Proposal

Introduction

Proposal ID 2015-058
Submitted January 16, 2015
Owner fhl
Department Friday Harbor Laboratories
Category Software
Funding Status Fully Funded
Metric Score None

Contacts

Primary
  • Name
  • Title
  • Email
  • Phone
  • Mailbox
  • Alan Cairns
  • Senior Computer Specialist
  • cairns@uw.edu
  • 206-616-0704
  • Please use US Mail (Campus 351812)
Budget
  • Name
  • Title
  • Email
  • Phone
  • Mailbox
  • Scott Schwinge
  • FHL Administrator
  • schwinge@uw.edu
  • 206-616-0708
  • Please use US Mail (Campus 351812)
Dean
  • Name
  • Title
  • Email
  • Phone
  • Mailbox
  • Dr. Lisa J. Graumlich
  • Dean, College of the Environment
  • graumlic@uw.edu
  • 206-221-0908
  • Box 355355

Descriptions

Abstract

Much of the research done at FHL now focuses on Marine Genomics, including invertebrates and algae. Genomics can be used in biodiversity studies, population studies and to study developmental and evolutionary processes. Students prepare DNA at FHL, do the PCR and send away the samples for sequencing. The sequences come back and must be assembled with a Sequencing Assembly Program. Two of the widely used sequencing assembly programs are Sequencher and MacVector. Both of these programs are important not only for their capabilities, but because they are easy to learn and help students understand genomics by the way that the programs are deployed. We originally purchased these programs with STF funding, but they are continually updated and we have not been able to update for several years. It is critical to receive the updates of these programs to stay current with state of the art genomics methods. Demand to use the software by students has increased beyond our existing licenses. We are requesting one new license of Sequencher , one upgrade to our existing Sequencher license, and two upgrades to our existing MacVector licenses.

Category Justification

This proposal meets the criteria for the Software category. It addresses students’ software needs for software that is not on the key server.

Background

The Friday Harbor Laboratories (http://depts.washington.edu/fhl) are the University’s primary field station for the study of marine biology and related disciplines.

We presently have as many as 70 students in residence full-time during any one session. Hundreds more (annually more than 1,500) make shorter, research oriented field trips to FHL. Undergraduate students attend for a full quarter in spring or autumn (10-11 weeks) receiving 15-16 credits, while in summer undergraduates and graduate students attend 5-week courses, of 9 credits each. Our Research Experiences for Undergraduates (REU) program has expanded, giving undergrads hands on experience in the areas of Integrative Biology and Ecology of marine organisms. Graduate students often conduct research on site for more than a year. Commonly three or more courses are taught simultaneously, and these are concurrent with the work of 20-30 graduate students and independent researchers.

In addition to the standard lectures and labs common on the Seattle campus, students in most FHL classes usually conduct a self-directed research project related to the course content. This involves collection of data in the field or lab, analysis of these data, and the presentation of their results through written and oral reports.

The Laboratories are a division of the UW College of the Environment, but our instructors are recruited from various departments. In 2014 we will have faculty participating from UW Oceanography, Biology, Fisheries, Program on the Environment, Sociology, the Applied Physics Lab, and even English (due to the new creative writing aspect of our fall MBQ class). Our visiting instructors will be coming from universities in California, Oregon, Hawaii, Arizona, New Mexico, Illinois, North & South Carolina, Alabama, New York, Canada, and Germany. Classes from the Seattle, Bothell, and Tacoma UW campuses visit the Laboratories on field trips. Thus, the learning experience at Friday Harbor is a collaborative effort in many disciplines, involving participation by many different academic units.

It is not uncommon to hear students say that their experience at FHL was “the most valuable of my academic career." Students especially value the free access to facilities and research tools at our Labs, as evidenced by these comments in our 2013 exit surveys:
"I have had a great and very memorable 5 weeks here. Thanks to the staff, professors and facilities at FHL. I would recommend it to others, and I hope to come back sometime soon." "Excellent experience -- thank you!" "This place is wonderful. I will truly miss it!" "I loved my experience here at FHL. I can't wait to come back."

Marine Genomics research at FHL is increasingly done by both undergraduate and graduate students at FHL. The demand to use Sequencher and MacVector now has students in both research apprenticeships and research components of genomics classes in line for single copies of each during our busy terms. Furthermore the existing licenses are in need of updating. MacVector was last updated in 2006 and Sequencher in 2011. In the fast evolving world of genomics this puts our students at a disadvantage.

Benefits to Students and the University

This software proposal provides needed software that is not available on the key server. This directly benefits students who need to conduct gene sequencing.

Departmental Endorsements

*** Dr. Billie J. Swalla, Director, Friday Harbor Laboratories
The University of Washington's Friday Harbor Laboratories continue to contribute to the major teaching and research initiatives of marine sciences in the College of the Environment and we appreciate that STF is a critically important partner. We have a world-class FHL research apprenticeship program for undergraduates to conduct research for a quarter, with a new endowment for student support. This intense training program includes major reliance upon state-of-the-art research tools to permit undergraduate students to learn how to plan, conduct and present (in public and publication modes) modern research.
FHL's undergraduate educational effort has also been supported generously by the Howard Hughes Medical Institute, Microsoft, Mary Gates Endowment, Washington Research Foundation, and others. In addition, the National Science Foundation (NSF) awarded FHL $303,000 for three years of undergraduate REU Program support, which has been combined with our existing Blinks endowment and money from BEACON to support 15-18 undergraduates conducting research at FHL each summer. Many of our other undergraduate classes, in fall spring and summer, also include research projects by the students.
FHL is continuously working to provide increased financial support to all its programs, including explicitly instructional and research training efforts, from non-State of Washington sources (private foundations, individuals, and federal sources). This initiative has resulted in development of support up to about 75% of the apprenticeship program from non-UW sources. However, this also requires, as a crucial prerequisite, stable support for our physical plant and supplemental support for student technology tools. Thus STF support continues to be fundamentally important leverage to keep our research equipment up to date.
This proposal is for critical software to conduct genomics research.
I strongly support this initiative by Alan Cairns, and urge its support by the STF.

***Dr. Paul W. Gabrielson, FHL Instructor of Marine Algae
Sequencher is essential software for any student who is doing molecular research at FHL. All DNA extracted and amplified at FHL is sent off site for sequencing, and those results posted on websites by the sequencing facilities. In order to see, check and make sense of that raw data Sequencher is essential. FHL has no other software available to do this. Without Sequencher, molecular research at FHL would not be possible and the labs would be back to 20th C biology. This would not serve students' needs.

Installation Timeline

This software will be ordered and installed asap after we receive acknowledgement of funding.

Resources Provided by Department

The software will be installed on common use computers both in the computer lab and Lab 10 where student genomics research takes place.

Access Restrictions (if any)

The software will be installed on all common use computers in the Computer Lab and Lab 10. A dongle is used with each license and can be checked out on an as needed basis. All students have access to the Computer Lab at all times using the key code provided at the beginning of the term. The Lab 10 keycode will be provided to all students who are doing genomics research.

Student Endorsements

***Shawn Luttrell, Graduate Student, Dept. of Biology
MacVector is a critical and essential program for my ongoing research at Friday Harbor Laboratories. I study an animal that lacks an annotated genome and MacVector allows me to reconstruct phylogenies, align gene sequences, and design primers for molecular studies. Many of the genes I work with have sequence similarities with other genes and therefore, MacVector is necessary to analyze coding regions and ensure I design primers specific for my gene of interest. Having the most current and up to date version of MacVector will provide an indispensible tool for completing my research at FHL.

***Kevin Kocot, Postdoctoral researcher in Marine Genomics, previous TA and graduate student at Friday Harbor Labs
Sequencher is by far the most popular piece of software for assembling 2+ reads from a Sanger sequencing run to get a consensus sequence. Although the software has a lot of features, the basics (and even many of the "bells and whistles") are very intuitive to use and it is easily picked up by even a relatively inexperienced student, following a demonstration by an experienced user and a little supervised hands-on time. I have personally used this software in my research and taught several undergraduate students how to use it for student research projects and the training phase has always gone very well. Notably, I have also used the comparable software DNASTAR but found Sequencher to be much more user friendly and efficient. Unfortunately, even in Linux, there is no comparable free software for this application.

Items

Group Funded Item Unit price Quantity Subtotal
None

MacVector (upgrade license)

$840.90 2 $1,681.80
Description

Justification

Sequencher (standalone license)

$2,500.00 1 $2,500.00
Description

Justification

Sequencher (upgrade license)

$825.00 1 $825.00
Description

Justification

Sales Tax

$480.65 1 $480.65
Description

Justification

Total requested: $5,487.45

Total funded: $5,487.45

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