RCN-UBE The genome consortium for active undergraduate
teaching using next-generation sequencing
Project Description.
Results of Prior Support.
As part of a prior National Science Foundation, Research Coordination Network –
Undergraduate Biology Education (RCN-UBE) incubator grant (DBI-1061893), Juniata College
formed a network of faculty named the Genome Consortium for Active Teaching using NextGeneration Sequencing (GCAT-SEEK). GCAT-SEEK initially included 13 primarily
undergraduate institutions in the Mid-Atlantic region in collaboration with the Pennsylvania State
University Genomics Core Facility (PSUGCF). GCAT-SEEK met in July, 2011 at Juniata and
solidified collaborations with PSUGCF to enable access to state-of-the-art sequencing
technology for incorporation of investigator-requested raw DNA sequence into undergraduate
research projects that are woven into new and existing curriculum. GCAT-SEEK provides the
opportunity for students primarily at small undergraduate institutions to utilize next-generation
sequence data to address fundamental questions in biology and bioinformatics and meet
educational and research goals of the Vision and Change Dialogues (1).
The outcomes of the initial network workshop were published (2) and the key achievements are
summarized below:

Successfully established a network structure to coordinate as GCAT-SEEK.

Established communications and data transfer protocols for network partners.

Proposed and implemented a pilot study to determine feasibility of large scale data
production.

Identified bottlenecks in the process and crafted remedies for those bottlenecks.

Developed realistic learning objectives for undergraduates.

Drafted a flexible instrument to assess student learning gains.
Over the past 11 months since the workshop, the RCN/UBE award facilitated a pilot study to
determine what practical challenges will be faced when investigators and undergraduates
collaborate with a research core sequencing facility. We chose ten representative projects from
network participants for sequencing. Through those, GCAT-SEEK identified challenges and
bottlenecks and considered/proposed solutions. GCAT-SEEK developed a standard operating
procedure (SOP) outlined in figure 1 (next page).
Each institution and faculty member in the network had different levels of expertise. This
variation provided a good test for the robustness of our approach. GCAT-SEEK established a
series of professional development interventions to be used as needed. Faculty requested help
on topics ranging from design of the sequence study (e.g., choice of platform, quantity of data
required, etc.) to resources required for data analysis (e.g., bioinformatics strategies including
using appropriate software, etc.). These interventions led to our current proposal to sponsor
faculty/student summer workshops led by advisory panels with expertise in the areas of
sequence data production, bioinformatic data analysis, pedagogy and assessment. Faculty will
apply to attend workshops by proposing to GCAT-SEEK a research project and classes to be
modified. The identified project and class will be their focus at the workshop. The applications
will be reviewed by the advisory panels for potential to impact the network. Successful
applicants will attend workshops and GCAT-SEEK members will mentor novice investigators
through meaningful projects using appropriate platforms that yield reliable sequence data. Our
workshops will have a strong focus on educational integration and publishing of educational
modules for dissemination to the network. To ensure quality design of research projects GCAT-
SEEK identified and secured appropriate expertise to support GCAT-SEEK members (see
advisors listed for the “Data Collection” and “Data Analysis” panels in figure 1). A third
“Educational Outcomes” panel will assist in developing pedagogies for broadest implementation,
and assess the degree to which we are connecting teaching with learning outcomes in the
context of next-generation sequencing.
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To maximize limited resources for sequencing, GCAT-SEEK explored the potential of combining
samples from different projects into a single sequencing run. We were concerned about
variation in sample quality but PSUGCF provides additional quality control (QC) screening on
their Agilent Bioanalyzer to validate samples before any sequencing is initiated. GCAT-SEEK
members typically generate more potential samples than can be accommodated in a single run.
If any samples fail QC screening, alternative samples are substituted immediately to provide the
maximum number of projects per run without delays. Optimal capacity is important for
maximizing the savings available only through a large and diverse network such as GCATSEEK. GCAT-SEEK structure provides PSUGCF the volume and flexibility needed to maximize
the impact of the collaboration. In the pilot study, sequence data from ten independent projects
has been acquired and successfully transferred to the GCAT-SEEK server at Juniata. Network
faculty teaching genomics classes have already begun to download datasets as examples in
their classes, but a focus on educational integration in a workshop setting is planned to solidify
module development.
GCAT-SEEK fully appreciates that data analysis (assembly, annotation, and statistical analysis)
is the most challenging aspect to introducing next-generation sequencing into the
undergraduate learning environment. Consequently, we assembled a panel of experts from
research-intensive institutions (Albert, Aguilar, Marden), as well as individuals who teach
bioinformatics at the undergraduate or graduate level to help with this aspect (Sakk,
Lamendella). Regina Lamendella will coordinate the activities of this panel and coordinate
GCAT-SEEK computational resources. Lamendella is an expert in meta-genomic analysis who
will join Juniata in June, 2012 as a tenure-track Biology faculty member (see Biosketch). Jim
Marden is a Penn State Biology faculty member and an associate editor of BMC Genomics with
specialization in transcriptomics. An HHMI award to Juniata College will support a 12 month
post-doctoral research associate that will be shared between the Marden laboratory and Juniata
College. The Marden postdoc will have as a primary responsibility facilitating RNAseq analysis
at each of these workshops. The data analysis panel will help to identify resources available
(additional mentors and software) to facilitate data analysis. With the help of the previously
mentioned HHMI grant to Juniata College, GCAT-SEEK has already negotiated and will obtain
obtain NextGENe and CLC Bio licenses for the network and their students. We will obtain a
cluster with 4 compute nodes (200GB RAM, 48 processors, 20TB storage) that will allow a
larger number of users to simultaneously run analyses on these platforms or run freeware such
as the Maker pipeline for automated eukaryotic genome annotation on many processors at once
(3,4).
GCAT-SEEK’s major focus is to use next-generation sequencing to actively engage
undergraduates in learning and acquiring the core concepts and competencies identified
through the Vision and Change dialogues (1). Core concepts include: 1) evolution, 2) structure
and function, 3) genetic information flow, exchange, and storage, 4) pathways and
transformations of energy and matter, and 5) interconnecting and interacting living systems.
Core competencies include 1) ability to apply the process of science, 2) ability to use
quantitative reasoning, 3) use modeling and simulation to understand complex biological
systems, 4) understand the interdisciplinary nature of science, and 5) communicate and
collaborate with other disciplines. Next-generation sequencing and bioinformatic analysis
provide a “real world” setting to expose students to these key concepts and competencies in
modern biology education (see prokaryotic genomics workshop module plan for a detailed
example). We have modified the “SALG” assessment instrument to begin to track progress in
student self-perception and direct understanding of these core areas, as well as the quantitative
competencies identified in Vision and Change (1; see description of assessment workshop
module below).
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GCAT-SEEK members currently developing curriculum will engage larger numbers of students
either through relevance to individual students (e.g. implications embedded in the human
genome) or through a relevant focus to a specific problem (e.g. environmental pollution/clean
water). It is clear that the number of students that an individual professor will teach biology to
using next-generation approaches typically depends on the faculty experience level. Professors
typically start learning by themselves, then involve one or a few research students, then a class
of research students, upper level classes of 20 students, and finally lower division
implementation of 50 to 100 students. Faculty workshops are an excellent means to provide
experience and accelerate implementation and dissemination of educational modules that can
be readily interwoven into one’s home curriculum.
Since its inaugural meeting in July 2011, GCAT-SEEK has grown from 13 to over 88 member
institutions (115 individuals). Members are primarily faculty at small undergraduate institutions,
as well as a dozen faculty and postdocs from research universities involved in undergraduate
education. The eagerness of faculty to join GCAT-SEEK is encouraged by critical factors:

An established genomics core to ensure quality data production.

Raw sequence data specific to their research program and courses.

Colleagues to help with data acquisition, analysis, and pedagogy.

The track record of success of the Genome Consortium for Active Teaching at Davidson
College (the original GCAT (5) after which the current GCAT-SEEK network and
workshops are modeled and named) in bringing genomics to undergraduates. GCAT
trained over 360 faculty and 24,000 undergraduates in the use and interpretation of
microarray data.
In the last year the research coordination network has proven its worth in a variety of ways. The
network forms a community of enthusiastic biologists with similar backgrounds and interests.
The network’s listserv has been a place where our intellectual synergies have been realized
with respect to questions on experimental design and execution, bioinformatic approaches,
pedagogic best practices, and assessment of student learning. By drawing from the expertise
of the community, a single institution with such breadth of specialization is not necessary and
intellectual resources are efficiently used. Because the smallest unit of sequence is oftentimes
much larger than required for a single project, combination of samples among investigators
greatly reduced run costs. Recognition of the role of our community has led to successfully
negotiation of software discounts from CLC Bio, Softgenetics, and Geneious software
companies for the network. Our network’s data is available for members to use in classes and
is being shared already. We have begun to create a database of highly purified barcoded
primers as well. Our network provides a forum for student input on biology education, with
students participating in our research programs, classes, and presentations at our workshops.
The workshop structure we propose now is tailored for undergraduate educators, and
will assist in all key stages from project development to pedagogical integration at the
home institution.
Narrative (What GCAT-SEEK Now Proposes)
The Guiding Premise of GCAT-SEEK
To transform undergraduate biology education, faculty must provide opportunities for students
to engage in the process of modern science. GCAT-SEEK will engage students in inquirybased learning that is grounded in the key concepts and competencies of modern
biology, and are connected to learning objectives and assessments (1,6,7). Genomics
and bioinformatics are dynamic fields, well-suited for capturing the imagination of
undergraduates. Current literature (5,8) indicates that raw data in the area of an educator’s
research can be the catalyst for transforming undergraduate education. In this proposal our
overarching goals are to increase network participation and dissemination, foster a sense of
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community among network faculty and students, and support efforts to communicate and
coordinate resource usage (Table 1). Our specific objectives are to i) support faculty/student
workshops and presentations, and ii) support faculty time for dissemination, assessment, and
communication efforts. These aims will empower our network faculty to begin to implement the
vision of GCAT-SEEK more broadly. Our vision is for faculty to direct their innate passion for
research into research projects of their choosing, which become the cornerstone of innovative
educational efforts that are assessed for student learning gains. Our network is predominantly
comprised of schools and technology centers in the mid-Atlantic region. In order to scale with
increased interest, a successful regional duplication of the workshops would greatly decrease
travel costs to workshops, thus increasing participation. In the same way that GCAT split into
GCAT-Chip, GCAT-Synbio, and GCAT-SEEK in 2011, a regional duplication of GCAT-SEEK
leadership would eventually allow expansion of resources and facilitate coordination of efforts
as interest broadens. Moving our workshops to different regions should facilitate this plan as we
work with local facilitators and genome cores in the workshops.
Table 1. Broad goals and specific objectives of this RCN-UBE proposal.
Specific Objectives
Broad Goals
Workshop
Increase network participation and
disseminate to other regions
X
Nurture sense of community among
young scientists and educators
X
Student
Presentations
Faculty Time
X
Support network communication,
assessment, and sharing of
resources
X
Challenges in Undergraduate Biology Education
Many reports and educational initiatives in STEM education have determined that the 21st
century curriculum should focus on two major goals: namely to 1) engage students in the
process of science and 2) to present science as a vibrant and active field (1,6,9,10). There is
extensive pedagogic research demonstrating that participation in open-ended research
endeavors enhances undergraduate learning and emphasizes the importance of crossdisciplinary approaches (6,9-13). Developing innovative approaches and empowering faculty
with the tools to implement novel strategies remains a challenge at all levels of undergraduate
education (6). GCAT-SEEK will empower faculty to engage students and create interest in
modern science while underscoring the cross-disciplinary nature of biology. The approach we
will use incorporates large data sets and computing skills that are considered core
competencies for future careers in life sciences research and biotechnology (1,6,9,14).
Recently, the Howard Hughes Medical Institute’s (HHMI) Science Education Alliance program
(15) , the Department of Energy’s (DOE) “adopt-a-genome” project (16,17), and the Genomics
Education Partnership (18) have put original genome sequences in the hands of
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undergraduates. The HHMI program supports a limited number of institutions to isolate and
determine the genome sequence for phage (15). The DOE program offers small undergraduate
institutions a similar opportunity to conduct original research involving the annotation and
bioinformatic analysis of recently sequenced genomes (15,17). The Genomics Education
Partnership focuses on chromosome number 4 of Drosophila and undergraduates learn to move
from preliminary sequence to high-quality finished sequence, while annotating genes and other
features (18). All of these programs demonstrate that undergraduate can make novel
contributions in genomics through original research, which engages the next generation
of talented research scientists.
While the DOE and HHMI programs provide novel sequence data and are valuable first
iterations for engaging and training future life scientists, they support a limited number of
projects. Furthermore, the research is predetermined by the funding agencies (DOE’s “adopt-agenome” project, GEP’s fly chromosome and HHMI’s phage genomes). The GCAT-SEEK
model seeks to expand this approach by providing sequence as a teaching tool to more
individuals and in their areas of research expertise (2,19). This may be more effective because
it is linked to existing research interests of individual faculty and students. Investigator-initiated
sequencing would empower many individuals who could use nucleotide sequence in their
individually selected research areas, ask new scientific questions and test hypotheses with the
help of undergraduates.
Central to this proposal, and previous GCAT microarray successes, is that the faculty
member attending a workshop controls the focus of the study (see figure 1). Controlling
the research focus embraces the key value of academic freedom, and ensures a sense of
ownership among the teacher and student investigators. Ownership assures that faculty will
understand the nature of the scientific question being addressed and the value of the
sequencing technology to scientific discovery and understanding. Ultimately, ownership allows
teachers to transform their classroom activities into open-ended inquiry delivered with
enthusiasm. Numerous studies have documented real research by undergraduates enhances
student engagement and learning and constitutes a high impact practice for undergraduate
education (5,10,18,20-22). The involvement of undergraduates in cutting-edge research is a
major focus of the recommendations of the Vision and Change initiative of AAAS/NSF (1) as
well as other groups concerned with STEM education and student retention (7).
Furthermore this approach overcomes some of the problems identified by Silverthorn and
colleagues using teaching modules developed by the American Physiology Society’s initiative to
create teaching modules (23). This study highlights the importance of faculty being familiar with
materials they use to teach and a sense of ownership and inclusion in the development of
teaching material (23). For these reasons the development of pedagogic activities envisioned in
figure 1 favors a parallel strategy in which the research component and the teaching
component are driven by the faculty member with appropriate support and advice from advisors
with expertise in discovery research and/or the Scholarship of Teaching and Learning (SoTL).
The range of projects envisioned (see table 2; 24) would allow the application of nextgeneration sequencing and bioinformatic analysis to be applied across a wide spectrum of
organisms (archaea, bacteria, and eukaria) and levels of biological organization (environmental,
ecology, organismal, and molecular). This will allow students to connect and reinforce the
fundamental biological concepts identified through the Vision and Change dialog (1) in a
pedagogically effective way.
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Table 2. GCAT-SEEK members that submitted letters of intent to participate in the first year.
Institution
Primary Investigator
Title
Type of NextGen
Analysis
Estimated
Student Impact
Juniata College
Norris Muth
Metagenomics and environmental DNA detection for early
detection of invasive fungal pathogens of forests.
Metagenomics
32/yr
*St. Edwards
University
Charles Hauser and
Monica Swartz
Plant‐fungal interactions: a soil metagenomics study.
Metagenomics
10/yr
Metagenomics
30/yr
Metagenomics
70/yr
Metagenomics
20/yr
Metatranscriptomics
20/yr
Metagenomic analysis of soil bacterial communities
across a thermal gradient overlying the Centralia,
Pennsylvania coalmine fire.
Environmental Biology: Benthic life in Abandoned Mine
Drainage
Analysis of Biotic Interactions Associated with Crohn's
Disease
Susquehanna
College
Tammy TobinJanzen
Mt. Aloysius
College
Mike Engle
Juniata College
Gina Lamendella
Bucknell
University
Emily Stowe-Evans
Comparative analysis of microbial communities in two
freshwater reservoirs in Pennsylvania and the affect of
light wavelength attenuation in the these reservoirs on
microbial community structure and function
Swarthmore
College
Nick Kaplinsky
Simultaneous mapping and cloning of a NudC modifier in
Arabidopsis thaliana
Juniata College
Jill Keeney
Regulation of transposable elements
Loyola
University of
Maryland
Lisa Scheifele
Resequencing of Saccharomyces cerevisiae strains
following lab evolution
Small genome
resequencing
Duquesne U.
Nancy Trun and
Becky Morrow
Gonzaga
University
Kirk Anders
Determining the genomic sequence of the pathogen
Streptococcus equi
Genomic Diversity of Novel Mycobacteriophages Isolated
from Soil in an Old Growth Forest
Small Genome
Sequencing
Small Genome
Sequencing
Correlation of Genome Sequence with Biolog Phenotype
Microarray Profile in Closely Related Bacteria
Species Identified by Undergraduates
Small Genome
Sequencing
200/yr
Determining the roles of the yeast 14-3-3 proteins in
rapamycin-mediated transcription
Analysis of the response of monocytes to Hepatitis C
Virus (HCV)
Molecular evolution of incipient speciation in Sebastes
rockfishes
Transcriptomics and
ChIP-seq
20/yr
Transcriptomics
16/yr
Transcriptomics and
Genomics
100/yr
Lycoming
College
Jeff Newman
St. Lawrence U.
Emily Dixon
California
Lutheran U.
Dennis Revie
Sequencing based
mapping and cloning
Small genome
resequencing
24/yr
25/yr
15/yr
32/yr
100/yr
Juniata College
Vince Buonaccorsi
Davidson
College
Malcolm Campbell
and Michael Dorcas
Migration of green tree frog into historically more
temperate regions. (Hyla cinerea )
Transcriptomics and
Genomics
20/yr
Rochester
Institute of
Technology
Irene M. Evans
What effect does a prion protein have on a yeast cell
grown under stressful conditions?
Transcriptomics
60/yr
Georgetown U.
Anne Rosenwald
and Gaurav Arora
Investigation of the pathogenicity island of Salmonella
enterica serovar Agona
Transcriptomics
25/yr
Genetic control of muscle growth in crustacean molting
and limb regeneration .
Transcriptomics
10/yr
Colorado State Kyle S. MacLea and
U.
Donald L. Mykles
Analysis of mRNAs that escape translational repression
Transcriptomics
under stress
Effects of increased mercury levels on smallmouth bass
Chris Grant and
Juniata College
Transcriptomics
Micropterus dolomie gene expression profiles.
Vince Buonaccorsi
Characterizing differential expression responses of
Transcriptomics and
King’s College
Jeramia Ory
Cryptococcus neoformans strains isolated from patients
Genomics
and the environment
*Minority serving institution. Twelve additional projects from the network are in development for year two.
U. Richmond
Angie Hilliker
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100/yr
20/yr
10/yr
The main focus of this proposal is to empower GCAT-SEEK faculty and student members
in both how to use the modern technology, and how to integrate it into the classroom in
pedagogically effective ways. Our proposal will catalyze faculty and student training in
modern biology and encourage research by removing barriers to initial engagement and
teaching. We will provide inexpensive access to state-of-the-art sequencing in addition to
technical support for data acquisition, bioinformatics analysis, and developing pedagogy based
on established GCAT-SEEK assessment of learning outcomes. Here we aim to broaden the
expertise of the network faculty, and strengthen our sense of community,
communications, and efforts of individuals in leadership positions.
Our approach stresses integration of basic biological concepts and modern bioinformatics with
the multi and cross disciplinary approaches generated by faculty interests. Genome and
transcriptome data challenges students to understand of the interacting network of genes and
proteins in an individual, how the organism interacts with its environment, and how organisms
have adapted over evolutionary time scales. With a relatively modest investment within the
existing scientific infrastructure, the GCAT-SEEK model of faculty-generated research projects
will reach more students and launch new areas of investigation in a diverse spectrum of species
and subdisciplines. The synergy offered by advances in education and basic science will
produce a transformative effect on the campuses involved.
GCAT-SEEK will become a national model in which an investigator’s innate passion for
research is channeled into improved teaching and training for undergraduates in a workshop
setting. Aggressively publishing our teaching modules and sharing workshop datasets will
foster broad participation by the network, in particular for those seeking to get involved without a
wet-lab experience.
Objective 1. Support for faculty/student workshops and presentations. We propose to
host faculty/student development workshops that will support novice faculty members and
students through the bottlenecks facing broad undergraduate engagement that were identified
in the prior NSF RCN/UBE supported incubator project. We propose to pair faculty into teams
across institutions or across disciplines within universities. Previous experience by
GCAT-CHIP (M. Campbell pers. comm.) and others (25) found that attendance by faculty teams
increases likelihood of successful curricular integration once professors return to their home
institution. Their sense of isolation is greatly decreased, and enthusiasm for the challenge of
change is maintained. In particular faculty combinations of biology, information technology,
biochemistry, mathematical modeling, and statistics would be highly beneficial for subsequent
collaboration and integration among disciplines at the home institution. Ability to communicate
and collaborate across disciplines is a core competency identified by the Vision and Change
dialogues (1) and the collaboration within an institution would model such activities for students.
Faculty pairs of biologists from different institutions will facilitate a sense of community and
collaboration that is not usually possible at small colleges.
Up to five faculty may opt, rather than bringing a faculty colleague, to invite an excellent
undergraduate research student with established leadership credentials or potential to attend
the workshop. Student participation helps create student leaders by further developing their
knowledge, communication skills and credentials. Student participation fosters a national
community of student researchers. As was documented in the Vision and Change Dialogues
(1), the student perspective is important, often overlooked, and ultimately deepens the
conversation.
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We propose to use the workshops to help participants get started in the pursuit of their own
inextricably linked genomic research and educational goals. Faculty applicants will be required
to propose a project and identify a class for modifications in January, the applications will be
reviewed and ranked by the advisory panels in the spring, and the GCAT-SEEK steering
committee will select applications demonstrating the highest potential to impact undergraduate
education by May. Projects must meet biosafety approval from Juniata, and meet any other
IRB, recombinant DNA or other regulatory issues before approval. The steering committee will
advise on best strategies for those not selected to be resubmitted the following year (figure 1).
Participants will ship in advance or bring their samples from which nucleic acid will be prepared
and tested for quality control. We anticipate that for many projects, samples may be ready to
send out for sequencing, but for some projects poor sample quality may delay or preclude
sequencing. This strategy will greatly improve effectiveness and enthusiasm for the workshop
as investigators will be making progress towards producing customized teachable modules
concurrently while pursuing a research question of innate interest to them.
Workshops will be organized into whole-group and small breakout sessions divided by
application type (see table 3, next page). A survey of the network showed (N=45) that 36% of
interests were in transcriptomics, 18% in bacterial genomics, 20% in meta-genomics, and 26%
in eukaryotic genomics. A technology overview will be provided for the whole group on the first
day led by genome core directors at PSUGCF. We will continue to develop relationships with
genome core directors from other regions as we finalize plans for movement of the workshop
(see MSI recruitment section below). Days two through four will divided into breakout
sessions by application, where wet lab sample preparation and bioinformatic approaches will be
covered (see prokaryotic genomics example below). In the afternoon of day four,
assessment strategies will be reviewed and participants will practice customizing instruments
(see assessment module below). Evening sessions will be focused on incorporation of the
day’s experiences and pre-designed teaching modules into a classroom setting adapted for
each faculty member (see pedagogical integration below). On day five faculty and student
participants will present their customized teaching module to other members, giving all
members an overview of the alternative applications and teaching approaches. There will also
be a session where faculty and student participants share their perspective on the modules and
workshop. Starting in year two, in the afternoon session on day five, students more broadly
drawn from the network will be invited to present their research using next-generation
sequencing (see student presentations below). We anticipate that overall, as a result of
workshops, participants will be able to:
1. Design experiments using next-generation sequencing technologies
2. Prepare nucleic acid samples and assess quality
3. Sequence and analyze their samples
4. Teach modules that integrate next-generation sequencing research into the classroom
5. Assess student learning goals and track outcomes
We are proposing to sponsor faculty development workshops that are hands-on, active learning
experiences. The teaching style itself will reflect recommendations of the Vision and Change
dialogues and the model of GCAT with approximately 10% of the time in mini-
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Table 3. Proposed GCAT-SEEK workshop schedule, teaching teams, and general content.
Teaching Team
Day
Setting
Theme
Content
1 PM
Group
NextGen
Deb Grove
Platforms
Experimental Design
Craig Praul
Experimental Design
Gina Lamendella
2
Breakout
Wet Lab
See below
3
Breakout
Bioinformatics
See below
4 AM
Breakout
Bioinformatics
See below
4 PM
Group
Assessing Student
Tammy Tobin
Customizing and Using
Learning Gains
Nancy Trun
the SALG
5 AM
Group
Faculty Presentations
Participants
Faculty teaching modules
5 PM
Group
Student
Presentations
Participants
Student presentations
lectures, accompanied by activities (1). Our modules will be connected to core concepts and
competencies identified by GCAT-SEEK (2) and the Vision and Change dialogues (1). We are
aiming for modules to be well developed and easily transferable to the home institution to help
facilitate implementation. Modules will be generic, in the sense that any dataset of the
appropriate general characteristics (e.g. RNAseq differential expression, prokaryotic genome)
will be able to plug into the analysis and educational framework developed. This will avoid a
problem identified by Silverthorn and colleagues (23) where lack of passion and knowledge of
the system inhibits faculty integration during the semester, even with high initial buy in. In the
initial GCAT model the role of academic freedom in the direction of any project was seen by
participants as a critical factor in their enthusiasm and engagement in the project and its
subsequent inclusion in their classroom activities. Modules will have clear learning objectives
and assessment instruments developed, increasing coherence of teaching and student learning
(26-29). Proposed topics, content, and teaching teams are shown in Tables 3 and 4. We will
consult with Istvan Albert, coordinator of Biostars and professor in the Michigan State
Bioinformatics Workshop when technological questions arise during the development stage of
the workshops (see letter of support). Our workshop leadership is therefore a mixture of
network and research intensive faculty providing a balance of state-of-the-art cutting edge
science and an awareness of the novice undergraduate learner entering this complex area of
modern biology. This ensures high quality research, high buy-in from participants, and
educational outcomes.
Workshop Example Modules. Here we provide a detailed example of the curriculum for one
breakout session, the assessment module, and the plans for development of customized
teaching modules in the evening by participants. Modules for transcriptomics, eukaryotic
genomics, and meta-genomics sections will parallel the structure detailed below for prokaryotic
genomics (Table 4).
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Table 4. Proposed GCAT-SEEK workshop breakout topics, teaching
teams, and content.
Topic
Teacher
Content
Genomic DNA prep
Jeff Newman
Prokaryotic Genomics
Assembly
Tammy Tobin
Annotation/Comparison
Genomic DNA prep
Andres Aguilar
Eukaryotic Genomics
Assembly
Vince Buonaccorsi
Annotation/Comparison
RNA prep
Marden Postdoc
RNAseq
Assembly/Mapping
Annotation/Comparison
eDNA prep
Gina Lamendella
Metagenomics
Annotation
Nancy Trun
Mapping
Prokaryotic genomics breakout session. The goals for the prokaryotic genome analysis
section will be for participants to prepare library-construction quality DNA and appropriate
documentation from their organism of interest and to perform de novo and/or reference-based
assembly, and automated annotation of a real dataset. In advance of the workshop, participants
will be asked to submit samples of their organism, provide any special growth information, and
register to use specific bioinformatics sites. The first day of the prokaryotic genomics breakout
session will begin with an overview and comparison of different approaches for gDNA isolation.
Participants will then isolate gDNA from the organism of interest and set up a quality-control
PCR using 16S rRNA universal primers. In the afternoon of the same day, participants will
work in the computer lab to review different types of next-generation sequencer output, file
types, quality scores, linkers, barcodes, assembly principles, algorithms (de novo vs
resequencing), and programs. Participants will begin assembly of a practice GCAT-SEEK
dataset using either the NextGENe, Geneious, and/or CLC Workbench suites on the Juniata
College GCAT-SEEK cluster. While the assemblies are running, participants will review
annotation methods focusing on RAST (Rapid Annotation with Subsystem Technologies) and
DOE-JGI IMG (Integrated Microbial Genome) tools (30,31). Upon completion, sequence
assemblies will be reviewed, and finishing strategies discussed. Assembled sequences and
reference sequences (if not already present) will then be loaded into RAST and/or IMG, and
annotation run overnight.
During the second and third days of the prokaryotic genomics breakout session participants will
assess DNA quality by Qubit quantification, Nanodrop spectrophotometric assay, and
electrophoresis of gDNA and PCR products. Participants will prepare documents to be sent
with samples to the sequencing facility. DNA samples that pass quality control standards will be
packaged and sent for sequencing. During the afternoon, participants will review the annotation
results, compare genomes of related organisms in terms of gene content (core genomes and
unique genes), subsystems present, metabolic mapping, dot plots for
synteny/inversions/translocations.
These activities incorporate all of the core concepts and competencies from the AAAS/NSF
Vision and Change “Call to action (1)” Assembly to a reference genome and comparison of
gene content and order illustrates evolutionary changes. The structure of operons and
organization of genes typically reflects common biological functions. The annotation of genes
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and identification of instances of horizontal gene transfer is critically dependent on our
understanding of information flow, exchange and storage. Integration of the annotated gene
products into subsystems will identify pathways used by the organisms to transform energy
and matter during growth. Based on knowledge of the organism’s biology and phenotypic
characteristics, participants will apply the process of science to make predictions about which
genes/subsystems should or should not be present. Quantitative reasoning will be used to
evaluate the raw sequence data based on quality scores and predict assembly metrics based
on read length and number. The metabolism of the organism will be modeled based on the
subsystems identified. Discussion of the algorithms used during assembly and the physicalchemical principles that underlie next-generation sequencing technologies will illustrate the
interdisciplinary nature of Genomics. Finally, the presentation of the prokaryotic genomics
methods during the day five portion of the workshop exploring the alternate applications of nextgeneration sequencing will provide practice in communication and collaboration with other
disciplines.
Assessment group session. A core objective of this project is to provide participating faculty
with the skills and tools necessary to incorporate research-based next generation sequencing
pedagogy into their classrooms. We hypothesize that the research-based pedagogical
innovations fostered by this project will enhance student learning, particularly in the core
competencies outlined in the Vision and Change 2011 report. We intend to test this
hypothesis by applying the GCAT-SEEK assessment instrument, which was developed based
on these core competencies, across all GCAT-SEEK projects. During the proposed
workshops, participants will thus learn to analyze student progress on both consortium and
course-specific learning goals using the GCAT-SEEK assessment instrument (32). The
resulting data can then be used to assess student progress as well as to modify and improve
course modules. This assessment process will ensure that student learning is continually
improving and that, as technologies change, the GCAT-SEEK consortium will ensure that
faculty skills and course modules change with them.
The GCAT-SEEK assessment instrument (32) was developed using the Student Assessment
of Learning Gains (SALG) website developed by Seymore in 1997, and updated by Seymore,
Carroll and Weston in 2007 (33). We have developed a separate assessment instrument for
each major area of next generation sequencing interest (eukaryotic genomics, prokaryotic
genomics, transcriptomics, meta-genomics). Regardless of application, each instrument has a
pre-course and a post-course version, and shares questions in the following common sections:
1) student reported assessment of their own biology, data analysis and next generation
sequencing knowledge; 2) student reported enthusiasm for the course material and
bioinformatics; and 3) a series of core bioinformatics questions that directly assess student
progress in the GCAT-SEEK/Vision and Change core competencies that are common to all
applications (evolution, information flow, etc.). Each different application instrument also has a
unique series of application-specific questions. Finally, the SALG instrument lets instructors
add assessment questions of their own. This combination of direct and indirect assessment will
allow GCAT-SEEK members to combine student perceptions and attitudes about their own
learning with questions that directly evaluate students’ progress on GCAT-SEEK and coursespecific core competencies.
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In order to assure that the participating faculty are able to collect assessment data that is not
only relevant to the project, but that is also relevant to their own courses and departments, a
half-day assessment workshop is planned during which faculty will:
1)
2)
3)
4)
Enhance their abilities to design meaningful, course-specific learning goals based on
the Vision and Change 2011 core competencies. In this portion of the workshop, faculty
will learn to use “backwards course design,” (34) to design their own courses. In backwards
course design, faculty first develop course learning goals, then they develop the assessment
instruments for those learning goals. Only after both of these steps are completed do they
move on to develop their course content and assignments. This portion of the workshop will
be a logical support and extension of the course module development that the faculty and
students will be involved with in the other portions of this workshop.
Learn to design assessment questions that monitor their students’ progress on these
learning goals. In this section of the workshop, faculty and students will work together to
design course-specific assessment questions that can be added to the GCAT-SEEK
assessment instrument.
Learn to use the GCAT-SEEK Student Assessment of Learning Gains (SALG)
instrument to gather and process assessment data. In the final portion of the workshop,
faculty and students will get direct hands on experience with the SALG site by adding their
course-specific questions to the GCAT-SEEK assessment template.
Provide feedback regarding the current core GCAT-SEEK questions. The workshop
surveys will include questions to elicit feedback and suggestions for improvement of the
GCAT-SEEK instrument so that it will be as relevant as possible when it ‘goes live’ this fall.
Dr. Tammy Tobin will facilitate this workshop. She is a professor of biology at Susquehanna
University and coordinated the university’s Center for Teaching and Learning for five years.
During that time she was a co-PI on a Teagle Foundation grant to develop regional instruments
to assess students’ progress as ‘intentional learners’ as defined by the AAC&U 2002 Greater
Expectations Report: A New Vision for Learning as a Nation Goes to College. She has over ten
years of total experience in faculty development to improve student learning. Jay Hosler,
director of the Juniata College SoTL center and an ASM/NSF bioscholar assessment fellow will
participate in the design and implementation of the assessment tools for the network. Dr. Nancy
Trun will assist with this workshop. Trun used novel and existing published assessments to
study a novel, community-based, multi-institution, NSF-supported teaching pedagogy that she
designed and tested. This effort involved two small PUIs and a community college.
Evening Sessions on Pedagogical Integration. We propose to use informal evening
homework sessions each night to focus on teaching module design. This section of the
workshop will be coordinated by Nancy Trun, and assisted by the workshop facilitators specific
to their breakout session. Teams will meet at a lounge area in their dormitory each evening and
adapt materials provided from the day’s workshop session to fit the research project they are
working on, and address goals of the course they identified in their application. Workshop
presenters will create a teaching modules aimed at lower division students as laboratory or
case-study, active-teaching experiences. Modules will contain goals, technical details and
protocols, student activities and assessments that can be used by participants to teach NextGen
technology. Some material and details may need to be adjusted depending on the details of the
experimental design and goals, and considerations such as class size and level. The workshop
participants will present to the entire group the outline of their module on the last day of the
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workshop. The facilitators will make sure the information in the presentation is accurate and that
the presentation is designed to engage the other workshop participants
The Day 1 evening session would involve editing biological context and experimental design
content. Days 2 and 3 would involve editing wet lab and bioinformatic protocols. Day 4 would
involve editing the student activities, assessment tools, and revising the teaching module as a
whole. Day 5 AM will involve faculty teams presenting to the whole group for 15-20 minutes,
and publishing their modules on the GCAT-SEEK website. The information to be included in the
presentation will focus on: i) how their sequencing technology works, ii) what question they are
using the technology for, iii) a brief overview of how their data will be analyzed, and iv)
limitations of the technology in addressing the research goal. Presentations will be video
recorded and published so that network members can see how the modules are supposed to
work from the designers themselves. The evening homework sessions will have three
purposes. First, they will reinforce what participants have learned during the workshop. Second,
they will give the workshop and network participants an overview for all of the NextGen
sequencing technologies. Third, they will produce accessible draft teaching modules that can
be widely adopted.
By the end of the workshop, participants will have prepared their samples for sequencing at the
workshop and sent them off to be processed. They will have practiced bioinformatic procedures
on datasets similar to those they are producing, and will have gained experience editing the
SALG. They will have produced education modules that will fit their research interests and data
when it arrives from the sequencing core. Network members will benefit from these efforts in
having available numerous completed, parallel projects by which they can engage genomics
students. Network members can optionally i) use the customized modules and data without
having to perform wet lab experiments themselves, or ii) use the generic modules to perform
customization themselves.
Objective 2. Support leadership with time for dissemination, assessment, and
communication efforts. Summer stipends for key leadership roles will guarantee the
outcomes that we are seeking with respect to publications of the work of the network, analysis
and publication of student learning gains, and web communications. Key roles are described
below in the management plan.
Management Plan. All network members will be able to apply to attend faculty workshops.
Faculty become members by free subscription to our listserv, with directions and conditions for
membership found on our web page. Panel members in Figure 1 will rank workshop
applications via potential impact on undergraduates. This will include both number of students
that will be impacted and a consideration of project feasibility and feasibility for curricular
integration. A maximum of 6 individuals from the home institution may attend the workshop if
space is limited. The task of maintaining and updating web communications is performed by
Jeff Newman. Web communications are essential to share the mission of GCAT-SEEK,
membership conditions and lists, next-generation technology overview, lab protocols,
bioinformatic approaches, curricular and assessment tools, completed projects and upcoming
conferences. Through the web site we coordinate use of resources, and nurture our sense of
community and expedite dissemination of the network to the world. Tammy Tobin and Nancy
Trun will be collecting, modifying and advising on assessment instruments, analyzing
assessment data and writing publications on student learning gains as a result of GCAT-SEEK
activities. Vince Buonaccorsi will be working to coordinate evaluation of applications, coordinate
overall activities, and publish accomplishments of the network. There will be a board meeting
before each workshop led by Vince Buonaccorsi and the local coordinator where appropriate at
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the workshop location. Newman, Trun, and Tobin will attend at least one board meeting per
year. Communications outside board meetings will be predominantly via e-mail to the steering
committee. Local coordinators (Buonaccorsi, Newman, Aguilar, Sakk, Fowlks) will be
responsible for the local aspects of hosting workshops including coordinating arrangements for
lab and meeting spaces, housing, food, and registration arrangements. Istvan Albert will need
to be available for technological questions as they arise during the development stage of the
workshops. Hosler is responsible for consulting on assessment development and performance
of the tools. We will encourage local coordinators to form relationships with their core directors
and begin regional subsections of GCAT-SEEK. We will record and report attendance at
workshops, publication of education modules, number of educational and discovery publications
within and about the network, and number of website visits and downloads of published
educational modules with Google Analytics. The SALG will allow monitoring of student learning
gains and demographics. Number of network members can be measured by listserv review.
Workshop data will be shared immediately on GCAT-SEEK servers, but under condition that
users will not publish on the dataset without consent of the originator and that it will be used for
undergraduate education only.
Coordination Plan. There is no similar network that we are coordinating with.
Increasing diversity. Our plan for MSI recruitment is tied to the workshop location. We plan to
offer the first workshop at Juniata College as our first test run in a setting of maximum
institutional support. In the second year we will move the workshop to Lycoming College as a
test of transferability and mobility. Lycoming was selected because Jeff Newman (Lycoming
faculty member) is in the steering committee of GCAT-SEEK, and has already taught a test
prokaryotic bioinformatics workshop at the Allegheny Branch meeting of the American Society
for Microbiology, in Fall 2011. After year two, workshops will be at both Juniata and a minority
serving institution until HHMI supplemental funds end at the end of year four of this grant. We
have identified three MSIs that are willing to host our workshops (see letters of support). In
year three, Morgan State, a historically black college will host a workshop with Dr. Erik Sakk as
local coordinator. Dr. Sakk is also a founding member of GCAT-SEEK (2). In year four, CSU
Los Angeles, a Hispanic serving institution has agreed to host the workshop, and network
member Andres Aguilar will be the local facilitator. Andres Aguilar is experienced at eukaryotic
comparative genomics, and will be a workshop facilitator starting in year one (Table 4). In year
five, Hampton University has agreed to host with Dr. Edison Fowlks serving as local coordinator.
We will solicit local genomics core facilities to host the technology overview to strengthen bonds
with additional sequence providers. Hosting the workshops will greatly facilitate involvement of
faculty and students at the home institution, thereby improving minority recruitment into the
program. This approach also demonstrates the feasibility and benefits of regionally based
networks, and ability of our network to scale with interest. Regionally based workshops vastly
decreases travel costs, thereby greatly increasing numbers of students and faculty that may be
involved. By moving our workshop location around, we prove that our approach is amenable to
duplication in other regions of the country.
In addition to our combined postdoctoral, research intensive, and PUI faculty facilitator staff, and
student participants in the workshop, we are also proposing a half-day of student research
presentations on the last day of the workshop in years two through five that will also increase
network diversity. This will provide a mainly regional forum for students to practice their
communication skills, and form a community of young scientists. Network faculty will encourage
appropriate students to apply and the administrative board of GCAT-SEEK will review quality of
abstracts and determine travel awards.
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