Student/Postdoc Information Booklet

Updated January 2012

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Table of Contents 1. What is BEACON?......................................................................................................3 Research at BEACON .................................................................................................................. 3 Education and Outreach at BEACON........................................................................................... 4 Diversity at BEACON.................................................................................................................... 4 Knowledge Transfer to Industry.................................................................................................... 4 2. What can BEACON do for you?................................................................................5 Community.................................................................................................................................... 5 Funding......................................................................................................................................... 5 Student/Postdoc Association ........................................................................................................ 5 Research Opportunities ................................................................................................................ 5 Education and Outreach Opportunities......................................................................................... 5 Professional Development............................................................................................................ 5 Mentoring and Support ................................................................................................................. 6 Opportunities with Industry ........................................................................................................... 6 3. What is expected from BEACON students and postdocs?....................................7 How to become a member............................................................................................................ 7 Participation in BEACON events .................................................................................................. 7 “Participant” vs. “Affiliate”.............................................................................................................. 7 BEACON Multidisciplinary Graduate Courses.............................................................................. 7 Reporting requirements ................................................................................................................ 8 RCR training ................................................................................................................................. 8 4. BEACON Activities and how to get involved...........................................................9 Friday seminars ............................................................................................................................ 9 BEACON Researchers at Work blog ............................................................................................ 9 Annual Congress .......................................................................................................................... 9 Education and Outreach ............................................................................................................... 9 5. Funding opportunities for BEACON Students and Postdocs..............................10 BEACON Recruiting Graduate Fellowships at MSU................................................................... 10 Project-based funding for students and postdocs....................................................................... 10 BEACON Distinguished Postdoctoral Fellowships ..................................................................... 10 Student/Postdoc Travel Funds ................................................................................................... 10 6. BEACON Student/Postdoc Association.................................................................12 7. Important Contacts ..................................................................................................13

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1. What is BEACON? The BEACON Center for the Study of Evolution in Action is an NSF Science and Technology Center, founded in 2010 with the mission of illuminating and harnessing the power of evolution in action to advance science and technology and benefit society. BEACON is headquartered at Michigan State University and has partners at North Carolina A&T State University, University of Idaho, University of Texas at Austin, and University of Washington. As an STC, BEACON has goals in the areas of research, education, diversity, and knowledge transfer to industry.

Research at BEACON BEACON research is interdisciplinary, uniting biology, computer science, and engineering. BEACON research falls under three thrust groups, which are based on natural levels of organization: genomes, behavior among individuals, and community-level dynamics. These thrust groups are united by three cross-cutting themes: biological evolution, digital evolution, and evolutionary applications. Thrust Group 1: Evolution of Genomes, Networks and Evolvability. The overall goal of this group is to understand the evolution of genome architecture and the processes that govern the production of genetic and phenotypic variation. Research projects in this thrust group fall into a number of common themes. Many investigators are studying the actual processes of speciation and adaptation—not just evidence that they have occurred in the past, but testing hypotheses about the way the process itself works. Other research themes include: environmental change and adaptation, interactions among genes, and applying an evolutionary perspective to synthetic biology. Thrust Group 2: Evolution of Behavior and Intelligence. Research in thrust group two focuses on the evolution of behavior of individuals, both in relation to the environment (e.g., navigation, foraging) and in relation to each other (communication, risk avoidance, cognition and social dynamics). Digital evolution has proven to be a powerful tool in which data gathered from biological organisms can be applied to recreate the evolution of complex behavior in digital organisms. By observing the evolution of self-replicating digital organisms, we can understand the conditions that led to the evolution of complex behaviors in biological organisms. Another major theme in this thrust group is using evolutionary computation to create better, smarter electronic and robotic systems, such as dynamic control systems that respond to the environment, improved detection systems for security, and robots that can navigate on their own through environments that may change unpredictably. Thrust Group 3: Evolution of Communities and Collective Dynamics. Research in this group focuses on the evolution, stability, and emergent properties of assemblages of organisms, considering both their ecological properties and their ability to perform collective tasks. Research themes include disease networks and transmission,

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metagenomics, maintenance of phenotypic variation through collective dynamics, and engineering applications of biological collective dynamics.

Education and Outreach at BEACON BEACON has both internal and external education goals. Internal education: BEACON has a two-semester sequence of multi-disciplinary graduate training offered at all five institutions. Graduate-level courses are offered at MSU, with distance participation by students at UI, UT, and UW; a parallel sequence is offered for upper-level undergraduates and graduate students at NC A&T. In the fall semester, biology students learn computer science skills, while computer science and engineering students learn the basics of evolutionary biology. In the spring semester, students from both of these courses come together to apply their new skills to interdisciplinary, collaborative research projects. BEACON also offers undergraduate learning and research opportunities. At UT Austin, there is a Freshman Research Initiative (FRI) stream led by BEACON members that focuses on evolution in action. BEACON also offers a Research Experiences for Undergraduates (REU) summer program at Kellogg Biological Station (MSU) and Friday Harbor Laboratories (FHL), as well as a Summer Research Opportunities Program (SROP) on the MSU campus in the summer. External educational outreach: BEACON has several external programs, including a one-week Summer High School Residential program at MSU, teacher-training workshops, and exhibits at affiliated campus museums at MSU, UT, and UW.

Diversity at BEACON Diversity is a core value at BEACON, as we strive to increase participation by underrepresented groups (including women, ethnic minorities, and people with disabilities) at all levels (pre-college, undergraduate, graduate, postdoctoral, and faculty). One of BEACON’s partner institutions, North Carolina A&T State University, is a historically black college/university (HBCU), and we are creating partnerships with other HBCUs across the country to form a pipeline for students at those institutions interested in pursuing graduate research at BEACON’s Ph.D.-granting partner institutions. Diversity is a consideration in BEACON’s internal project funding decisions. By increasing the diversity of experience in the people who make up BEACON, we can increase the diversity and strength of our thought and scholarship.

Knowledge Transfer to Industry BEACON aims to engage in knowledge exchange with industry partners. This exchange can take many forms, including: company-provided “challenge problems” and data for BEACON researchers to analyze, student internships at companies, and the adoption of BEACON tools by industry partners.

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2. What can BEACON do for you?

Community First and foremost, BEACON is a community of interdisciplinary scholars. Through regular weekly seminars, research collaborations, the annual Congress, and the website, members at all five BEACON institutions come together regularly to exchange ideas. We have a large space on the MSU campus, located in 1441 BPS Building, with a conference room, seminar room, desk and office space for a number of students, postdocs, and faculty, as well as a large lounge. The seminar room and conference room are equipped with videoconferencing technology, allowing us to meet with our partners at other institutions on a regular basis. We strongly encourage communication across disciplines and institutions, and new research collaborations regularly emerge from these interactions.

Funding BEACON provides funding for students and postdocs in several different ways, including graduate and postdoctoral fellowships, project-based funding, and travel awards. See Section 5 (Funding Opportunities for Students and Postdocs) for more details.

Student/Postdoc Association The BEACON Student/Postdoc Association provides support (social, moral, and financial) for all BEACON undergraduates, graduate students, and postdocs, and has representation on BEACON committees. See Section 6 (BEACON Student/Postdoc Association) for more details.

Research Opportunities By participating in BEACON, you can receive interdisciplinary training through classes, and find research opportunities with a wide range of faculty at five different institutions. See our “People” page on the website (http://www.beacon-center.org) for a listing of faculty associated with BEACON.

Education and Outreach Opportunities Interested in K-12 science education or outreach to the public? BEACON has many different kinds of education and outreach projects, and there are many opportunities for students and postdocs to get involved. Contact Education Director Louise Mead (lsmead@msu.edu) for more information.

Professional Development BEACON provides many professional development opportunities, such as grant-writing workshops, science communication workshops, and training in mentoring undergraduate research. At MSU, we are partnering with the Center for Academic and

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Future Faculty Excellence (CAFFE, http://grad.msu.edu/caffe) to provide some of these opportunities and encourage participation in CAFFE’s large menu of other professional development opportunities.

Mentoring and Support BEACON is dedicated to providing an inclusive environment for all members. Diversity Director Judi Brown Clarke (jbc@msu.edu) is always available for support and advice. For graduate students, postdocs, and faculty interested in involving undergraduates in research, we offer training in mentorship so that everyone can get the most out of the research experience.

Opportunities with Industry Many BEACON faculty members maintain strong contacts with people in industry. We are developing an online resource where students interested in internships and other opportunities can post their CVs, and where potential employers can find qualified students to work with them. Contact Knowledge Transfer Manager Betty Cheng for more information (chengb@cse.msu.edu).

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3. What is expected from BEACON students and postdocs? How to become a member Any student or postdoc whose primary advisor is a BEACON faculty member can join BEACON. Contact Managing Director Danielle Whittaker (djwhitta@msu.edu) to be added to the database and mailing lists.

Participation in BEACON events While we don’t expect you to participate in every activity available, we do encourage students and postdocs to be regularly involved in BEACON events. Ideally, students should do some or all of the following:

• Regular attendance of Friday BEACON seminars, and presenting at least once a year once the student has commenced her/his own research

• Completion of BEACON multidisciplinary courses • Participation in BEACON-sponsored or BEACON-relevant research • Embracing a multi-disciplinary and multi-institutional perspective • Presenting research at BEACON Congresses and in poster sessions at special

events • Contributing to the BEACON blog

“Participant” vs. “Affiliate” According to NSF’s definitions, a Center “participant” is someone who participates in Center activities at least 160 hours per year. This includes taking BEACON courses, being involved in BEACON research (whether it is directly funded by BEACON or not), attending or presenting at the Friday seminars and the Congress, or any other BEACON activities. If you are affiliated with BEACON but not at the 160-hour level, then NSF considers you an “affiliate.” Please be sure that your designation in your online profile is correct (more below, under Reporting Requirements).

BEACON Multidisciplinary Graduate Courses BEACON graduate students are expected to take the multidisciplinary graduate courses offered at all five BEACON institutions. Graduate-level courses are offered at MSU, with distance participation by students at UI, UT, and UW; a parallel sequence is offered for upper-level undergraduates and graduate students at NC A&T. In the fall semester, biology students learn computer science skills, while computer science and engineering students learn the basics of evolutionary biology. In the spring semester, students from both of these courses come together to apply their new skills to interdisciplinary, collaborative research projects. Graduate course names and numbers at MSU (students at UI, UT & UW, please check with your BEACON leads for your university’s course numbers): • Computational Science for Evolutionary Biologists, Instructor Titus Brown: CSE 891 • Evolutionary Biology for Non-Life Scientists, Instructor Alexander Shingleton: ZOL

890

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• Multidisciplinary Approaches to the Study of Evolution, Instructors Charles Ofria and Ian Dworkin: CSE 891

Course names and numbers at NC A&T: • Evolutionary Biology for Engineers and Computer Scientists, Instructor Joseph

Graves: COMP 790.003 for graduate students, COMP 590.005 for undergraduates • Computational Science for Evolutionary Biologists, Instructors Gerry Dozier and

Greg Goins: Biology 499

Reporting requirements As a member of BEACON, you should maintain an up-to-date profile on the BEACON intranet (http://secure.beacon-center.org). We ask that you regularly report your BEACON outputs and activities on the intranet, including but not limited to: publications, degrees completed, awards received, and education/outreach activities. When publishing work that was supported by BEACON, please be sure to acknowledge it by putting BEACON as one of your affiliations and, if allowed by the journal/conference, listing NSF support in the acknowledgments section with the following wording:

This material is based in part upon work supported by the National Science Foundation under Cooperative Agreement No. DBI-0939454. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

RCR training All BEACON students and postdocs, whether or not they are directly receiving funding, are required by NSF to complete Responsible Conduct of Research (RCR) training. We have put together a BEACON RCR policy that can be found on the BEACON Intranet. Since nearly all of our participants are already required by their home institutions and departments to complete this training, we do not require any additional training – only that you report it to us in addition to your home institution/department. In the future, we hope to be able to integrate reporting systems with other entities to lessen the burden.

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4. BEACON Activities and how to get involved Friday seminars Every Friday at 3:30 PM Eastern, 1441 BPS Building (MSU), or in videoconference rooms at partner institutions. We rotate through 5 themes: Thrust Groups 1, 2, and 3; Education and Outreach; and an "All-BEACON" category. We occasionally offer "BEACON 101" talks on broad areas of research designed to be helpful to people who are not specialists. Typically 1-2 people give a talk each Friday. These talks are not intended to be polished, finished projects. Instead, we want talks on works in progress, with the intention of getting feedback and interest across BEACON. All five partner institutions participate via videoconference. If you are interested in presenting, please contact the appropriate thrust group leaders or the Managing Director, Danielle Whittaker (djwhitta@msu.edu). You can see the current schedule at any time by going to the “BEACON Events” tab on the website and click the link below the calendar for “Read-only spreadsheet showing Friday seminar themes and speakers.”

BEACON Researchers at Work blog Every Monday morning, we feature a blog post written by students and postdocs. These posts describe their BEACON research at a level that can be easily understood by the public, and are designed to communicate your research not only within BEACON but also to the outside world. If you are interested in writing a post, please contact Managing Director Danielle Whittaker (djwhitta@msu.edu).

Annual Congress Every summer, BEACON holds the BEACON Congress at the MSU headquarters. This annual meeting is a great opportunity to share your research, learn what other research is going on, and brainstorm about new collaborations with other BEACON members at all 5 institutions. Travel for this Congress is covered by BEACON. [Because the largest number of BEACON members is at MSU, it would be prohibitively expensive to hold the Congress at another partner institution.]

Education and Outreach There are many opportunities to get involved in BEACON education and outreach activities, including:

• Mentoring a summer research undergraduate student • BEACON High School summer residential program at MSU • Museum exhibits at MSU, UT, and UW

We’re always looking for new ideas, too. If you are interested in participating, contact Education Director Louise Mead (lsmead@msu.edu).

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5. Funding opportunities for BEACON Students and Postdocs BEACON Recruiting Graduate Fellowships at MSU BEACON offers “top-up” fellowships to new Michigan State University students who receive University Fellowships (http://grad.msu.edu/universityfellowships/) or external funding, such as from NSF. Students must be nominated for these fellowships by a BEACON faculty member. If an applicant is awarded a BEACON Top-Up Recruiting Fellowship, they will receive between $3,000 and $5,000 in additional fellowship funds for each year they participate in BEACON activities, for up to a maximum of five years. If the applicant receives an NSF or other similar fellowship already providing $30,000 or more in annual support, BEACON will offer a one-time fellowship supplement of $5,000. Students receiving these fellowships are required to take the two BEACON multidisciplinary graduate courses (see Section 3: What is Expected from BEACON Students?). The funds for these fellowships come from matching funds from MSU, not from NSF, so we are unable to offer them at partner institutions. For more information on MSU graduate funding opportunities, see http://grad.msu.edu/funding/.

Project-based funding for students and postdocs Projects chosen for funding in the annual BEACON budget allocation process typically include funds for graduate research assistantships, postdocs, and/or undergraduate hourly pay. Students and postdocs who are affiliated with BEACON faculty on a funded project may be supported by one of these projects, and will conduct research related to the goals of that project. This funding is available at all five partner institutions. Typically, these funding requests are submitted by BEACON faculty, but graduate students and postdocs can be co-PIs on these requests. In some cases postdocs can also be the lead PI on funding requests, as long as BEACON faculty are included as co-PIs. BEACON faculty can now advertise open, funded positions for students and postdocs on the BEACON website (under “Available Positions”). To have a position listed here, please send the information to Managing Director Danielle Whittaker.

BEACON Distinguished Postdoctoral Fellowships Beginning in 2012, BEACON will offer one competitive 2-year fellowship per year to an outstanding interdisciplinary postdoctoral scientist. The fellow will be based at MSU (again, funds are provided by MSU matching funds) but will need two faculty sponsors, one of which may be from a different BEACON institution. Application instructions are available on the BEACON website (under “Available Positions”).

Student/Postdoc Travel Funds Students and postdocs at all five institutions may apply for funding to travel to conferences, workshops, etc., if the travel is related to BEACON research. Many

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BEACON-funded projects explicitly include such travel funds, but other travel funds are available for those not supported on such projects. To apply for travel funds, download the application form on the BEACON website and follow the instructions there (look under the menu item “For Current Members” and choose “Student/Postdoc Travel Funds).

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6. BEACON Student/Postdoc Association The first goal of the BEACON undergraduate, graduate, and postdoc association is to promote communication, both within- and among BEACON institutions. Towards this goal, we have chosen liaisons at all 5 partner universities, each of whom is planning to build a strong network among students and postdocs at their home institution. These groups will have regular social interactions such as "lunches and lab tours" to learn about different BEACON-related activities at their institutions. The group of liaisons communicates regularly in order to share successes and keep each of the sites connected. We also plan to elect representatives to the various committees within BEACON so that students and postdocs have a voice in the directions of BEACON. These representatives will receive feedback from and communicate to the entire body of BEACON students and postdocs about the activities of these committees. Additionally, the organization aims to use some of its funds to support between-institution travel outside that of funded projects in order to foster new collaborations and maintain a cohesive body of students and postdocs. This collaboration both within and among partner institutions is a major priority of the student and postdoc association. Through events such as a student and postdoc retreat, scheduled to take place before BEACON Congresses, students and postdocs can learn about work being done at other institutions as well as form new collaborations. To support potential collaborations, students and postdocs can submit requests for small, fixed-amount awards that are provided by the association in order to help begin new or maintain existing cross-discipline and cross-institution collaboration. Another major component of the BEACON student and postdoc association is to prepare BEACON alumni for wherever their careers take them. This training is accomplished through the interaction of undergraduates and graduate students as well as graduate students and postdocs, so that each of these groups can learn from those in the next phase of their academic careers. This training is extended through planned local outreach programs funded by the student and postdoc organization, in which high school students are invited to meet with and observe researchers in BEACON. By interacting with BEACON members, these students can gain a greater understanding of science in action, and how students are educated. Additionally, the small awards available can be used to fund personal development and/or outreach activities such as invited speakers during the student and postdoc retreat preceding the BEACON Congresses. By these means, we hope this organization will cater directly to the needs of its constituents, since the activities are created and dictated by them. For more information, contact your local Student/Postdoc Association Liaison (see section 7: Important Contacts).

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7. Important Contacts

BEACON Leadership Title Name Email Phone

Director Erik Goodman goodman@egr.msu.edu 517-355-6453 Deputy Director Charles Ofria ofria@msu.edu 517-355-8389 Managing Director Danielle Whittaker djwhitta@msu.edu 517-884-2561 Education Director Louise Mead lsmead@msu.edu 517-884-2560 Diversity Director Judi Brown Clarke jbc@msu.edu 517-353-5985 Administrative Assistant Connie James jamesc@msu.edu 517-884-2548 Accounts Manager Darcie Zubek zubek@msu.edu 517-884-2556 Knowledge Transfer Mgr Betty Cheng chengb@cse.msu.edu 517-355-8344 NCAT co-lead Gerry Dozier gvdozier@ncat.edu 336-334-7245 ext.467 NCAT co-lead Joseph Graves gravesjl@ncat.edu 336-285-2858 (Mon,

Spring 2012) 919-684-0577 (Tu-Fri, Spring 2012)

UI lead James Foster foster@uidaho.edu 208-885-7905 UT lead Risto Miikkulainen risto@cs.utexas.edu 512-471-9571 UW lead Benjamin Kerr kerrb@u.washington.edu 206-221-3996 Thrust Group 1 lead Titus Brown ctb@msu.edu 517-355-1646 Thrust Group 1 lead Tom Schmidt tschmidt@msu.edu 517-884-5400 Thrust Group 2 lead Kay Holekamp holekamp@msu.edu 517-432-3691 Thrust Group 2 lead Rob Pennock pennock5@msu.edu 517-432-7701 Thrust Group 3 lead Fred Dyer fcdyer@msu.edu 517-353-9864 Thrust Group 3 lead Phil McKinley mckinley@cse.msu.edu 517-353-4396

BEACON Student/Postdoc Association Title Name Email

MSU Co-Liaison Brian Connelly bdc@msu.edu MSU Co-Liaison Caroline Turner cturner@msu.edu MSU Co-Liaison Luis Zaman luis.zaman@gmail.com NC A&T Liaison Daniel Opoku dopoku@ncat.edu UI Liaison Matt Pennell mwpennell@gmail.com UT Liaison Art Covert covertar@gmail.com UW Liaison Carrie Glenney cglenney@uw.edu