C A T
E E K
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of Buonaccorsi, Vincent P
(BUONACCORSI)
Sent: Friday, May 18, 2012 10:54 AM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: Vision and Change Leadership Fellows
Hi everyone,
In case you haven’t seen this yet…
Initiative Launched to Change Undergraduate Biology Education
A new national initiative promises to improve college biology education by engaging faculty members in an effort to change how post-secondary life sciences departments approach education. PULSE, which stands for
Partnership for Undergraduate Life Sciences Education, is a collaborative effort funded by the National Science
Foundation (NSF), National Institutes of Health (NIH), and the Howard Hughes Medical Institute (HHMI).
Program organizers also announced today that they are accepting applications from faculty members interested in becoming Vision and Change Leadership Fellows - individuals who will lead a national effort to stimulate systemic change in how post-secondary educational institutions approach biology education. The intent of the program is to develop a strategy to implement the findings from a 2011 report.
College students and faculty members have long argued that the approach to undergraduate education in the life sciences should be modernized to reflect what we now understand about how students learn. Twenty-first century science demands that students develop scientific and technical skills, and also the capacity to work beyond traditional academic boundaries. Undergraduate students, regardless of their major, deserve and need a life sciences education that helps then understand biology and how scientific research is conducted. Informed decision-making, whether managing one's health, deciding what food to eat, or understanding how individual actions influence the environment, requires an appreciation of the nature of science.
In 2006, the NSF initiated a multi-year conversation with the scientific community, with assistance from the
American Association for the Advancement of Science. That dialogue, which was co-funded with the National
Institutes of Health and the Howard Hughes Medical Institute, generated the 2011 report, Vision and Change in
Undergraduate Biology Education: A Call to Action.
The scientific community actively informed the recommendations in the Vision and Change report. Among these were a recognition that a 21st century education requires changes to how biology is taught, how academic
GCAT-SEEK Listserv Archive May 2012 Page 1

departments support faculty, and how curricular decisions are made.
"There is now broad consensus about the change that is needed," said HHMI's Cynthia Bauerle. The way biology is taught needs to change in order to "spark student interest in science and prepare them for the challenging scientific problems we face in the 21st century."
Prior efforts to reform post-secondary life sciences education have focused on helping individual faculty members improve their teaching methods. These initiatives have created points of excellence at institutions across the country, but have failed to produce the systemic change that is needed to fundamentally improve college-level biology education.
To foster this widespread change, the NSF, NIH, and HHMI have partnered to launch the PULSE program.
Supporting the effort are Knowinnovation and the American Institute of Biological Sciences.
The PULSE initiative will facilitate the systemic change that was identified as a national priority in the Vision and
Change report.
Clifton A. Poodry of the National Institute of General Medical Sciences, the division of NIH providing funding to
PULSE, notes that NIH has a long-standing commitment to training the next generation. "We look forward to furthering this goal through our partnership with NSF and HHMI to implement recommendations of the Vision
and Change report for improving undergraduate biology education," said Poodry.
This year PULSE will select 40 Vision and Change Leadership Fellows. The selection process will identify individuals experienced in catalyzing undergraduate biology education reform at institutional, departmental, or divisional levels in the nation's colleges and universities. The Fellows will represent research universities, regional or comprehensive universities, liberal arts colleges, and community colleges. The Fellows will be engaged in a yearlong effort to develop an implementation strategy for the Vision and Change report.
"What we are trying to achieve is systemic change, transformation of undergraduate biology education in this country," stated Judith Verbeke of the NSF. This is why the PULSE effort is encouraging current or former biology department heads to apply. "The focus is intentional," said Verbeke, "because it's at the level of the department that so many decisions are made. We are looking to the department as the most appropriate unit to make real change."
Ideal applicants will be aware of the history and discourse of reforming undergraduate life sciences education; have undergraduate teaching experience as well as experience mentoring, motivating and evaluating other faculty; and will have experience as current or former chairs or department heads. Applicants should be active in cultivating the mix of scholarship in teaching and life sciences research appropriate to their type of institution.
Successful candidates will have a record of working collaboratively and creatively with individuals from different backgrounds.
It is through diversity of perspective that we achieve change, Bauerle said, "We seek not only those who are already members of the choir, but also committed life scientists and educators who question how best to proceed."
GCAT-SEEK Listserv Archive May 2012 Page 2

Applications for the Vision and Change Leadership Fellows program will be accepted through July 9, 2012.
Information about the PULSE program, including application guidelines, is available at www.pulsecommunity.org . The Vision and Change report is online at http://visionandchange.o
rg/finalreport.
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of Buonaccorsi, Vincent P
(BUONACCORSI)
Sent: Wednesday, May 23, 2012 3:35 PM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: quick survey
Hi Everyone!
I am presenting a talk about our network at the “Bioinformatics workshop for Student/Scientist Partnerships” in a few weeks at HHMI headquarters in Maryland. I would really appreciate it if you could take this quick survey, so I know a little more about you, your school, your background and needs, and the potential collective impact of our group on undergraduate education. I have not set this up to be anonymous, but I will keep your answers strictly confidential. I am expecting 90% of us to be novices at this point with respect to the new technology... that’s why we have the network! Keep in mind that you are in no way obligated to respond, and blanks are fine if you don’t want to answer particular questions. Please simply reply to me. Thanks!!
1. Name:
2. School:
3. Approximate total number of undergraduates at your school:
4. Minority Serving Institution?: Yes/No
5. Your Department:
6. Your primary field (within your department):
7. Are you or have you been a department chair? Yes/No
8. Position (please pick from below):
Undergrad
Instructor
PostDoc
Assistant Prof
Assoc.Prof
Full Prof
Other please specify
9. Genus/species of organism(s) of sequencing interest:
GCAT-SEEK Listserv Archive May 2012 Page 3

10.Type of sequencing project(s) of interest, please pick from below. You can list more than one or ALL:
Bacterial Genome de novo
Bacterial Genome resequence
Small Eukaryote Genome (<300Mb) de novo
Small Eukaryote Genome (<300Mb) resequence
Large Eukaryote Genome (>300Mb) de novo
Large Eukaryote Genome (>300Mb) resequence
Transcriptomics
Metagenomics
Other, please specify
11. Number of freshmen and sophomore undergrads you teach in your department on average each year:
12. Number of junior and senior undergrads you teach in your department on average each year:
13. Number of undergraduate research students you teach each year:
14. Familiarity with Unix or Linux operating system (1 to 5, with 5 as highest):
15. Familiarity with Perl or Python (1 to 5, with 5 as highest):
16. How many raw Next Generation sequencing datasets have you tried to analyze up to this point from any source, using any software?:
17. How many years have you been a member of either GCAT or GCAT-SEEK?:
18. Familiarity with literature on assessment of student learning gains (1 to 5, with 5 as highest):
19. How many years of experience teaching undergrads:
20. Open commentary:
Again, thanks so much for your help!
Vince
GCAT-SEEK Listserv Archive May 2012 Page 4

-----Original Message-----
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of Buonaccorsi, Vincent P
(BUONACCORSI)
Sent: Thursday, May 24, 2012 12:04 PM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: Fuel for the fire!
Hi Everyone,
1) Thank you for your quick response so far with the survey. I've already received 15. Just 100 to go!
2) I am also very pleased to announce that Juniata College was selected by Howard Hughes Medical Institute to receive a 1M award entitled, "The Genomics Leadership Initiative at Juniata College."
( http://www.hhmi.org/news/hhmicolleges20120524.html
). I am serving as PI of our Hughes award and want to let you know that our research coordination network was seen as highly meritorious by reviewers... an effective vehicle for implementing change in undergraduate education.
The network has received:
-funding for summer faculty development workshops for the network -funding for a very brainy computer capable of assembling large Illumina datasets for our collective use -support for some shared bioinformatics software (TBA)
3) For your reference, the Aims of our pending NSF-TUES proposal are complementary to the Hughes award: a)
Obtain raw sequence in a network faculty member's research area, b) storage servers, bioinformatics tools, and cloud time that would better enable larger number of students to get involved, c) support for developing and implementing pedagogical and assessment tools for the network to ensure faculty and student progress on core
GCAT-SEEK learning goals.
4) We will be submitting a full NSF RCN/UBE proposal shortly as well, again designed to be complementary to the Hughes award. We will be asking for a) matching support for the summer workshops, b) time for key persons to administer network activities and publications, c) perhaps support for a national competition for network students that would allow them to attend disciplinary meetings and/or a collaborative long distance nanocourse in bioinformatics (do you like those ideas?).
I would like to give special praise to Malcolm Campbell and the GCAT-SEEK steering committee (Nancy Trun:
Duquesne, Jeff Newman: Lycoming, Tammy Tobin: Susquehanna) for their critical roles in getting this effort off the ground.
If you have questions about any of this, please don't hesitate to ask.
Vince
GCAT-SEEK Listserv Archive May 2012 Page 5

-----Original Message-----
From: gcatseek-l [mailto:gcatseek-l@listserv.davidson.edu] On Behalf Of Campbell, Malcolm
Sent: Thursday, May 24, 2012 12:45 PM
To: gcatseek-l
Subject: Re: Fuel for the fire!
Great news and congratulations!! So happy for you and all of us who will benefit from your vision and community minded proposal.
Malcolm
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of JEFF NEWMAN
Sent: Thursday, May 24, 2012 12:47 PM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: Re: Fuel for the fire!
Wooohooo! Way to go. Congrats!
Connected by DROID on Verizon Wireless
-----Original Message-----
From: Laura L. Hoopes [mailto:LLH04747@pomona.edu]
Sent: Thursday, May 24, 2012 1:28 PM
To: JEFF NEWMAN; GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: RE: Fuel for the fire!
Off to a great start, congratulations to you and Juniata!
Laura Hoopes
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of Todd Eckdahl
Sent: Thursday, May 24, 2012 1:49 PM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: Re: Fuel for the fire!
Wow! Great news, Vince. Congratulations. This is the beginning of something that will benefit many, many faculty and students.
Todd
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of Charles Hauser
Sent: Thursday, May 24, 2012 2:02 PM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: Re: Fuel for the fire!
Vince,
Congrats!
A great step forward for students to utilize the next greatest tool!
Charles
GCAT-SEEK Listserv Archive May 2012 Page 6

-----Original Message-----
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of Buonaccorsi, Vincent P
(BUONACCORSI)
Sent: Tuesday, May 29, 2012 7:48 AM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: quotes and offers
Hi Everyone,
1) Please keep sending in your surveys!
2) Attached is an updated Illumina quote from Operon. Note that it extends only until end of June. Let me know if you have money for a run this summer and we can talk about whether it makes sense to try and combine experiments for cost savings.
3) If you are interested in the extended two month CLC Bio Genomics Workbench 2-month trial license for this summer, please let me know by next Wednesday June 6.
4) If you have any students that would benefit from using the Geneious software package this summer, the company has offered to give them a free 8-week Geneious Pro license. The company is also offering GCAT-SEEK members 25% off on all their other license types including annual or lifetime licenses. Geneious is what we (at
Juniata) use for most of our Sanger sequence manipulation and organization, designing primers, making alignments, and tree building. For nextgen it is useful for creating searchable blast genomic databases, Batch blasting NCBI, and there are plugins for various applications including whole genome alignment. If you've never used it, you can download the free geneious pro trial and see whether you are interested in requesting free licenses for your students. Please let me know by next Wednesday June 6. See below for more information.
5) Please remember that these offers apply only to GCAT-SEEK members and their undergraduate students.
Best wishes,
Vince
________________________________________
Geneious as a Teaching Tool:
* Geneious uses many industry standard algorithms and embeds useful applications such as ClustalW, Primer3,
Paup* and Mr.Bayes.
* The collaboration features in Geneious will allow you to share files and course data with your students and the simple export features make producing graphics a breeze.
Take a quick video tour of Geneious by visiting our Education page< http://www.geneious.com/default,774,education.sm
>, browse our catalog of beautiful screenshots< http://www.geneious.com/default,1255,screenshot_gallery.sm
>, or read more about the features and benefits that Geneious provides on our Features page< http://www.geneious.com/default,1228,features.sm
>.
"Geneious is the perfect combination of ease-of-use and bioinformatic refinement!" – Asst Prof Joshua Udall –
Brigham Young University Kind regards,
The Geneious Team sales@biomatters.com<mailto:dipti@biomatters.com
>
GCAT-SEEK Listserv Archive May 2012 Page 7

-----Original Message-----
From: GCAT SEEK [mailto:GCATSEEK-L@LISTSERV.DAVIDSON.EDU] On Behalf Of Tobin, Tammy
Sent: Tuesday, May 29, 2012 8:28 AM
To: GCATSEEK-L@LISTSERV.DAVIDSON.EDU
Subject: Re: quotes and offers
Hi all,
I have been playing around with the CLC Bio Genomics Workbench this spring, and thus far I really like it. Its
BLAST interface is a bit clunky, but otherwise the program seems to do a good job. It is also available for Mac platforms - unlike many of the other programs out there.
Happy sequencing!
Tammy
GCAT-SEEK Listserv Archive May 2012 Page 8