a blog series off the Health Sciences Library website called
Bioinformatics Bites, and a lot of the blog posts were basically answering
reference questions – either ones that I made up, or variations on ones
that I received through the library’s help desk – and this allowed me to
establish my name around campus because even if people didn’t know that I was
there it was pretty easy to find online if they googled “Health Sciences Library”,
“Anschutz”, and “bioinformatics”. I also started
a workshop series soon after beginning at CU Anschutz before I had
the training and I felt like I needed to establish the connection between
bioinformatics in the library. So I
started the series populated mostly with bioinformatics experts on campus that
I’ve been introduced to so I didn’t do a lot of teaching at the beginning but by
the end of the workshop series I was integrating a lot of NCBI database
training in there so essentially I would pick a database and have it very
question inquiry-based learning that okay this is type of information I
want to find and I would show them all the ins and outs of searching the
databases and along with these any of the instruction that I did within the
NCBI databases I created a LibGuide with all the
information that was from the classes so if somebody couldn’t attend a class, or they
wanted review the information after the class that was up there and this
LibGuide should still be online if you guys want to take a look, sorry I didn’t
include a URL on the slide. Another thing
that I realized as I was working there is that communication was a really big
deal. There wasn’t very good ways to
advertise events around campus, so I the first thing that I did is I created
a listserv and populated it with email addresses with people who came to the
workshops. So I already knew they were
interested in bioinformatics so this is a good way for me to re-contact people
that I already knew were interested, and we also created an event calendar off of
the research pages so that anyone on campus with a research or bioinformatics
related event could add their event to the calendar. It’s kind of surprising to me
that there wasn’t really a centralized event calendar for the whole campus, but
as you can see by all the things that are on the calendar here it got a lot of
use and most of them weren’t added by me. And so that’s about it for me and I
guess we are on to Poll 4, so I will pass the control back to Peter. Thank you, Tobin. You should be seeing
Poll 4 in your polling module there. Please answer the questions as before Okay, the poll has ended now. Thank you
very much for responding. I’m going to go
ahead and turn the presentation over to our next speaker who is Robyn Reed who
does bioinformatics support at Penn State’s medical campus in Hershey
Pennsylvania. Thanks Peter. As Peter just mentioned, I am at the
Hershey campus at Penn State. In case you
don’t know where that is, it’s just outside of
Harrisburg. We are not the main campus of
Penn State, Penn State has several campuses but I’m at the med school. This first slide is really just about
the environment where I am and a little bit about me. I am in the Harrell Health
Sciences Library. We serve about 11,000
people between the Penn State College of Medicine and Penn State Health. In terms
of various programs here, the various academic programs, we have biomedical
graduate programs, Masters, and PhD programs, as well as of course the med
school so it’s an MD program, various nursing and physician assistance
programs, but we don’t have any undergraduates here. So it is
graduate and above, but the challenge is the library based in terms of
bioinformatics is when I started here in 2012 we had little or no role to
bioinformatics, no paid bioinformatics analysis tools, or resources and we don’t
to this day. We really don’t pay for
anything per se, and I wanted to try to change that and put some sort of bioinformatics
spin to the library. My
personal background is that in my job I am a liaison to the basic science areas
here. I do have a scientific background
and work experience. I have undergraduate
and graduate level training in scientific areas, and then I worked in
research labs for a number years before I went into librarianship. So I took the
training that Peter mentioned earlier, the Librarian Guide class to get my feet
wet again, or at least in a different area of working in the lab. And from
after that training I started workshops here and I have them bulleted list and
the bulleted list here that you see on this
slide and what I did was I open them up to all everybody here: all faculty, staff,
students, postdocs, and targeting the basic science areas. And generally
speaking they were well attended. I got
some good feedback, I did receive a few questions afterwards that were
bioinformatics-related since those workshops, not an awful lot but some. So it
did seem to be going pretty well and also in addition to the workshops I’ve
done some course integrated instruction. We have, as I mentioned, the PhD programs
here and there is a something called a biomedical sciences program, and I have
taught in a couple of those courses. And
what I’ve actually done in this classes is I put a part of an assignment
I reviewed the use of the Gene and conserved domain databases because I
related to an assignment that they were working on and I also went over Blast,
which is a sequence alignment tool. And
what this did is it gave me a little bit of time to go a little bit more in depth
with these students as they were PhD candidates and I think it’s important
for them to understand that the other faculty agreed but I was able to go to a
level that I wasn’t that comfortable with because I probably taught 90% of
that section but I also worked with a protein biochemist where he was able to
draw it a little bit more and get a student’s thinking about exactly how
substitution matrices work and be if interaction the amino acids and that
kind of thing where I would just probably give an example or two and he
was able to take it to a probably another level that I wouldn’t be able to
do at that time. And the other classroom
I taught I also want to be using the Gene database and finding basic
information on DNA and protein sequences and then I well in there certainly you
look at all related information that NCBI links to because I’ve basically
that’s really important and I went to a specific example with that. The other
course that I have taught is an undergraduate course for chemistry
majors once a semester at Condon University Park campus to teach this
class. And what we do there because this is a
survey class I have gone over some bio chemistry which is really just looking
for basic gene information because they don’t happen anywhere else in their
program, and then I also focus on PubChem which they find to be very helpful. So
the outcome from all this have been pretty good. I’ve been invited back each
year semester to do this I am looking for other things to do
to expand a little bit. As Karen and
Julie mentioned you know starting somewhere is always a great idea
even if you don’t feel comfortable you should try it anyway. You don’t know
what you can do until you try really. I
found the partnering when somebody was very helpful and if anybody has any
questions and wants to talk to me about this further I’m happy to talk to you
offline afterwards if you want to. Thanks
for having me and I will pass this back to Peter. Thank you, Robyn. You should be seeing the
fifth poll which is asking you about whether you would like to learn about
our NCBI sequence similarity search Service, which is called Blast. Please
respond as before into the polling pod on the right hand side. [Music]
Okay, thanks for responding to the poll. I’m going to go ahead and pass the
presentation on to Elliott Smith who is our next
presenter and he’s from the University of California at Berkeley. Thank you. Peter. When I was appointed a
selector and liaison for molecular and cell biology at UC Berkeley in 2012, one
of the goals I developed was to expand the library’s bioinformatics support. My
own undergraduate and graduate training was in chemistry and so this was a new
area for me, but when I was asked to take on the subject specialty I identified
bioinformatics support as a clear need that in the past had not been
systematically served. My supervisor Sue
Koskinen the head of the library’s Life and Health Sciences Division, has
supported me in these efforts from the first. A few years ago there were no
regularly recurring training programs on campus focused on using bioinformatics
Tools. Upper division undergraduates and
graduate level courses seemed to assume pre-existing knowledge of these tools. In
surveys of incoming molecular and cell biology graduate students, more than
two-thirds of my respondents said that they would be interested in an
introduction to NCBI bioinformatics resources. The need for bioinformatics
tools crosses many disciplines not only molecular and cell biology but plant and
microbial biology, integrative biology, biochemistry, neuroscience, and Public
Health. UC Berkeley has academic and
research programs in all of these areas. So it was clear that a program to
provide bioinformatics support might have a substantial impact. I’m going to
focus in this presentation on a 50-minute workshop and an accompanying
guide I developed entitled NCBI Bioinformatics Resources an
Introduction. I based the workshop and
guide on materials and examples presented during a Librarians Guide to
NCBI, which I attended in March 2015. Rather than giving a general
introduction to the range of NCBI Resources, there are more than 40 of them,
I decided to focus on how these interlinked resources can be used to
answer three common research questions. The first is how to find genes and
proteins associated with a particular Disease, syndrome, process, or other topic. The second is how to find a protein
sequence and a gene coding region starting with an organism and a protein. And the third was how to compare
sequences and identify a protein or a gene starting with a sequence. Each
research question has a separate tab in the guide. Find Genes and Proteins shows
how to search PubMed by topic and then use NCBI’s interlinking functions to go
to the relevant records in Gene, Protein and Structure databases. Find Sequences
shows how to search the gene database by organism and protein to find gene coding
and protein sequences. And Compare
Sequences shows how to use Blast to identify a protein or a gene from a
sequence. The outcomes to date are that I
have offered the workshop three times and it has gotten a fairly good response. I’ve had about 35 attendees over the
three workshops, a mix of undergraduates graduate students and at least one
faculty member. The online guide has been
viewed about 1,500 times over the past Year. The workshop and guide have also
led to individual research consultations and so raised the library’s visibility
in this area. It is also increased
outreach to faculty. An instructor in the
plant and microbial biology department has asked me to give the workshop
specifically to his class. So this
workshop is becoming course-integrated instruction, as well as general
bioinformatics support. My future plans
include offering the workshop again this semester and next fall. I’m also
developing workshops on additional topics including advanced Blast and
genomic analysis. There are possibilities
for collaboration with a campus supported Computational Genomics
Research Laboratory which has begun to offer some training and consultation. A
challenge is staying abreast of this rapidly evolving field when
bioinformatics support is only one part of my responsibilities. But my experience
shows that even without an advanced degree
in the field it’s possible to provide meaningful bioinformatics support. Thank
you for your attention and I’d be happy to answer any questions you might have
after the presentations are complete, or by email. And now I’ll turn it back over
to Peter for a poll question. Thanks
Elliot. So you’re now seeing poll six in
your polling module there on the right hand side. It’s about whether you teach
users about bioinformatics so please answer the poll and we’ll proceed once
we get the results. Thank you. Thanks for responding to the poll. We’ve
collected all the information. I’m going
to go ahead and turn it over to our final speaker who is Rob Wright from
Johns Hopkins Medical School. Thanks Peter. So I’m Rob Wright. I’m the basic science
informationist is at the Welch Medical Library at Johns Hopkins University. And
I’m going to talk about the five roles that I play as a bioinformatics
librarian, which will echo what all of my colleagues have been talking about today. They are navigator, searcher, teacher,
connector, and student. So as a navigator,
I’m helping direct users to databases and tools, and sometimes that’s all they
need is to be pointed in the right Direction. And a lot of times that
navigation will be toward a couple of Portals, one from NCBI and the other from
EMBL-EBI. Although sometimes I’ll find a
tool that’s not available from either of those sources but is perfectly suited to
answering a question, something like the Human Protein Atlas. And I’ve co-created
a bioinformatics portal which has core omics databases and tools and this is a
tool I can just point people to if they have questions about a particular topic. It’s also a resource that really helped
me when I was starting providing bioinformatics services to orient me to
the landscape of bioinformatics. And it’s
also a tool that I go to sometimes when I don’t know where to begin with a
particular question and I tend to find
resources there that can help me get Started. As a searcher I’m returning
results from searches of bioinformatics databases and these are just some
examples of tools that I’ve searched recently so I’ve looked for clinically
significant gene variants in ClinVar, used BioMart to
get batch sequence from a family of Genes, searched
InterPro to find proteins that have common domain architecture, and use GEO
and ArrayExpress to get gene expression data for a systematic review. So as a
teacher I’m instructing researchers and bioinformatics topics, and as many of my
colleagues have mentioned I’m also providing sort of introductory level
instruction in the use of NCBI databases and tools. I’m also working currently on
a online module to show an overview of what goes into a next-generation
sequencing experiment. So similar to the
research life cycle that Rolando mentioned earlier, this is part of a
larger project funded by the Big Data to Knowledge program and other modules
included in that project are ones to help researchers understand the effects
involved with next-generation sequencing data and also best practices for sharing
that data via repositories like dbGap. I’m also a connector, so there are
certainly instances where I don’t have the expertise to answer a question and
in those cases I’ll reach out to my network which includes the Librarians
Guide to NCBI online discussion group, folks on my campus who are expert Galaxy
Users, as well as faculty from the Hopkins Center for Computational
Genomics. I’ve also brought in staff from
NCBI and UCSC to give hands-on workshops on their tools. And then finally I’m a
student. So bioinformatics is a really broad
complex and constantly changing field and I try to keep up as I can. So certainly the Librarians Guide to
NCBI course was a great sort of immersion into research use cases and
how NCBI guide tools can be used to adjust those, but I also have taken advantage of
short courses lectures workshops, etc. at Hopkins and most recently took a
semester long introductory course in the our statistical software suite which a
lot of my users use to analyze their data. So those are my five role. Thanks a
lot and I’ll reconnect to Peter. Peter is muted. Yeah, apparently I am sorry
about that. [Music]
So the poll here is about whether you want to participate in a focus group and
so there’s a couple of dates there with some additional information if you want
to select another date you we contact you about that. You need to enter your email address for
that to happen, or any of these things to happen. Okay so we’re going to leave this open
and I’m going to go ahead and proceed to the next thing. This is a link to the evaluation form on
this slide. Molly Knapp is also sharing that link in
the chat box, I believe. So once you fill
this form out your CE certificate will generate automatically. Once you finish
the evaluation then you can fill in your name and print and save the certificate. Also on this slide is the email address
the National Training Office in nto.utah.edu. You can write to them if you have
any problems with a certificate or the Evaluation, and you can also write to
that address if you have additional questions that we’re not able to get to
perhaps, or that you think of after the webinar. [Music] Okay so I think what I’m going to do now
is to let Kate be the presenter, and I think we have time for a few questions. She’s going to direct the questions to
the panelists either directed to or one of the organizers will answer them. Okay, thank you Peter. There have been a couple of
questions that have come in via chat. We
have a few minutes left so if there are additional questions please enter them
into the chat panel and send them to all Panelists. Okay so our first question was
“To those of you who bring in external speakers or instructors from vendors. Are
these folks coming in free of charge, or is it being treated as a purchase
training session. And if the latter, how
is it being budgeted, for example, by the library or by the requesting department?” So I saw that
Rolando had an answer to this, but Rolando, if you don’t mind unmuting
maybe you could share your answer verbally? OK. Thank you, Kate. And yeah we
do not pay. We rarely, we
never pay in these 2.5 years. We never
pay for any speaker, people we’ve invited, they come for free. We don’t pay for their time, we just pay
for their traveling expenses and staying here if they are coming from outside the
institution. We got a grant to bring in
Marci to teach Cytoscape, so that paid for the traveling expenses, her
expenses. And the vendors provide a
training that is included in the price of the license. So in the case of
of the software you don’t need to worry about
maintenance, you want to worry about any troubleshooting support. They do offer
101 support questions and everything, and they provide training. Also included in the
Price. The library doesn’t have to pay. The library doesn’t have to budget for all
these expenses. So that’s, I don’t know if
that answer the question. Thank you, Rolando. Great. Would any of
the other panelists like to address that question? This is Elliott Smith, and I would just
echo what Rolando said the vendors that we have brought in for bioinformatics
databases have generally been happy to provide trainings for free. Many of them
are either based in this area or they will combine a trip to do trainings at
UC Berkeley with trainings at other institutions in the area. So we to date
have not ever had to pay travel expenses. The vendors have provided the service. It’s a way of promoting their database
and getting more usage and then of course that gives us an incentive to
continue to license it. Great, thanks
Elliott. That’s really good to know. There
is one other question so far that we’ve received from our attendees and that’s
another question really for all of our panelists. The question is, “Are there
in-person trainings or seminars that you would recommend if I was interested in
learning more about how to train in Bioinformatics?” Who would like to address
this question first? Perhaps Julie or Karen? In terms of in-person trainings or
seminars, I haven’t really had much beyond what we happened with the
librarians guide um and and what has been offered locally but one of the
things that has often been very helpful is finding videos on YouTube. The NCBI
has quite a bit of material there and typically those videos are also linked
with paper and pencil of materials, with information from the slides and
sometimes with information about activities that are presented in the
videos so that you’re not just watching the video but that you can follow along
on your own computer. Thanks Julie. Anyone else have recommendations for
Training? This is Elliott Smith again, and
I would just say that as someone new to the area of bioinformatics I did find
the Librarians Guide to NCBI the week-long intensive class offered at a
NIH and NCBI and NLM to be extremely helpful. It was focused, as I think Rolando may
have mentioned, or Rob, it was focused on specific use cases involving the
resources and that was a very helpful way for me to learn how to make use of
these resources. Thanks Elliott. Okay there are actually no
other questions that have come in the chat panel that I can see. I’m going to
give the ball back to Peter. Thanks Kate. And thanks to everybody who
participated in the webinar today. I just wanted to finish with this slide
that actually I stole from Julie and Karen. You heard from eight different
librarian today who have diverse backgrounds and they come from very
different institutional settings. All of
them provide bioinformatics support. For
most of them I think it should be clear to you that with some basic
knowledge it’s possible for you to expand your support role to include
bioinformatics tools and databases. And
I’m leaving you with the set of concluding points from their slides,
Karen and Julie slides, the tips on how to support bioinformatics: start
Somewhere, trust your ability to learn, partner with people if you can, look for
and take opportunities get help, and keep Going. So thanks again everyone for
attending and I’m going to go ahead and end the webinar for everyone. Thank you
again. [Music]

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