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EcoPod in Biology Journal

Our second paper on EcoPod, which describes the underlying algorithms that drive the user interface is now published in BMC Bioinformatics. This publication is our first in the Biology literature, after a number of other contributions to Computer Science venues.

PhotoSpread Widely Noted

Our first draft of a spreadsheet metaphor for Photo tagging, search, and organization has found interested audiences. Hector presented the system at the ETH in Switzerland, in Mexico, and at a government meeting. Sean presented our paper at CHI 2008, and Andreas briefly discussed PhotoSpread at MIT. Eric also found interest for the software in the Biology community. A video of PhotoSpread is available on YouTube.

Congratulations to our BioACT graduates!

Jeannie Stamberger received her Ph.D. in Biology; Merrie Ringel Morris, creator of TeamTag and TeamSearch, earned her Ph.D. in Computer Science. Aswath Manoharan received a Masters with distinction in research for his work on optimizing the EcoPod question sequence in the presence of historic abundance data. YuanYuan Yu also left us with a Masters degree after he created the EcoPod software.

BioACT releases paper UI toolkit

Ron Yeh constructed a R3 toolkit for building paper user interfaces with the Anoto system. Designers draw the interface regions on paper. The toolkit generates the event handler stubs and other code. Ron deployed the toolkit to a project class at UC Berkeley. After intensive work with the students there, a new version of the toolkit emerged and was released as open source.

BioACT paper wins Best Student Paper award at JCDL 2006

Our paper "EcoPod: a mobile tool for community based biodiversity collection building" won the Best Student paper award at the 2006 6th ACM/IEEE-CS joint conference on Digital Libraries. The paper's authors are YuanYuan Yu, Jeannie A. Stamberger, Aswath Manoharan, and Andreas Paepcke. We describe a handheld tool for identifying plants and animals in the field. The tool attempts to minimize the number of interactions required to reach a conclusion.

BioACT paper wins Brian Shackel Award at Interact 2005

One of our BioACT papers received the Brian Shackel Award at the recent Interact conference. This award is to recognise the most outstanding contribution in the form of a refereed paper submitted to and delivered at the Conference.

The award committee felt that our paper, "Visual Interface and Control Modality: An Experiment About Fast Photo Browsing on Mobile Devices" "combines theory with experiment and produces surprising results that can be explained in terms of the theories used to generate the initial hypotheses." They decided that "the paper is timely, could guide current product development and is good science. The design work is as good, with the theory driving the design options and underpinning evaluation. It thus is strong in all the key areas critical to HCI."


Project Summary

This work will help biodiversity researchers Acquire digital materials in the field, manage these online holdings (Curate), and Transfer the knowledge (or disseminate) to other researchers, museums, and the public. We will create three sets of tools: (i) tools for speedy data entry and small-group collaboration in the field, (ii) tools for large scale collaboration in distributed collection curation, and (iii) tools for semidirected search and browsing of digital biodiversity materials.Jasper Ridge


Biodiversity is commonly characterized as having three levels of organization: genetic, organismal, and ecosystem. At all levels, scientists endeavor to describe the elements of diversity, their spatial and temporal distributions, and to understand the processes that create and sustain diversity. Therefore, the project is a collaboration with Stanford University's Jasper Ridge Biological Preserve and the California Academy of Sciences. The two institutions have extensive experience studying biodiversity, the latter at the organismal level, and the former at the ecosystem level. Their past and current projects will form the basis for the tools and prototypes we will produce. The work of these two groups is described below, to clarify our area of work. 

Stanford University's Jasper Ridge Biological Preserve is a 1,200 acre area in the foothills of the Santa Cruz mountains, just outside the Stanford campus. The area has been a Preserve for the past 30 years, but scientists have studied the region since 1891. Since 1928 aerial photographs have been shot. Starting with 1994 aerials were taken every year and were geo-rectified. Efforts are under way to reach back and geo-rectify at least one of the earlier aerials per decade. This collection is joined by a large number of ground level photos and collected specimens. Biologists at the Preserve record changes in the local climate, and have studied the relationship between biodiversity and the intensity and type of neighboring urban development. Many of the Jasper Ridge studies involve long-term experiments. For example, the Preserve gave researchers an opportunity to observe over multiple years an invasion of Argentine ants and its effect on native ant communities [21, 40]. Ant colonies were mapped and their distributions recorded as the invading species progressed. This research was successful in itself. An important capability, however, is missing that might expand this work further. The biologists cannot easily take advantage of already existing data. For example, the aerial photographs might reveal other changes that took place over the course of the study in the areas surrounding the colonies. It is not possible to quickly retrieve the relevant portions of that valuable photo collection. Similarly, a number of other projects in this well-surveyed stretch of land have been producing data that might well impact the Argentine ant study. Underground humidity measures that are collected for other reasons over selected plots in the area, for example, might coincidentally be of interest to the ant invasion researchers. 

In contrast to the locally focused Jasper Ridge Preserve, the charter of the California Academy of Sciences in San Francisco is more broadly to gather and maintain collections that document biodiversity around the globe, and to educate students and the public about all aspects of natural history. The Academy organizes expeditions to all parts of the world. Participating scientists collect data on plants and animals, and return with specimens and large collections of photographs. This material is prepared, preserved, and maintained in permanent collections back in San Francisco. Identifying and cataloging the volume of material being collected still poses a tremendous challenge to Academy staff, while the diversity of data being gathered is also increasing. Beyond research in biodiversity the Academy helps raise sensitivity to ecological considerations abroad. Academy herpetologists have, for example, worked with colleagues in Myanmar to establish a biodiversity museum. Academy botanists and entomologists are establishing a field station in Madagascar to help study and preserve the long-isolated and now extremely threatened biota of that ancient island.  

This project is supported by the National Science Foundation (Grant Nos. 0430448 and 0534662).




Hector Garcia-Molina Stan Blum Nona Chiariello Rodolfo Dirzo Scott Klemmer Andreas Paepcke Martin Theobald Terry Winograd


Eric Abelson SeanKandel Stephen Whang

Student Alums

Related Publications by this Group

TitleAuthorDate of publicationTypeSubject group
PhotoSpread: A Spreadsheet for Managing Photos Sean Kandel, Eric Abelson, Hector Garcia-Molina, Andreas Paepcke, Martin Theobald 2008 Conference Photo browsign
Optimizations for the EcoPod Field Identification Tool Aswath Manoharan, Jeannie Stamberger, YuanYuan Yu, Andreas Paepcke 2007 Other Mobile Computing
Fine-Granularity Virtual Tags on Physical Objects Nikhil Raghavan and Andreas Paepcke 2007 Other Mobile Computing
Iterative Design of a Paper + Digital Toolkit: Supporting Designing, Developing, and Debugging Yeh, Ron; Klemmer, Scott; Paepcke, Andreas; Bastııa-Forte, Marcello; Brandt, Joel; Boli, Jonas 2007 Other Digital Libraries
Mediating Group Dynamics through Tabletop Interface Design Meredith Ringel Morris, Anthony Cassanego, Andreas Paepcke, Terry Winograd, Anne Marie Piper, and Anqi Huang 2006 Conference or Journal Paper Digital Libraries
TeamSearch: Comparing Techniques for Co-Present Collaborative Search of Digital Media Morris, Meredith Ringel; Paepcke, Andreas; Winograd, Terry 2006 Conference or Journal Paper Digital Libraries
TeamTag: Exploring Centralized versus Replicated Controls for Co-located Tabletop Groupware Morris, Meredith Ringel; Paepcke, Andreas; Winograd, Terry; Stamberger, Jeannie 2006 Other Miscellaneous
Physical-digital ensembles for mobile interaction Ron Yeh 2006 Other Digital Libraries
ButterflyNet: A Mobile Capture and Access System for Field Biology Research Yeh, Ron B; Liao, Chunyuan; Klemmer, Scott R; Guimbretiere, Francois; Lee, Brian; Kakaradov, Boyko; Stamberger, Jeannie; Paepcke, Andreas 2006 Conference or Journal Paper Mobile Computing
EcoPod: A Mobile Tool for Community Based Biodiversity Collection Building Yu, YuanYuan; Stamberger, Jeannie A.; Manoharan, Aswath; Paepcke, Andreas; 2006 Conference or Journal Paper Digital Libraries; Mobile Computing
Piles Across Space: Breaking the Real-Estate Barrier on PDAs Hsieh, Tony; Wang, QuianYing; Paepcke, Andreas 2005 Conference or Journal Paper Digital Libraries
Visual Interface and Control Modality: An Experiment about Fast Photo Browsing on Mobile Devices QianYing Wang, Susumu Harada,Tony Hsieh, and Andreas Paepcke 2005 Other Mobile Computing
Multi-User Piles Across Space QianYing Wang, Tony Hsieh, Meredith Ringel Morris, and Andreas Paepcke 2005 Technical Report Digital Libraries
Piles Across Space---Breaking the Real-Estate Barrier on PDAs Tony Hsieh, QianYing Wang, Andreas Paepcke 2005 Conference or Journal Paper Miscellaneous
ButterflyNet: Mobile Capture and Access for Biologists Yeh, Ron B; Klemmer, Scott R 2005 Other Miscellaneous
ButterflyNet: A Mobile Capture and Access System for Field Biology Research Yeh, Ron B; Liao, Chunyuan; Klemmer, Scott R; Guimbretiere, Francois; Lee, Brian; Kakaradov, Boyko; Stamberger, Jeannie; Paepcke, Andreas 2005 Technical Report Miscellaneous
Field Notes on Field Notes: Informing Technology Support for Biologists Ron B. Yeh and Scott Klemmer 2004 Other Miscellaneous


Sites relevant to the project include: InfoLab home page, Digital Libraries project home page.  


On-site photos:


Annual report 2004/05.

Annual report 2005/06.

Annual report 2006/07.

NSF Support. This material is based upon work supported by the National Science Foundation under Grant Nos. 0430448 and 0534662. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.