Issue 2, November 2012 to January 2013
Genomics Leadership Initiative Newsletter HHMI grant supports Juniata Student and Faculty Conference Presentations, Workshops, & Fellowships
We have a new web page!
Check out a preliminary description of our certificate program, research, and leadership programs, along with past editions of the newsletter at: www.juniata.edu/projects/hhmi
Workshops: Steve Strutt’13 and Dr. Gina Lamendella (Biology) travelled to San Francisco to study how to properly identify genes in novel bacterial genomes at the Joint Genome Institute (JGI). This will help Steven complete his senior research project, “Sequencing of oil-amended biotrap isolates from the Deepwater Horizon Oil Spill”. Additionally, the JGI will provide Steven with two days of intensive training on high-throughput sequencing technologies. Steven is intending on a graduate career in molecular microbiology and this experience would afford him access to these cutting edge sequencing technologies. Dr. Lamendella also traveled to the lab of Dr. Robert Knight at U. Colorado, Boulder to receive personalized training in cloud computing and multivariate statistics for metagenomic analysis. Such training will be of use in her microbiology classes as well as a summer faculty/student bioinformatics workshop that Juniata is holding this summer. Conferences: Alex Sickler’14 (Biology) presented, “Genome Annotation of Two Pacific Rockfishes Differing in Longevity” at the 21rst Plant and Animal Genome meeting in San Diego, CA, accompanied by his research mentor Vince Buonaccorsi. Alex states: “The talks and interactions with so many scientists were really inspiring. I was able to get new ideas on how to approach research questions and maximize my productivity back at Juniata.” Dr. Buonaccorsi presented, “The Genome Consortium on Active Teaching using Next-Generation Sequencing”. Fellowships: Andy Maul ’14 (Biology) was awarded an extraordinary research opportunity (EXROP) fellowship to perform summer research with HHMI professors at the HHMI Janelia Farm research campus. HHMI invites colleges, universities, and professors that have active HHMI awards to nominate qualified students from their universities, with a special emphasis on minority inclusion. Andy was one of approximately 80 of 380 students to receive the award.
Summer Research Program at Juniata College Drs. Keeney, Muth, Buonaccorsi, Dries, and Lamendella were awarded HHMI summer research fellowships at Juniata through the GLI grant. They will each be mentoring one or two HHMI-supported students (eight students total this year), and will each use cutting edge nextgeneration sequencing genomic technologies as part of their work. Research experiences are essential for students wishing to go to graduate school, and help medical students understand and appreciate the process of scientific inquiry.
Students: How can you get involved in the summer research program?
Look for College e-mails and announcements advertising positions that are not already filled and the program in general. Talk to professors sponsoring research programs. Inquire about getting involved in their research program during the semester. Consider taking a “course-based undergraduate research” class, such as Molecular Techniques, Genetics Research Methods, or even Field & Stream. Take classes in molecular biology, biochemistry, genetics, statistics, and IT.
Progress towards a Certificate in Genomics, Ethics, and Society We’ve been working hard to plan and implement the central curricular piece of our grant, a certificate program in genomics, ethics, and society. Certificates are not common at Juniata, but certificates can provide an interdisciplinary curriculum that is not available within any single academic unit. As we envision it, a certificate offers the possibility of a more cohesive general education experience for students. In the certificate program, classes from many different departments are oriented around a common theme, have common inter-departmental learning objectives and assessments, and will be supported by ongoing faculty learning communities related to the grant. Comprised of seven courses, the proposed certificate addresses both the science and the broader ethical, legal and social implications (ELSI) surrounding progress and discoveries in the field of genomics. No area of modern biology provides a more appropriate focus for combining the humanities and sciences than the ethical, social and legal implications (ELSI) of the human genome project and the evolution of the field of personalized medicine. The certificate’s faculty learning communities apply the unique perspectives of undergraduate liberal arts study to a subject that cannot be completely addressed without the input of specialists working across disciplinary boundaries. The ethical, legal and social issues surrounding advances in genomics provide a strong focus for practicing a breadth of knowledge and skills while understanding the acts of judgment and social contexts involved in the development and application of scientific knowledge; the understanding of the scientific foundation of genomics provides the focus for developing an interdisciplinary base and cross disciplinary understanding of the life sciences in an era of “big data”. The certificate is aimed at biology POEs, but is open to all students. It is currently pending approval of Juniata’s Curriculum Committee.
ELSI Learning Community The ELSI group focused its recent meetings and conversations on: • • •
Understanding each other’s work in its relationship to genomics and developing a common vocabulary to discuss this with students Planning the workshops for the summers of 2013 and 2014 Developing an initial list of courses for the ELSI part of the genomics certificate and making certain a sufficient number of them would be offered in academic year 2013-14 for students to be able to start work on the certificate.
We accomplished the following: Member of the group met and later communicated by email about articles in the various fields of which ELSI is composed, and also discussed the relationship between ELSI, the liberal arts, and critical thinking. We agreed we will use our work together to create a Juniata dictionary of ELSI and genomics terminology. The idea is to notice what words we are using and keep a list of how different fields and individuals use them. Andrew Fletcher agreed to lead this effort. Also two members of the group, Jim Roney and Wade Roberts, are presenting papers at a conference in Ottawa, Canada on core courses in the liberal arts on science, ethics, and art. The title of the conference is: Re-thinking the Liberal Arts through Core Texts: Science, Poetry, Philosophy and History (The Annual Conference of the Association of Core Texts and Courses). Dr. Roberts will be presenting: Life-World, Normativity and Weber's “Science as a Vocation”. Dr. Roney will be presenting: We or I: Fundamental Questions on Human Dignity, Science, and the Role of Reason in a Russian Dystopian Classic. These papers were greatly improved by their experiences in the ELSI learning community.
The group wrote, discussed, modified, and approved daily plans for the topics of the two faculty workshops and identified faculty who would be responsible for each day. We also have a list of possible presenters and have scheduled the workshop for 2013 for late May. The title of the 2013 workshop is: Nature, Justice, and Genomics. The title of the 2014 workshop is: Genomics Research, Health, and Leadership. The challenge now is to carry out this plan and to schedule speakers for the workshops and the next year and a half. We also decided what courses individuals will be developing at the workshop and identified a list of participants.
The difficulty we faced in developing the courses for the certificate is that they have to be submitted before the workshop at which the courses will be developed. We decided that the team-taught courses on Genomics, Ethics, and Society will become the gateway course to the program and that students will choose from a menu of other courses taught by participants in the
ELSI learning community who have attended the workshop. Genomics, Ethics, and Society will be taught as an IC next year. Students may also take courses on the Social History of Medicine, Science and Human Values, Judgment and Decision, or Medicine, Doctors, and Russian Literature. These courses will be a focus during part of the workshop and will be taught next year.
Integrative Science Learning Community The Integrative Sciences learning group met once in November to discuss potential courses to address the themes of the GLI. To meet requirements of the proposed Genomics Certificate several strategies were suggested. For integrative science and genome science learning goals, the Biology department suggested that Biology II cover this material, but Human Biology and Sensory Biology could serve as non-biology major alternatives. For the statistics area the learning group thought any of the statistics courses would suffice. However, we are examining whether certificate learning goals may need to be in the class specifically to maintain cohesiveness of the program. For the bioinformatics area, the new HHMI Bioinformatics postdoc wishes to offer a bioinformatics course or integrate bioinformatics into existing offerings. To cover large data sets, Information Discovery (IM 241) or Database Management System (CS 370) could be used but they require Computer Science I as a prerequisite. Loren is proposing a course CS 110G that would have a focus on the handling of large data in the context of Computer Science I. Some of the courses mentioned are taught by faculty who were not at the meeting.
Further discussions with those faculty will take place at our learning group meetings in the spring, including a focus on approaches to better integrate the sciences within individual classes. Contact Loren Rhodes to make sure you are included in the group!
New Course on Unix Operating System Much of genomics software is developed and processed by Unix systems. Starting this spring, the IT/CS department is offering a 1-credit Unix Programming course each semester to serve the needs of the GLI and needs within the CS and IT POEs. Over 20 students are enrolled this semester! The objectives of this course include the following: Experience learning a programming language "on your own" as is commonly the case in industry • • •
Understand the syntax and semantics of the Unix language Understand how to develop and implement various types of programs in Unix Understand pattern matching using regular expressions
The student should develop or enhance skills in the following areas: • • •
Proficient editing and script building Design and revision of Unix scripts Debugging techniques appropriate for the Unix language
HHMI/NSF Super Computers at Juniata To help support the intense computational bioinformatics needs of the GLI and the GCAT-SEEK network (gcat-seek.org) more broadly, Juniata purchased a dedicated server last year from PSSC labs with 16GB RAM, 16 AMD processors, and a 3TB hard drive using funds from a grant from the National Science Foundation. With our HHMI grant, Dr. Lamendella has coordinated the
Suggest a name for the Cluster!
If you can think of a clever name for the purchase and acquisition of a Nor-Tech compute cluster, send to
[email protected], cluster to extend our capabilities. The Nor-Tech subject “Contest”. The person suggesting compute cluster will have 528GB total RAM, 144 the winning name will receive a 4Gb flash AMD cores, and a 20TB hard drive. This cluster drive in the shape of an Illumina MiSeq will be used to perform the jobs that can’t be easily sequencer. performed elsewhere on the web or current cloud platforms. The cluster will also serve as a cost-free “sandbox” for network members and their students to learn computationally intensive programs that would be costly to use on the cloud without having extensive experience first.
HHMI Post-doctoral Research Associate In a collaborative effort, Juniata and Penn State hired PhD candidate Mark Peterson for the HHMI Bioinformatics postdoctoral position. He will teach at Juniata and perform research at Penn State. Mark is currently a graduate student at IU Bloomington, plans to graduate in April, and start working at Juniata on June 1. He will be working closely with Vince Buonaccorsi at Juniata and Jim Marden from the Biology Department at Penn State University. Mark has worked for five years studying how the behavioral and genetic response of dark eye juncos (a bird) to testosterone differs among the sexes. In the process of nailing down a biological story about Juncos, he has picked up some very valuable computational, statistical, and teaching skills. By simultaneously participating in Juniata’s intimate teaching setting and the fast-paced world of high intensity research, Mark will be in a position to bring the latest technology to our classrooms, the GCAT-SEEK faculty, and student research efforts. He will be preparing our students to become future leaders, while he prepares himself for a career that balances scholarship and teaching endeavors.
Juniata awarded a $445,000 NSF Grant to support GCAT-SEEK research coordination network for undergraduate biology education Juniata has received its third grant to support its Genomics Leadership Initiative. This grant extends the scale and scope of the GCAT-SEEK summer workshops that HHMI is co-sponsoring. The focus of this NSF project is to support and expand participation in the newly formed Genome Consortium for Active Teaching using Next-generation Sequencing (GCAT-SEEK), that is coordinated by Juniata College, in a collaboration with Lycoming College, Susquehanna University, Duquesne University, and Penn State. Genomics and bioinformatics are dynamic fields well-suited for capturing the imagination of undergraduates in both research laboratories and classrooms. However, high costs, demanding technical skills, and high rates of change inhibit integration of next-generation sequencing approaches into the undergraduate curriculum. GCAT-SEEK aims to generate and use massively parallel sequencing data associated with the research interests of network members as the catalyst for producing innovative and broadly disseminated educational modules that offer authentic research experiences to students. The goals of this project are to increase network participation, produce and disseminate educational modules that are assessed for student learning gains, foster a sense of community among network faculty and students, and support network communications. Hands-on faculty/student workshops centered on participant research projects are the key implementation strategy.
Anticipated outcomes include improved faculty expertise, increased authentic student research experiences for undergraduates, and production of innovative, effective educational modules that improve student preparation for graduate, technical and research careers. We anticipate impacting thousands of students via this project. Workshops will be moved around the country to include three minority serving host institutions to bolster participation by groups underrepresented in STEM disciplines.
This project is being jointly funded by the Directorate for Biological Sciences and the Directorate for Education and Human Resources, Division of Undergraduate Education as part of their efforts towards support of Vision and Change in Undergraduate Biology Education.
Business Details The Internal Advisory Board met three times in November and December, and had extensive email correspondence in December as we prepared our application to curriculum committee for the certificate program. The main focus of the internal board meetings during this time has been on the goals and strategies of the integrative science learning community, and on submission of the genomics certificate to Juniata’s curriculum committee. The ELSI learning community started meeting every other week during November. It is comprised of Jim Roney (World
Languages); David Sowell, Andrew Fletcher (Biology); Jack Barlow (Politics); Phil Dunwoody (Psychology), Will Dickey (English); Jill Keeney (Biology); Kathy Baughman, Marlene Burkhardt (Economics &Business). The Integrative Science learning community met for their first time to discuss implementation of the certificate program. In attendance were Jeff Demarest, Vince Buonaccorsi, Jill Keeney, Andrew Fletcher (Biology), Jamie White (Physics), Jerry Kruse, Kim Roth (Math) and Loren Rhodes (IT). A technology working group met once to discuss qualities of the cluster that we plan to purchase in support of the bioinformatics initiatives associated with the grant. In attendance were Dave Fusco, Anne Wood, Chris Walls, Gina Lamendella (Biology), Vince Buonaccorsi (Biology), Loren Rhodes(IT), and Chris Sowell. Buonaccorsi also met with Leo Osborn, John Wall, and Colin Brislawn ‘14 about strategies to market and communicate our programs on the web.
