Using ImageJ in Teaching and Research
Organized by: Stokes Baker, 4001 W. McNichols Rd., Detroit, MI
Donna Hazelwood, 820 N. Washington Ave., Madison, SD
Beverly Brown, 70 Varinna Drive, Rochester, NY
ImageJ is powerful image analysis software distributed
free by the National Institutes of Health. Because of the availability
of inexpensive
digital cameras, ImageJ has many applications for both teaching and research.
Participants will learn how to make quantitative measurements. Additionally,
instructions on how to make and analyze time-laps video using readily
available cameras will be taught. Examples of how ImageJ has been
used in undergraduate
instructions will be presented. Participants are required to bring
their own laptop computers. Software will be distributed at the session.
Symbiota: a software package for virtual floras
Organizer: Dr. Corinna Gries, Institute of Limnology, University
of Wisconsin, Madison, WI 53706
Edward Gilbert, 2831 E. 18th St, Tucson, AZ 85716, phone: 520-481-7638;
egbot@asu.edu
Leslie Landrum, SoLS, Arizona State University, Box 874501, Tempe, AZ 85287-4501
Thomas H Nash III, SoLS, Arizona State University, Box 874501, Tempe, AZ
85287-4501
The workshop will emphasize exercises to explore
the full functionality of Symbiota, a software package developed
to aid regional natural history collections integrate and publish
their specimen data in an online virtual flora (or fauna) format.
First we will cover the basic user interface which allows one to
search for specimens by various parameters, and generate distribution
maps and checklists. We will then demonstrate how species checklists
generated from specimen data can be integrated with morphological
character data to create dynamically interactive identification tools
for any given area. Species identification is aided by extensive
information in species profile pages which are illustrated with images
from a separate database. In this exercise, educators may generate
custom checklists and keys for areas as large as an extensive field
trip or as small as a school yard and establish this as a project
within Symbiota for their students. Bring your computer for the exercise
or follow along the presentation. We will also walk collection curators
through data maintenance within Symbiota. This will involve data
loading, tuning data presentation, discussion of the taxonomic thesaurus
and managing the character and character state information for dynamic
keys. If there is interest, we will briefly discuss setting up a
Symbiota node for interested collections or consortia without getting
into the technical detail.
More information on Symbiota may be found at http://symbiota.org/tiki/tiki-index.php.
The Symbiota package is currently used by three nodes, SEINet with vascular
plant records from the Southwestern US taken from 20 herbaria
(http://swbiodiversity.org/seinet/index.php),
the Consortium of North American Lichen Herbaria with records from 8 herbaria
(http://symbiota.org/nalichens/index.php)
and the Cooperative Taxonomic Resource for American Myrtaceae with records
from 4 herbaria (http://symbiota.org/cotram/index.php).
Photographing plants: Standarized photographs and their use in
plant identification
Organizer: Bruce K. Kirchoff, UNCG, Department of Biology, P.O.
Box 26170, 312 Eberhart, 321 McIver St., Greensboro, NC 27402-6170
We are at a turning point in how we teach plant identification and
identify unknowns, but the revolution has yet to be codified into
a coherent formula. Still, the pieces are in place to create a unified
teaching and identification environment that can be used as easily
by novices as it can by experts. The key to this claim is the use
of standardized plant images. The author has used standardized photographs
in a program that teaches visual tree identification, and in a new
type of visual key. The workshop will cover the photographic standards
that have been developed to date, their rational, the need for development
additional standards, and will demonstrate the power of standardized
images in teaching plant identification. - Interested participants
are invited to a post-workshop foray to photograph plants within
walking distance of the conference venue. Bring your cameras.
PlantingScience: Fostering Student Scientific Thinking
Through Mentoring
Organizers: Eric H. Jones, Department of Biological
Science Florida State University Tallahassee FL 32306-4295
Laura Super University of British Columbia, Kelowna BC 3333, University Way
Laura Lagomarsino, Harvard University, Herbaria 22 Divinity Ave, Cambridge,
MA 02138
Lindsey K. Tuominen, Warnell School of Forestry & Natural Resources, 180
E Green Street. The University of Georgia Athens, GA 30602-2152
PlantingScience fosters science literacy in elementary,
secondary, and undergraduate students via scientific inquiry curricula
and online scientific mentoring. This workshop is aimed at providing
a means for the PlantingScience community (although people new to
PlantingScience are welcome) to learn how to better cultivate an
appreciation for science among our students from our collective experience.
The sessions will focus on four topics:
- engaging students in formulating scientific research questions,
- guiding students through testing their hypotheses,
- the challenges and benefits of mentoring online, and
- an open
forum discussion.
The sessions will be beneficial for current mentors and teachers,
and will enable the future development of the PlantingScience program.
An introduction to next-generation sequencing
Organizer: Aaron Liston, Department of Botany & Plant Pathology,
Oregon State University, Corvallis, Oregon 97331-2902
Next generation sequencing describes technologies that produce
billions of base pairs of sequence data per experiment, at a cost
of less than a dollar per megabase. Many universities have acquired
next-generation sequencing technology in the past two years, but
few plant biologists are aware of how to utilize this in their research.
A major goal of the workshop will be to give participants enough
information so that they can develop and initiate their own projects
in phylogenetics, population genetics, and gene expression using
this technology.
In the morning, we will describe the available technologies, applications,
and protocols for sample preparation and sequencing. We will also present strategies
such as multiplexing for reducing costs. In the afternoon, we will describe
options for computational infrastructure and the analytical pipeline. Participants
will then have an opportunity to work with provided data, and generate assembled
sequences.
Participants will need to bring their own laptop for the "hands
on" part of the workshop. We will email programs and data to
install prior to the workshop.
Teaching Evolution: A Discussion
Organizer: Beverly J. Brown, Nazareth College, 4245
East Ave., Rochester, NY 14618
Botany 2010 Plenary Speaker, Dr. Ken Miller will join us for a discussion of
the challenges instructors face when they teach evolutionary theory. This is
an opportunity to bring your questions and successes to share with the group.
This discussion will be especially useful for those new to teaching evolution,
and those dealing with heterogeneous student populations, such as community
colleges.
Exploring Land Plant Evolution, Coal Balls
and Insectivorous Plants in a Class
Organizer: Jon Wallace, 111 Birden St., Torrington, CT 06790
This workshop will try to put plant evolution into perspective.
I will start with the early Devonian (~400 MYA) land plants and show
numerous examples of fossils which exemplify the tremendous diversity
of this kingdom. Particular attention will be paid to the Carboniferous
Period (~ 350 MYA) and participants will make their own coal ball
peel to take home.
Each participant will receive a CD copy of my PowerPoint presentation
on land plant evolution, two booklets I made to help identify Carboniferous
coal ball peel plants, as well as a set of labs I use with Venus
Flytraps. I will have some coal balls (about 15) to give out to interested
participants as well.
Helping Students use a HOT Skills Wheel™ to
enhance Higher Order Thinking on Botany (and other Science) Topics.
Organizers: J S Shipman, Ph. D.. 54 Bryon Road,
CH 02467 c/o 1860 Route 211 East Middletown, NY 10940
Suzanne Kapelari
Stan Rice
Building higher order thinking skills is important to studies in
botany. Participants in this symposium will make a H.O.T. Skills
Wheel™ and use it in small groups to study some botany so they
will have first hand experience to share with their own students.
Participants will also access Plants Cafe and other plant-oriented websites
for use in developing lessons.
After trying the wheel for various botany topics, participants will share their
experiences. After returning home, participants are encouraged to use the new
H.O.T. skills wheels™ with their classes and submit their results for
possible publication in text or on the web.
Participants should bring a journal article or portion of text
that they would like to incorporate into their H.O.T. Skills Wheel™ lesson,
and may bring colored pencils, markers or crayons (6 light colors),
other art or music supplies(guitar, if you'd like to use it in your
lesson, for example), and a folder.
Participants should be prepared to purchase booklets cost $12.00
each at the workshop.
I've Completed the Research, Compiled the Results
and Written My Manuscript: Now What? Behind the Scenes at an Editorial
Office
Organizers: Amy McPherson, Managing Editor, American Journal of Botany,
BSA, P.O. Box 299, St. Louis, MO 63166-0299
Richard Hund, Production Editor, American Journal of Botany, BSA, P.O. Box 299,
St. Louis, MO 63166-0299
This workshop, designed for graduate students, early-career scientists, or those
new to publishing, is intended to give a brief yet detailed look at what happens
from manuscript submission to final publication in a scientific journal. Questions
to be addressed include:
- How do I identify the best journal for my manuscript?
- What should I include---and not include---in my cover letter?
- What can I expect in the manuscript submission process?
- What common pitfalls can I avoid?
- What happens during the peer-review process?
- What should be included in the response-to-reviews letter?
- What does the editor expect from me as a reviewer?
- What happens when the manuscript is sent to production (or why am I discouraged
from making major changes in proof)?
The session is designed to give the new-to-publishing researcher
a chance to see what happens before and after they hit "Submit" for
their manuscript submission.
Sustainable Teaching
Organizer: Clare Hasenkampf, Associate Professor Biological Sciences,
Director of the Centre for Teaching and Learning, UTSC, 1265 Military
Trail, Scarborough, Ontario, M1C1A4
Summary: For the teaching of a course to be emotionally and intellectually satisfying
there must be learning. For such teaching to be sustainable the amount of effort
must be reasonable.
What does it take to create a course that is satisfying and do-able, for the
long haul?
In this workshop I will consider some ideas about
- Student learning
- Principles of a well-aligned course
- A ‘common sense’ checklist for sustainability
I hope that the ideas presented will help you find your way to teach courses
that regularly provide a rich learning experience for students and a satisfying
intellectual endeavor for yourself.
Workshop is primarily for graduate students, post docs and faculty early in
teaching careers.
DNA Subway Puts Students On Fast Track To Gene Annotation And Genome
Analysis
Organizer: Uwe Hilgert, iPlant Collaborative/Dolan DNA Learning
Center, Cold Spring Harbor Laboratory; PO Box 100; Cold Spring
Harbor, NY 11724
Annotating and comparing genome sequences can bring
to life elements of gene structure and function that previously
could only be approached as
abstractions. Assembling gene models and comparing genes engages students
in their own learning,
as they acquire a range of conceptual and process knowledge. DNA Subway (http://dnasubway.org)
is a simplified and intuitive bioinformatics platform to annotate
DNA sequences, construct gene models, build phylogenetic trees,
and analyze next-generation sequencing data. Workshop participants will use
DNA Subway
to upload and analyze DNA and protein data and learn how to integrate genome
analysis into their own teaching.
Cladonia Systematics: What can we infer from morphology and molecules?
Organizers: James C. Lendemer, Institute of Systematic
Botany, The New York Botanical Garden, Bronx, NY 10458-5126,
Brendan Hodkinson Department of Biology, Box 90338, Duke University, Durham,
NC 27708
Michele D. Piercey-Normore, Dept. of Biological Sciences, University of Manitoba,
Winnipeg, Manitoba, Canada, R3T 2N2.
Participants will spend an afternoon exploring an emerging area of lichen systematics
that involves the integration of molecular and morphological data to elucidate
taxonomic relationships at the species-level. The workshop will focus on examples
from the genus Cladonia as a model for this type of unified approach. The main
objective is to facilitate an understanding of the morphological identity of
members of Cladonia and to provide insight into processes involved in the evolutionary
patterns observed with morphological, chemical and molecular characters. It
will include lecture and discussion of molecular and morphological methods
as well as hands on examination of specimens in the genus, Cladonia.
Forming a BSA Student Chapter: Benefits, Experiences
and Connections
Organizers: Heather Cacanindin, Botanical Society
of America 4475 Castleman Ave, St. Louis, MO
William Dahl, Botanical Society of America 4475 Castleman Ave, St. Louis, MO
Dr. Chris Martine, SUNY-Plattsburgh
Megan Ward, SUNY-Plattsburgh
Many active botany clubs exist at community colleges and universities
around the country. However, only a few have signed on to become
BSA Student Chapters.
There are some tangible and significant benefits to belonging to a BSA Student
Chapter. This workshop will feature presentations, discussion and a question/answer
session by the leaders and members of BSA Student Chapters as well as BSA
staff who support and facilitate their efforts. While some BSA
Student Chapters are
well-established, many are just starting to take off and connect with other
botanical clubs around the country. Come learn about what BSA Student Chapters
can do, how they benefit your members, save you money, connect you to diverse
opportunities, and grow the botanical community in meaningful ways. This
workshop is targeted to undergraduates, graduate students, and
potential professionals
in the field who wish to learn more about BSA Student Chapters.
Bioinformatic applications in the research of the model moss
Physcomitrella patens: using predicted protein-protein interaction
to construct interacting and regulatory network.
Organizers: Dr. Matt Geisler, Department of Plant Biology, MC6509,
Southern Illinois University Carbondale, Carbondale, IL 62901
Mr.
Scott Schuette, Department of Plant Biology, MC6509, Southern Illinois
University Carbondale, Carbondale, IL
62901
Background: A plant interactome is a map of all physical interactions between
all proteins, and is an essential part of systems biology. Predicted interactomes
are the fore-runner to experimentally determined interaction maps and the only
type of interactomic data that will likely be available for bryophytes in the
foreseeable future. Plant interactomes and network visualization software are
currently available but not sufficiently user friendly for non-bioinformatics
specialists to take full advantage of these tools.
Our workshop will provide instruction and demonstrations
for participants to utilize the predicted interactomes generated
for Arabidopsis (Geisler-Lee et al., 2007) and a pre-publication
release of the Physcomitrella patens predicted interactome. Participants
are encouraged to bring lists of their genes of interest to the
workshop (use the old or new moss accession numbers) and can walk
away with a map of all predicted interactions for their proteins.
A moss predicted interactome allows significant progress in the identification
and annotation of unknown genes, interacting partner genes, and the filling
in of pathways in plant regulation, signaling and metabolism. While these predictions
provide insight for only the portions of the genome which show evolutionary
conservation with plants, fungi and animal model systems, they are not restricted
to well characterized genes, and include many completely unknown yet conserved
proteins.
Preparing Digital Images for Publication
Organizer: Mike Vanderberg, PO Box 558, Havana, FL 32333
This workshop covers general Digital Art Submission
Guidelines for publishing figures in both print and online journals.
It will include live demonstrations
in Adobe Photoshop and Illustrator on the following topics: Imaging Foundations,
RGB Image Submission and Color Management, Preparation Tips, plus a brief discussion
on Image Integrity.
What is a Teaching Philosophy, Teaching Dossier (Portfolio)
and why develop one?
Organizer: Clare Hasenkampf, Associate Professor Biological Sciences,
Director of the Centre for Teaching and Learning, UTSC, 1265 Military
Trail, Scarborough, Ontario, M1C1A4
The Teaching Portfolio (or Teaching Dossier) is a collection
of documents that support critical reflection and/or analysis of
a
body of teaching work. The purpose of
this workshop is to help
you understand how to use a teaching portfolio as an effective tool to improve
your teaching, and to create a teaching dossier that documents your approach,
progress and teaching achievements.
The learning goals for the workshop are:
- You will understand
the difference between the Teaching philosophy,
teaching dossier (narrative) section, dossier appendix and archive
of teaching
evidence
- You will be able to use learning goal 1 to assemble
into a compelling
portrait of your teaching.
- You will feel empowered to start/continue
to assemble your dossier
Workshop is primarily for senior graduate students, postdocs and
pre-tenure faculty.
Building the US National Virtual Herbarium (USVH)
Organizers: Mary Barkworth, Zack Murrell
This workshop,
which will also be the annual meeting of the USVH project, will
hear reports of the current status of the project
within the various regions plus steps being taken to further
its development. The focus will be on what is required to accelerate
digitization efforts around the country.
