Botany 2011 Workshops

WS01 - Plants, People & Pictures - See Agenda

Organized by: Kim Bridges, Retired Professor Univ. of Hawai`i at Manoa

Bill Dahl, Botanical Society of America

We are going to explore digital photography in the context of both Point-and-Shoot and Digital SLR cameras. The focus is on typical botanical and ethnobotanical themes. The overall aim is to help everyone, from beginner to competent photographer, better understand the capabilities and features of this emerging digital medium. Special attention will be given to macro-photography. The workshop includes discussions, demonstrations and hands-on opportunities. All participants are asked to bring their camera gear as there will be an outdoor photo shoot. Two sessions: 1:00-5:00 PM and 7:00-8:30 PM.

WS02 - iPlant Discovery Environment and API:  Integration of Biological Data-sets, Computational Tools, and Analytical Workflows

Organized by: Ann Stapleton, University of North Carolina

Uwe Hilgert, iPlant Collaborative, Dolan DNA Learning Center, Cold Spring Harbor Laboratory

Eric Lyons, University of Arizona

With current high-throughput data collection methodologies, plant biologists often find themselves overwhelmed by the amount of data to process. Similarly, there are many analytical tools from which to choose when processing these data, many of which require knowledge of using the command-line interface and high performance computers. iPlant's web-based Discovery Environment allows biologists to easily manage and share biological data, computational tools, and analytical workflows. Furthermore, iPlant provides two APIs (Application Programming Interfaces) to allow researchers to integrate additional tools and to access tools and data through the web.

This workshop will focus on using iPlant's web-based Discovery Environment to create and share workflows to process data and on using iPlant's APIs to integrate new tools.

WS03 - DNA Subway Places Students On Fast Track To Plant Genome Analysis and DNA BarCoding

Organized by: Uwe Hilgert, iPlant Collaborative, Dolan DNA Learning Center, Cold Spring Harbor Laboratory

Genome analysis provides opportunities for students to discover basic principles of molecular biology while embarking on research projects. DNA Subway is an educational platform for gene annotation and comparison. It bundles research-grade bioinformatics tools and databases into intuitive workflows and presents them in an appealing interface using the metaphor of a subway map. Riding on any of four different DNA Subway lines, users can predict and annotate genes in up to 150 kb of DNA (Red Line), identify homologs in sequenced genomes (Yellow Line), analyze DNA barcodes and construct phylogenetic trees (Blue Line), and analyze RNAseq data (Green Line). Work can be saved for later use and/or shared with other users. 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.

WS04 - Sustainable Teaching: Getting started and keeping going

Organized by: Clare Hasenkampf, University of Toronto

In this workshop I will consider some ideas about Student Llearning Principles of a well-aligned course and 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, but all are welcome.

WS05 - Best Practices for Image use in Keys and Guides

Organized by: Bruce K. Kirchoff, University of North Carolina at Greensboro

Although illustrations have played an important role in identification keys and guides since the 18th century, their use has varied widely. Some keys lack all illustrations, while others are heavily illustrated. Even within illustrated keys and guides the way in which images are used varies considerably.

During this workshop we will review image use in selected keys and guides, and present a set of suggested best practices for image use. The best keys and guides use multiple standardized images, displayed at sizes that are easy to see, and arranged in a standardized manner so that similar images can be compared across species. It is not possible to form an adequate taxonomic concept from a single photograph. The failure to use multiple images for each species is the most common shortcoming of illustrated keys and guides. Illustrated keys and glossaries should contain multiple images for each character state so that the user can judge variation in the state. When used in glossaries, a single drawing is best used to illustrate several terms, and each term is best illustrated with several drawings. Scale bars should be used with discretion. They are not needed on every illustration and, when used indiscriminately, can distract the user's attention from the salient features. Iconic symbols and colored marginal bands can make the key easier to use, and should be used where appropriate.

WS06 - Preparing Digital Images for Publication

Organized by: Mike Vanderberg, Sheridan Press

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.

WS07 - Teaching Philosophy, Teaching Statements and teaching Dossiers-How to and Why

Organized by: Clare Hasenkampf, University of Toronto

In this workshop we will look at the Teaching Philosophy and Teaching Dossier as a tool for a reflective teaching practice.  We will also look at the Teaching Statement and Dossier as parts of job applicatins, promotion files and for Teaching awards.

WS08 - Workshop and Roundtable Discussion: Successful Manuscript Preparation and Publication

Organized by: Amy McPherson, Managing Editor, American Journal of Botany
Richard Hund, Production Editor, American Journal of Botany

This workshop, designed for graduate students, early-career scientists, and those new to publishing, is intended to give a brief yet detailed description of what happens from manuscript submission to final publication in a scientific journal. This round-table discussion, with members of various editorial teams (including the American Journal of Botany) and your peers, will serve as a forum for questions and answers regarding successful or not so successful article publication in a scientific journal. Questions may be submitted before the workshop. The session is designed to give the new-to-publishing researcher a chance to discuss the publishing process from the author's and editor's perspectives.

WS09 - US Virtual Herbarium Project; Progress made, goals to achieve

Organized by: Mary Barkworth, Intermountain Herbarium

The workshop, which is also the official annual meeting of the US Virtual Herbarium Project, will focus on sharing of new developments and approaches to the digitization of herbaria and examples of how such information is being used or can be expected to be used in the very near future. There will also be a summary presented of some of the intermediate steps that have been taken towards attainment of the overall goal of digitizing all specimens and developing resources that enable diverse publics to benefit from access to the digitzed information.

WS10 - Floristic projects:  who does what, with Flora of North America as a case study.

Organized by: Nancy R. Morin, Flora of North America

This workshop will be useful to anyone involved in any of the floristic projects currently underway and will provide an opportunity for participants in various projects to compare notes. Flora of North America (FNA) provides a case study.  It is a massive collaborative project to produce a Flora of North America north of Mexico in print and electronic forms.  Sixteen out of the projected 30 volumes have been published. The project involves more than 900 botanists in North America and elsewhere.  

Missouri Botanical Garden is an FNA editorial center and also the center for botanical illustration and composition. This workshop will focus on a behind-the-scenes look at how treatments are processed and what authors, regional and taxonomic reviewers, editors, and artists do.  Break out sessions will provide time for different groups (e.g. authors, regional reviewers, editors) to discuss problems and solutions.  The workshop will include a tour of the composition and illustration facilities and the Missouri Botanical Garden library.  It will finish with a reception for everyone interested in the project.  

JUST Added!

WS11 - Professional Development: Applying to Graduate Programs

Organized by Ann Sakai

This workshop is primarily for undergraduates interested in applying to graduate programs, master's degree students applying to doctoral programs, and faculty who work with these students, but all are welcome.  The workshop will consist of a brief presentation of the "ins and outs" of applying to graduate school before and during the application process.  This presentation will be followed by a question and answer session between the participants and several panelists. The latter will include current graduate students, as well as faculty experienced in graduate admissions procedures, from several different institutions.