IMG-ACT

IMG Annotation Collaboration Toolkit (IMG-ACT) is a multi-platform toolkit created to assist instructors in integrating microbial genome annotation into the undergraduate curriculum. Building on the architecture of genomic data in the Integrated Microbial Genomes (IMG) system, JGI developed the Annotation Collaboration Toolkit (ACT) as a "plug-in" to IMG with both the instructor and student in mind. For instructors, IMG-ACT provides a platform to organize course materials, assign gene and pathway annotation research, as well as efficiently review the results of student annotations. For students, IMG-ACT displays assignments, provides tutorials, encourages teamwork, and stores key information about genes and pathways. An important consideration of IMG-ACT is that data is exportable in a format compatible with IMG. IMG-ACT also contains an Instructors Resources site, which provides a reference for tool use and serves as a collaborative forum in which instructors can share curricular materials, ideas, and resources. This forum is also an avenue of communication among instructors, project managers, and technical support. Finally, IMG-ACT houses the Online Lab Notebook pages that students populate with data they have accumulated throughout the annotation process. There are individual Student Wiki pages for each gene annotation or pathway step annotation, allowing students to store sequences, alignments, images, comments, and references. The format of the Lab Notebook pages that students fill out as they go through an annotation is presentable in a final publication page. IMG-ACT supports the “Interpret a GEBA genome” Education Program.

Go to IMG-ACT (login required)

Acknowledgments

Several groups at the Joint Genome Institute and Lawrence Berkeley National Laboratory developed and currently maintain the Integrated Microbial Genomes (IMG) system. Members of the JGI Informatics Department (Anthony Kosky, René Perrier, Joni Fazo, David Hays, Leila Hornick, and Kristen Taylor) developed and currently maintain IMG-ACT according to system and content requirements provided by the JGI Education Outreach Program (Cheryl Kerfeld, Edwin Kim, and Seth Axen.) JGI’s Educational Advisory Committee (Sharyn Freyermuth at the University of Missouri, Brad Goodner at Hiram College, and Kathleen Scott at the University of South Florida) assisted in the design of IMG-ACT. A core group of college and university professors nationwide (see below) provided input based on their experience in annotating a microbial genome in the initial phase of the project (with technical support from Folker Meyer’s team at Argonne National Laboratory.)

JGI’s Collaborative Genomics Annotation Team

Kelynne Reed, Austin College
Zhaohui Xu, Bowling Green State University
Ferda Soyer, Izmir Institute of Technology
Robert Britton, Michigan State University
Rick Johns, Northern Illinois University
Christopher Kvaal, Saint Cloud State University
Erin Sanders-Lorenz, University of California, Los Angeles
Cheryl Bailey, University of Nebraska, Lincoln
Sabine Heinhorst, University of Southern Mississippi
Jayna Ditty, University of Saint Thomas
Shari Freyermuth, University of Missouri, Columbia
Kathleen Scott, University of South Florida
Brad Goodner, Hiram College