Building Biodiversity Information Education: Next Generation Bioinformaticians

P. Bryan HeidornCarole PalmerDan Wright

Graduate School of Library and Information Science University of Illinois at Urbana-Champaign

Information Power Tool Training

• Who needs bioinformaticians?

• What is a bioinformatician?

• Who are the bioinformaticians?

• What do bioinformaticians need to know?

• Proposed training programs

Reports on cyberinfrastructure and e-science initiatives recognize the shortage in qualified professionals to manage the increasing stores of scientific data (National Science Board, 2005)

Who needs bioinformaticians?

What is a bioinformatician?

preparing information specialists to work in such “information-rich environments and to participate as peers in problem solving” requires cross training in library and information science and discipline knowledge of scientific domains. Florance et al. (2002)

Who are the bioinformaticians?

• Biologists at all degree levels self trained in information technology

• Information technologists at all degree levels self trained in biology (I.e. clueless for X months)

• Professional Bioinformaticians

Audiences for TDWG Training

• Practicing Biology Researchers• Practicing Computer/Information

Scientists• Bachelors/Masters/PhD Students

– Biology– CS– Biological Informatics

Settings

• Online Documentation– Standard itself– Primer– PowerPoint (added audio stream)

• Just in time • Workshops (e.g. DigIR training)• [A]Synchronous Distance Education

Granularity

• University training (Semester Granularity)– Masters in Biological Informatics (National

Science Foundation under Grant No. IIS-0534567 to Carole L. Palmer and P. Bryan Heidorn.)

– MSLIS Data Curation Concentration (Institute of Museum and Library Services RE-05-06-0036-06 )

– Individual Courses

What do bioinformaticians need to know

Abstract Skill Sets1) Evaluation and implementation of

information systems: user based assessment and continual quality improvement for the development of tools that work and are used.

2) Information acquisition, management, and dissemination: development of digital libraries, data archives, institutional repositories, and related tools.

3) Information organization and integration: ontology development, structuring information for optimal use and sharing, and standards development.

Six step plan

1) Spur interest in BDI education and outreach among TDWG members or potential members.

2) Develop and ever changing list of the knowledge and skills required in biodiversity informatics.

3) Define educational units which might include key documents, a bibliography, and optional venues to face-to-face and Internet classes.

Six step plan

4) Maintain pointers to relevant educational units where they exist outside of TDWG.

5) Make educational materials where they do not exist, so that it easy for prospective learners can most easily acquire the knowledge.

6) Identify the dependencies among required skills and knowledge so that learners can plot a meaningful path through educational units.

Technology dependencies

• What must you know to use a standard?• Darwin Core

– requires a transport layer (DigIR then TAPIR)

– XML editors/validators (not all equal XMLSpy, Oxygen, …)

• DigIR requires PHP, SQL• General Computational Compatency• TDWG pointers to learning about these

technologies

What do new students in botany, entomology, X-ology need to learn about computation before getting to your lab or museum?

What (if anything) falls beyond TDWG’s purview?

Biological Informatician’s Skill Sete.g. UIUC, MS in Bioinformatics

Core Requirements

Computer Science

Biology

Bioinformatics

CS 411: Database Systems CS 473: Algorithms

18 to choose from

(= computational biomolecular informatics)Applied BioinformaticsBioinformaticsLaboratory Techniques in BioinformaticsAlgorithms in bioinformatics**Principles of SystematicsComputing in Molecular BiologyGenomics, Proteomics, and Bioinformation

Concentration / Disciplinary

• Natural Science Ontologies• Science Communication• Biodiversity and Ecology Informatics

Representing and Organizing Information

Interfaces to Information Systems

Building Digital Libraries Indexing and Abstracting

Health Sciences, Information Services and Resources

Architecture of Networked Information Systems

Information Sources and Services in the Sciences

Implementation of Information Retrieval Systems

Use and Users of Information

Electronic Publishing

Document Modeling

Current CoursesNew this SemesterProposed

Scientific data and procedure standards Sociotechnical perspectives on scientific practice

Scientific classifi cation and vocabulary State-of-the-art informatics resources and tools Ontology development Scientific literatures and bibliometrics Data curation and long-term data management Open access repositories Discovery informatics and data mining Project management Interdisciplinary scientific collaboration

Biodiversity Informatics

• Data Quality and Data Curation• Natural History Museum Informatics• Social Factors in Data Sharing• Interactive Keys• Field Monitoring• Geographic Information Systems• Information Federation in Biology• Computational Ecology• Biodiversity Ontologies• Molecular Bioinformatics

Educational Objects

• Education materials are type 3 documents.

• Need templates.• Parts of educational objects

– Standard– Dependencies– Primer– Demonstrations– Exercises– …

Synchronous Distance Ed

ClassroomInstructorStudents

VOIPConference

Skype

Video/Desktopsharing

Conferencee.g.Webhuddle

InternetStudent

Student

Scientist

TDWGMeeting