Developing a cyberinfrastructure: Experiences from a regional network of plant taxonomists

Zack Murrell, Derick Poindexter, and Zack Murrell, Derick Poindexter, and Michael DenslowMichael Denslow

Appalachian State UniversityAppalachian State University

murrellze@appstate.edu SERNEC.ORG

SERNEC: SouthEast Regional SERNEC: SouthEast Regional Network of Expertise and Network of Expertise and

CollectionsCollections

A National Science Foundation A National Science Foundation

Research Coordination NetworkResearch Coordination NetworkRCN Award # 0542320

FIVE YEAR PROJECT TO BUILD A REGIONAL FIVE YEAR PROJECT TO BUILD A REGIONAL

BIOINFORMATICS RESEARCH TOOLBIOINFORMATICS RESEARCH TOOL

SERNEC: SouthEast Regional Network of SERNEC: SouthEast Regional Network of Expertise and CollectionsExpertise and Collections

215+ herbaria in 215+ herbaria in the regionthe region

Colleges Colleges

UniversitiesUniversities

State and State and federal parksfederal parks

Private Private collectionscollections

SERNEC

GoalsGoals

1.1. Network the 215 herbaria in 15 states in Network the 215 herbaria in 15 states in southeastern North Americasoutheastern North America

2.2. Develop a strategy for advancing each state’s Develop a strategy for advancing each state’s ongoing databasing effortongoing databasing effort

3.3. Publish online botanical resources that will be Publish online botanical resources that will be available to scientists, land managers, state and available to scientists, land managers, state and federal agencies, educators and the general federal agencies, educators and the general publicpublic

murrellze@appstate.edu SERNEC.ORG

State of Herbaria in the Southeast USA

Data derived from Index Herbariorum (http://www.nybg.org/bsci/ih/ih.html) .

• Collections vary in size from 3,000 to 750,000 specimens.

• Curators are taxonomists, ecologists, paleobotanists, population biologists.

• Some institutions with significant budgets, IT support and curatorial staff.

• Some institutions are single person operations without budgets or IT support.

• ESTIMATED 15 MILLION SPECIMENS FROM THE SOUTHEAST. “Highest fruit on the tree”

or

“Least Common Denominator”

http://www.sernec.org/

MOBILIZATION AND COMMUNICATIONMOBILIZATION AND COMMUNICATION

WORKING GROUPS:WORKING GROUPS:1.1. IT and infrastructure - FacebookIT and infrastructure - Facebook2.2. Libraries and literature - LinkedINLibraries and literature - LinkedIN3.3. Images (specimen and live) - DrupalImages (specimen and live) - Drupal4.4. Education and outreach -DrupalEducation and outreach -Drupal5.5. Taxonomic concept mapping - DrupalTaxonomic concept mapping - Drupal6.6. State working groups - NING and listservState working groups - NING and listserv

““IT TAKES A VILLAGE”IT TAKES A VILLAGE”

murrellze@appstate.edu SERNEC.ORG

http://www.herbarium.unc.edu/seflora/firstviewer.htm

SERNEC Partners

• US Geological Survey NBII/SAINUS Geological Survey NBII/SAIN

• SunSITE – Univ. of Tennessee-KnoxvilleSunSITE – Univ. of Tennessee-KnoxvilleImplementation of emerging and advanced Implementation of emerging and advanced technologies and applications.technologies and applications.

• University of North Carolina and the Interdisciplinary University of North Carolina and the Interdisciplinary Geospatial Research Geospatial Research Center, Univ. Tenn-Chattanooga Center, Univ. Tenn-Chattanooga Dynamic mapping of Southeast collectionsDynamic mapping of Southeast collections

• Robert Sandusky - University of Chicago Robert Sandusky - University of Chicago E-Research: The Contexts, Processes, and Social Order of Distributed Collective PracticeE-Research: The Contexts, Processes, and Social Order of Distributed Collective Practice

• Developing collaborations with HERBIS, MORPHBANK and Developing collaborations with HERBIS, MORPHBANK and FILTERPUSHFILTERPUSH

digitize clean

Portal- individual herbarium

Portal- individual herbarium

SERNEC

Federated Database

Concept mapping

MORPHBANK

SERNEC-NBII

portal

Herbarium

w/out Server

Herbarium

w/ Server

Automated

Automated-data provided

Automated-Data provided

Experts

View Data

(LOGIN and annotate)

Public

Educators K-12

Corporate users

Decision-makers

Curators

scientistsSunSITE

Data storage/curation

SERNECCommunity

CuratorsScientistsEducators

Artists

Mirrored data storage/curation

Data transfer

Annotation

Data transfer

Annotation

Notify of Annotation

Annotation

Notify of Annotation

Annotation

GIS mapping

Virtual workbenchSHC portal w/

herbarium Tools

Using the Society of Herbarium Curators Using the Society of Herbarium Curators for for governance structuregovernance structure

State consortia

Regional Chapter

Decision-makingConsensus buildingConflict resolution

Utilize existing organization’sconstitution structure

http://www.societyofherbariumcurators.org/

Community tool development: “Idiot’s guides”Compiling listserv threadsSeeking contributions

Networks and collaborations on Networks and collaborations on this scale do not develop this scale do not develop

overnightovernightThe potential success of this network is rooted in the The potential success of this network is rooted in the

significant contributions made by biologists in the region significant contributions made by biologists in the region over the past century that provide a solid foundation for over the past century that provide a solid foundation for this effort. Meeting annually for the past 60 years.this effort. Meeting annually for the past 60 years.

The Association of Southeastern Biologists (ASB) The Association of Southeastern Biologists (ASB) The Southern Appalachian Botanical Society (SABS) The Southern Appalachian Botanical Society (SABS)

How can we identify “natural” groups?How can we identify “natural” groups?Associations and journals, annual gatherings, taxon based Associations and journals, annual gatherings, taxon based

societies.societies.

http://www.asb.appstate.edu/http://www.asb.appstate.edu/

Initiative to develop an Initiative to develop an all-taxa database of all-taxa database of collections in the collections in the Southeastern USASoutheastern USA

Symposium April 4, 2009Symposium April 4, 2009

Birmingham, AlabamaBirmingham, Alabama

Sponsored by:Sponsored by:

CollectionsWeb (NSF CollectionsWeb (NSF RCN)RCN)

SERNEC (NSF RCN)SERNEC (NSF RCN)

Biodiversity Informatics: Progress and Potential in the Southeastern USA

Expand domain network to all-taxa regional network

Modified from: www.theodora.com/maps

New England

SERNEC

Great LakesNorthern Great Plains

Pacific Northwest

California Consortium of Herbaria

Arizona & New Mexico

CIRH

Central Great Plains TORCH

Developing Herbarium Networks

United States Virtual Herbarium United States Virtual Herbarium (USVH)(USVH)

Will use regional networks for Will use regional networks for organizational structureorganizational structure

Support from National Biological Support from National Biological Information Infrastructure (NBII)Information Infrastructure (NBII)

What can networks do?What can networks do?

Drive change in behavior by accepting best practices Drive change in behavior by accepting best practices (mark-up new descriptions at time of publication).(mark-up new descriptions at time of publication).

Develop high quality data through analysis and Develop high quality data through analysis and annotations.annotations.

Assemble species pages and interactive keys.Assemble species pages and interactive keys. Provide information on phylogenetics and Provide information on phylogenetics and

phyloinformatics.phyloinformatics. Identify gray literature/scan literature.Identify gray literature/scan literature. Provide expertise for concept mapping (to literature and Provide expertise for concept mapping (to literature and

use).use).

How can we mobilize social networks?How can we mobilize social networks?

Support typical workflow (layman’s guide to Support typical workflow (layman’s guide to technical jargon).technical jargon).

Develop education modules for bioinformatics Develop education modules for bioinformatics (for both curators and students). (for both curators and students).

Provide training modules for literature mark-Provide training modules for literature mark-up.up.

Collaborate on development of standards Collaborate on development of standards within taxonomic groups.within taxonomic groups.

DS/CS/Inf

DS/CS/InfDS/CS/Inf

DS/CS/Inf DS/CS/Inf DS/CS/Inf

Herb Network

Museum Network

Regional Network

Herb Network Herb Network

Domain Network

“US”TDWGDS/CS/Inf

Domain ScientistsComputer ScientistsInformaticists

{Evangelical model

SERNECSERNECSouthEast SouthEast Regional Regional

Network of Network of Expertise Expertise

and and CollectionsCollections

www.sernec.owww.sernec.o

rgrg

SERNEC